iccmse 2007 short abstracts

ICCMSE 2007

SHORT ABSTRACTS

25 – 30 September 2007

ICCMSE 2007 Short Abstracts A. Normal Submissions

SIMULATION OF TURBULENT FLOW THROUGH POROUS MEDIA EMPLOYING A V2F MODEL Reza Bahoosh Kazerooni* and Siamak Kazemzadeh Hannani* *

Center of Excellence in Energy Conversion, School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran Email:[email protected]

Abstract. In this article a v2f model is employed to conduct a series of computations of incompressible flow in a periodic array of square cylinders simulating a porous media. Galerkin/Least-Squares finite element formulation employing equal order velocity-pressure elements is used to discretize the governing equations. The Reynolds number is varied from 1000 to 50,000 and different values of porosities are considered in the calculations. Results are compared with the available data in the literature. v2f model exhibits superior accuracy with respect to k − ε results and is closer to LES calculations. The macroscopic pressure gradients for all porosities studied, showed a good agreement with Forchheimer-extended Darcy's law, in the range of large Reynolds number. Keywords: Turbulence, Porous Media, v2f model. PACS: 02.60.Cb

Usefulness of Neuro-Fuzzy Models’ Application for Tobacco Control Sonja Petrovic-Lazarevic, Jian Ying Zhang Monash University, Department of Management, 26 Sir John Monash Drive, Caulfield East, VIC3145, Australia Abstract. The paper presents neuro-fuzzy models’ application appropriate for tobacco control: the fuzzy control model, Adaptive Network Based Fuzzy Inference System, Evolving Fuzzy Neural Network models, and EVOlving POLicies.We propose further the use of Fuzzy Casual Networks to help tobacco control decision makers develop policies and measure their impact on social regulation. Keywords: fuzzy control model, neural networks models, evolving policies, fuzzy casual networks.

Reconstruction of a destroyed ‘Dead Leaves’ tessellation from its fragments via the puzzle fitting function Wilfried Gille Martin-Luther-University Halle-Wittenberg, Institute of Physics, Hoher Weg 8, D-06120 Halle, E-mail: [email protected] Abstract. An isotropic ensemble of a large number of puzzle pieces is given. These pieces are separated, homogeneous particles with a maximum diameter L0 . Then, in respect to their analysis, the so-called puzzle fitting function Φ r
L0  can be determined from elastic scattering experiments of (electromagnetic) waves of a certain wavelength, followed by a discussion of the behavior near the origin. The latter yields either Φ 0
L0  1 or Φ 0
L0  1. If the second relation is fulfilled, the origin of the particles can be traced back to a destroyed tessellation, which is based on a ‘Dead Leaves’ model (DLm) of a certain grain shape. This approach is explained in more detail for hemispherical grains of constant radius R, making possible practical applications in several fields, for example in archeology, biology, geography and materials science. The method can be seen as part of the large field of automatic image analysis, although no image material is made use of directly. Keywords: Dead Leaves model, Fragments of a tessellation, Puzzle fitting function PACS: 42.30.Wb, 42.30.Sy, 42.25.Dd, 87.57.Gg, 61.12.Ex

INTRODUCTION In many areas, reaching from sizes of some nanometers to thousands of kilometers, the destruction of a tessellation leads to single, independent objects. Obviously, these objects can be considered to be the pieces of a puzzle, see the examples in Figure 1 or inspect The BROWN UNIVERSITY S.H.A.P.E. Web Side: http://www.lems.brown. edu/shape/; Here, mathematical procedures about reconstructions of archeological findings; - applications, projects and references are involved.// Furthermore, there exist applications in many fields. Basic denotations and functions for investigating the question whether the pieces given fit together or not have been introduced [1, 2], closely connected to the foundations of scattering theory [3] and the theory of chord length distributions (CLDs) [4, 5] and stochastic geometry geometry [6, 7, 5, 8]. The working function for the following consideration is the so-called small-angle scattering correlation function (CF), γ  r L , connected with the set covariance C  r L , C  0  L  c, C  ∞  L  c2 , and the volume fraction of the particles c via γ  r L  C  r L  c  c   1  c ; 0  r  L, c  1. This function is defined for a certain order range L. In the following, this length parameter is not given explicitly in the equations, but γ  r  γ  r L is written. For a single particle (actually for a grain or for a puzzle piece of volume V and surface area S), the CF possesses the basic properties γ  0  1,  γ   0  S   4  V  1  l and γ  r  0, if r  L, see [8]. The mathematical analysis of such puzzle particle arrangements, see Figure 1, requires the assumption of a certain model, describing the background of the fragments as puzzle pieces. Based on the assumption that the origin of the random particle shapes goes back to a Dead leaves model (DLm) [9], the so-called puzzle fitting function Φ  r has been introduced [2]. This assumption requires that there is no connection between the puzzle pieces and their geometric shapes. In cases, when the shapes of the puzzle pieces are not independent, the assumption of a DLm is an approximation, which remains useful for practical application. As well as the Boolean model [7], the DLm has been well checked in stereological practice [5, 7]. Recently, scattering intensities, involved in this type of model, have been determined in the special case of a so-called puzzle-interlayer model.

From Femtosecond Dynamics to Breast Cancer Diagnosis by Raman Spectroscopy H. Abramczyk*+, I. Placek* , B. Brożek-Płuska*, K. Kurczewski*, Z. Morawiec++, M. Tazbir++ *

Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Technical University of Łódź, The Faculty of Chemistry, 93-590 Lodz, Wroblewskiego 15, Poland, phone: (+48 42) 631-31-88, 631-31-75, email: [email protected], +Max-Born-Institute, Max-Born-Str. 2A, 12489 Berlin, Germany, email: [email protected], ++Kopernik Hospital, Oncology Ward, Lodz, Poland

Abstract. This paper presents new results based on Raman spectroscopy and demonstrates its utilisation as a diagnostic and development tool with the key advantage in breast cancer research. Applications of Raman spectroscopy in cancer research are in the early stages of development. However, research presented here as well as performed in a few other laboratories demonstrate the ability of Raman spectroscopy to accurately characterize cancer tissue and distinguish between normal, malignant and benign types. The main goals of bio-Raman spectroscopy at this stage are threefold. Firstly, the aim is to develop the diagnostic ability of Raman spectroscopy so it can be implemented in a clinical environment, producing accurate and rapid diagnoses. Secondly, the aim is to optimize the technique as a diagnostic tool for the non-invasive real time medical applications. Thirdly, the aim is to formulate some hypothesis based on Raman spectroscopy on the molecular mechanism which drives the transformation of normal human cells into highly malignant derivatives. To the best of our knowledge, this is the most statistically reliable report on Raman spectroscopy-based diagnosis of breast cancers among the world women population.

1

Quantal cumulant dynamics for dissipative systems Yasuteru Shigeta Department of Physics, Graduate School of Pure and Applied Science, Tsukuba University, Tennodai 1-1-1, Ibaraki 305-8571, Japan. Abstract. We develop a quantal cumulant dynamics method for the quantum tunneling in dissipative environment. Reduced equations of motion of classical and quantal cumulant variables without bath degrees of freedom are derived. We observed suppression of the tunneling that depends on the sign of a friction constant for an Ohmic approximation and on the magnitude of a bath frequency for a single bath mode approximation. A possible mechanism of the suppression is explored by analyzing an effective quantal potential of the tunneling path. Keywords: dissipative tunneling PACS: 03.65.Ge,03.65.Sq,03.65.-w,03.65.Xp

INTRODUCTION The motion of a quantum particle interacting with harmonic bath modes is of considerable interest, with a broad range of applications including tunneling in biological long-range electron and short-range proton transfer reactions. Nevertheless, the many-body quantum simulation is limited to some degree, because it costs too much. Path integral techniques developed by Feynman [1] and Caldeira-Leggett [2] allow a rigorous formal elimination of the bath degrees of freedom, and result in a reduced description for the particle coordinates alone. However, evaluating the necessary path integrals using the nonlocal action in the phase space remains a complex task. Therefore it is desirable to establish an efficient scheme in order to understand the many-body quantum tunneling in dissipative systems. Instead of the full quantum dynamics, a wide variety of methods based upon semi-classical and quantal dynamics has been proposed. Recently, Prezhdo and co-workers developed the quantized Hamilton dynamics (QHD) approach derived from a different route, i.e. Heisenberg’s equations of motion [3, 4, 5, 6, 7, 8]. We have applied the QHD method to the molecular vibrational analysis, and found that the method gives less error in the vibrational frequency that the classical dynamics does [9]. Nevertheless, the QHD in a general potential has not been done yet, because of its tedious derivation. Recently we have developed a new methodology for one-dimensional quantum systems called quantal cumulant dynamics (QCD) as an alternative to the QHD, where coordinates, momenta, and cumulants are central variables [10, 11]. The key ideas in this work are that a shift operator acting on an arbitrary operator is introduced and a cumulant expansion is applied to evaluate the expectation value of the shift operator. The expectation value of the shift operator is independent of the Hamiltonian so that the scheme is applicable to the general potential. In this paper, we derive reduced equations of motion of cumulants for one-dimensional cases in order to investigate tunneling motion in dissipative systems based on the QCD method. An extension to the multi-dimensional cases is straightforward.

THEORY The Hamiltonian of a one-dimensional system coupled with classical bath degrees of freedom is given by   2
p2j mωj2 x2j p ˆ ˆ= H + V (ˆ q) + + cj xj qˆ , + 2M 2mj 2 j

(1)

where the first term denotes the kinetic energy operator, the second term is the potential energy operator, and third term is Hamiltonian of the classical bath and coupling between the classical bath and the quantum particle. The ordinary commutation relation for qˆ and pˆ holds, [ˆ q , pˆ] = i (¯ h = 1).

Potentials of Mean Force of Two Hydrophobic Amino-Acid Side Chain Models Dependent on Orientation Mariusz Makowski and Lech Chmurzyński Faculty of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland

Abstract. The potentials of mean force (PMFs) dependent on orientation were determined for system involving formation of hydrophobic dimer composed of modelling side chain - side chain interaction in water, using the TIP3P water model. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for a system modelling side chain – side chain interactions of a pair Val-Phe, in water. The PMFs dependent on orientation were calculated by using the Weighted Histogram Analysis Method (WHAM). The shape of PMFs for the dimer dependent on side-chain orientation is characteristic for hydrophobic interactions with contact and solventseparated minima, and desolvation maxima. The position of all these minima and maxima change with the distance between centres of interactions. Keywords: potential of mean force, side chain – side chain interactions, weighted histogram analysis method, molecular dynamics simulations. PACS: 87.15.By

Data Intensive Analysis of Biomolecular Simulations T. P. Straatsma Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, P.O.Box 999, MSIN K7-90, Richland, WA 99352, USA

Abstract. Biomolecular simulations are resulting in increasingly large molecular time trajectories. This contribution describes a data intensive analytics capability that is designed to effectively use massively parallel computing resources to carry out and visualize large scale molecular dynamics trajectory analyses. Keywords: Data intensive analysis, Molecular simulation. PACS: 87.15.Aa

A Java Library for the Calculation of Molecular Descriptors Irene Luque Ruiz, Miguel Ángel Gómez-Nieto University of Córdoba. Department of Computing and Numerical Analysis. Campus de Rabanales. Albert Einstein Building. E-14071 Córdoba (Spain). Abstract. In this paper, we describe a Java free tool for the calculation of molecular descriptors. Molecular descriptors are invariants extracted from graphs (molecular graphs) representing chemical compounds, and they are used for the development of QSAR models for the prediction of properties and activities of chemical compounds and drugs. The Molecular Descriptors (MDC) library developed is based on the open source code CDK (Chemical Development Kit) extending the scope of this software to the calculation of a large number of molecular descriptors. The large number of molecular descriptors included in MDC makes this library a powerful tool for Computational Chemistry and Chemometric researchers. Keywords: Molecular descriptors, MDC, Java library, QSAR, CDK. PACS: 01.50.hv, 07.05.-t, 01.50.Lc, 07.05.Bx, 07.05.Wr

Contraction Maps on Complexity Spaces and ExpoDC Algorithms S. Romaguera∗ , M.P. Schellekens† , P. Tirado∗ and O. Valero∗∗ ∗

Departamento de Matemática Aplicada, IMPA-UPV Universidad Politécnica de Valencia, 46071 Valencia, Spain † Department of Computer Science National University of Ireland, Western Road, Cork, Ireland ∗∗ Departamento de Matemática e informática Universidad de la Islas Baleares, 07122 Palma de Mallorca, Baleares, Spain. Abstract. We present a mathematical model, based on techniques of Denotational Semantics, for the complexity analysis of expoDC algorithms. This is done by showing that the recurrence inequation associated to an expoDC algorithm gives rise to a contraction map on a suitable quasi-metric space of complexity functions. We prove that this contraction has a unique fixed point which is the maximal element, with respect the order induced by the quasi-metric, of the set of solutions of the recurrence inequation. The complexity of such an algorithm is represented by this maximal element. Keywords: complexity quasi-metric space, contraction mapping, fixed point, expoDC algorithm, recurrence inequation. MSC(2000): 11Y16, 68Q25, 54E50, 54H25.

INTRODUCTION Throughout this paper the letters N and ω will denote the set of natural numbers and nonnegative integer numbers, respectively. Our basic reference for quasi-metric spaces is [3]. Following the modern terminology [9], by a quasi-metric on a set X we mean a function d : X × X → [0, ∞) such that for all x, y, z ∈ X : (i) d(x, y) = d(y, x) = 0 ⇔ x = y; (ii) d(x, y) ≤ d(x, z) + d(z, y). Let us recall that quasi-metric d on a set X induces a partial order ≤d on X given by: x ≤d y ⇐⇒ d(x, y) = 0. A quasi-metric space is a pair (X, d) such that X is a set and d is a quasi-metric on X. If d is a quasi-metric on X, then the function d s defined on X × X by d s (x, y) = d(x, y) ∨ d(y, x), for all x, y ∈ X, is a metric on X. A quasi-metric space (X, d) is said to be bicomplete if d s is a complete metric on X. By a contraction map on a quasi-metric space (X, d) we mean a self-map f on X such that d( f x, f y) ≤ kd(x, y) for all x, y ∈ X, where k is a constant with 0 ≤ k < 1. The number k is called a contraction constant for f . It is clear that if f is a contraction map on a quasi-metric space (X, d) with contraction constant k, then f is a contraction map on the metric space (X, d s ) with contraction constant k. In order to help to the reader we formulate the following detailed form of the Banach contraction principle, which will be useful later on. Theorem 1. Let f be a contraction map on a complete metric space (X,d). Then, for any x ∈ X, the sequence of iterations ( f n x)n∈ω is convergent in (X, d) to a point x0 which is the unique fixed point of f. The theory of complexity (quasi-metric) spaces, introduced by M. Schellekens in [8], constitutes a part of the research in Theoretical Computer Science and Topology and provides a mathematical model for the complexity analysis of algorithms for which the execution time depends on one parameter. Applications of fixed point methods on complexity spaces to the complexity analysis of Divide and Conquer algorithms are also presented in [8]. Further contributions to the development of the theory of complexity spaces and other related structures, and its application to Quicksort algorithm may be found in [2], [4], [7], and [6], and in [5], respectively. Let us recall ([8]), that the complexity (quasi-metric) space is the pair (C , dC ), where C = { f : ω → (0, ∞] :

∞

1

∑ 2−n f (n) < ∞},

n=0

An Accurate Finite-Difference Scheme on Second Order Partial Differential Equations in 3D N. Niakas*, V. C. Loukopoulos** and C. Douskos* * **

Faculty of Engineering, University of Patras, Patras, 26500, Greece Department of Physics, University of Patras, Patras, 26500, Greece

Abstract. A numerical technique is presented for the approximate solution of second-order partial differential equations in three dimensions. With the temporary introduction of two unknown functions of the coordinates the initial equation is separated into three parts that are reduced to ordinary differential equations, one for each dimension, associated with a finite-difference scheme. The use of suitable manipulations and the elimination of the unknown functions, gives finally a linear system of algebraic equations that is solved using an iterative method. The numerical technique is tested on an example of fluid mechanics: the equation of steady-state molecular diffusion of a substance in a continuous medium moving in a straight tube of square cross-section. The numerical results based on the present technique are more accurate than those of the standard relaxation treatment and the ADI method, when the contribution of the first-derivative terms in the initial equation is dominant. In all cases the comparison of the numerical results with those of the analytical solution, demonstrates the reliability of the presented numerical code. Keywords: Finite Difference, Partial Differential Equations, Convection-Diffusion, 3D. PACS: 02.70.Bf

Numerical Solution of the Velocity-Vorticity Navier-Stokes Equations in Three Dimensions for an Incompressible Newtonian Fluid V. C. Loukopoulos and G. T. Karahalios Department of Physics, University of Patras, Patras, 26500, Greece Abstract. A numerical scheme based on a finite-difference technique is presented for the approximate solution of the velocity-vorticity Navier-Stokes equations of a viscous incompressible Newtonian fluid in three dimensional flows. Introducing in each component two auxiliary functions of the coordinate system and considering the form of the initial equation on lines passing through the nodal point ( x0 , y0 , z0 ) and parallel to the coordinate axes, we can separate it into three parts that are finally reduced to ordinary differential equations, one for each dimension. The present technique gives finally a system of linear equations in which the matrix of the coefficients of the unknowns is diagonally dominant. Keywords: Navier-Stokes Equations, Three Dimensions, Numerical Solution. PACS: 47.11.Bc

Application Of The CVP Method On 3D Internal Flows Polycarpos K. Papadopoulos* and Pavlos M. Hatzikonstantinou* *Department of Engineering Science, University of Patras, Patras GR26500, Greece Abstract. The CVP computational method is applied to three-dimensional flow problems. The CVP method is accurate, converges easily and it is easily implemented, particularly in the case of complex geometries associated with generalized curvilinear coordinate systems. The validity of the method is illustrated by presenting results for the laminar, incompressible, developing flow in curved ducts of square cross-sections. Keywords: CVP Method, 3D Laminar Incompressible Flow. PACS: 47.11.-j, 47.11.Bc, 47.15.-x, 47.15.Rq

INTRODUCTION Three dimensional incompressible flows are commonly found in a wide range of industrial devices. One of the many challenges in computational fluid dynamics is to create numerical methods that solve this kind of problems with accuracy and efficiency. A relatively new method that has been developed for this purpose is the CVP method. Its basic characteristic is the solution of a set of correction equations which are based on three variational equations for the continuity, the vorticity and the pressure. It was pioneered by Hatzikonstantinou et al.[1] and over the recent years it has been successfully applied to the quasi-2D problem of fully developed flow in curved and helical ducts of square, circular and elliptical cross-sections [2-4]. These applications have shown that the CVP method is capable of producing accurate results that are in excellent agreement with experimental data, even when it is applied on problems of complex geometry. The advantages and disadvantages of the CVP method have been detailed in a comparison study [5] with the well known SIMPLE method of Patankar and Spalding [6]. The results of the comparison have shown that CVP can be easily implemented and solve different flow problems, since its correction equations are constructed independently of the discretization process and they can be expressed in any coordinate system without much effort. It has also been shown that CVP has increased independence from the grid size and it can produce accurate results even on meshes with deformed cells. On the other hand, it incorporates more correction equations than SIMPLE and hence it is more time consuming. The present work presents the implementation of CVP for the simulation of internal 3D problems. The system of the NavierStokes equations is solved in the parabolic and the fully elliptic formalism and the governing and correction equations are transformed to a generalized coordinate system that follows the geometry of the flow passage. The results of the simulation are compared with experimental data of the existing literature and excellent agreement is observed. The present implementation of CVP shows that the method is capable of simulating accurately, laminar, incompressible 3D flows, using generalized coordinates. This is a very important step in establishing the efficiency of the method and paves the way for its generalization to turbulent and compressible flows.

CVP METHOD In order to outline the steps of the CVP procedure we consider the general case of three-dimensional unsteady incompressible G internal flow. The non-dimensional velocity vector V and the pressure p satisfy the nondimensional continuity equation:

G G ∇⋅V = 0 and the momentum Navier-Stokes equations

(1)

Ab initio FMO-MD method reimplemented and applied to pure water Yuto Komeiji*, Takeshi Ishikawa #, Yuji Mochizuki #, Hiroshi Yamataka #, Tatsuya Nakano + *Research Institute for Computational Sciences, AIST Central 2, Tsukuba, 305-8568, Japan Department of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Tokyo 171-8501, Japan + National Institute of Health Sciences, 1-18-1 Kamiyoga, Tokyo 153-8501, Japan

#

Abstract. The Fragment Molecular Orbital based Molecular Dynamics method (FMO-MD, Komeiji et al., Chem. Phys. Lett. 372, 342, 2003) was reimplemented by combining the latest versions of PEACH and ABINIT-MP programs. Several simulations were performed for a spherical cluster of 125 water molecules at HF/6-31G* level to examine methods in FMO-MD. It was found that use of a molecular configuration prepared by annealing with classical MD lead to a better stabilization of the subsequent FMO-MD simulation. It was also found that use RATTLE bond length constraint in the heating stage could save computational time. These data are expected to serve as a basis for future simulations of solvated molecules. Keywords: FMO, MD, PEACH, ABINIT-MP, Water. PACS: 82.20.Wt

Modeling of hydrogen storage materials: A reactive force field for NaH Ojwang’ J.G.O.∗ , Rutger van Santen∗ , Gert Jan Kramer∗ , Adri C. T. van Duin† and William A. Goddard III† ∗

Schuit Institute of Catalysis, Eindhoven University of Technology, Postbus 513, 5600 MB, Den Dolech 2, Eindhoven, The Netherlands. † Material Research Center, California Institute of Technology(Caltech) , 1200 East California Boulevard Pasadena, California 91125, U.S.A.

Abstract. Parameterization of a reactive force field for NaH is done using ab initio derived data. The parameterized force field(ReaxFFNaH ) is used to study the dynamics governing hydrogen desorption in NaH. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by the parameterized force field. To gain more insight into the mechanism governing structural transformation of NaH during thermal decomposition a heating run in a molecular dynamics simulation is done. The result shows that a clear signature of hydrogen desorption is the fall in potential energy surface during heating. Keywords: hydrogen storage, reactive force field, abstraction, desorption, cluster, metastable state PACS: 64.30.+t, 31.15.Ew, 36.20.Ey

INTRODUCTION Bogdanovic [1] pioneered the interest in the complex metal alanates by establishing that the thermal decomposition process of NaAlH4 could be reversed by doping with metal catalysts of which, titanium is the most thoroughly investigated. However, there are still unresolved problems in understanding of H2 dissociation process in the system. Among these include the role of titanium (is it a dopant or a catalyst?) and long range transport mechanism of Al during the dissociation process. Briefly, the conventional (de)sorption steps occurs as follows: NaAlH4 Na3 AlH6

1 2 Na3 AlH6 + Al + H2 (3.7wt%) 3 3 3 ↔ 3NaH + Al + H2 (1.9wt%) 2 ↔

(1) (2)

We are developing a reactive force field(ReaxFFNaAlH4 ) to study the structural and dynamical details of hydrogen (de)sorption processes in NaAlH4 system. We aim to elucidate on the long range transport mechanisms of Al atoms during (de)sorption process and the dynamics governing hydrogen desorption. Towards this end we are parameterizing a force field, ReaxFF[2], to simulate large clusters containing NaH, Na3 AlH6 , NaAlH4 and Al phases plus catalysts atoms. ReaxFF has already been shown to be able to accurately predict the dynamical and reactive processes in hydrocarbons[2], silicon/silicon oxides[3], aluminum/aluminum oxides[4] and nitramines[5]. As a run-up towards parameterizing ReaxFFNaAlH4 , we have already sufficiently parameterized ReaxFFNaH , which is a reactive force field for sodium and sodium hydride, to adequately describe H2 desorption process in NaH. In this work the details of the parameterizations of ReaxFFNaH , the diffusion mechanism of hydrogen atoms and hydrogen molecules in NaH and abstraction process of surface molecular H2 in NaH cluster are examined. It will be shown that a clear signature for H2 dissociation is the fall in potential energy surface during heating process in a molecular dynamics simulation run.

Psycho-Diagnostic Problems of Personalized Teaching Systems Waheeb A. Abu-Dawwas, Rashed M. Al-Azzeh, and Mohammed H. Abu-Arqoub Department of Computer Science, Faculty of Information Technology, University of Petra, P.O. Box 840344, Amman 11181, Jordan {waheeb, ralazzeh, abu-arqoub }@uop.edu.jo Abstract. The paper is an attempted to discuss one of the must important components in the architecture of personalized teaching systems - the testing system. One of the aims of the paper is to propose a definition of cognitive state, which can be used in designing personalized teaching systems. Keywords: Tutor, Personalized Teaching System, Testing system, Cognitive state. PACS: 07.05.Mh

Theoretical Investigation Of The Unexpected Red Shift In The Halothane…Acetone Complex Kristýna Pluháčková and Pavel Hobza Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Centre for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic; e-mail: [email protected] Abstract. Halothane…acetone and fluoroform…acetone complexes were studied using the MP2 method with a cc-pVTZ basis set and the DFT method with TPSS functional and a TZVP basis set. Whereas fluoroform shows a pronounced blue shift upon complexation, halothane exhibits a small and surprisingly red shift. To explain this we have performed the SAPT and NBO analyses. Although the composition of the total stabilisation energy of each complex gained different results it did not provide a satisfactory explanation for the difference in the spectral shifts. The origin of the difference in the shifts was interpreted to be a result of the interplay of the hyperconjugation and rehybridisation mechanisms. The blue-shift of the C-H stretch frequency upon complexation exhibited by fluoroform...acetone complex was explained by concerting of the two above-mentioned mechanisms. On the other hand, in the halothane...acetone complex the hyperconjugation and rehybridisation mechanisms compensate and it results in small red shift of the C-H stretch frequency. The calculated shift of the C-H stretch vibration frequencies of halothane (+27 cm-1) agreed with the experimental value of +5 cm-1. Keywords: Blue-shifting H-bonding, nature of bonding, halothane…acetone, fluoroform…acetone. PACS: 03.67.Lx

Molecular Dynamics Simulation of Crystallization under Quiescent and Shearing Conditions A. Jabbarzadeh and R. I. Tanner School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006, Australia Abstract. We report molecular dynamics simulation of crystallization of model alkane systems conducted under constant pressure conditions. We studied n-eicosane (C20H42) and n-Hexacontane (C60 H122 ) both under quiescent and steady shear conditions and monitored their crystallization dynamics. We have compared an order parameter used in the simulations against one analogous to that used in dilatometry experiments. For both alkanes applying steady shearing significantly speeds up the crystallization process. The crystallization kinetics follows that of Avrami and we have calculated Avrami growth function and exponent for many cases. The Avrami exponent calculated using our order parameter for defining degree of crystallinity, agrees well with that obtained in the experiments. Keywords: molecular dynamics simulation, crystallization, shear induced crystallization, rheology, shear flow. PACS: 61.46.Hk, 64.70.Dv, 81.10.–h, 36.20.Ey

The cyclic coordinate descent in hydrothermal optimization problems with non-regular Lagrangian L. Bayón, J.M. Grau, M.M. Ruiz and P.M. Suárez University of Oviedo, Department of Mathematics, E.U.I.T.I. Campus of Viesques, Gijón, 33203, Spain. Abstract. In this paper we present an algorithm, inspired by the cyclic coordinate descent method, which allows the resolution of hydrothermal optimization problems involving pumped-storage plants. The proof of the convergence of the succession generated by the algorithm was based on the use of an appropriate adaptation of Zangwill’s global theorem of convergence. Keywords: Optimal Control, Hydrothermal Coordination, Coordinate Descent PACS: 02.30.Yy; 02.60.Cb; 89.30.Ee

INTRODUCTION The coordinate descent method enjoys a long history in convex differentiable minimization. Surprisingly, very little is known about the convergence of the iterates generated by this method. Convergence typically requires restrictive assumptions such as that the cost function has bounded level sets and is in some sense strictly convex. The problem of minimizing a strictly convex function subject to linear constraints is considered in [1]; a convex function of the Legendre type subject to linear constraints is considered in [2]; while in [3], the author considers the objective to be pseudoconvex in every pair of the coordinate blocks and regular in some natural sense. In a prior study [4], it was proven that the problem of optimization of the fuel cost of a hydrothermal system with several thermal plants may be reduced to the study of a hydrothermal system made up of one single thermal plant, called the thermal equivalent. A necessary minimum condition was established in [5] for the optimization of hydrothermal problems involving one single hydraulic pumped-storage plant, thereby considering non-regular Lagrangian and non-holonomic inequality constraints. The present paper addresses the generalization of this problem to several hydro-plants with pumping capacity. We introduce a relaxation numerical method for its resolution. The proof of the convergence of the succession generated by the algorithm was based on the use of an appropriate adaptation of Zangwill’s global theorem of convergence [6]. Finally, we present the solution of a hydrothermal optimization problem in which the potential of the proposed algorithm is evidenced.

STATEMENT OF THE PROBLEM Let us consider a hydrothermal system comprised of n thermal plants and m hydro-plants, assuming, with no loss in generality, that of the m hydro-plants, the first k are of the pumped-storage type (non-regular Lagrangian). The problem consists in minimizing the cost needed to satisfy a certain power demand during the optimization interval [0, T ]. Said cost may be represented by the functional J(z) =

Z T 0

L(t, z(t), z˙ (t))dt

(1)

¶ µ k S L(·, ·, ·) is the class C2 [0, T ] × R2m − Si and L(·, ·, z˙ ) is the class C2 ([0, T ] × R2m ), such that i=1

L(t, z(t), z˙ (t)) = Ψ (Pd (t) − H(t, z(t), z˙ (t))) over the set

¡ ¢m Θ := {z ∈ C1 [0, T ] / z(0) = 0 , z(T ) = b , Hi min ≤ Hi (t, z(t), z˙ (t)) ≤ Hi max }

where Ψ is the function of thermal equivalent cost, Pd (t) is the power demand, z = (z1 , · · · , zm ) is the vector of admissible volumes, zi (t) being the volume that is discharged up to the instant t by the i-th hydro-plant, z˙ =(˙z1 , · · · , z˙m )

New MP2 Database of Nucleic Acid Base Trimers: How Well Reproduce DFT Methods Structure and Binding Energies? Martin Kabeláč[a], Haydee Valdes[a], Edward C. Sherer[b], Christopher J. Cramer[b] and Pavel Hobza[a] [a] Dr. Martin Kabeláč, Prof. Pavel Hobza Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules. Flemingovo nám. 2, 166 10 Prague 6, Czech Republic Fax: (+) 420 220 320 E-mail: [email protected] [b] Dr. Edward C. Sherer, Prof. Christopher J. Cramer Department of Chemistry and Supercomputing Institute, University of Minnesota207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA

Abstract. A new database of nucleic acid base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to other databases, this one includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in real biomolecules. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms is unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BH&H, and the self-consistent charge density functional tight binding method augmented with an empirical dispersion term (SCC-DFTB-D) were assessed for their abilities to accurately compute structures and energies. The best reproduction of the BSSE corrected RI-MP2 stabilization energies was achieved by the TPSS functional (TZVPP basis set) combined with empirical dispersion; removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of potential energy surfaces of biopolymers. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking. The whole database of geometries and interaction energies of the complexes can be found on the web page: http://www.rsc.org/suppdata/CP/b7/b707182e/index.sht

Keywords: nucleic acid bases, ab initio, DFT, trimers, database. PACS: 03.67.Lx

Influence of Temperature on the Offset Voltage of Piezoresistive Pressure Sensors Mohamed Ras lain and Abdelhafid chaabi Département d’électronique, Faculté des sciences de l’ingénieur, Université de Constantine Route Ain el bey , Algeria Microéléctronic technology and the silicon micromachining allow for the development of low cost miniature pressure sensors.Curruntly their design as well as their optimization of their performances complex issues. Based on the phenomena of displacement of the majority carriers in silicon and based on the assumption that each piezoresistor of a silicon pressur sensor has its own temperature coefficients (TCRs of the first and second order), this study gives an explanation on the existence of the offset volage in the piezoresitif pressure sensors and its thermal behaviour. Using different models of majority carriers mobility in silicon, this paper presents a new formula for the first and the second temperature coefficient α and β in function of doping concentration N (cm-3).On the other hand, this new presentation enable us to present the thermal behaviour of piezoresistive pressure sensors in function of two parameters namely the doping concentration N (cm-3) and temperature T (°C) then we report the effect of the temperature on the offset voltage. This theoretical aspects of the thermal variations of the offset voltage of silicon piezoresitive pressure sensors have been developed by assuming that there exists a difference in the doping concentration of the four piezoresistors constituting the Wheatstone bridge. The numerical model of α and β obtained in this work allowed us to obtain a new formula for these two coefficients of temperature. Then using the interpolation program we obtained the variations of these two coefficients in function of the doping concentration N only. With these formulas we can obtain usually a thermal variation of the offset voltage only in function of two parameters, temperature T and doping N. This new method for driving α , β in function of N , ΔV in function of N and T should be of interest to people working in the field of sensors where we they can easily extract the numerical values of the two coefficients α and β and use them in the formula of the offset voltage.

Keywords: Silicon, temperature coefficient, doping concentration, temperature, offset voltage.

Theoretical study of 1,8-Diaminonaphthalene Polymerization Mohammad R. Nateghi* and F. Kalantari† *Department of Chemistry, Azad University, Yazd-Branch, Yazd Iran † Department of Chemistry, Kashan university, Kashan, Iran Abstract. The polymerization of 1,8-diaminonaphthalene (1,8-DAN) was studied by a theoretical approach based on HartreeFock calculations. Investigation of relative stability of most possible dimers, trimers and tetramers yields very useful data concerning the regioselectivity of the coupling reaction as well as the final structures of the polymeric chains. The mechanism is more likely to occur via a radical-radical pathway and leads to mixture of compounds through ortho-C-C and para-C-N linkages. Keywords: Hartree-fock calculations; 1,8-diaminonaphthalene; polymerization PACS: 80- 82- 82. 35. cd-82. 35. x

Acoustic analysis of a sandwich non metallic panel for roofs by FEM and experimental validation P.J. García Nietoa, J.J. del Coz Díazb, J.A. Vilán Vilánc and F.P. Alvarez Rabanalb a

Department of Mathematics, Faculty of Sciences, University of Oviedo, C/ Calvo Sotelo s/n, 33007 Oviedo, Spain b Department of Construction, EPSIG, University of Oviedo, Departmental Building 7, 33204 Gijón, Spain c Department of Mechanical Engineering, University of Vigo, Campus de Lagoas-Marcosende, 36200 Vigo, Spain Abstract. In this paper we have studied the acoustic behavior of a sandwich non metallic panel for roofs by the finite element method (FEM). This new field of analysis is the fully coupled solution of fluid flows with structural interactions, commonly referred to as fluid-structure interaction (FSI). It is the natural next step to take in the simulation of mechanical systems. The finite element analysis of acoustic-fluid/structure interactions using potential-based or displacement-based Lagrangian formulations is now well established. The non-linearity is due to the ‘fluid-structure interaction’ (FSI) that governs the problem. In a very considerable range of problems the fluid displacement remains small while interaction is substantial. In this category falls our problem, in which the structural motion influence and react with the generation of pressures in two reverberation rooms. The characteristic of acoustic insulation of the panel is calculated basing on the pressures for different frequencies and points in the transmission rooms. Finally the conclusions reached are shown. Keywords: Finite element modeling; acoustic insulation; fluid-structure interaction; numerical methods. PACS: 43.40.At, 43.55.Ev, 43.20.Tb, 02.70.Dh, 02.60.Cb

INTRODUCTION Sound proofing or ‘acoustic insulation’ is any means of reducing the intensity of sound with respect to a specified source and receptor [1]. There are several basic approaches to reducing sound: increasing the distance between source and receiver, using noise barriers to block or absorb the energy of the sound waves, using damping structures such as sound baffles, or using active anti-noise sound generators. Sound proofing affects sound in two different ways [1]: noise reduction and noise absorption. Noise reduction simply blocks the passage of sound waves through the use of distance and intervening objects in the sound path. Noise absorption, on the other hand, operates by transforming the sound wave. Noise absorption involves suppressing echoes, reverberation, resonance and reflection. The damping characteristics of the materials it is made out of are important in noise absorption. Sound waves are reflected when they hit a hard surface. Providing an absorbent surface can reduce some of the reflected sound. In a "hard" room, soft materials such as absorbent ceiling panels, carpeting on the floor, and drapes or special absorbent wall coverings, will reduce noise by reducing the reflected sound. Only reflected sound can be treated as described, while direct sound will not be affected. In this paper, we have proceeded to study the acoustic behavior of a typical sandwich non metallic panel for roofs by the finite element method (FEM). The panel has 2.8 × 3.6 m dimensions, with thickness of 0.109 m, and it is constituted by three layers (see Fig. 1). The external side is made up of water-repellent agglomerate (WAG). The insulating nucleus is made of extruded polystyrene (XPS), and the finish side is made of natural spruce wood (NSW). In evaluating materials for their ability to absorb sound energy, its ability to absorb sound is usually provided in the form of an absorption coefficient. The absorption coefficient is defined as the ratio of sound energy absorbed by a given surface, to the sound energy incident upon that surface. The absorption coefficient can vary from 0 to 1. If, for example, the absorption coefficient is 0.9, then 90% the sound energy will be absorbed by that material. Most porous absorbers are more efficient at high frequencies, while improving the materials thickness, or mass, can increase low frequency absorption.

Regularity and discrete schemes for the heat equation on non-smooth domains 1

Pius W. M. Chin∗ , Jean M.-S. Lubuma∗ and Kailash C. Patidar† ∗

Department of Mathematics and Applied Mathematics, University of Pretoria, Pretoria 0002, South Africa Department of Mathematics and Applied Mathematics, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa

†

Abstract. In [1], the solution of the heat equation on a polygonal domain is decomposed into regular and singular parts. Here, it is shown that the solution is globally regular by using a suitable weighted Sobolev space. This result is used to design an optimally convergent semi-discrete finite element method (FEM) where the mesh size is suitably refined. As full discrete schemes, the Fourier series and the non-standard finite difference methods coupled with the FEM are presented. AMS Subject Classification (2000): 35K05, 44A10, 46E35, 65M60, 65M99. Keywords: Heat equation, singularity, regularity, Fourier series, finite element/difference method.

REGULARITY AND SINGULARITY OF THE SOLUTION Consider the heat equation

∂u − ∆u = f in Ω × (0, +∞), u(x, 0) = 0 and u = 0 on ∂ Ω × (0, +∞), ∂t

(1)

where Ω is a polygonal domain Ω ⊂ R2 with boundary ∂ Ω ≡ Γ. Following [2], the origin of the plane, viewed as the center of polar co-ordinates (r, θ ), is assumed to be the only non-convex vertex of the polygon with angle ω such that one of the two sides adjacent to the origin is on π the abscissa axis. We will make use of the function S = ψ r ω sin ωπ θ , ψ ≡ ψ (r) being a smooth cut-off function that is equal to 1 near 0. £The datum f is¤ supposed to be in the Lebesgue space of square integrable functions: f ∈ L2 [Ω × (0, +∞)] ≡ L2 (0, +∞), L2 (Ω) . Given a Hilbert space X, we will more generally use the Sobolev space e s [(0, +∞), X] stands for the space of functions v ∈ H s [(0, +∞), X] such that the H s [(0, +∞), X] . The notation H extension ve by 0 outside (0, +∞) belongs to H s [(−∞, +∞), X]. In practice, X will be the Sobolev space H m (Ω) or H0m (Ω) (see [3]). £ ¤ £ ¤ e 1 (0, +∞), L2 (Ω) satisfying Theorem 1 [1] Let u ∈ L2 (0, +∞), H01 (Ω) ∩ H kukL2 [(0,+∞),H 1 (Ω)] + kukHe 1 [(0,+∞),L2 (Ω)] ≤ Ck f kL2 [(0,+∞),L2 (Ω)] 0

be the unique solution of (1). There holds the singular decomposition u = uR + [K ?t φ (r,t)] S £ ¤ £ ¤ e 1 (0, +∞), L2 (Ω) , K ∈ H e 12 − 2πω (0, +∞), φ (r,t) = where uR ∈ L2 (0, +∞), H 2 (Ω) ∩ H01 (Ω) ∩ H 0 and 0 for t ≤ 0, with the estimate kuR kL2 [(0,+∞),H 2 (Ω)] + kKk

1

π

e 2 − 2ω (0,+∞) H

1

Corresponding author: [email protected]

≤ Ck f kL2 [(0,+∞),L2 (Ω)] .

2

1 − r4t √ e t

for t >

Designing a Software Tool for Fuzzy Logic Programming

1

José M. Abietar, Pedro J. Morcillo and Ginés Moreno Department of Computing Systems, University of Castilla-La Mancha, EPSA 02071 Albacete, Spain [email protected], [email protected], [email protected] Abstract. Fuzzy Logic Programming is an interesting and still growing research area that agglutinates the efforts for introducing fuzzy logic into logic programming (LP), in order to incorporate more expressive resources on such languages for dealing with uncertainty and approximated reasoning. The multi-adjoint logic programming approach is a recent and extremely flexible fuzzy logic paradigm for which, unfortunately, we have not found practical tools implemented so far. In this work, we describe a prototype system which is able to directly translate fuzzy logic programs into Prolog code in order to safely execute these residual programs inside any standard Prolog interpreter in a completely transparent way for the final user. We think that the development of such fuzzy languages and programing tools might play an important role in the design of advanced software applications for computational physics, chemistry, mathematics, medicine, industrial control and so on. Keywords: Fuzzy Logic, Reasoning under Uncertainty, Languages and Software Systems, Logic in Artificial Intelligence PACS: 03B52, 68T37, 68T35, 68T27

INTRODUCTION Logic Programming [1] has been widely used for problem solving and knowledge representation in the past. Nevertheless, traditional LP languages do not incorporate techniques or constructs to treat explicitly with uncertainty and approximated reasoning. To overcome this situation, during the last decades several fuzzy logic programming systems have been developed where the classical inference mechanism of SLD–Resolution has been replaced with a fuzzy variant able to handle partial truth and to reason with uncertainty. Most of these systems implement the fuzzy resolution principle introduced by Lee in [2], such as languages Prolog-Elf [3] and Fril [4]. Following this line, in the original version of [5], a fuzzy logic program is conceived as a set of weighted formulas, where the truth degree of each clause is explicitly annotated. The task of computing and propagating truth degrees relies on an extension of the resolution principle, whereas the (syntactic) unification mechanism remains untouched. Continuing this trail, one of the most modern, flexible and evolved fuzzy dialects of Prolog which follow this scheme, is the one presented in [6]. Informally speaking, in the multi-adjoint logic framework, a program can be seen as a set of rules each one annotated by a truth degree, and a goal is a query to the system, i.e., a set of atoms linked with connectives called aggregators. A state is a pair hQ, σ i where Q is a goal and σ a substitution (initially, the identity substitution). States are evaluated in two separate computational phases. During the operational one, admissible steps (a generalization of the classical modus ponens inference rule) are systematically applied by a backward reasoning procedure in a similar way to classical resolution steps in pure logic programming, thus returning a computed substitution together with an expression where all atoms have been exploited. This last expression is then interpreted under a given lattice during what we call the interpretive phase, hence returning a pair htruth degree; substitutioni which is the fuzzy counterpart of the classical notion of computed answer traditionally used in LP. In what follows, we present a short summary of the main features of our language (we refer the reader to [6] for a complete formulation). We work with a first order language, L , containing variables, function symbols, predicate symbols, constants, quantifiers (∀ and ∃), and several (arbitrary) connectives to increase language expressiveness. In our fuzzy setting, we use implication connectives (←1 , ←2 , . . . , ←m ) and also other connectives which are grouped under the name of “aggregators” or “aggregation operators”. They are used to combine/propagate truth values through the rules. The general definition of aggregation operators subsumes conjunctive operators (denoted by &1 , &2 , . . . , &k ), disjunctive operators (∨1 , ∨2 , . . . , ∨l ), and average and hybrid operators (usually denoted by @1 , @2 , . . . , @n ). Although the connectives &i , ∨i and @i are binary operators, we usually generalize them as functions with an arbitrary number of arguments. In the following, we often write @(x1 , . . . , xn ) instead of @(x1 , @(x2 , . . . , @(xn−1 , xn ) . . .)). By

1

This work was supported by the EU, under FEDER, and the Spanish Science and Education Ministry (MEC) under grant TIN 2004-07943-C04-03.

A conservative Galerkin-characteristics algorithm combined with a relaxation scheme for two regions nonlinear solute transport problem in porous media Mohammed Shuker Mahmood Department of Applied Mathematics, Mechanical Engineering Faculty, University of Žilina, 010 26 Žilina, Slovakia 1. Abstract. Numerical scheme based on the modified method of characteristics with adjusted advection combined with a relaxation scheme for solving strongly nonlinear degenerate convection diffusion problem which arises in the contaminant transport in porous media with dual porosity. A series of computational experiments and comparisons with other solutions are carried out to illustrate the rate of convergence, the behavior and the capability of the scheme. Keywords: dual porosity, nonlinear degenerate equation, convection dominant diffusion, characteristics method PACS: 65M25, 35K57

INTRODUCTION Numerical modelling of transport problems has to capture the mathematical properties of physical systems. For the transport of contaminant in porous media characterized by convection, diffusion and adsorption the conservation of mass, accuracy and minimal numerical dispersion (also nonoscillation) are highly recommended to the numerical schemes. Modified method of characteristics MMOC [1, 2] is viable and one of the efficient front tracking scheme. However, it fails to conserve the mass specifically for nonlinear problems. Various attempts based on MMOC have been introduced to produce conservative schemes, e.g. Eulerian-Lagrangian (localized adjoint ELLAM) and characteristicsmixed finite element methods are other variants that conserve the mass, see [3, 4, 5, 6, 7]. Modified method of characteristics with adjusting advection MMOCAA is already proposed by [7] to conserve the mass globally. The implicit adjusting of the advection is studied in [8, 9, 10] for nonlinear degenerate parabolic problems (single porosity) combined with a relaxation scheme [11, 12]. In this paper we investigate the extension of MMOCAA (implicit adjusting) combined with a relaxation scheme to the two regions (also called two domain, dual porosity or mobile and immobile ) model of reactive solute transport in porous media. A macroscopic model can be formulated based on the mass conservation law as, see e.g. [13, 14] (see also [15]), ∂ (θm cm + ρψ (cm )) (1) + div(θm vcm − θm Dm ∇cm ) = α (cm − ci ) in (Ω × (0, T )) , ∂t ∂ (θi ci + ρφ (ci )) = α (ci − cm ) in (Ω × (0, T )) , (2) ∂t where Ω ⊂ Rd , d = 1, 2, is a bounded domain and T is a constant. Here cm and ci are the dissolved concentrations in the mobile and immobile water regions respectively, v is the (Darcy) velocity field of water, Dm (t, x) is the diffusion (dispersion) tensor, ρ > 0 is the bulk-density, ψ and φ are the adsorption isotherms of porous media, θm and θi are the mobile and immobile phases porosities and α is the mass transfer coefficient. As α → ∞ the mass exchange becomes instantaneous between mobile and immobile phases and the total porosity is θ = θm + θi , but as α → 0 the mass exchange becomes negligible and the total porosity is θ = θm . The functions θm (x), θi (x), v(t, x) and ρ (x) are assumed to be continuous and bounded. It should be noted that in the immobile phase (solid matrix) the advection is negligible.

1

(email:[email protected])

Transport Properties of Uranium Dioxide by Molecular Dynamics Simulation Seçkin D.Gunay, Unsal Akdere, Birtan Kavanoz and Çetin Taşseven Yildiz Technical University, Faculty of Science, Department of Physics, Davutpaşa Campus, 34210 Esenler, Istanbul-TURKEY Abstract. A semi empirical interionic potential model has been parameterized to investigate UO2 by molecular dynamics simulation at solid and liquid phase (2000K-3200K). Contrary to the other potential models in literature, it has been shown that potential in this study is adequate to provide reasonable information at low and high temperatures. The transition to superionic phase and melting has been successfully reproduced. Keywords: Uranium dioxide; Molecular dynamics simulation, Interionic potential, Diffusion PACS: 61.20.Ja; 61.43.-j; 66.10.-x; 66.30.-h

Forecasting Electricity Prices in an Optimization Hydrothermal Problem J. M. Matías∗ , L. Bayón† , P. Suárez† , A. Argüelles∗∗ and J. Taboada∗∗ ∗

Dpt. of Statistics, University of Vigo, ETSEM, Lagoas - Marcosende, 36310 Vigo, Spain Dpt. of Mathematics, EUITI, University of Oviedo, Campus de Viesques, 33204 Gijón, Spain ∗∗ Dpt. of Natural Resources, University of Vigo, ETSEM, Lagoas - Marcosende, 36310 Vigo, Spain †

Abstract. This paper presents an economic dispatch algorithm in a hydrothermal system within the framework of a competitive and deregulated electricity market. The optimization problem of one firm is described, whose objective function can be defined as its profit maximization. Since next-day price forecasting is an aspect crucial, this paper proposes an efficient yet highly accurate next-day price new forecasting method using a functional time series approach trying to exploit the daily seasonal structure of the series of prices. For the optimization problem, an optimal control technique is applied and Pontryagin’s theorem is employed. Keywords: Control problem, electricity markets, forecasting, functional models, time series analysis PACS: 02.30.Yy, 02.60.Ed, 05.45.Tp, 89.30.Ee

INTRODUCTION During the last decade, the electricity supply industry is moving from a centralized operational approach to a competitive one. This is the case for Spanish utilities since January 1st, 1998. In this paper the new short-term problems that are faced by a generation company in a deregulated electricity market are addressed and an optimization algorithm is proposed. Our model of the spot market explicitly represents the price of electricity as an uncertain exogenous variable. We represent generation units with high level of detail and our model distinguishes individual generation units and considers inter-temporal constraints such as hydro reserves. The methodology presented could be applied to any deregulated system based on bids. However, the Spanish regulation [1] has been used as reference market model. Since next-day price forecasting is an aspect crucial of the problem, Since next-day price forecasting is an aspect crucial, this paper proposes an efficient yet highly accurate next-day price new forecasting method. Price forecasting techniques in power systems are relatively recent procedures. In [2] the model is based on the probability density functions of forecast prices. In [3] dynamic regression and transfer function models are proposed. In [4] electricity prices models are reviewed and a novel classification is proposed. Trying to exploit the seasonal daily structure of the time series of prices, in this work we model the series using a functional approach which considers hourly prices as observations of daily functions of prices. Therefore, within this approach, the series of prices consists of a sequence of real-valued functions defined on the interval [0, 24]. We model this functional time series with a linear autoregressive functional model (functional input – functional output) which formulates the relationships between each daily function of prices and the functions of previous days. So, this paper generalizes two previous papers of the authors. In [5] our model of the spot market explicitly represents the price of electricity as a known exogenous variable, and in [6] the volatility of the spot market price of electricity is represented by a stochastic model. We search for past spot market sessions that can be considered similar to the session that the company is about to face using clustering techniques.

STATEMENT OF THE HYDROTHERMAL PROBLEM In this section the optimization problem of one company is described. Let us assume that our hydrothermal system accounts for one hydro-plant and m thermal plants (is easy to generalize to n hydro-plants as we can see in [6]). Let Ψi : Di ⊆ R −→ R (i = 1, . . . , m) be the cost functions (Euro/h) of the m thermal plants. In general, the cost functions

Taiwan’s Information Security Policy Enhancement: An Analysis of Patent Indicators and Patent Documents Nai-Wen Hsu*, Jr-Shiuan Liang* and Yi-Chang Chen† *

Science & Technology Policy Research and Information Center, NARL, No. 106, Sec. 2, Heping E. Rd., Taipei, Taiwan

†

Dept. of Information Management, National Pingtung Institute of Commerce, No 51, Minsheng E. Rd., Pingtung, Taiwan Abstract. Information security policy in Taiwan stems the gap between expectation and reality. For this, the paper presents an analysis of patent indicators and patent document attempt to conclude the overview of the information security technology development. The paper also identifies the leading countries and cutting-edge areas with potential trends. Finally, several practicable and valuable strategies after this work are generalized to achieve the goals of Taiwan information security policy. Keywords: Information security policy, Patent indicators, Document analysis. PACS: 07.05.Kf

Atomic calculations applied to semiconductor hetero structures L. Pedesseau, J. Even, F. Doré and C. Cornet FOTON-INSA Laboratory, UMR 6058 au CNRS, INSA de Rennes, 20 avenue des Buttes de Coëmes, CS 14315, 35043 RENNES Cedex, FRANCE Abstract. We present results of a study from first principles modeling using ABINIT packages. Firstly, we would like to calculate the characteristic bulk properties of InAs and GaAs crystals and to use them in a kp model in order to study piezoelectricity in a truncated cone quantum dot. Secondly, we focused our attention on electronic properties of highly strain InAs/GaP interface. Special emphasis is put on variations of the InAs lattice parameter that we strained up to the lattice parameter of GaP crystal and on agreement of InAs behavior either with Chuang calculations and ab initio. Keywords: Ab initio, kp method, semiconductor, quantum dot, piezoelectricity, . PACS: 71.15.Mb, 71.20.-b, 71.20.Nr, 73.21.La, 78.20.Hp, 79.60.Jv

Coupled Perturbed Hartree-Fock calculation of the static polarizability for periodic systems. Implementation in the CRYSTAL code. M. Ferrero∗, Michel Rérat†, R. Orlando∗∗ and R. Dovesi∗ ∗

Dipartimento di Chimica IFM, Università di Torino and NIS -Nanostructured Interfaces and Surfaces - Centre of Excellence, http://www.nis.unito.it Via P. Giuria 7, 10125 Torino, Italy † Equipe de Chimie Physique, IPREM UMR5254, Université de Pau, 64000 Pau, France ∗∗ Dipartimento di Scienze e Tecnologia avanzate, Università del Piemonte Orientale, Via Bellini 25/G, 15100 Alessandria, Italy

Abstract. The Coupled Perturbed Hartree-Fock (CPHF) scheme has been implemented in CRYSTAL06, periodic ab initio computer code that uses a gaussian type basis set, in order to obtain the polarizability of crystalline systems (3D), slabs (2D), polymers (1D) and, as a limiting case, molecules (0D). The formulation is presented, together with applications referring to diamond, silicon and SiC. It turns out that, for a given hamiltonian and basis set, high numerical accuracy can be achieved at relatively low cost compared to the Finite Field perturbation method (FF), that uses a saw-tooth electric potential. Correctness of the CPHF results was tested with reference to FF calculations with CRYSTAL. Keywords: calculation, CPHF, crystalline systems, dielectric constant PACS: 71.15.-m, 71.15.Ap, 71.15.Dx, 71.45.Gm, 74.25.Jb,77.22-d, 78.20.Ci, 78.40.Fy

INTRODUCTION In presence of an electric field, the single-particle Hamiltonian operator is: 1 (1) (~pe − e~A(~r,t))2 + eφ (~r,t) + VC (~r) 2m ~pe ≡ h¯i ~∇r is the momentum of the electron,~r its position, ~A(~r,t) and φ (~r,t) the vector and scalar potentials defining ~ the electric field (~ F = −~∇r φ − ∂∂At ) and VC (~r) the Coulomb potential energy without outer field. Then, the calculation of the static polarizability, which is the response of the electronic system in the presence of a static electric field and corresponds to the second-order perturbation energy, is generally done in the gauge where the electric field is only described by φ . As the field is uniform in the real space, the Hamiltonian operator becomes: H=

H = H (0) − e~r · ~F

(2)

where H (0) is the unperturbed Hamiltonian operator and the second term is the well-known classical dipole moment field interaction. In the following, we will consider a periodic system interacting with a static (UV-visible) field. In this case, the electric dipole approximation used for finite systems cannot be used anymore because the electric perturbation breaks periodicity. A possible solution to this problem is to use a periodic “saw-tooth” electric potential, as proposed by Baldereschi et al. [1], in combination with a supercell scheme like in Ref. [2]. This approach permits to compute the dielectric tensor elements. However, the process is extremely demanding computationally. We can therefore introduce a different perturbation operator that preserves translational symmetry and does not imply the use of supercells. (see also Refs. [3, 4, 5, 6, 7, 8, 9, 10, 11, 12]).

Molecular Dynamic Simulation of Detonation Phenomena A.V. Utkin, I.F. Golovnev, V.M. Fomin Institute of Theoretical and Applied Mechanics, Russian Academy of Science, 4/1 Institutskaya Str., Novosibirsk 630090, Russia Abstract. In the present study, the molecular dynamics method has been used to examine the influence of the thermal effect of the chemical reaction on processes in a detonating molecular crystal. Molecular dynamics data are compared with predictions of the continuum theory of detonation; in particular, fulfillment of the Chapman-Jouguet condition is verified. Keywords: Molecular dynamics, Detonation, Equation of State. PACS: 71.15.Pd 82.40.Fp

Interpretation of Electronically Excited States by Means of Configuration Analysis Kiyotada Hosokawa and Shin-ichiro Sato Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering Hokkaido University, North 13, West 8, Sapporo Japan, 060-8628 The configuration analysis (CA), that is a procedure to analyze and interpret the excited electronic configuration obtained by the self-consistent field molecular orbital (SCF MO) calculations including configuration interactions (CI) in terms of fragment reference molecular orbitals, was extended to nonplanar molecular system. We can investigate the extent of contribution of local excitation (LE), charge transfer (CT), or charge resonance (CR) in each electronic state from the results of CA. The method was applied to a meso-meso linked orthogonal porphyrin dimer and trimer as well as a planar fused dimer and trimer. We successfully extended the CA method to non-planar and large molecular system. We found that (1) only the excited states that show large shifts to longer wavelength region possess noticeable contributions from the CR configurations in meso-meso type of oligomers, and (2) all the excited states of doubly fused oligomers have larger contributions of CR configurations than those of meso-meso linked oligomers. Keywords: Configuration Analysis, Porphyrin oligomer PACS:31.90.+s

Online Visual Quality Inspection for Weld Seams Maike Löhndorf∗ , Herbert Ramoser∗ and Luigi Cambrini† ∗

Advanced Computer Vision, Donau City Straße 1, A-1220 Vienna Austrian Research Centers, Donau City Straße 1, A-1220 Vienna

†

Abstract. Arc welding is a widely used technology in almost all sectors of industrial production. Many tasks are automatically performed by robots. This paper presents a flexible vision based quality management system to detect defects online during the weld process. Keywords: Digital image processing, online inspection, arc welding, machine learning PACS: 42.30.Tz, 42.30.-d, 42.62.Cf, 89.20.Bb, 89.62.Ff

INTRODUCTION Arc welding is an important technology in industrial production of many key products, e.g. automobiles, ships, airplains, pipelines. An ever growing amount of welding tasks is performed automatically by robots driving the demand for automatic quality control. Steps have been undertaken in that direction using different approaches. One main field is concerned with the online tracking of the seam path ahead of the torch using cameras and lasers, e.g. [1], [2]. Others deal with the post manufacturing inspection: [3] use shape from shading to reconstruct the 3D shape of the weld bead. Shape from shading depends on stable light conditions which do not exist during the weld process due to the weld arc, making it an offline system. [4] classifies weld defects on x–ray images using support vector machines. This approach realizes offline inspection and needs an x–ray imaging device. Others use laser lines to recover the geometry. The system presented in this paper differs from the known approaches in two main points: (1) The system learns the required quality from training seams that are considered to be sufficiently well welded. (2) The system runs online. Defects should cause an interruption to save weld material and time or, ideally, the quality management should give feed back to correct the robot. A single camera mounted on the weld arm observes the currently welded seam behind the weld head. The observed features are the position and the width of the seam as well as the light distribution in the vicinity of the arc. An additional advantage of the system is that it just needs one off–the–shelf camera and that it poses no restriction on the robot’s freedom of movement. This paper is organized as follows. We first describe the system setup and the flexible calibration framework. This is then applied to the brightness evaluation around the weld torch and the geometric shape of the seam.

SYSTEM DESCRIPTION The hardware of the system consists of a welding robot, a camera system rigidly mounted on the robot arm near the welding torch, and a PC used for the image processing. The camera’s field of view contains the end of the torch and the first few centimeters of the newly welded seam. The camera is linked with the robot’s control unit which also controls the imaging process. The vision system is adaptable to individual welding tasks with their respective quality requirements. This flexibility is achieved by allowing for a learning phase when the robot is set up for a new task. The quality parameters are learned from a set of welded seams, called training seams, selected by a weld engineer from samples exhibiting sufficient quality. The measurements of the training seams are combined to form reference values with tolerance intervals. The learning phase is performed just once before the robot is really employed to work. It is therefore not time–critical. During the weld process the seam’s quality is monitored online. This is called verification phase. The verification is based on a frame–by–frame comparison of the current work with the reference values. The robot’s control and the synchronization with the camera assure the required synchronicity. The assessed features are currently the light distribution in the vicinity of the weld torch, and the position and width of the seam.

Weld Spot Detection by Color Segmentation and Template Convolution Luigi Cambrini*, Jürgen Biber†, Dieter Hönigmann†, Maike Löhndorf† *

Austrian Research Centers GmbH – ARC, Image Processing, Video- and Safety Technology, 1220 Vienna, Austria † Advanced Computer Vision GmbH – ACV, Donau-City-Straße 1, 1220 Vienna, Austria Abstract. There is a need of non-destructive evaluation of the quality of steel spot welds. A computer-vision based solution is presented performing the analysis of the weld spot imprints left by the electrode on the protection bands. In this paper we propose two different methods to locate the position of the weld spot imprint as a first step in order to verify the quality of the welding process; both methods consist of two stages: (i) the use of the X channel of the XYZ color space as a proper representation, and (ii) the analysis of this image channel by employing specific algorithms. Keywords: Quality inspection; welding process; color segmentation; template convolution. PACS: 89.20.Bb; 89.20.Ff; 42.30.Tz; 42.30.-d; 42.62.Cf.

A step towards planification of focused ultrasound thermoablation Luis Kabongo∗,† , Pascal Desbarats∗ and Erik Dumont† †

∗ LaBRI, 351 cours de la Libération, 33405 Talence, France Image Guided Therapy, 2 Allée du Doyen George Brus, 33600 Pessac, France

Abstract. Focused ultrasound devices are used in thermal ablation therapy. Their utilization implies to planify the focal point trajectory before the intervention. Our final objtective is to provide clinicians with a planification tool.In this article, different methods for trajectory planification are presented and then evaluated on 3D synthetic objects taking into account the total intervention duration. Finally, a discussion on the efficiency of the methods in clinical use is proposed. Keywords: thermotherapy, focused ultrasound, intervention planification, 3D simulation PACS: 43.80.Sh, 87.50.Kk, 87.54.Br, 87.54.Hk

INTRODUCTION Hyperthermia has become a major technique used in medical interventions such as tumour ablation [1], treatment of heart arrhythmias [2], local drug delivery with thermo-sensitive microcarriers [3, 4] and control of gene therapy using heat-sensitive promoters [5]. The objective of any thermal procedure is to provide adequate treatment of the entire target volume while sparing adjacent biological structures. Tumour ablation using hyperthermia consists in overheating tumorous tissues by applying locally a lethal energy dose. This over-heating can be achieved using different kinds of energy as radiofrequency (RF) [6], microwaves [7, 8], laser [9] or focused ultrasound [10]. MR-compatible techniques have the advantage to allow a real-time non-invasive monitoring of temperature with MRI [11, 12] for security and efficiency estimation during and after intervention. In focused ultrasound surgery (FUS), temperature elevation is produced by a modified sonography transducer that emits ultrasounds at higher power. Its main principle is to focus ultrasound waves emitted by a spherical surface into a small region of space (the focal point). If the first FUS transducers had a single vibrating parabolic surface which concentrates naturally the energy at the focal point, modern transducers consists in the aggregation of vibrating surfaces called elements distributed on a parabolic surface. Contrary to older systems it is possible to displace the position of the focal point by changing electronically the phase (it is the reason why they are called phased-array transducers). This ensures a faster and more precise focal point positioning than using mechanical translation systems. Earlier planification techniques consisted in shooting at one point of the tumour, waiting for a cooling period to control thermal diffusion and then to displace the focal point and shoot again. These techniques allow a precise control of the induced thermal dose (TD) [13] which is the sum of temperature along time, but take a long time to achieve a total ablation of the tumour. There is a direct link between TD and necrosis [14, 15]. On the other hand, most recent techniques [16, 17] try to take advantage of thermal diffusion by taking into account the overlap effects in energy deposition induced by multiple FUS shots along a given trajectory. In this article, we present several methods to obtain such trajectories and there accuracy in the intervention simulation for synthetic objects. Finally, we will discuss about the efficiency of each methods in terms of integration in clinical routines.

MATERIAL AND METHODS All computations in this article were performed on an Intel Core Duo 2 GHz laptop computer with 2 GB RAM. All methods were integrated in a simulation chain process previously published [18]. Our main objective is to obtain a trajectory that will be followed by the focal point during the intervention. To minimise the duration of the ablation this trajectory must take into account overlapping thermal effects. In order to

THE KEPLER PROBLEM IN ROTATING REFERENCE FRAMES: TOPOLOGICAL STUDY OF THE PHASE FLOW M.C. Balsas∗ , E.S. Jiménez∗ and J. A. Vera∗,† ∗

Consejería de Educación y Cultura de la Región de Murcia. Murcia, Spain. † Departamento de Matemática Aplicada y Estadística. Universidad Politécnica de Cartagena. Cartagena (Murcia), Spain.

Abstract. This paper studies the topology of the phase flow of a Keplerian motion in a rotating reference frame, with help of some analytical and graphics tools. By means of Liouville-Arnold theorem and some specifics techniques, we obtained a complete topological classification of the phase flow associated to this system. Keywords: Liouville-Arnold theorem, Kepler problem, amended potential, Hill regions. PACS: 91.10.Sp, 95.10.Ce, 45.50.Jf

INTRODUCTION This paper presents the exact qualitative study of the phase flow of a Keplerian motion in a rotating reference frame. To the best of our knowledge, a comprehensive study of this problem is not included in classical theoretical mechanics textbooks, nor in orbital mechanics ones. This is surprising, because this problem models numerous types of body motion such as satellite motion with respect to a frame positioned on Earth, relative orbiting motion and formation flying satellites. We describe the Hamiltonian dynamics, associated to the Kepler problem in rotating coordinates by means of Liouville-Arnold theorem (see for details [1, 2]) and some specifics techniques. We obtained a complete topological classification of the phase flow associated to this system. The dynamics of the canonical hamiltonian system is described by the Hamiltonian H : E−→ R

(1)

given by 1 H= 2



p2r +

p2θ r2



+ αpθ −

1 r

(2)

where α > 0 and is a real structural constant of the system with E = R+ × S1 × R2 the phase space, where the Hamiltonian is defined. Note that H = HKepler + αpθ (3) where HKepler represents the Kepler Hamiltonian associated to the two body problem and the term αpθ adds to the dynamics of the Kepler problem the effect associated to rotation of the reference frame. If we want to do a qualitative study of the dynamic associated to the Hamiltonian system we have to consider the following sets Ih = {(r, θ, pr , pθ ) ∈ E : H (r, θ, pr , pθ ) = h} Ik = {(r, θ, pr , pθ ) ∈ E : pθ = k} (4) Ihk = Ih ∩ Ik These sets are invariant by the Hamiltonian flow associated to the Hamiltonian system being H and pθ two first integrals, independent and in involution. Hence, the Hamiltonian system (2) will be integrable. The main results of this paper are the description of the foliation of (i) The phase space E by the invariant sets Ih .

Image Normalization and Discrete Wavelet Transform Based Robust Digital Image Watermarking Cabir Vural1 and Serap Kazan2 1

Electrical-Electronics Engineering, Sakarya University, 54187 Esentepe, Sakarya, Turkey. Email: [email protected], Fax: 90 264 2955601 2 Computer Engineering, Sakarya University, 54187 Esentepe, Sakarya, Turkey. Email: [email protected] Fax: 90 264 2955608

Abstract. In this study, a new digital image watermarking algorithm that combines the strengths of the moment based image normalization and two dimensional discrete wavelet transform is proposed. Normalization provides robustness against geometrical degradations, whereas discrete wavelet transform achieves immunity for compression, linear and non-linear filtering by taking the properties of the human visual system into consideration. The method is shown to resist numerous image manipulations. Furthermore, the method is easy to implement and suitable for real time applications. Keywords: Digital image watermarking, moment based image normalization, discrete wavelet transform. PACS: 07.05.Pj

Aggregative Learning Method and Its Application for Communication Quality Evaluation Dauren F. Akhmetov 1 and Minoru Kotaki 2 1

NTTDoCoMo Hokkaido, Inc., Sapporo, 060-0001, Japan [email protected] 2 School of Eng., Hokkaido Tokai University, Sapporo, 005-8601, Japan [email protected] Abstract. In this paper, so-called Aggregative Learning Method (ALM) is proposed to improve and simplify the learning and classification abilities of different data processing systems. It provides a universal basis for design and analysis of mathematical models of wide class. A procedure was elaborated for time series model reconstruction and analysis for linear and nonlinear cases. Data approximation accuracy (during learning phase) and data classification quality (during recall phase) are estimated from introduced statistic parameters. The validity and efficiency of the proposed approach have been demonstrated through its application for monitoring of wireless communication quality, namely, for Fixed Wireless Access (FWA) system. Low memory and computation resources were shown to be needed for the procedure realization, especially for data classification (recall) stage. Characterized with high computational efficiency and simple decision making procedure, the derived approaches can be useful for simple and reliable real-time surveillance and control system design. Keywords: Time Series, Identification, Prediction, Model, Algorithm, Wireless, Communication, Quality.

The convolution method in neutrino physics searches V. Tsakstara∗ , T.S. Kosmas∗ , J. Sinatkas † , V.C. Chasioti∗ and P.C. Divari∗ Theoretical Physics Section, University of Ioannina, GR 45110 Ioannina, Greece Department of Informatics and Computer Technology, TEI of Western Macedonia, GR-52100 Kastoria, Greece ∗

†

Abstract. We concentrate on the convolution method used in nuclear and astro-nuclear physics studies and, in particular, in the investigation of the nuclear response of various neutrino detection targets to the energy-spectra of specific neutrino sources. Since the reaction cross sections of the neutrinos with nuclear detectors employed in experiments are extremely small, very fine and fast convolution techniques are required. Furthermore, sophisticated de-convolution methods are also needed whenever a comparison between calculated unfolded cross sections and existing convoluted results is necessary. Keywords: Integral transforms and operational calculus, convolution methods, interpolation techniques, neutrino-nucleus interaction, supernova neutrino spectra PACS: 2.30.Qy, 2.60.Ed, 13.15.+g, 26.50.+x

INTRODUCTION The convolution (or folding) is a well known basic operation used in many areas of research (physics, mathematics, engineering, informatics, etc.) to extract information from images [1, 2]. This operation takes two functions, f and g, and produces a third function C that, in a sense, represents the amount of overlap between f and a translated version of g. Thus, for two continuous one-dimensional (simplest case) integrable functions f and g, the convolution is defined by the integral C(t) ≡ ( f ? g)(t) =

Z β α

f (t 0 )g(t − t 0 )dt 0

(1)

(notice the shifted function g in the integrand). Equation (1) shows that the convolution blends one function with another and constitutes a particular kind of integral transform that expresses the overlap of the function g as it is shifted over the function f . The integration range in Eq. (1), depends on the domain on which f and g are defined and it could be a finite range, but often we take α = −∞ and β = +∞ by extending either periodically or with zeros the integration range in both directions. Of special interest is the convolution defined for discrete functions (discrete convolution) written as c(κ ) =

∞

∑

f (λ ) g(κ − λ )

(2)

λ =0

(we have adopted infinite sequences in the sense of using extensions with zero coefficients, if necessary, as mentioned before). We also mention the specific type of convolution defined between distributions. Convolution with distributions is very often used in physics where three-dimensional convolutions are usually needed. We note two such examples: (i) The folding of the nucleon-centers charge (or matter) density distribution ρ (r) of a nucleus with the single nucleon charge (matter) density distribution ρn (r) which is written as [3],

ρ f (r) =

Z

ρ (r0 )ρn (r − r0)d 3 r0 .

(3)

(ii) The folding of the cross section σ (υ ) of a cold dark matter particle of the Universe scattered off a nuclear target with a velocity distribution f (υ ), where υ denotes the velocity of the dark matter candidate [4]. Usually, a Maxwellian type velocity distribution f (υ ) is employed for the dark matter particles (see Ref. [4] for expressions of the convolution). In such cases the convolution might be a very complicated problem [4]. In the present work, we restrict ourselves in one-dimensional convolutions and focus on their applications to neutrino studies in nuclear and astro-nuclear physics, which are interesting research topics in modern physics [5, 6, 7, 8]. There, the role of f in Eq. (1) plays an energy-distribution function of the neutrinos produced by a specific source (Sun,

Numerical Simulation of the Static Stiffness Problem on a Catenary by using Threads 1

A. Alberto∗ , E. Arias† , T. Rojo† , F. Cuartero† and J. Benet∗∗ Albacete Research Institute of Informatics, Universidad de Castilla-La Mancha, Avda. España s/n, 02071-Albacete † Dept. Sistemas Informáticos, Escuela Politécnica Superior, Universidad de Castilla-La Mancha, Avda. España s/n, 02071-Albacete ∗∗ Dept. Mecánica Aplicada, Escuela Politécnica Superior, Universidad de Castilla-La Mancha, Avda. España s/n, 02071-Albacete ∗

Abstract. The static problem on the pantograph/catenary interaction consists on obtaining an optimal design of the interaction pantograph/catenary, ensuring suitable placement of the line with the contact wire that has to be parallel to the ground, so that the pantograph can obtain the energy from the line. The loss of contact between the pantograph head and the catenary produces in the train a loss of energy and, consequently, a decrease in the speed. In this paper, we will present a High Performance (HPC) implementation that has been carried out on various algorithms to solve the equilibrium equation of the system in a catenary model. This HPC has been carried out by exploiting some special properties of the involved data structures (iterative methods with preconditioning have been used for the resolution of this system) and on the other hand by applying parallelism. The last point is really very important due to the fact that currently, multicore architecture are present on our desktop, laptop, etc [1]. But, the programmers do not develop the applications taking into account the new features of this architectures and, in fact, they do not take beneffits of number of processors in it. So, also in this paper, a shared memory implementation based on threads is presented for solving the static problem on the pantograph/catenary interaction. This implementation allows to reduce dramatically the execution time in order to be able to carry out the whole simulations in a reasonable time. All these algorithms have been integrated with a user friendly interfaz in a tool software, which is currently used in the industry. Keywords: structure catenary, static stiffness problem, interaction pantograph/catenary, equilibrium equation, high performance computing, software tool

CONTENTS Introduction

1

Static stiffness problem in a catenary model

2

Experimental Results

4

Conclusion and future work

5

INTRODUCTION In the last few years, the user, demand greater comfort and safety in railway transport, so, it has been evolved by adapting itself to new user requirements. This, however, is bound up with a decrease in journey time,which implies an increase in the speed of the train. The high-speed trains can travel at a speed over 350Km/hour. In order to reach these speeds, it is important to provide of constant energy to the train. For this reason, it is necessary to carry out an optimal design of the interaction pantograph/catenary, ensuring suitable placement of the line, with the contact wire parallel to the ground, so that the 1

This work has been supported by regional project ”Algoritmos de Altas Prestaciones para el Calculo de la Ecuacion Dinamica de en la Interaccion Pantografo-Catenaria en Trenes de Alta Velocidad” (CEDIPAC), JCCM-PCI-05-019

© 2004 AIP Numerical Simulation of the Static Stiffness Problem on a Catenary by using Threads 2 13/07/2007 1

Towards Simulations of Outer Membrane Proteins in Lipopolysaccharide Membranes T. A. Soares and T. P. Straatsma Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, P.O.Box 999, MSIN K7-90, Richland, WA 99352, USA

Abstract. Atomistic simulations of the outer membrane of Pseudomonas aeruginosa constituted of monolayers with 64 LPS molecules and 160 PE molecules were performed. The Amber96 force field and our extensions of the Glycam93 force field were used together with periodic boundary conditions the smooth Particle Mesh Ewald method. Simulation derived properties of LPS membranes are shown to exhibit good agreement with available experimental data within the time scale simulated, chosen force field and simulation conditions. The molecular model used offers an accurate representation the high asymmetry and low fluidity characteristics of outer membranes Keywords: Molecular simulation, Lipopolysaccharide membranes, Outer membrane proteins. PACS: 87.15.Aa

ICCMSE 2007 Short Abstracts B. Symposia

Computer Assisted Structure Determination of Large Clusters: XRD and DFT Reinhart Ahlrichs Institute of Physical Chemistry, University of Karlsruhe, Kaiserstraße 12, 76131 Karlsruhe X-ray diffraction (XRD) is the most powerful tool for quantitative structural analysis. The importance of XRD can hardly be overestimated since it provides the basic characterization of molecules: topology, bond distances and angles, and very often even the chemical composition if other methods for elemental analysis fail. XRD investigations may encounter problems, however, and here is a list of frequent difficulties. 1. Conformational disorder of protecting ligands, e. g. PEt3 or PPh3, or of end groups such as –NPr2, Pr = propyl. 2. Orientational disorder: a molecule may be oriented differently at different sites; plastic phases are an extreme case. 3. Occurrence of various isomers distributed statistically within a crystal. 4. Atoms with similar atomic number cannot be distinguished since they have similar form factors. Measurements of disordered crystals, as in 1-3, yield difficult to analyze diffraction patterns of ensemble averages, which invariably cause large uncertainties, e. g. in bond distances. The 4th problem persists even if good crystals are available. As a consequence of the partial failure of XRD to characterize molecules, other methods have to be employed for this purpose. Molecular electronic structure calculations are very well suited to complement and correct XRD. This will be demonstrated for selected cases where chemical composition and structure could only be determined with the help of quantum chemical treatments. The examples presented include the clusters: [Ag26In18S36Cl6(R2PCH2PR2)10]2+, [Cu7Se20In4Ph20], [Cu45Sb16(PEt2Me)16], [Ag28(µ6-S)2(ArP(0)S2)12(PPh3)12] which have been synthesized by the group of Dieter Fenske. Aspects of methodology, e. g. choice of DFT functionals and basis sets, and effect of protecting ligands will be briefly mentioned. References [1] Ahlrichs, R.; Eichhöfer, A.; Fenske, D.; Hampe, O.; Kappes, M.; Nava, P.; OlkowskaOetzel, J. Angew. Chem. Int. Ed. 2004, 43, 3823-3827 [2] Weigend, F.; Schrodt, C.; Ahlrichs, R. J. Chem. Phys. 2004, 121, 10380-10384 [3] Weigend, F.; Schrodt, C. Chem. Eur. J. 2005, 11, 3559-3564 [4] Ahlrichs, R.; Fenske, D.; Rothenberger, A.; Schrodt, C.; Wieber, S. Euro. J. Inorg. Chem. 2006, 6, 1127-1129 [5] Ahlrichs, R.; Crawford, N.R.M.; Eichhöfer, A.; Fenske, D.; Hampe, O.; Kappes, M.; Olkowska-Oetzel, J. Eur. J. Inorg. Chem. 2006, 345-350 [6] Shi, W.; Ahlrichs, R.; Anson, C. E.; Rothenberger, A.; Schrodt C.; Shafaei-Fallah, M. Chem. Commun. 2005, 47, 5893 - 5895 Acknowledgments This work was sponsored by the Center for Functional Nanostructures, Karlsruhe.

Elementary Energetic Effects of Radiation Damage to DNA and RNA Subunits Partha P. Bera and Henry F. Schaefer III Center for Computational Chemistry, Athens, Georgia 30602-2525

E-mail: [email protected], [email protected]

Abstract. Elementary products of radiation damaged DNA and RNA base pairs are investigated using density functional methods. Relative energies, pair dissociation energies, and bond dissociation energies of radicals of the AT, GC and AU base pairs are presented here. Such radicals may be produced by the direct or indirect consequences of radiation, low energy electrons (LEEs), or by reactions with OH radicals. The predicted energetic properties may facilitate the identification of radicals in present and future experiments and thus create possibilities for unraveling DNA and RNA damage mechanisms. The results obtained in this research show the relative ease with which some of the damaged base pairs can be unpaired. This in turn creates the possibility of single and double strand breaks (SSB and DSB).

Prediction of Fluid Phase Behavior from Molecular Models K. Lucas Chair of Technical Thermodynamics, Aachen University Schinkelstrasse 8, 52062 Aachen Abstract. Setting up molecular models for the prediction of fluid phase behavior rests on an interdisciplinary basis of foundation, of which quantum mechanics and statistical mechanics are particularily relevant. Quantum mechanics provides molecular properties such as the geometry, multiple moments and polarizabilities or alternative formulations of the molecular charge distribution, which are required to calculate the energy of a molecular system. Statistical mechanics provides relationships between the molecular energy of the system and the macroscopic fluid phase behavior. Solving the statistical mechanical equations for the general case is possible by computer simulation. Due to the excessive amount of computer time required for the execution of such calculations this route is restricted to particular applications and to model development. For practical purposes solutions using simplifications tailored to the application under consideration are established. This paper reviews the field from an application oriented perspective.

Exploiting the degrees of freedom of intermediate effective Hamiltonians J.P.Malrieu Toulouse

Applications of a Novel Spin-free Combinatoric Open-shell Coupled Cluster (COS-CC) Theory to Single-reference Doublets Dipayan Datta1 and Debashis Mukherjee1, 2, ∗ 1

Department of Physical Chemistry, Indian Association for the Cultivation of Science, Calcutta 700 032, INDIA. 2 Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore 560 064, INDIA. We describe in this paper a compact spin-free coupled cluster (CC) theory for simple openshell configurations, like doublets and biradicals, which are not necessarily single determinants. A new cluster Ansatz for the wave-operator is introduced, in which the cluster operators with direct valence spectator scatterings are replaced by closed-shell-like single and double excitation operators. The cluster operators with exchange valence spectator scatterings and the pure valence excitation operators are allowed to contract among themselves through the spectator orbitals. The novelty of the Ansatz is in the choice of a suitable automorphic factor accompanying each composite of non-commuting operators, ensuring that each such composite appears only once. This leads to CC equations which terminate exactly at the quartic power of the cluster amplitudes, reminiscent of the closed-shell CC theory. As a pilot example application, we compute the state energy of the ground state of the Fluorine radical with three different basis sets, and assess the performance of the theory by comparing with the benchmark full CI result in the same basis sets. The results show the power and the efficacy of the method.

I.

INTRODUCTION

Despite the spectacular success of closed-shell coupled cluster (CC) theories [1–3], a generalization of the CC formalisms to open-shell systems leading to an explicitly spin-free correlation model has neither been straightforward nor easy. Several methodologies have emerged during the last two decades to treat states with open-shell or multireference character of arbitrary complexity. Most of these methods are based on effective Hamiltonian strategy [4] using reference functions spanning a model space. The more widely used among these are the Valence-Universal Multi-reference Coupled Cluster (VU-MRCC) theories [5–7], which are widely used to compute energy differences of states with varying degrees of ionization relative to a closed-shell ground state. These formalisms are explicitly spin-free, but require hierarchical generation of cluster amplitudes of various valence ranks. Valence-Specific (VS) (or equivalently State-Universal (SU)) [8] theories, on the other hand, use reference functions spanning a Hilbert space of a fixed number of valence electrons and therefore generate the state energies per se, without solving the hierarchy. At a lower level of complexity, there are simple open-shell reference configurations about which a cluster expansion can be effected. Such exercises have been attempted using unrestricted Hartree-Fock (UHF) or restricted open-shell HartreeFock (ROHF) determinants as references and defining the cluster operators in terms of spin-orbitals [9–11]. The major disadvantages of these latter methods are their relatively high computational cost, since the number of cluster amplitudes is roughly three times more in the spin-orbital basis than in the orbital basis and also they lead generally to spin-broken solutions. These methods, however, retain the simplicity and compactness of the single-reference coupled cluster (SRCC) methods and generate CC equations which are at most quartic in cluster amplitudes. In the symmetry-adapted-cluster (SAC) expansion formalism, developed by Nakatsuji et. al. [12], the cluster operator generates only those excitations from the reference, which belong to the same symmetry. The symmetryadapted CC expansion, therefore, generates a pure spin-state, but the spin-adapted expressions are unwieldy. Janssen and Schaefer [13] first pointed out that utilization of the full flexibility of the spin-space requires the use of spinfree cluster operators, and in addition to excitation operators, one must generally include operators with spectator scatterings involving the indices of the open-shell (valence) orbitals. Unlike in a closed-shell theory or spin-orbital based open-shell theory, these operators are non-commuting and therefore can be joined among themselves in all powers. As a result, the Baker-Hausdorf expansion does not terminate after the quartic term. In their work, Janssen and Schaefer [13] came across terms involving up to eight-fold commutators. An orthogonally spin-adapted open-shell CC formalism based on unitary group approach (UGA) to many-electron correlation problem has been discussed by Li and Paldus [14]. The chief difficulty arising out of the Janssen and Schaefer method [13] is present in this method too and terms with up to eight-fold commutators are present.

∗ Electronic

address: [email protected]

At the Cutting Edge of a Petascale Computing World: An Overview of Petascale System Interconnect Project Kazuaki J. Murakami Leader of Petascale System Interconnect Project Department of Informatics and Research Institute for Information Technology, Kyushu University, Japan [email protected]

Feng Long Gu, Mutsumi Aoyagi, and Takeshi Nanri Research Institute for Information Technology, Kyushu University, Japan

Koji Inoue Department of Informatics, Kyushu University, Japan Abstract. This talk presents an overview of the Petascale System Interconnect (PSI) project. The PSI project is one of the national projects on “Fundamental Technologies for the Next Generation Supercomputing” of MEXT (Ministry of Education, Culture Sports, Science and Technology), Japan. The goal of the PSI project is to develop technologies enabling petascale supercomputing systems with hundreds of thousands of computing nodes. The PSI project consists of three subprojects to tackle with the three fundamental technologies: subproject 1 is for the small and efficient optical packet switches; subproject 2 is for the low-cost & high-performance MPI communications; and subproject 3 is for the methodologies of evaluating and estimating the performance of petascale systems. With the successful completion of the PSI project, the Japan Next-Generation Supercomputer R&D Center (NSC) will take the technologies to build Japan’s next generation supercomputer, which is expected to be over 70 times faster than the current fastest supercomputers.

Mechanisms of Nucleotidyl Transfer Catalyzed by the Yeast RNA Polymerase II Rui Zhu and Dennis R. Salahub Department of Chemistry and Institute for Biocomplexity and Informatics University of Calgary 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4 Abstract. It has been proposed that all classes of nucleic acid polymerases use the same two-metal-ion mechanism for nucleotide incorporation. The main chemical kinetic scheme is that the oxygen atom of the 3’-OH group of the transcript primer, acting as a nucleophile, forms a phosphodiester bond with the first phosphate of the (deoxy)nucleoside triphosphate and the other two phosphates form a pyrophosphate leaving group. While some molecular modeling studies on DNA polymerases have been performed to investigate the detailed chemical steps involved in the kinetic scheme, few theoretical studies on RNA polymerases are available in the literature. Here, we report a molecular dynamics study of nucleotidyl transfer catalyzed by the yeast RNA polymerase II, which is based on the most recently published crystal structures. We particularly focus on the creation of the nucleophile, i.e., deprotonation of the 3’-OH group. Two pathways are examined: (i) proton transfer to the conserved Asp485 residue of the active site in association with nucleophilic attack and (ii) proton transfer to a nearby water molecule before nucleophilic attack. All the molecular dynamics simulations are carried out by a recently developed reactive force field, ReaxFF, whose parameters are derived directly from quantum chemical calculations. The rate-limiting step of the reaction in both cases is the dissociation of the pyrophosphate leaving group, which needs about 23 kcal/mol of activation energy. The nucleophilic attack needs about 19 kcal/mol of activation energy for pathway (i) and 17 kcal/mol of activation energy for pathway (ii). The water-assisting deprotonation just needs about 7 kcal/mol of activation energy. These data indicate that pathway (i) is comparable to pathway (ii). If water misses the deprotonation of the 3’-OH group before nucleophilic attack in the latter pathway, the general base (Asp485) of the polymerase active site can readily perform the deprotonation in the attack through the former pathway.

Electron Momentum Spectroscopy and Its Applications to Molecules of Biological Interest Feng Wang Centre for Molecular Simulation, Swinburne University of Technology, P. O. Box 218, Hawthorn, Melbourne, Victoria, 3122, Australia

Abstract. Energy and wave function are the heart and soul of Schrödinger quantum mechanics. Electron momentum spectroscopy (EMS) so far provides the most stringent test for quantum mechanical models (theory, basis sets and the combination of both) through observables such as binding energy spectra and Dyson orbital momentum distributions. The capability of EMS to measure Dyson orbitals of a molecule as momentum distributions provides a unique opportunity to assess the models of quantum mechanics based on orbitals, rather than on energy dominated (mostly isotropic) properties. Recently, the author introduced a technique called dual space analysis (DSA), which is based on EMS and quantum mechanics to analyze orbital based information in the more familiar position space as well as the less familiar momentum space. In this article, the development of EMS and DSA is reviewed through the applications to molecules of biological interest such as amino acids, nucleic acid bases and recently nucleosides. The emphasis is the applications of DSA to study isomerization processes and chemical bonding mechanisms of these molecules.

Interatomic (Intermolecular) Decay Processes in Clusters: Current Status and Outlook V. Averbukh and L. S. Cederbaum Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany Abstract. Since their theoretical prediction a decade ago, interatomic (intermolecular) Coulombic decay (ICD) and related processes have been in the focus of intensive theoretical and experimental research. The spectacular progress in this direction has been stimulated both by the fundamental importance of the new electronic decay phenomena and by the exciting possibility of their practical application, for example in spectroscopy. We review the current status of the research of interatomic (intermolecular) decay phenomena in clusters and discuss some perspectives of this new field. Keywords: Interatomic Coulombic decay, environmental effects on electronic decay PACS: 31.15.Ar, 31.50.Df, 31.70.Dk, 32.80.Dz, 36.40.-c

INTRODUCTION Core vacancy states of atoms and molecules represent very highly excited states of the corresponding atomic or molecular ions, typically lying above the double or even multiple ionization thresholds. As a result, these states decay by electron emission in a specific type of autoionization process named after its discoverer, P. Auger [1]. Kinetic energies of the electrons emitted in the course of Auger decay are given by the differences between the bound states of singly and doubly charged species and thus are quantized. This property explains the great spectroscopic value of the Auger electron spectroscopy (AES) [2], as well as its importance for numerous analytical applications, e.g. in surface science (see, for example, Ref. [3]). Auger decay is typically an intraatomic process, only modestly affected by the environment. Usually, such an effect is manifested in the so-called chemical shift of the Auger electron lines (see, for example, Ref. [4]). As an extreme example of the effect of the environment on Auger decay, one can cite the interatomic Auger effect in ionic solids [5]. In 1997, the authors of the theoretical work [6] took a pioneering approach to the issue of the environment effects on the decay of vacancy states. The question posed by the researchers was: “Can a vacancy decay non-radiatively only due to the effect of the environment?”. Surprisingly, it turned out that such an environment-mediated decay is not only possible, but is also a general phenomenon, typical of relatively low-energy inner-shell vacancies in a wide variety of clusters [6]. In order to get an idea of the new decay process discovered by Cederbaum and co-workers, one can consider the decay of 2s vacancy of neon, once in an isolated ion and once in a cluster, e.g. in Nen . The 2s−1 state of the isolated Ne+ lies below the double ionization threshold of Ne and thus cannot decay by Auger mechanism. As a result, (2s−1 ) Ne+ decays radiatively on a nanosecond time scale. However, if (2s−1 ) Ne+ is allowed to interact with an environment, e.g. with other Ne atoms, the situation changes dramatically. Indeed, in Nen cluster, one can consider not only the high-energy Ne2+ Nen−1 doubly ionized states, but also the ones of the type (Ne+ )2 Nen−2 . The latter states are relatively low in energy due to the separation of the positive charge between two neon atoms. In fact, the charge-separated states lie several electron-volts lower than (2s−1 ) Ne+ Nen−1 . This leads to a very interesting interatomic decay process in which 2p electron of the ionized Ne fills the 2s vacancy, while 2p electron of another Ne atom is ejected into continuum. Since such a process is enabled by the Coulombic interaction between the electrons of the two Ne atoms, it has been called interatomic Coulombic decay (ICD). In a small loosely bound cluster, such as neon dimer, the repulsion between the two charges created by ICD leads to Coulomb explosion of the system [7] (see Ref. [8] for an exception). Under such conditions, the excess energy of the initial vacancy state is partitioned between the outgoing electron and the separating positively charged fragments. Thus, while Auger decay leads to quantized Auger electron energies, ICD in small clusters makes the total of the electron and the cluster fragment energies to be quantized. The kinetic energy of the relative motion of the fragments is often called kinetic energy release (KER). The last several years have witnessed a series of remarkable advances in the experimental study of ICD. Hergenhahn, Möller, and co-workers have presented the first experimental evidence of ICD by clearly identifying the new process

Nonlinear ac dielectric response in polyelectrolytes Jean-Louis Déjardin Laboratoire de Mathématiques et Physique des Systèmes, Groupe de Physique Statistique et Moléculaire, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France Abstract. The problem of the nonlinear harmonic response in dielectric relaxation of polyelectrolytes is considered in the context of coupled (rotation-translation) kinetic equations. Perturbation theory is used to derive the complex dielectric increment for an assembly of non-polar rodlike macroions surrounded by small counterions and acted on by a strong dc bias electric field superimposed on a weak ac field. The approach starts from a Smoluchowski equation in configuration space of molecular orientations ( ϑ ) and displacements (x) first used for Kerr effect relaxation by Szabo et al. [J. Chem. Phys. 85, 7472 (1986)]. By solving this equation for the stationary regime, we calculate the expectation value of

(

) ( ) where P and H stand for the first Legendre and Hermite polynomials, characterizing the

P1 cos ϑ H1 x

1

1

first harmonic component of the electric polarization of the macroion. The results so obtained in the form of analytic expressions are illustrated by Cole-Cole-like diagrams and three-dimensional dispersion and absorption plots in order to show the influence of the coupling parameter a measuring the importance of the rotational motion over the translational one.

Molecular Currents and Aromaticity P. W. Fowler Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK

Abstract. A widely used criterion of aromaticity is based on magnetic response properties: an aromatic (anti-aromatic) π-conjugated system is defined as one that sustains a global diatropic (paratropic) ring current when perturbed by a perpendicular external magnetic field. If this criterion is accepted, there is a direct theoretical test of aromaticity: calculate the first-order response of the current density for the molecule of choice, map it and inspect the map for the sense, strength and global distribution of the current. Calculation of induced current densities by the specific distributed-gauge method known as the ipsocentric approach offers practical and conceptual advantages in that physically realistic distributions of current density are obtained with modest basis sets, so that the method is economical, but more importantly, and only with the ipsocentric choice, molecular orbital contributions are free of unphysical occupied-occupied mixing and they therefore give the foundation for an interpretation of current patterns in terms of frontier orbital symmetries, energies and nodal structure. The key role of orbital symmetry/topology in the theory suggests construction of a simplified ‘pseudo-π’ model calculation that can be applied to much larger systems, without significant loss of accuracy in the predictions of currentdensity patterns. Applications to a monocycles and polycyclic aromatic hydrocarbon molecules are reviewed.

Temperature Dependence of the Polarizability of Sodium Clusters: An all-electron Density Functional Study Patrizia Calaminici, Andreas M. Köster, Gabriel U. Gamboa Martinez Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740 México D.F. 07360 México

Abstract. In this contribution we report first-principle all-electron density functional theory (DFT) calculations on small sodium clusters with less than 10 atoms employing the linear combination of Gaussian type orbital DFT program deMon2k. Born-Oppenheimer molecular dynamics (BOMD) simulations over more than 200 ps (> 100,000 time steps) with gradient corrected functionals in combination with DFT optimized all-electron double-zeta valence polarization are presented. In order to study the temperature dependency of the cluster polarizabilities BOMD trajectories from 50 to 900 K are recorded for each cluster. The polarizability tensor is then calculated along these trajectories employing all-electron triple-zeta valence polarization basis sets augmented with field induced polarization functions. The analysis of the BOMD results shows that the temperature dependency of the sodium cluster polarizability varies strongly with cluster size. Moreover, characteristic changes in the polarizability per atom as a function of temperature are observed. The mismatch between theoretical and experimental polarizabilities will be discussed in the light of these new results.

Genetic Algorithm for Structural Optimization of Tubular Nanostructures Teresa E.B. Davies∗ , Mihail M. Popa† and Cristian V. Ciobanu∗ ∗

†

Division of Engineering, Colorado School of Mines, Golden, CO 80401, USA School of Automation, Computers, and Electronics, University of Craiova, 1100 Craiova, Romania

Abstract. Why can metals or oxides form nanotubes, sometimes even chiral ones? How could silicon, which has little or no propensity for sp2 hybridization, form nanotubes akin with the well understood carbon nanotubes in which the atoms are unequivocally sp2 hybridized? It would be perhaps beneficial, if not expected, for the theory to step up to the plate and engage in the discovery of credible growth mechanisms and atomic structures for the tubular and multi-shell structures that can determine future directions in nanoscience and nanotechnology. In an effort to contribute to answering these questions, we present here a global optimization method designed specifically for tubular structures. Due to the recent success of the genetic algorithms in elucidating structures of 1- and 2-dimensional nanoscale materials, we base our optimization procedure on the same evolutionary principles. We have found that the cross-over operations based on planar cuts (which were so successful previously) are not sufficient to ensure convergence to lowest energy structures, and design new ones. The application of the new and more diverse cross-over operations has resulted in converged structures for different materials, which provides confidence in pursuing the application of genetic algorithm for finding the structures of new tubular materials. 1 Keywords: genetic algorithms, modified embedded atom method, Tersoff potentials, Lennard-Jones, nanotubes, nanowires, global optimization PACS: 61.46.Fg, 68.70.+w

1. INTRODUCTION One-dimensional (1-D) nanostructures presently show tremendous technological promise due to novel and potentially useful properties. For example, gold chains on stepped silicon surfaces [1, 2] can have tunable conduction properties, rare earth nanowires and bismuth nanolines have unusual straightness and length [3] and can thus be useful as nanoscale contacts on chips or as templates for the design of other novel structures. Atomic wires on stepped silicon surfaces have also been recently evidenced in the Ga/Si(112) system [4]. The structure of step edges on Si surfaces is of key interest, for it can help trigger a step-flow growth mode [5] useful for preparing high-quality wafers. Understanding the formation, properties, and potential applications of these intriguing 1-D nanostructures requires knowledge of the atomic positions of the adsorbate atoms, as well as of the location of the silicon atoms at the step edges. In recent years, the fundamental and technological efforts towards viable uses of nanostructures have markedly switched from carbon nanotubes to semiconductor nanowires, as the latter allow for a more diverse range of structures and, hopefully, for more control over their properties. Silicon nanowires (SiNW) offer, in addition to their appeal as building blocks for nanoscale devices, the benefit of simple fabrication techniques compatible with the currently well-developed silicon technology. Fervent strides are underway to synthesize nanoscale wires for nano-electronics applications [6], because of the realization that such wires can operate both as nanoscale devices and as the leads that connect them [7]. Currently, the widely used methods of synthesis [8, 9, 10, 11] can produce silicon nanowires (SiNWs) with diameters ranging from several tens of nanometers down to 1 nm. The SiNWs are usually crystalline with a prismatic shape bounded by facets that are parallel to the axis of the wire [9, 10, 11, 12, 13]. Interestingly, while efforts based on rationally controlled growth of SiNWs are underway across the world, three laboratories appear to have achieved silicon nanotubes (SiNTs) instead [15, 14, 16]. The formation of silicon nanowires is by now well understood – so how can Si nanotubes be formed instead of nanowires? The question of nanotube formation in carbon has been answered long ago [17], and the answer is very simple: carbon can readily hybridize and form π bonds which bond the atoms strongly in plane in a honeycomb lattice. The out-of-plane bonding between the such parallel lattices is weak,

1

Email for correspondence: [email protected]

Nuclear quantum effects on the structural properties of solids Iván Scivetti∗ , David Hughes∗ , Nikitas Gidopoulos† , Alfredo Caro∗∗ and Jorge Kohanoff∗ ∗

Atomistic Simulation Centre, Queen’s University Belfast, Northern Ireland, UK † Isis Facility, Rutherford Appleton Laboratory, Chilton, Didcot, England, UK ∗∗ Lawrence Livermore National Laboratory, CA, USA

Abstract. A method to take into the account the effect of quantization of vibrations on the structural and dynamical properties of solids is presented. It is based on mapping a suitable subspace of the vibrational manifold and solving the Schrödinger equation in it. A number of increasingly accurate approximations is described, and results for different models and for ab initio potentials are presented. In particular, we focus on quantum nuclear effects on the lattice constant and interatomic distances for a simple anharmonic monoatomic chain and for hydrogen-bonded systems. We analyze the influence of Brillouin zone sampling. Keywords: Quantum nuclei, isotope effect, lattice dynamics PACS: 61.50.Ah, 63.20.Dj, 67.80.Cx

INTRODUCTION Structural properties of solids like interatomic distances, bond angles and equilibrium lattice parameters are usually calculated by assuming that atomic nuclei (or ionic cores) are classical particles. While this is justified for heavy atoms, whenever light atoms such as hydrogen are involved, this assumption becomes questionable. To obtain the equilibrium volume a useful, widely-used improvement is the quasi-harmonic approximation (QHA). In the QHA the ground state energy is supplemented with the zero-point-energy (ZPE) corresponding to harmonic vibrations. The ZPE depends on the volume in a way characteristic of the type of bonding. For covalent bonding it increases upon compression, while for hydrogen-bonding there is a competition between increasing and decreasing frequencies. The combination of ground state and zero-point energies leads to a modified E vs. V curve, with a minimum located at the quantumcorrected equilibrium volume. The QHA has the additional advantage that it lends itself naturally to the incorporation of thermal effects, in addition to quantum. If ωi (k) are the 3N vibrational bands of the solid, then the QHA free energy is given by   Z 3N Z h¯ 3N h¯ ωi (k) ) dk , (1) FQHA = E + ∑ g(k)ωi (k) dk + kB T ∑ g(k) ln 1 − exp(− 2 i=1 kB T i=1 where the integral extends to the whole vibrational Brillouin zone. Internal structural parameters (distances and angles) are unaffected by the QHA, apart from variations mediated by volume changes. The reason for this is that the quantum average position of a harmonic oscillator coincides exactly with the classical position. It requires some degree of anharmonicity to modify the internal geometry. The general treatment of vibrations in solids or molecules is based on a Taylor expansion of the potential energy in terms of the atomic coordinates. Truncating the expansion at second order results in the harmonic approximation. The dynamical matrix, given by the second derivatives of the potential with respect to the coordinates, can be diagonalized thus leading to a set of orthogonal eigenvectors or normal modes Q µ . Normal modes do not interact at the harmonic level. Additional terms in the Taylor expansion lead to anharmonicity, which can come essentially in two flavors: intra-mode anharmonicity when the vibrational modes remain non-interacting, but the potential seen by one or more modes cannot be approximated by a quadratic expression. This type of anharmonicity can be accounted for in a rather simple way, by solving the one-dimensional Schrödinger equation in each one of the non-quadratic modes. The second type of anharmonicity is due to mode-coupling. When the excursions along a vibrational normal coordinate are large, the approximation of small oscillations implicit in the second-order expansion breaks down. n Successive terms in the expansion involve products of modes of the form Qm µ Qν (and higher-order terms involving more than two modes). Which pairs of modes are coupled depends very much on the specific system. Group theory can be used to discard some couplings, but only if the expansion is truncated at a certain order m + n. In general there

Spin-Orbit Coupling Effects in Di-Hydrides of ThirdRow Transition Elements Shiro Koseki Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan Abstract. Spin-orbit coupling (SOC) effects were investigated for low-lying electronic states in the dihydrides of third-row transition elements by using MCSCF+MRMP2, +FOCI, and +SOCI methods with the SBKJC basis sets augmented by a set of f functions for transition elements and a set of p functions for hydrogen atoms, where MCSCF, MRMP2, FOCI, and SOCI are abbreviations of multi-configuration selfconsistent field, multi-reference second-order Møller-Plesset, first-order configuration interaction, and second-order configuration interaction, respectively. Before the inclusion of SOC effects, six di-hydrides (LaH2, HfH2, TaH2, WH2, OsH2, and IrH2) are lower in energy than the corresponding dissociation limits (transition element and a hydrogen molecule). All of these di-hydrides have bent structures at their energy minima, and the ground states are 2A1, 1A1, 4B1, 5B2, 3B2, and 2A1, respectively. After the inclusion of SOC effects, the ground states are assigned to E1/2, A1, E1/2, A1, A1, and E1/2 in the double-group representation of C2v symmetry. It can be concluded that SOC effects are not so important in LaH2, HfH2, and TaH2, while they become important in describing bending potential energy curves of low-lying electronic states in WH2, OsH2, and IrH2. B

B

B

Approximate Procedures in Multireference Perturbation Theory: Successes and Limitations. Joseph J.W. McDouall * and David Robinson School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK Abstract. We study a number of simplifications to the MRMP2 variant of multireference perturbation theory, with a view to enabling this type of methodology to be applied to a wider range of systems. We consider in turn: the elimination of the orbital optimization stage in preparing the reference wavefunction; the truncation of the configuration expansion in the active space; the combination of the two previous approximations and finally the spin-component scaling of the dynamic correlation energy that has proved very advantageous in single reference MP2 applications. These approximations have important formal and practical consequences, which we illustrate. We test these schemes on diatomic potential energy curves and polyatomic reaction barriers. While the approximations introduced are not applicable in all circumstances we find that many commonly encountered situations are amenable to treatment by these simplified procedures. Accordingly it is hoped that the realm of application of the MRMP2 method will be increased.

*

Corresponding author: [email protected]

Applications of response theory with relaxation Patrick Norman Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden Abstract. Based on the Ehrenfest theorem, an equation-of-motion that takes relaxation into account has been presented in wave function theory, and the resulting response functions are non-divergent in the off-resonant as well as the resonant regions of the spectrum. The derivation of the linear and first-order nonlinear response functions includes exact state theory as well as single determinant approximate state theory thereby including time-dependent Hartree–Fock and Kohn–Sham theories. The response functions in this theory are complex and the methodology is coined the complex polarization propagator technique. The real and imaginary parts of the response functions may correspond to different physical observables. The present work includes applications that involve electric- and magnetic-dipole molecular properties in the visible, ultra-violet, and X-ray regions of the frequency spectrum. The real and imaginary parts of the electric-dipole polarizability and the mixed electricdipole–magnetic-dipole polarizability are determined for S-methyl oxirane in order to calculate the polarizability, linear absorption cross section, optical rotatory dispersion, and electronic circular dichroism. The linear absorption cross section is determined in the ultra-violet region and at the carbon K-edge. The polarizability with an imaginary frequency argument is determined for formaldehyde, acetaldehyde, acetone, and methyl oxirane and the related C6 dispersion interaction coefficients are determined from the Casimir–Polder integral. As a single application of the nonlinear response function, the two-photon resonant enhanced second-harmonic generation response is determined for a “two-dimensional” π -conjugated system. Keywords: response theory, polarization propagator, relaxation, second-harmonic generation, optical activity, dispersion forces, X-ray absorption PACS: 31.10.+z, 31.15.Md, 33.15.Kr, 33.20.-t, 33.20.Kf, 33.20.Lg, 33.20.Rm, 33.55.-b, 33.55.Ad, 34.20.Gj

1. INTRODUCTION Propagator methods were introduced in atomic and molecular physics in the mid-sixties but had already been extensively used in solid state, nuclear, and statistical physics. At first one focused at molecular ionization and excitation processes but, later, more general considerations of molecular response properties were made. An early milestone in the development of molecular polarization propagator methods is the work of Linderberg and Öhrn in 1973 [1]. A modern formulation, based on second quantization, of molecular response properties in approximate electronic structure theory is found in the work by Olsen and Jørgensen in 1985 [2]. This work has served as the foundation for a series of program implementations of linear and nonlinear response functions for a variety of electronic structure methods, and, in the literature of today, there exist numerous successful applications of these approaches. The framework for the theory is very general and applies to perturbations that are time-independent and time-dependent, external and internal, and electric, magnetic, or geometric, and the limitations are basically set by the use of perturbation theory and Fourier decompositions so that, in the present form, it is not readily adopted to time-resolved spectroscopies. In 1998, a re-formulation of response theory based on the differentiation of a time-averaged quasi-energy was made by Christiansen, Jørgensen and Hättig [3]. The main motivation for this work was to achieve a common formulation of response theory in variational and non-variational electronic structure theories, and it has served as the basis for the development of time-dependent coupled cluster theory. It is noteworthy that, although perturbation theory is the common denominator for the mentioned work, it can be applied to situations in which the perturbation field is in resonance with an electronic transition in the molecule (i.e. the quantum mechanical system). The response functions are formally divergent at these points in the frequency spectrum, but their poles and residues are shown to be related to spectroscopic observables. The simplest example is given by the poles and residues of the linear response function which correspond to the excitation energies and transition moments, respectively, of the system, and, although a transition moment in itself is not a physical observable, its absolute square governs the strength of linear absorption. More intriguing examples of the residue analysis of response functions are given by the identification of transition matrix elements for multi-photon absorption and excited state properties. All of these aspects have been the subject of computational studies in the literature and the virtues and limitations of the residual approach for the standard wave function parametrizations are well understood. It stands beyond doubt that response theory in quantum chemistry is mature and has a reached a point where it can

Constrained variational response to Fock-space multi-reference coupled-cluster theory: Formulation for excited-state electronic structure calculations and some pilot applications Prashant Uday Manohar, and Sourav Pal∗ Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India

Abstract Fock-space (FS) multi-reference (MR) coupled-cluster (CC) method has emerged as compact tool to account for electronic structure of open-shell systems and molecules in low-lying excited states. Development of linear response (LR) has been one of the challenging problems in FSMRCC due to multiple-root nature of effective Hamiltonian. The recently developed constrained variational approach (CVA) has opened up a promising tool for efficient evaluation of analytic response properties. In this article, we present formulation of the method for excited state calculations. We discuss the decoupling of equations as a result of spin-adaptation and present some preliminary results for analytical dipole moments and polarizabilities of some molecules in low-lying triplet excited states. ∗

Email: [email protected]

The Linear and Non-Linear Optical Properties of Some Noble Gas Compounds Manthos G. Papadopoulos and Aggelos Avramopoulos Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 116 35, Greece. e-mail: [email protected]. Abstract The linear and nonlinear optical properties (L&NLO) of HArF, HXeOH and HXeSH are reported. The very significant effect, which the inserted noble gas atoms, has on the properties of the resulting derivative, is discussed and interpreted. The property values have been computed by employing a systematically built series of basis sets, aug-cc-pVnZ, and a hierarchy of computational techniques (HF, MP2, CCS, CCSD(T)). Electronic and vibrational contributions to L&NLO properties are presented. We have also discussed the effect of the local field (LF) on the L&NLO properties of HXeOH and HXeSH. The LF is created by the surrounding Xe atoms, since the molecules of interest are synthesized in a Xe matrix. It has been found that the effect of LF on some L&NLO properties is remarkable.

Molecular dynamics and Monte Carlo simulations of organic compounds adsorbed on ice surfaces. S. Picaud , P.N.M. Hoang , L.B. Partay† , G. Hantal† and P. Jedlovszky† 

Institut UTINAM - UMR 6213, CNRS - Université de Franche-Comté, F-25030 Besançon Cedex, France † Institute of Chemistry, Laboratory of Interfaces and Nanosize Systems, Eötvös Loránd University Pázmány Péter stny. 1/a, H-1117 Budapest, Hungary Abstract. The adsorption characteristics of small, partially oxidized hydrocarbons, such as methanol, formaldehyde, ethanol and acetic acid molecules on an ice Ih(0001) proton disordered crystal have been studied on the basis of computer simulations performed at tropospheric temperatures. Molecular dynamics simulations as well as Grand Canonical Monte Carlo calculations have been performed to determine the configurations of the molecules in their adsorption sites, the adsorption energies, the saturation coverage of one monolayer above the ice surface, and the corresponding adsorption isotherms. The results of these simulations are in close agreement with experimental data, and demonstrate that the main driving force for the adsorption of these partially oxidized hydrocarbons on ice is the formation of hydrogen bonds, not only with the water molecules of the ice surface, but also within the adsorbate. Keywords: Molecular dynamic simulation; Monte Carlo simulation; ice; Partially oxidized hydrocarbons; adsorption. ˝ 02.70.Uu, 31.15.Qg, 42.68.Ge PACS: 68.43.Uh,

INTRODUCTION Recent measurements in the upper troposphere have revealed the presence of small, partially oxidized hydrocarbons (POHs) such as methanol, formaldehyde, acetone, formic and acetic acids, which may play a non negligible role in the chemistry of this region. Indeed, the upper troposphere defines a region of the atmosphere between 8 and 12 km, where the temperature is in the 188 K - 228 K range. In this cold environment the photo-oxidation of the POHs can provide a substantial source of HOx radicals that drive photochemical cycles involving ozone production and loss in the atmosphere[1]. Moreover, upper tropospheric air may become supersaturated with respect to water, leading to the formation of cirrus clouds that are largely made of ice particles below 233 K[2, 3, 4, 5] and that can cover up to 30 % of the Earth’s mass at any given time[6]. Hence, the presence of ice particles may promote numerous heterogeneous reactions which are not observed in the gas phase, and which have to be taken into account to better understand the physical chemistry of this region of the atmosphere. In particular, POHs may be scavenged by ice particles, and thus cirrus clouds may influence the partitioning of the different species between the gaseous and solid phases. For this reason, a growing number of experimental[7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] and theoretical[18, 19, 20, 21, 22, 23, 24, 25] studies have recently been devoted to the characterization of the interaction between POHs and ice, in order to provide details on their adsorption, incorporation, diffusion and release mechanisms at the surface and in the bulk of ice crystals. For instance, Knudsen cell and coated-wall flow tube experiments have been performed to characterize the uptake of POHs on ice as a function of their functional groups (e.g., C=O, O-H, C(O)H, C(O)OH) and of their size. These studies, which targeting the adsorption behavior of ketones[9, 12, 13, 14, 16], alcohols[7, 10, 17, 21], carboxylic acids[8, 15], and aldehydes[7, 10] have shown that most of these POHs are physisorbed on ice, and the corresponding adsorption energies are between 70 and 50 kJ/mol. The only exception is formaldehyde, which exhibits a very low affinity for the ice surface. Despite these recent experimental investigations, fundamental questions, such as how trace gases interact with ice, where they prefer to locate at the ice surface and, or whether there is a competition between hydrogen-bonding to ice and lateral hydrogen-bonding between adsorbed species, remained unanswered. These points can be tackled at a theoretical level by means of atomistic simulations. In a series of previous papers, we used molecular dynamics (MD) and/or Monte-Carlo (MC) simulations to investigate the adsorption of acetone[18], methanol[20, 23], formaldehyde[20, 25], ethanol[21], and acetic acid[15] on ice. Indeed, MD and GCMC simulations allow a realistic

Vibrational analysis from quantum mechanic molecular dynamics trajectories. Philippe Carbonniere, Alain Dargelos and Claude Pouchan

Groupe de Chimie Théorique et réactivité, IPREM UMR CNRS 5254, Université de Pau et des Pays de l’Adour 2 rue Jules Ferry, F-64000 Pau, France In this paper we report a vibrational analysis from Quantum Mechanic dynamic DFT based approaches. After a brief presentation of the dynamic simulation using the Atom Centered Density Matrix Propagation (ADMP) formalism, we compare in the case of methyl amidogen the vibrational spectra obtained from a Vibrational Configuration Interaction formalism and the molecular Dynamic approach. Except for the CH stretching modes, the results converge giving a good agreement with the experimental data. The second example concerns a larger sized molecular system, the Glycine radical. An interpretation of all the fundamental bands is given in the MIR area between 150 to 4000 cm-1.

Quantum Chemical Models for Accurate Theoretical Thermochemistry Krishnan Raghavachari* Department of Chemistry, Indiana University Bloomington, IN 47405 Larry A. Curtiss Materials Science and Chemistry Divisions Argonne National Laboratory, Argonne, IL 60439

Accurate quantum chemical techniques such as CCSD(T) have made it possible to evaluate the bond energies of small molecules from first principles with chemical accuracy. In recent years, we have developed “composite theoretical models” such as G3 theory that have made it possible to extend such accuracy for larger molecules. In these methods, high level correlation calculations [e.g., CCSD(T)] with moderate sized basis sets are combined with results from lower level calculations (e.g., MP4, MP2, or even HF) using larger basis sets to approximate the results of more expensive calculations. In this work, we discuss the recently developed fourth generation model, labeled Gaussian-4 (G4) theory, and illustrate its performance for a comprehensive test set of first- and second-row molecules. Extensions to molecules containing heavier elements (main-group as well as transition metals) are also discussed. Finally, new strategies for obtaining accurate density functional thermochemistry for large molecules are outlined.

*

Electronic mail: [email protected]

A dynamically adaptive refinement in muliresolution multiwavelet basis for dynamical quantum wavefunctions Hideo Sekino and Shinji Hamada Toyohashi University of Technology 1.1 Hibarigaoka Tenpakucho Toyohashi 441-8580 and JST Abstract. A dynanically adaptive grid scheme is introduced for the representation of quantum wavefunctions by Multiresplution Multiwavelet (MRMW) basis. A restricted direct product of individual dimension is introduced for representing the Cayley operator and it proves to reduce drastically the computational time and storage space for high dimension problems where the straightforward application of MRMW is too complicated. The efficiency of the scheme is tested in a semi-classical dynamics simulation of molecular electronic system. The time evolution of the wavefunction is stable.

The Electronic Flux in Chemical Reactions Patricio Flores, Soledad Gutiérrez-Oliva, Bárbara Herrera and Alejandro Toro Labbé QTC, Departamento de Química Física,Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile. Abstract. The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used to shed light on reaction mechanisms. Keywords: electronic flux,chemical potential,reaction mechanisms PACS: 31.15.Ar

THE REACTION FORCE. The course of a one-step chemical reaction, or of an individual step in a more complex process, is commonly described by the path of minimum potential energy that links the transition state to the reactants and products and defines the intrinsic reaction coordinate ξ . Recently, the reaction force concept has been introduced to get insight on the mechanism of chemical reactions, the reaction force is the derivative of the potential energy (E(ξ )) with respect to the reaction coordinate ξ [1]: dE (1) . dξ For a generic potential function presenting an energy barrier separating the reactants, located at ξR , and the product at ξP , F(ξ ) exhibits two critical points (at points ξ1 and ξ2 ). These are used to define three reaction regions along ξ : the reactant region (ξR ≤ ξ ≤ ξ1 ) where the reactants gets prepared for the reaction mainly through structural reordering[2, 3, 4, 5, 6]; the transition state region (ξ1 < ξ < ξ2 ) which is characterized by a marked electronic reordering and the product region (ξ2 ≤ ξ ≤ ξP ) that is mainly characterized by structural relaxation leading to the products[2, 4]. F(ξ ) = −

CHEMICAL POTENTIAL AND FLUX. The electronic chemical potential (µ) is a key property to understand the changes of the electronic structure since it accounts for the escaping tendency of electrons from an equilibrium distribution. Chemical potential arises in the Euler-Lagrange equation of the energy functional of Density Functional Theory (DFT) as a Lagrange multiplier to comply with the condition that the electronic density integrates to N, the total number of electrons of the system[7]. It is conceptually useful to examine the profile of chemical potential that for a N electron system with total energy E and external potential v(~r) is defined as[7]:   ∂E µ= , (2) ∂ N v(~r) Owing to the discontinuity of the variable N, chemical potential can be computed through the use of finite difference approximation and the Koopman’s theorem through the following expressions [7]: 1 1 µ ≈ − (I + A) ≈ (εL + εH ), 2 2

(3)

Computational methods for fundamental studies of plasma processes N. Ning∗ , G. Dolgonos∗ , W. Morscheidt† , A. Michau∗∗ , K. Hassouni∗∗ and H. Vach1∗ ∗

LPICM, Ecole Polytechnique, CNRS, 91128, Palaiseau, France LGPPTS, Université Pierre et Marie Curie, ENSCP, 75005 Paris, France ∗∗ LIMHP, CNRS-UPR1311, Université de Paris Nord, 93430 Villetaneuse, France †

Abstract. We present a combination of a wide range of computational methods that permits us to perform in-depth numerical studies of processes taking place in silicon/hydrogen plasma reactors during the fabrication of solar cells by means of Plasma Enhanced Chemical Vapor Deposition (PECVD). Notably, our investigations are motivated by the question under which plasma conditions hydrogenated silicon Sin Hm (n ≤ 20) clusters become amorphous or crystalline. A crystalline structure of those nanoparticles is crucial, for example, for the electrical properties and stability of polymorphous solar cells. First, we use fluid dynamics model calculations to characterize the experimentally employed hydrogen/silane plasmas. The resulting relative densities for all plasma radicals, their temperatures, and their collision interval times are then used as input data for detailed semi-empirical molecular dynamics (MD) simulations. As a result, the growth dynamics of nanometric hydrogenated silicon Sin Hm clusters is simulated starting out from the collision of individual SiHx (x=1-3) radicals under the plasma conditions derived above. We demonstrate how the plasma conditions determine the amorphous or crystalline character of the forming nanoparticles. Finally, we show a preliminary absorption spectrum based on ab initio time-dependent densityfunctional theory (DFT) calculations for a crystalline cluster to demonstrate the possibility to monitor cluster growth in situ. Keywords: silicon, hydrogen, plasma, PECVD, fluid dynamics model, time-dependent DFT, semi-empirical molecular dynamics simulations, cluster growth dynamics, crystallization, absorption spectrum, nanostructures, polymorphous silicon, solar cells PACS: 81.10.Bk, 61.46+w, 81.05.Zx, 81.07.Bc, 52.27.Lw

1. INTRODUCTION Recent experimental studies carried out in our laboratories showed that hydrogenated polymorphous silicon (pm-Si:H) solar cells have higher efficiencies and are more stable with respect to standard amorphous (a-Si:H) solar cells, which makes them economically more attractive. Hydrogenated silicon nanocrystals, incorporated into the amorphous matrix, are thought to be responsible for this improvement. While this discovery might have an important impact on potential industrial applications, very little is yet known concerning the origin and properties of the involved nanocrystals [1]. Recently, it was demonstrated that those nanocrystalline silicon particles are actually produced in the gas phase of the plasma and not on the substrate itself [2]. However, no mechanism has yet been proposed to explain under which experimental conditions those nanoparticles take an amorphous or a crystalline structure. In the following, we will therefore present a semi-empirical MD simulation of the growth dynamics of nanometric hydrogenated silicon particles in the gas phase of a plasma reactor. In the first section, we will characterize the employed plasma by means of a fluid dynamics model. Then, we will investigate the cluster growth under quasi-realistic experimental plasma conditions using semi-empirical molecular dynamics. In the last section, we will then show our first absorption spectrum obtained with a time-dependent DFT approach.

1

Corresponding author, Fax 0033 1 69 33 30 06, [email protected]

Elongation method applied to aperiodic systems --random polypeptides, high spin alignment, polymer in solvent, and DNA Y. Aoki1, F. L. Gu1, Y. Orimoto1, S. Suhai2 and A. Imamura3 1

Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580, Japan (Correspondence to: Y. Aoki, E-mail: [email protected]) 2

Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D69120 Heidelberg, Germany 3 Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan

Abstract. A theoretical method, which makes us possible to efficiently obtain the electronic states of random polymers by combining oligomers at a time, is proposed. This technique is developed at the both levels of semi-empirical method by incorporating it into MOPAC and ab initio method into GAMESS program packages. The reliability and the efficiency of this method are confirmed by applying mostly to aperiodic systems such as random polypeptides, open-shell system with spin helix, polythiophenes in solvent, and DNA.

On The Frontier Bond Location In The QM/MM Description Of Peptides And Proteins. Pierre-François Loos, and Xavier Assfeld Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239, 54506 Vandœuvre-lès-Nancy Cedex, France.

Abstract. We propose to consider two different Quantum Mechanics/Molecular Mechanics partitions of peptides. Not only the usual Cα–Cβ bond is considered as the frontier but also the less common C–N and N–C peptide bonds are investigated as putative QM/MM boundaries. When the frontier atom is a C atom then the partial double bond character of the peptide bond is naturally taken into account by our scheme. However, when the frontier atom is nitrogen, then special care has to be taken. Instead of the usual mono valence electron description that was previously proposed, the N frontier atom is described with 5 electrons (2 core and 3 valence) to allow him to share part of his valence electrons with the carbon atom, and then to recover the partial double C–N bond of the peptide.

Molecular response properties calculated and analyzed using static and time–dependent DFT Jochen Autschbach Department of Chemistry University at Buffalo State University of New York Buffalo, NY 14260–3000, USA email: [email protected] Abstract. Computations of static and frequency–dependent properties of closed–shell molecules are considered. Among the topics that are discussed are analyses of nonlinear optical properties by with the help of localized orbitals, the embedding of such analysis tools in computations with spin–orbit coupling, and the computation of frequency–dependent magnetic response. The formalism to calculate frequency–dependent molecular properties within the framework of time–dependent density functional theory (TD–DFT) is summarized. Keywords: Electric and magnetic properties of molecules, density functional theory, time–dependent density functional theory, nonlinear optical properties, relativistic effects PACS: 31.15.Ar, 31.15.Ew, 33.15.-e, 33.15.Kr, 42.65.An, 71.15.-m, 71.15.Rf, 78.20.Ci

INTRODUCTION The past 2 decades have seen a surge in first–principles computations of molecular response properties, i.e. theoretical studies of what happens to a molecule when it is subject to external fields, internal perturbations such as from nuclear spins, and so on. Here, some of our recent developments for the computation of static and time–dependent response of molecules computed within the framework of static and time–dependent density functional theory (DFT and TD–DFT) [1, 2] will be reviewed. A TD–DFT response property module for molecules which makes use of Slater–type atomic– orbital (AO) basis functions, numerical integration, and density fitting was developed in our group over the past few years years. It can perform linear, quadratic, and cubic response computations along with chemically intuitive analyses of these properties. Our research has for some time been focussed on the analysis of response properties calculated from first principles theory with the help of orbital–based tools [3–5]. Recently, we have adopted the Natural Bond Orbital (NBO) machinery developed by Weinhold and coworkers [6–9] for this purpose. Our response module can perform an analysis of the results in terms of NBOs and associated “natural localized molecular orbitals” (NLMOs) [7]. Recently, this technique was applied to analyses of dynamic first (ˇ) and second ( ) electric dipole–hyperpolarizabilities in nitroaniline and derivatives thereof [10, 11]. In the following, some of the technical details of the implementation, demonstration of its computational performance (linear scaling features), etc. will be presented. Results for the NBO analyses of nitroaniline and derivatives will be presented. The NBO analysis has recently been extended to static properties computed within a two–component (spin–orbit) relativistic DFT formalism [12]. As an example, the role of delocalization for the magnitude of the Pt–Tl nuclear spin–spin coupling in a Pt–Tl bonded dinuclear metal complex as revealed by the NBO analysis will be discussed briefly. We will then discuss computations of linear response involving an external magnetic field perturbation. Recent efforts in our group were directed towards computing the magnetizability of a molecule not only in the static case but also as a function of frequency [13]. Unlike in the static case, the magnetic–dipole magnetic–dipole polarizability has to be combined with other linear response tensors in order to yield a physically meaningful origin–independent linear magnetic response. Computations of the origin–independent magnetic linear response will be presented for M– hexahelicene and SF6 . We will also discuss computations of a linear intensity differential by which the time–dependent dipole–dipole magnetizability may be extracted from experimental data. The last section will conclude with some remarks about the static limit of magnetizabilities and other magnetic response properties calculated from “uncoupled” linear DFT response and the relation of these computations to the usual sum–over–states (SOS) theory.

Induced Rayleigh and hyper-Rayleigh spectra. Pair hyperpolarizability Tadeusz Bancewicz Nonlinear Optics Division, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Pozna´n, Poland Abstract. Collision-induced (CI) Rayleigh and hyper-Rayleigh (HR) light scattering spectra are briefly discussed. The CI hyperpolarizability for D∞h molecule–atom system is studied. Results are applied to the case of H2 -Ar pair. Spherical (s,1) (s,1) (s,1) (s,1) components ∆β01 (R) ∆β21 (R), ∆β23 (R) and ∆β45 (R) of the dipole part of the H2 -Ar first hyperpolarizability tensor ∆β (s,1) are computed. Keywords: collision-induced spectra, hyper-Rayleigh scattering, CI hyperpolarizability, MP2, SCF, H2 -Ar PACS: 33.80.Gjxa,34.30.th

June 28, 2007

INTRODUCTION Molecular interactions are known to influence the scattering spectra of molecules. Generally, contributions of interaction (collision)-induced effects to scattering intensities depend on the symmetry of the microsystems involved [1, 2, 3, 4]. For atoms and optically isotropic molecules the second-order dipole2 polarizability tensor ααβ is isotropic and it results in completely polarized monomer radiation [5, 6, 7, 8, 9, 10, 11] of Rayleigh and Raman scattering. However Rayleigh radiation is weakly depolarized due to collision-(and/or interaction-) induced pair polarizability. The hyper-Rayleigh light scattering process depends on the first hyperpolarizability tensor βi jk which vanishes for centrosymmetric microsystems [12, 13, 14, 15, 16, 17, 4, 18]. The third-rank hyperpolarizability tensor is odd under − → coordinate inversion, whereas the inversion leaves the the centrosymmetic molecule and consequently the β tensor − → unchanged [19, 20, 21] Hence, β must vanish for centrosymmetrics microsystem. Still, in systems composed of centrosymmetic species HRLS appears due to intermolecular interactions. To study these HR phenomena the CI pair − → hyperpolarizability tensor ∆ β is needed. In this paper we investigate the CI hyperpolarizability for D∞h molecule – atom system. The H2 –Ar pair is considered in detail. Moreover, the CI Rayleigh and hyper-Rayleigh light scattering is briefly reviewed. Complete permutational symmetry of indices of the polarizability ∆αi j as well as hyperpolarizability ∆βi jk tensor is assumed.

CI RAYLEIGH LIGHT SCATTERING DIFFERENTIAL CROSS SECTION The quantum-mechanical expression for the pair Rayleigh scattering double differential scattering cross section (DDCS) has the form [7, 22]: 

∂ 2σ ∂ ω∂ Ω

Introducing the dyad W(R)



R

=



ωs4 c

4 Z∞ −∞

→ → α (0) · e)(n∗ · ∆− α (t) · e)∗ i dt e−iω t hn∗ · ∆− | {z }

Wi j = n∗i e j

(1)

(R)

Fn (t)

(2)

Phenomenological and Microscopic Description of Molecular Layer and Crystal Optical Polarization M. Mestechkin 12773 Seabreeze Farms Dr. # 33, San Diego CA 92130, USA Abstract. The optical polarization of molecular layers and crystals in the strong field is characterized by nonlinear susceptibilities (NSC), which are obtained from hyperpolarizabilities (HP) of free molecules in any order. NSC, distinct in layer and bulk, are also described at the microscopic level by means of inclusion of the Madelung interaction potential (MIP) into the Hartree-Fock equations (HFE) for molecular crystal. The phenomenological approach is deduced from the microscopic one, in particular, the known Bloembergen formula and χ(ω)=α(ω)(vα(ω)L)-1 are derived from HFE for crystal HP. The calculations demonstrate that NSC, computed by both methods for fullerene crystal, coincide at all frequencies. Small deviations are determined by the anisotropy of the Madelung polarization interaction (MPI), which is expressed through the Lorentz tensor in the 2nd order in interelectron distances. MPI anisotropy in cubic cell appears in the 4th order.

The rôle of metals in amyloid aggregation: a test case for ab initio simulations V. Minicozzi , S. Morante ,† , G.C. Rossi and F. Stellato 

Dipartimento di Fisica, Università di Roma “Tor Vergata” and INFN, Sezione di Roma “Tor Vergata” Via della Ricerca Scientifica, 00133 Roma, Italy † CRS - SOFT c/o Dipartimento di Fisica - Università di Roma “La Sapienza” P.le A. Moro, 00185 Roma, Italy

Abstract. First principle ab initio molecular dynamics simulations of the Car–Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and β -amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2 3 ps. We present structural results which confirm indications coming from NMR and XAS data. Keywords: β -amyloids, Car–Parrinello MD PACS: 61.10.Ht,31.15.Ar

1. INTRODUCTION Owing to the recent spectacular technical and architectural advances in the design of new high performance computers, extremely powerful platforms are today available to the scientific community which allow to attack problems of unprecedented complexity in many research fields ranging from high energy particle physics to disordered systems, from material science to systems of biological interest. In this short contribution we would like to present ab initio simulations of the Car–Parrinello (CP) type in two paradigmatic examples. One is the study of the Cu coordination mode in the Prion Protein (PrP) binding sites located within the N-terminal octarepeat region. The second is a feasibility study of a comparative analysis of copper and zinc structural arrangements in β -amyloid–metal complexes. Good reviews on the subject of CP Molecular Dynamics (CPMD) simulations, as well as references to the original papers can be found in [1, 2]. The alternative road to CPMD simulations is that of using either quantum chemistry methods or hybrid approaches (like QM/MM). In general these methods have the virtue that they allow tackling model systems of more realistic sizes. The price to pay when using the first kind of approach is that one must know a priori the atomic structure of the system, which is often to a large extent unknown, while in the second case one has to employ classical mechanics for a large portion of the system and set up a delicate matching procedure in the region of the system where quantum and classical mechanics will have an overlap. Both the above strategies have been used for investigating challenging problems like enzymatic reactions and protein structural properties. A non-exhaustive list of methodologically useful papers can be found in refs. [3, 4, 5, 6]. It is worth noticing that, although there are many interesting works dealing with the analysis of the geometrical structure of the copper binding site in PrP (among which the previously cited [3, 4, 5]), not much has been done on the important issue of the specificity of transition metals binding properties in Aβ aggregation processes (see however [7]). We end this brief report with some conclusions and an outlook of possible future lines of investigations.

2. METHODS In all cases we have considered CPMD simulations have been carried out employing the freely available QuantumESPRESSO package [8, 9], in the version which makes use of Vanderbilt’s ultra-soft pseudo-potentials and PBE exchange-correlation functional [10]. Periodic boundary conditions have been imposed on the super-cell containing

EOM-CCSDT study of the low-lying ionization potentials of CO2 , CS2 and OCS Monika Musiał Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland Abstract. The equation-of-motion coupled-cluster (EOM-CC) method with full inclusion of triples is applied to evaluate the vertical ionization potentials (IP) of carbon dioxide, carbon disulphide and carbonyl sulfide for relatively large basis sets. The theoretical results are accurate enough to define a consistent set of vertical ionization potentials. IP-EOM-CCSDT (IP-EOMCC Singles, Doubles, Triples) improves the IP-EOM-CCSD values by up to 0.4 eV for CO2 , 0.5 eV for CS2 and OCS. Keywords: Coupled-Cluster, Equation-Of-Motion, ionization potentials, connected triple excitations PACS: 01.30.Cc, 31.15.Dv, 31.50.Bc

INTRODUCTION In the Coupled Cluster (CC) [1, 2] theory, photoionization energies can be obtained from the equation-of-motion (EOM) [3, 4, 5, 6, 7] formalism in full analogy with the similar excitation energy (EE) [7, 8, 9, 10] and electron affinity calculations [7, 11, 12]. Hence the EOM-CC offers an approach that is conceptually simple, inexpensive, and allows straightforward applications. The development of IP-EOM-CCSDT (Ionization Potential EOM-CC Singles, Doubles, Triples) scheme [5] in the fully vectorized and factorized form makes it possible to obtain highly accurate vertical ionization potential which is our objective. The IP states that correspond to the ionized reference can be obtained by diagonalizing H¯ (≡ e−T HeT ) in the basis of determinants containing N −1 electrons where N refers to the number of electrons in |Φ o i. Using a proper factorization procedure, described in Ref. [5], the IP-EOM-CCSDT method can be applied to relatively large basis sets [5, 6]. In this paper we apply IP-EOM-CCSD and IP-EOM-CCSDT methods using a sequence of basis sets to determine the vertical IP’s of CO2 , CS2 and OCS molecules.

THEORY The basic idea of the IP-EOM-CC formalism is quite simple. The starting point for the approach is a ground state single reference CC calculations. Ionized state |Ψk i, different from the ground (or reference) state, |Ψo i, is parametrized in a linear fashion as: |Ψk i = R(k)|Ψo i with R(k) =

R(k) = R1 (k) + R2 (k) + R3 (k) + · · · 1 1 ∑ ri (k)iˆ+ 2 ∑ ∑ riaj (k)aˆ† jˆiˆ+ 12 ∑ ∑ riabjl (k)aˆ† bˆ †lˆ jˆiˆ+ · · · a ij i ab i jl

(1) (2) (3)

where standard convention for indices is used, i.e. indices a, b, ... (i, j, ...) refer to virtual (occupied) one-particle levels ˆ j, ˆ ...) represent creation (anihilation) operators. The effect of the R(k) operator is to remove an electron and aˆ† , bˆ † , ... (i, from the |Ψo i state (R1 ), which can be accompanied by single (R2 ) and double (R3 ) excitation process. These two states satisfy the Schrödinger equations: H|Ψo i = Eo |Ψo i and H|Ψk i = Ek |Ψk i. By choosing to represent the ionized state eigenfunction as in Eq. (1) it is readily obtained [5] that ¯ (HR(k)) c

= ωk R(k)

(4)

¯ ¯ or in matrix form (HR(k)) c = ωk R(k) where ωk is the energy change connected with the ionization process and H is the similarity transformed Hamiltonian, in terms of connected diagrams defined as: H¯ = e−T HeT = (HeT )c and subscript c indicates that only connected terms are considered in the expansion.

Second Hyperpolarizabilities (γ) of 1,3-Dipole Systems: Diradical Character Dependence of γ Masayoshi Nakano *#, Ryohei Kishi#, Akihito Takebe#, Masahito Nate#, Hideaki Takahashi#, Takashi Kubo†, Kenji Kamada§, Koji Ohta§, Benoît Champagne¶, and Edith Botek¶ #

Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, JAPAN † Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, JAPAN § Photonics Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, JAPAN ¶ Laboratoire de Chimie Théorique Appliquée Facultés Universitaires Notre-Dame de la Paix (FUNDP), rue de Bruxelles, 61, 5000 Namur, BELGIUM Abstract. The static second hyperpolarizabilities (γ) of 1,3-dipole molecules in singlet states are investigated using various ab initio molecular orbital (MO) electron correlation methods and density functional theory (DFT) methods with extended basis sets. Substantial dependences of γ as a function of the method of calculation are observed. At the UCCSD(T) level of theory, we observe the enhancement of γ in the intermediate diradical character regions as compared to those of small and pure diradical character regions.

*

Corresponding author. E-mail address: [email protected]

Evaluation of the performance of parallel sparse-matrix multiplications and the effect of dynamic load-balancing Takeshi Nanri∗ , Takeshi Soga† , Koji Kurihara∗∗ , Feng Long Gu∗ , Hiroaki Ishihata‡ and Kazuaki Murakami∗∗,∗ ∗

Research Institute for Information Technology, Kyushu Univ., 6-10-1 Hakozaki Fukuoka, 812-8581, Japan † Fukuoka IST ∗∗ Graduate School of Information Science and Electrical Engineering, Kyushu Univ. ‡ Fujitsu Ltd.

Abstract. This paper proposes and evaluates an algorithm of parallel matrix multiplication on compressed sparse-matrices. In addition to that, to overcome the problem of imbalanced distribution of non-zero elements over processors, a technology for dynamic load-balancing is examined. Measurements of the performance shows that the algorithm achieves sufficient speed up. The experiments in this paper could not show the significant effect of the dynamic load-balancing. It requires more analysis to determine the reason of this. Keywords: Sparse matrix, Parallel computing, Load balance PACS: 89.20.Ff

INTRODUCTION Operations on sparse matrices play important role on large-scale scientific computings. In many cases, sparse-matrices are compressed in some common format, such as CCS(Compressed Column Storage) or CRS(Compressed Raw Storage), so that values and positions of only non-zero elements are stored [6], to reduce the computation time and the amount of memory. Among many operations, matrix multiplication is becoming an important operation in some scientific problems. For example, in order to avoid cubic scaling in diagonalization for the decomposition of the overlap matrix, Jansik et al [1] introduced a scalable method of calculating the matrix square-root by using iterative matrix multiplications. However, there have been almost no approach for parallelizing this operation on compressed sparse-matrices with MPI. Therefore, this paper proposes a parallel algorithm of matrix multiplication on sparse matrices with CCS format and evaluates the performance of it. In this algorithm, the root rank decompresses and broadcasts one row of the compressed sparse-matrix, while the other ranks receive the row and calculate their part of the matrix with it. The decompression and the calculations are overlapped to achieve the higher scalability. In addition to that, this paper applies a dynamic load-imbalancing technology on this program. One of the most important problem on operating the compressed sparse-matrices is the load-imbalance in parallel computing. This problem is caused by the difficulty of dividing non-zero elements equally to the processors. The authors have developed a dynamic load-balancing technology on MPI programs[5]. This technology adjusts the implementation of collective communication in MPI library according to the dynamic information of load-balance. This paper evaluates the effect of dynamic loadbalancing on the parallel sparse-matrix multiplication program. The next section of the paper introduces some related works. Section 3 presents the detailed algorithm of parallel sparse-matrix multiplication. Section 4 describes the dynamic load-balancing technology. Section 5 shows results of performance measurements and discusses over them.

RELATED WORKS Many approaches are proposed to parallelize the matrix-vector multiplication on a compressed sparse-matrix and a vector such as [2]. In addition to that, there is an attempt on parallel computing of sparse-matrix multiplication on special patterns of sparsity [3]. However, there has been no attempts to parallelize the matrix-matrix multiplication on compressed sparse-matrices with general sparsity patterns.

Vibrational Normal Modes Contributions to the Vibrational First Hyperpolarizability in a Sample of TICT Molecules. Amar Saala,b, Mahfoud Hadj Ben Alia, Ourida Ouameralia a

Laboratoire de Physico-Chimie Théorique et Chimie Informatique faculty of chemistry USTHB university, Algiers 16111, Algeria. b Department of Chemistry, UMMTO university, Tizi-ouzou 15000, Algeria

Abstract. The vibrational normal modes contributions to the total vibrational first hyperpolarizability have been evaluated at the HF/6-31G level for a set of twist intramolecular charge transfer (TICT) molecules. From this study we tried to obtain a relationship between the vibrational contribution of a normal mode and its type, its frequency as well as with the interring twist angle.

Predictive Quantum Chemistry: A Step Toward “Chemistry Without Test Tubes”*

*

Quoted from an article Rod published in the University of Florida’s College of Liberal Arts Sciences news letter, CLAS.

Ajith Perera Department of Chemistry, Quantum Theory Project, University of Florida, Gainesville, FL 32611 Abstract. The merits of the claims made in two recent papers entitled “First generation of pentazole (HN5, pentazolic acid), the final azole, and a zinc pentazolate salt in solution: A new N-dearylation of 1-(pmethoxyphenyl) pyrazoles, a 2-( p-methoxyphenyl) tetrazole and application of the methodologyto1-( pmethoxyphenyl) pentazole” (R. N. Butler, J. C. Stephan and L. A.Burke, J. Chem. Commun. 2003, 10161017) and “First generation of the pentazolate anion is solution is far from over” (T. Schroer, R. Haiges, S. Schneider and K. O. Christe, Chem. Commun. 2005,1607-1609) are verified by predictive quality theoretical methods. Knowing whether the CF3OH in HF solution undergoes protonation to form CF3[OH2]+ is critical to the success of the recently proposed synthetic route to form the prototype perfluorinated alcohol, CF3OH. Chirstie and co-workers first considered the 13C and 19F shielding constants to distinguish CF3OH and CF3[OH2]+, but it turns out that they both have similar chemical shifts. Furthermore, they noted that the computed 13C chemical shifts differ by 11 ppm from the measured ones and claimed that “These findings presented a dilemma because either experimental or the calculated shifts has to be seriously flawed and, therefore chemical shifts alone it was impossible to decide whether CF3OH in liquid HF is protonated or not”. Instead of chemical shifts, they propose to use 13C-19F NMR spin-spin coupling constants and argue that the observed 20 Hz difference of 1J(13C-19F) to the increase in the covalent character upon protonation. The reported discrepancy in computed and measured chemical shifts is reexamined and the spin-spin coupling constants results are verified by the predicative-level calculations.

Band Structure of Polymer Extracted from Oligomer Calculations Anna Pomogaeva a), Feng Long Gu a),b), Bernard Kirtman c), and Yuriko Aoki a) a)

Department of Material Science, Faculty of Engineering Sciences, Kyushu University, 6-1 KasugaPark, Fukuoka 816-8580, Japan b) Current address: Research Institute for Information Technology, Kyushu University, Japan c) Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 931069510, U.S.A. Abstract. A method to build band structure of polymers from oligomer calculations has been developed. The correspondence between calculated energies of finite molecular chain and wave vector is obtained by projecting molecular orbitals (MOs) on the model Bloch functions. On the example of polydiacetylene, the reliability of the method for different computational methods (Hartree-Fock (HF), Density Functional Theory (DFT) with different basis sets) is shown.

Multi-physics Extension of OpenFMO Framework Toshiya Takami∗ , Jun Maki∗ , Jun-ichi Ooba∗ , Yuuichi Inadomi† , Hiroaki Honda† , Ryutaro Susukita∗∗ , Koji Inoue‡,† , Taizo Kobayashi∗ , Rie Nogita∗ and Mutsumi Aoyagi∗,† ∗ Research Institute for Information Technology, Kyushu University, Fukuoka 812–8581, Japan PSI Project Lab., Kyushu University, 3–8–33–710 Momochihama, Sawara-ku, Fukuoka 814–0001, Japan ∗∗ Fukuoka IST Foundation, Acros Fukuoka Nishi Office 9F, 1–1–1 Tenjin, Chuo-ku, Fukuoka 810–0001, Japan ‡ Department of Informatics, Kyushu University, 6–10–1 Hakozaki, Higashi-ku, Fukuoka 812–8581, Japan †

Abstract. OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the subsequent development planning corresponding to MPS is presented. It is discussed which should be selected as a scientific software, lightweight and reconstructable form or large and self-contained form. Keywords: fragment molecular orbital method, reference interaction site model, multi-physics simulation, open-source software PACS: 02.70.-c, 05.10.-a, 31.15.-p

INTRODUCTION AND OVERVIEW Multi-physics simulation is widely used even in complex scientific simulations. Such a calculation is often constructed by combining multiple theories including different degrees of approximations and different scales of description. Since reality and accuracy are required increasingly, these simulations have become larger and more complicated year by year. Grids, distributed computer resources over wide-area networks, are expected to execute such complicated scientific applications, and have been installed all over the world in order to demonstrate large-scale heterogeneous simulations with the help of middlewares [1]. On the other hand, the next generation supercomputer with a petascale performance is already planned in several countries[2]. Thus, the development of high-performance computing environments is fast and transient. As a scientist, it is important to watch the trend of those computer resources. In the present contribution, multi-physics calculations by the fragment molecular orbital (FMO) method [3] are considered under the distributed computing environments. The new FMO code toward a “peta-scale”[4] is extended to multi-physics simulations. It is also discussed what architecture and development policy should be effective under the fast-moving world of computing.

GRID-ENABLED CALCULATIONS OF FMO Before entering the main subject, we briefly review the grid-enabled FMO implementations have been developed in the NAREGI project[1]. These are based on the famous MO package, GAMESS[5].

Implementation of a Loosely-coupled FMO Although it is usually considered as an approximation to ab initio MO, the FMO algorithm is a multi-layered problem (see Fig. 1(b)) with the MO calculations for each fragment and the electro-static (ES) interaction between fragments. In the MO-layer, the quantum mechanical interactions of all the atoms and electrons within a fragment are included to obtain the fragment energy. On the other hand, only the classical ES interaction is considered when we go over the boundary of fragments. Since the MO-layer calculations can be executed independently, we can break the program into loosely-coupled components corresponding to the large-scale parallel execution in distributed computing environments (Fig. 1(c)).

ΛCCSD(T) Energies and Forces: Improving Upon CCSD(T) Andrew G. Taube and Rodney J. Bartlett Quantum Theory Project, University of Florida, Gainesville, FL, USA Abstract. Coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] is a high-accuracy reference to which other methods are measured; however, away from equilibrium RHF based CCSD(T) often fails. To remedy this failure, the ΛCCSD(T) method was introduced and implemented for both energies and gradients within the ACESII program system. Like CCSD(T), ΛCCSD(T) is extensive, orbitally invariant, and scales O(N 7 ). Applying ΛCCSD(T) to molecules at equilibrium shows little degradation of the CCSD(T) results. For bond-breaking ΛCCSD(T) is shown to be a significant improvement over CCSD(T). Keywords: Coupled-cluster, bond-breaking, perturbative approximations PACS: 01.30.Cc, 31.15.Dv, 31.50.Bc

INTRODUCTION Coupled-cluster theory is recognized as the most generally applicable and accurate quantum chemical method for medium-sized molecules of chemical interest [1]. This statement is embodied most fully in the coupled-cluster singles, doubles, and perturbative triples method: CCSD(T). For equilibrium properties CCSD(T) is considered the "gold standard" to which other methods are compared. Unfortunately, CCSD(T) shows profound failures when one moves away from equilibrium. Due to the perturbative nature of the (T) correction, as bonds are stretched, and orbitals become degenerate, the triples energy correction diverges, which leads to unphysical dissociation behavior for non-van der Waals bonded molecules. For example, this failure manifests itself in what one might imagine are simple singly-bonded molecules, such as lithium fluoride. Fig. 1 shows a comparison between the CCSD(T) bond-breaking curve and the Full Configuration Interaction (Full CI) curve [2, 3] for LiF. As the ground state dissociation curve approaches an avoided crossing with the ionic first excited state, the (T) correction diverges, yielding unphysical results for bond lengths longer than approximately 12 a.u.

−106.9 RHF CCSD(T) Full CI

Energy (Hartree)

−106.95

−107

−107.05

−107.1

−107.15 2

4

6

FIGURE 1.

8 10 Bond Length (a.u.)

12

LiF bond-breaking

14

16

Implementation of CCNUGrid-based Computational Environment for Molecular Modeling Kai Liu†, Changhua Luo¶, Yanliang Ren†, Jian Wan†,* and Xin Xu‡,* †

Key laboratory of Pesticide and Chemical Biology of Ministry of Education of China and College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China ¶ Platform Computing Incorporated Company at Beijing, Beijing 100083, China ‡ State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Center for Theoretical Chemistry, Xiamen University, Xiamen 361005, China

Abstract. Grid computing technology has being regarded as one of the most promising solutions for the tremendous requirement of computing resources in the field of molecular modeling up to date. Contrast to building a more and more powerful super-computer with novel hardware in a local network, grid technology enable us, in principle, to integrate various previous and present computing resources located in different location into a computing platform as a whole. As a case demonstration, we reported herein that a campus grid entitled CCNUGrid was implemented with grid middleware, consisting of four local computing networks distributed in College of Chemistry, College of Physics, Center for Network, and Center for Education Information Technology and Engineering, respectively, at Central China Normal University. Visualization functions of monitoring computer machines in each local network, monitoring job processing flow, and monitoring computational results were realized in this campus grid-based computational environment, in addition to the conventional components of grid architecture: universal portal, task management, computing node and security. In the last section of this paper, a molecular docking-based virtual screening study was performed at the CCNUGrid, as one example of CCNUGrid applications.

*

Corresponding authors.

Utilizing the fact that among all trial functions orthogonal to an approximate Ground State, Φ0, the closest, Φ1+, to the Exact First Excited State, ψ 1, has lower energy than the Exact: E[Φ1+] < E[ψ 1] Naoum C. Bacalis Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vasileos Constantinou 48, GR-11635 ATHENS, Greece Abstract. The truncated configuration interaction (CI) approximations of the Hamiltonian eigenstates suffer from lack of simultaneous accuracy: If they are orthogonal as a result of optimization of one state, the other states are poorly approximated; and if they are independently optimized, then they cease to be mutually orthogonal. The fact that: Among all functions, orthogonal to an approximate ground state, the one closest to the (unknown) exact first excited state, of the same symmetry, has lower energy than the exact, leads to the conclusion that: Minimizing the energy of a first excited state approximation, orthogonally to an approximate ground state, should be avoided, because it will depart, instead of approaching, the exact first excited state. Further analysis suggests a method to construct CI approximations of the ground and of the first excited state, which are mutually orthogonal and both closer to the exact than the independently optimized (non-orthogonal) ones. Keywords: Orthogonal Excited States PACS: 31.15.xt, 31.15.-p, 31.10.+z, 02.70.?c

1. In the following the Hamiltonian expectation value of a wave function, Ψ, is denoted by EΨ and is called energy of Ψ. For a non-degenerate Hamiltonian of unknown bound eigenstates of a specific symmetry ψ 0 , ψ 1 , ... and eigenenergies E ψ 0 < E ψ 1 < ..., minimizing the energy, EΦ1 , of the 1st excited state approximation Φ1 , while keeping orthogonal to a good (known) approximation of ψ 0 , say Φ0 , with energy EΦ0 (Φ1 orthogonal to Φ0 ), must lead to an energy minimum, say EΦ1ε < E ψ 1 , while the Hylleraass - Undheim - MacDonald (HUM)[1] 2nd root of the secular equation has 1 energy EHUM > E ψ 1: All wave functions are normalized to 1; by analysis, first an upper bound functional of an excited state E ψ n is reported, ­ i ¯ ® ¯2 i ¯ ¯ EΦ − ∑n−1 i=0 E ψ | ψ Φ n n 0 1 n−1 E ψ ≤ U [ψ , ψ , ...ψ |Φ] = n−1 i 1 − ∑i=0 | h ψ | Φi |2 which serves as a (negative) criterion for the quality (rejection) of Φ0 : If, for some function Φ, U 1 [Φ0 |Φ] < EΦ0 , then Φ0 is far from ψ 0 and must be rejected. Incidentally, EΦ0 cannot be lower than ¯ ®¯ E ψ 0 + (E ψ 1 − E ψ 0 )(1 − |hΦ0 ¯ψ 0 ¯2 ) > E ψ 0 this being the lowest value that an actual calculation can report, higer than variational limit E ψ 0 . © the ª 0 0 1 0 1 If a “good" Φ (i.e. with EΦ < E ψ ) were in the plane space of ψ , ψ , then the minimum energy of Φ1 , orthogonal to Φ0 , would occur at the closest state to ψ 1 among all states orthogonal to Φ0 , say Φ1+ , ­ ® ψ 1 − Φ0 Φ0 |ψ 1 1+ Φ ≡p 1 − |hΦ0 |ψ 1 i |2 with energy

Information-Theoretic Biodescriptors for Proteomics Maps: Applications to Rodent Hepatotoxicity Subhash C. Basak*, Brian D. Gute*, Kevin T. Geiss† and Frank A. Witzmann¶ *University of Minnesota Duluth, Natural Resources Research Institute, 5013 Miller Trunk Hwy., Duluth, MN 55811, USA † Human Effectiveness Directorate, Air Force Research Laboratory, 2610 Seventh Street, Wright-Patterson AFB, Ohio 45433, USA ¶ Department of Cellular & Integrative Physiology, Indiana University School of Medicine, 1345 West 16th Street, Rm 308, Indianapolis, Indiana 46202, USA Abstract. This paper describes an approach using information theory to derive a complexity measure for proteomics maps generated using 2-dimensional gel electrophoresis (2DE gel). The maps used in this study were partitioned into 5x5 grids and total protein abundance in each grid square was compared to the total abundance for the entire map. Next, Shannon's relation was applied to characterize the distribution of protein abundance across the entire map. Details of the approach are discussed, including an example of the calculations for one proteomics map containing 200 spots. Finally, results for the Map Information Content index are presented for a set of six maps calculated using 200, 500, and 1,400 protein spots. It is hoped that the application of information-theoretic techniques to characterize the complexity of these maps, thus reducing the amount of information presented to the researcher, will help in comparing maps containing a great deal of information and yield information useful in computational toxicology. Keywords: 2DE gel; biodescriptor; complexity; halocarbon; hepatotoxicity; information theory; map information content; proteomics; proteomics maps. PACS: 87.14.Ee; 87.15.Aa; 87.15.Tt

INTRODUCTION Following the completion of the Human Genome Project, the emerging technologies of genomics, proteomics, and metabolomics are taking an increasingly important role in the prediction of biomedicinal activity and toxicity of chemicals. Whereas microarray studies provide an assessment of cellular transcriptional processes, proteomics provides a better understanding of cell function because the intracellular proteins are the workhorses of living systems. The field of proteomics employs such technologies as two-dimensional gel electrophoresis (2DE), matrixassisted laser desorption-ionization (MALDI), surface-enhanced laser desorption ionization (SELDI), and isotopecoded affinity tagging (ICAT) for the analysis and characterization of cellular proteins. Many authors have used 2DE gel technology in understanding the molecular basis of chemical toxicity [1,2]. In this method the tissue or cell exposed to the toxicant is homogenized and the proteins are separated by charge and mass through two-dimensional electrophoresis. The magnitude of each spot after separation gives the abundance of a particular type of protein, or a closely-related set of proteins which comprise an individual spot. A typical 2DE gel can result in the isolation and identification of 1,500–2,000 proteins. An important goal of toxicoproteomics is to study the perturbation of protein expression in tissues under the influence of toxins. However, characterizing patterns consisting of 1,500 or more objects is a daunting task which cannot be accomplished simply through visual inspection; it requires rigorous mathematical/statistical methods for a thorough and objective analysis of such patterns. Our group has been involved in characterizing toxicoproteomic patterns using four different techniques: a) invariants of graphs associated with proteomics maps [3], b) spectrumlike representations of proteomics maps based on projections of the 3-D space (mass, charge, and abundance) onto

Modeling the IR spectra of acetaldehyde from a new vibrational configuration interaction method Didier Bégué and Claude Pouchan Université de Pau et des Pays de l’Adour Equipe de Chimie Théorique et Réactivité UMR 5254 – CNRS IPREM IFR Rue Jules Ferry – BP 27540 64075 Pau – France

Abstract. In this paper we present a new vibrational configuration interaction method known as a parallel vibrational multiple window configuration interaction P_VMWCI which generates several VCI matrices and enables the variational treatment of medium size molecular systems. Application to acetaldehyde gives a new interpretation of the MIR experimental data.

Stability and structure of Na+Krn (n = 1-20) clusters J. Dhiflaoui1, H. Bouzouita1 and H. Berriche* 1, 2 1

Laboratoire de Physique et Chimie des Interfaces, Département de Physique, Faculté des Sciences de Monastir, Avenue de l’Environnement, 5019 Monastir, Tunisia 2

Physics Department, Faculty of Science, King Khalid University, P. O. B. 9004, Abha, Saudi Arabia.

Abstract: We have investigated the structure and stability of Na+Krn (n=1-20) small clusters. The potential energy surface of the system is described using additive potentials VNa+Kr and VKr-Kr, which represent the pair interactions taken from the best available CCSD ab initio calculations. Both potentials have been fitted by Tang and Toennies and Lennard-Jones (LJ) analytical forms. In addition, the potential energy surface has been explored by the Monte Carlo conjugate gradient method in order to determine the geometry of each Na+Krn cluster and its isomers. Their relative stability was studied by calculating the energy per Krypton atom, the first derivative and the second derivative. It was shown that n=6, 8, 9, 10, 12 and 16 correspond to the magic numbers related to the most stable clusters.

Theoretical study of the CsLi molecule beyond the Born-Oppenheimer approximation N. Mabrouk1, H. Berriche*1, 2 and F. X. Gadea3 1

Laboratoire de Physique et Chimie des Interfaces, Département de Physique Faculté des sciences de Monastir, Avenue de l’Environnement 5019 Monastir, Tunisia. 2 Physics Department, Faculty of Sciences, King Khalid University, P. O. B. 9004, Abha, Saudi Arabia. 3 Laboratoire de Physique Quantique, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Cedex, France Abstract. The adiabatic and diabatic, potential energy curves, the spectroscopic constants and the transition dipole moments of the lowest electronic states of the CsLi molecule dissociating into Cs (6s, 6p, 5d, 7s, 7p, 6d, 8s) and Li (2s, 2p, 3s) have been performed. We have used an ab initio approach based on non-empirical pseudopotential, parameterized l-dependent polarization potentials and full configuration interaction calculations. Our spectroscopic constants of the ground and the first excited states are in good agreement with the available theoretical works.

Similarity and dissimilarity of DNA/RNA sequences D. Bieli´nska-Wa¸z˙ ∗ , P. Wa¸z˙ † , W. Nowak∗ , A. Nandy∗∗ and S. C. Basak‡ ∗

Instytut Fizyki, Uniwersytet Mikołaja Kopernika, ul. Grudzia¸dzka 5, 87-100 Toru´n, Poland † Centrum Astronomii, Uniwersytet Mikołaja Kopernika, ul. Gagarina 11, 87-100 Toru´n, Poland ∗∗ School for Environment Studies Jadavpur University, Calcutta 700 032, India ‡ Natural Resources Research Institute, 5013 Miller Trunk Highway, Minnesota 55811-1442 USA Abstract. Multi-dimensional aspects of similarity studies of DNA/RNA sequences are emphasized. The new graphical representation presented in our recent papers and its descriptors are used as numerical examples of the multi-dimensionality. Keywords: DNA/RNA sequences, descriptors, method of moments PACS: 02.50.-r, 87.14.Gg

INTRODUCTION The aim of this paper is an analysis of general aspects of the way similarity-dissimilarity should be interpreted. Similarity is like a beauty: It is strongly dependent on the properties being considered, on the weights given to each property and on the function connecting the properties. A pair of objects can be identical taken into account property 1 and another pair of objects if property 2 is considered. There is no universal answer about similarity relations for a set of complex objects. In this work these aspects of similarity are illustrated using DNA/RNA sequences. Recently, many methods aiming at characterizations of the sequences appeared. A group of very intuitive methods constitute all kinds of graphical representations. Several approaches to the graphical representation of DNA, from 2D to 6D methods have been introduced (see review [1]). The original method of plotting DNA sequences as a walk in 2D-space using four orthogonal directions that represent the four bases was introduced in Refs. [2], [3], and [4]. However, such a representation may lead to some parts of the sequence being hidden if the walk is performed back and forth along the same trace. In order to eliminate, or to minimize, the degeneracy caused by the repetitive walks, the 2D-methods have been modified and also multi-dimensional representations have been introduced. However, only 2D-methods can be really recognized as good visualization techniques. Higher order dimensions do not play their role. They are not a convenient tool for the visualization. A key point in such studies is a correct choice of the descriptors characterizing the nature of the plots. Numerical characterization are the basis of studies of a large number of sequences. There are two classes of approaches to defining such descriptors: The geometrical ones [5], [6], [7] and the graph-theoretical ones [8], [9], [10], [11]. A review of the graph-theoretical representations and descrip-

Protein dynamics and spectroscopy for ferryl intermediate of Cytochrome c Oxidase: A molecular dynamics approach Vangelis Daskalakis *†, Stavros C. Farantos *† and Constantinos Varotsis* *

Department of Chemistry, University of Crete, POBox 2208, 71305, Voutes-Heraklion, Crete, Greece Foundation for Research and Technology-Hellas (FORTH), POBox 1385, 71110, Voutes- Heraklion, Crete, Greece

†

Abstract. Cytochrome c oxidase is the membrane bound terminal enzyme in the respiratory chain. Molecular oxygen is reduced to water in its heme Fe/CuB active site. The O–O bond cleavage produces the ferryl-oxo (FeIV=O) intermediate. Molecular Dynamics calculations for a part of the protein containing over 8600 atoms are employed to probe the frequencies of vibrational modes which involve the stretching of Fe-O during protonation/deprotonation events near the active site. The role of protein frame for the spectroscopic properties of the ferryl intermediate is proved to be significant, as the intensity of the oxygen sensitive bands is controlled by conformational changes. In addition, the mechanism of the release of the produced water molecules is examined by changing the protonation state of a residue in the entrance of a proton pathway in the enzyme. B

Comparative theoretical study of Poly[3-(4-Octylphenyl)thiophenes] and Poly[3-(4octylphenoxy)thiophenes] as promising photovoltaic cells materials Ahmed Dkhissi and Claude Pouchan

Groupe de Chimie Théorique et réactivité, IPREM UMR CNRS 5254, Université de Pau et des Pays de l’Adour 2 rue Jules Ferry, F-64000 Pau, France The geometric and electronic structure of [3-(4-Octylphenyl)]Thiophenes (POPT) and [3-(4-octylphenoxy)thiophenes] (POPOT) oligomers, ranging in size up to the octamer (240 atoms), have been calculated with density functional theory (B3LYP/6-31G*). The knowledge of the geometries for these polymers is of utmost importance in order to understand their optical properties in different phase (solution and condensed phase) . The calculations indicate that, in opposition to the first polymer where the introduction of the pendant phenyl disturb the planarity for the backbone of the conjugated segment, the second polymer has a nice organisation where the conjugated chain still planar even the presence of octylphenyl groups. The optical spectra are calculated with TDDFT and Zindo approaches on the basis of the geometries provided by DFT, and compared to experimental data.

INTRODUCTION Conjugated organics polymers are of interest in the field of materials for solid-state electronics1 since they can be solutionprocessed, and because the techniques of synthetic organic chemistry can be employed to generate a large variety of structures. 2 These materials are now utilized in several industrial applications such as photovoltaic cells. 3 In a recent review, are recalled the most significant papers devoted to the the study of the low band gap polymers for organic photovoltaic.4 One of the most successful excitonic solar cell (XSCs) is based on a polymer/fullerene blend.5 In particular, a ~5% power conversion efficiency reported 6 for the poly-3-hexylthiophene (P3HT)/fullerene device is quite encouraging. While there could be a number of physical processes limiting the efficiency, the control of electronic and optical properties of the polymer itself is of great interest to optimize the efficiency. So in order, to support, or even guide , the synthesis of novel materials with enhanced properties, quantum chemical calculations are increasingly applied, in particular for the prediction of the optical properties of Π-conjugated polymers. The optical bandgap is a key parameter that controls, for instance, the efficiency of light absorption in solar cells. As poly-3-hexylthiophene (P3HT) are the most promising candidate for cell solar applications, the search of novel material, in order to optimize more the physico-chemical properties, based on P3HT is expected to be the best way. Poly[3-(4Octylphenyl)Thiophenes] (POPT) and Poly[3-(4-octylphenoxy)thiophenes] (POPOT) seem to be a good choice, since the introduction of a phenyl ring into the side chains would enhance conjugation and thermal stability.7 The regioregularity in the polymer is of great importance for the characteristics of the polymer such as conductivity and charge carrier mobility and transport.8-9 In the case of P3HT, several reports have investigated the regioregularity and its effects on packing of the polymer.10-11 In the photovoltaic applications, substitued polythiophenes should demonstrated a high degree of regioregularity in order to allows a self-organisation of the polymer in the solid state to give a maximum of Π- Π interactions. Based on these remarks, two interesting polymers are synthesized: POPT and POPOT with higher regioregularity (i.e 94%). The polymers have been characterized using several experimental techniques as NMR, UV-Vis and X-ray diffraction etc...The experimental data indicate that the absorption spectrum of POPT is largely redshifted (0.6 eV) from solution to solid phase while their corresponding shift is only of 0.16 eV for POPOT. These difference is not yet fully understood experimentally. So, the motivation of this work, by using quantum chemical calculations, is to give an explanation to the experimental finding and in the same time doing a comparative theoretical studies for these polymers. Based on the several approaches used in the field of Conducting Polymers, we used the so-called oligomer approach, in which the properties of oligomers of increasing chains length are first calculated, and then extrapolated to ideal infinite polymers.12 Even the oligomer approach requires calculating the properties of rather large systems, containing up to 242 atoms (POPOT), the method used herein are relatively cost efficient (DFT) for electronic structure calculations on large systems in comparison to those usually used in the conjugated sytems (semiempirical Hartree-Fock methods). The use of DFT again low-cost computational approaches is due to the nature of the systems studied here where the twisting is expected to be important due to the substitued groups. In general DFT with B3LYP hybrid functional is recommended for twisting of conjugated polymers.13

SMMH - A Parallel Heuristic for Combinatorial Optimization Problems

Guilherme Domingues 1,2), Yoshiyuki Morie 1,2) , Feng Long Gu 2), Takeshi Nanri 2), and Kazuaki Murakami 2,3) 1) Institute of Systems & Information Technologies, Fukuoka, JAPAN 2) Research Institute for Information Technology, Kyushu University, JAPAN 3) Department of Informatics, Kyushu University, JAPAN Abstract. The process of finding one or more optimal solutions for answering combinatorial optimization problems bases itself on the use of algorithms instances. Those instances usually have to explore a very large search spaces. Heuristics search focusing on the use of High-Order Hopfield neural networks is a largely deployed technique for very large search space. It can be established a very powerful analogy towards the dynamics evolution of a physics spin-glass system while minimizing its own energy and the energy function of the network. This paper presents a new approach for solving combinatorial optimization problems through parallel simulations, based on a High-Order Hopfield neural network using MPI specification.

Induced hyper-Rayleigh spectra. Theoretical and numerical analysis of spectral moments. Waldemar Głaz ∗ , Tadeusz Bancewicz ∗ , Jean-Luc Godet† and George Maroulis∗∗ ∗

Nonlinear Optics Division, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Pozna´n, Poland † LaborLaboratoire des Propriétés Optiques des Matériaux et Applications, Université d’Angers, 2 boulevard Lavoisier, 49045 Angers, France ∗∗ Department of Chemistry, University of Patras, GR-26500 Patras, Greece

Abstract. Theoretical and numerical methods of evaluating spectral moments characterizing properties of the collisionally hyper-Rayleigh scattered light (CHRS) shall be presented. In order to calculate the moments we have extended the theory so that it could include the (hyper)polarizabilities of higher rank. Numerically obtained ab initio hyperpolarizability values have been used. The values have been obtained for three diatomic noble gas systems: HeNe, HeAr and NeAr, and for several temperature points. The semi-classical and the quantum computations have been performed in order to achieve the goal; both from the sum rule method as well as from the spectral profiles. A brief outline of the methods used is presented in the sections hereafter. Keywords: collision-induced spectra, hyper-Rayleigh scattering, CI hyperpolarizability, spectral moments PACS: 33.80.Gjxa,34.30.th

July 18, 2007

NUMERICAL DETAILS In this study we have considered spectral moments of the light scattered by the systems of He-Ne, He-Ar and NeAr noble gas mixtures, of which the CHRS spectral profiles were studied in our previous work [1, 2, 3]. For these supermolecules the ab initio hyperpolarizability surfaces b˜ 1 (R) and b˜ 3 (R) computed by Maroulis et al. [4, 5, 6] and the interatomic potentials reported by López-Cacheiro et al. [7] were used. The classical zeroth, second and the fourth spectral moments of the collisionally induced hyper-Rayleigh spectra were directly computed for the dipolar (related to the component of rank L=1 of the hyperpolarizabilty tensor) and octopolar (L=3) parts of the CHRS intensity for each heterodiatom. The semi-classically corrected CHRS zeroth, first and second moments were computed. Quantum-mechanical calculations have been also performed. For the supermolecular collisions like these of interest in this work no general analytical solutions of the Schrödinger equations are expected to be available. Therefore, the problem of finding the necessary sets of wavefunctions was sorted out by having recourse to one of the standard numerical techniques: the Numerov procedure of solving differential equations was applied, with two initial points derived from the WKB approximation. As a result of the strategy assumed we arrived at the values of of the zeroth, first and second order moments for every system considered and at a variety of temperatures. The figures yielded by both the quantum and the semi-classical codes were compared. In the subsections that follow a short summary of the basic procedures, on which the numerical computations are subsequently based, is presented .

Reduced Density Matrices in Quantum Electronic Transport R. J. Bartlett, G.Fagas, and J.C. Greer Currents across molecules bonded between two metal electrodes are commonly treated as single electrons tunnelling through an effective potential barrier; this independent particle picture is well-known to describe many aspects of tunnelling. Examining quantum transport with explicit many-body treatments of the molecular region, we examine criteria for establishing effective single particle models to study tunnelling in metal-molecule-metal junctions. We find maximizing the overlap of the reduced density matrix derived from a single Slater determinant to the exact reduced density matrix defines the best single particle picture for transport [1]. This criterion leads directly to the problem of determining the natural orbitals on the molecular region within the tunnel junction. Non-equilibrium Green’s function (NEGF) approaches to quantum transport do not directly consider the oneelectron (1e) reduced density matrix when calculating current-voltage characteristics. However, the relationship

ρ(r,r ′) =

1 dωG(r,r ′;ω) 2πi ∫

(1)

allows us to relate approximations leading to the reduced density matrix and Green’s function. In this context, Pickup and Goscinski have shown that correcting the Green’s function through second order in the self-energy Σ(2) leads to improved prediction of ionization potentials (IPs) and electron affinities (EAs), as well the reduced density matrix calculated from eq. 1 becomes accurate to second order in electron correlation [2]. We discuss the impact of improving IPs and EAs, and hence the electro-negativity, on prediction of currents across single molecules and relate these approximations to transport methods that rely on a direct determination of the reduce density matrix [3].

REFERENCES 1. G. Fagas, P. Delaney, and J.C. Greer, Phys. Rev. B 73, 241314(R) (2006) 2. B.T. Pickup and O. Goscinski, Mol. Phys. 26, 1013 (1973) 3. P. Delaney and J.C. Greer, Phys. Rev. Lett. 93, 036805 (2004)

Investigating the Performance of Collective Communications on SMP Clusters: a Case for MPI_Allgather Feng Long Gu, a) Hyacinthe NZIGOU M., b) Guilherme de Melo Baptista Domingues, c) Takeshi Nanri, a) and Kazuaki Murakami a,b) a) Research Institute for Information Technology, Kyushu University, Japan b) Department of Informatics, Kyushu University, Japan c) Institute of Systems & Information Technologies, Kyushu, Japan Abstract. Message-passing interface (MPI) is a specification targeting parallel processing on Multiple instruction stream, multiple data stream (MIMD) architectures. Collective operation in MPI specification needs intensive communications. This paper reports an investigation on the performance of collective operations on PC clusters and multi-core Symmetric MultiProcessor (SMP) computers. MPI_Allgather is one of the most relevant MPI collective communications. From the comparison between the different MPI Allgather algorithms (Ring and Pairwise) on different platforms, we describe how multi-core systems can take the best advantage by exploiting difference between inter-node and intra-node communications.

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Are There Frame-Distortion Contributions To Collision-Induced Absorption And Collision-Induced Light Scattering? Uwe Hohm Institute of Physical and Theoretical Chemistry, Technical University of Braunschweig, Hans-SommerStr. 10, D-38106 Braunschweig, Germany Abstract. Collision-induced spectroscopy, such as collision-induced absorption (CIA) and collisioninduced light scattering (CILS), can give valuable information on permanent electric moments, polarizabilities and intermolecular-interaction potentials. In general the collision-induced spectra of the pure rare-gases and their binary mixtures are understood fairly well. However if at least one of the collision partners is a molecule then in some cases the spectra show features which can hardly be explained by current theories which deal with the case of undistorted molecules. Here we discuss the possibility of collision-induced frame distortion as an additional effect to be considered in collisioninduced spectroscopy.

Implementation and Evaluation of Fock Matrix Calculation Program on the Cell Processor Hiroaki Hondaa), Tetsuo Hayashib), Yuichi Inadomia), Koji Inouea) and Kazuaki J. Murakamia,b) a)

Research Institute for Information Technology, Kyushu University 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan b) Faculty of Information Science and Electrical Engineering, Kyushu University 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Abstract. Various processor architectures have been proposed until today, and the performance has improved remarkably. Recently, the Chip Multi-processors (CMPs), which has many processor cores onto a chip, are proposed for further performance improvement. The Cell processor is one of such CMP and shows high computational performance. Although this processor is designed for the multimedia, that high performance character can be utilized to molecular orbital calculation. In this study we implemented Fock matrix construction program on the Cell processor, and evaluated computational performance. As a result, there were two kinds of main stalls by the branch prediction and the data alignment, which are controlled by software mechanism for the simplification of the Cell processor hardware. It is possible to improve the performance about 30%, if the branch prediction hit ratio could be improved to 99%. For data alignment stall, a part of stalls, which is originated by data shuffle pipeline, could be decreased by preparing hardware data alignment mechanism.

Electric Dipole Polarizability Of Aluminum Phosphide Clusters AlnPn (n=2-9) And Electron Delocalization Panaghiotis Karamanis1 and Demetrios Xenides2,3 1

Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA. 2 Laboratory of Computational Sciences, Department of Computer Science and Technology, University of Peloponnese, Terma Karaiskaki, GR-22100 Tripolis, Greece, 3 Division of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria. Abstract. We have calculated the static dipole polarizabilities of stoichiometric AlnPn clusters with n=2-9 at HF, B3LYP, B3PW91 and mPW1PW91 levels of theory using basis sets of increasing size. Our results show that AlP clusters behave like the well studied GaAs clusters and their per-atom polarizabilities decrease rapidly with cluster size. At HF and the DFT levels the per-atom-mean polarizability saturates with size after n=4. Finally, from the methodological viewpoint, our results show that for those clusters, the different hybrid density functionals we used converge in the computation of the per-atom-mean polarizability as the size of the cluster increases.

Computational Studies on Dihalogen Complexes of N-methyl Imidazoline-2-thione and N-methyl Imidazolidine-2-thione Agnie Mylona Kosmasa and Demetrios K. Papayannisb a

Division of Physical Chemistry, Department of Chemistry, b Department of Material Science and Engineering , University of Ioannina, Ioannina, Greece 45 110

Abstract. The structural and energy characteristics of N-methyl Imidazoline-2-thione and N-methyl Imidazolidine-2-thione molecular complexes with the dihalogens I2, IBr and ICl have been investigated using quantum mechanical techniques. In all cases the planar geometries have been found to be favoured over the perpendicular structures which present a vertical arrangement of the dihalogen IY axis with respect to the imidazolethione plane. The results also reveal interesting trends regarding the correlation of various properties such as the S-I boning distance, the N-H stretching frequency shifting, the enthalpy of complexation and the interaction between the amidic hydrogen with the electron-acceptor dihalogen ability and the electronegativity of the Y atom.

Halogenated Methyl Nitrates, CX3ONO2 (X=F, Cl). A Computational Study of their Properties and Capacity to Act as Sink Compounds in the Troposphere Agnie M. Kosmasa and Antonija Lesarb a

b

Division of Physical Chemistry, Department of Chemistry, University of Ioannina, Greece 45110, Department of Physical and Organic Chemistry, Insitute Jožef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia

Abstract. Quantum mechanical techniques are employed to investigate the structure and stability of halogenated methyl nitrates CX3ONO2 (X=F, Cl). The calculations indicate the severe influence of the halogen electron withdrawing effect on the structural parameter changes and the stabilization of the halogenated species compared to the plain methyl analogue, CH3ONO2. On the basis of these findings, the significance of alkyl nitrate intermediate formation in the tropospheric oxidation of halocarbons is discussed.

Field-Theoretical Approach to Many-Body Perturbation Theory: Combination of MBPT and QED Ingvar Lindgren Physics Department, Göteborg University, Göteborg, Sweden Abstract. Many-Body Perturbation Theory (MBPT) is today highly developed. The electron correlation of atomic and molecular systems can be evaluated to essentially all orders of perturbation theory—also relativistically (RMBPT)—by means of techniques of Coupled-Cluster type. When high accuracy is needed, effects beyond RMBPT will enter, effects of retarded Breit interaction and of radiative effects (Lamb shift), effects normally referred to as QED effects. These effects can be evaluated by means of special techniques, like S-matrix formulation, which cannot simultaneously treat electron correlation. It would for many applications be desirable to have access to a numerical technique, where effects of electron correlation and of QED could be treated on the same footing. Such a technique is presently being developed and gradually implemented at our laboratory. Preliminary numerical results will be given.

Introduction Many-Body Perturbation Theory (MBPT) can effectively treat electron correlation of atomic and molecular systems to essentially all orders, using methods of Coupled-Cluster type [1], and it can also handle quasi-degeneracy problems using the "extended model-space technique" [2]. Quantum-electrodynamical (QED) effects, however, can be combined with standard MBPT only in the form of first-order energy corrections [3]. QED effects alone can be treated with higher accuracy. using S-matrix formulation or related numerical techniques [4], but these techniques cannot treat the electron correlation beyond second order. It would be desirable to have access to a technique capable of treating QED and electron correlation on the same footing. The Covariant-Evolution Operator technique, recently introduced at our laboratory for QED calculations [5, 6, 7], has such a potential, and this is presently being explored at our laboratory. The covariant evolution operator represents the time evolution of the relativistic state vector. This operator contains singularities in the form of unlinked diagrams or intermediate model-space states, and eliminating these leads to finite residual contributions, model-space contributions (MSC), like the folded diagrams of MBPT. The remaining regular operator, referred to as the Green’s operator, plays a central role in the new formulation. It is quite analogous to the Green’s function of field theory and at the same time closely related to the many-body wave operator and effective Hamiltonian. Therefore, this operator serves as a link between field theory and MBPT and makes it possible to treat quantum-electrodynamics systematically within the framework of many-body perturbation theory. Treated to all orders, the procedure leads for two-electron systems to the Bethe-Salpeter equation. The technique is presently being applied to light heliumlike ions, where quasi-degeneracy appears in excited states and where effects of electron correlation as well as of QED might be important. Presently no other numerical technique is available for such calculations.

Basic formalism In standard time-independent MBPT a number of target states are considered, satisfying the Schrödinger equation ˆ which transforms the model states to the full target states, H|Ψα i = E α |Ψα i. The basic tools are the wave operator Ω, and the effective Hamiltonian Heff , which operating on a model state yields the corresponding exact energy [2] ˆ α0 i; |Ψα i = Ω|Ψ

Hˆ eff |Ψ0α i = E α |Ψα0 i

(1)

The model states are the projections of the target states on the model space (intermediate normalization) |Ψ0α i = P|Ψα i. The wave operator satisfies in the general open-shell case the generalized Bloch equation in the linked-diagram form £ ¤ ¡ ¢ ˆ H0 P = Q V Ω ˆ − ΩV ˆ eff Ω, P (2) linked

Improvements in algorithms for two electron repulsion integrals evaluation in Gaussian type basis sets Marcin Makowski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, Cracow, 30-060, Poland e-mail: [email protected] Abstract. Some optimizations of the algorithms computing two electron repulsion integrals in Gaussian type basis sets are presented. Two typical cases arising in actual calculations are discussed. One of them concerns the evaluation of integrals over low contracted basis functions, the other applies to the integrals over the basis functions of low angular momentum and high degree of contraction. Efficiency of the algorithms obtained by the optimization techniques presented here is compared to the other known approaches. Keywords: two electron integrals, gaussian basis sets PACS: 31.15.Ar

INTRODUCTION Since the advent of so-called direct methods for ab inito quantum chemical calculations, in which two-electron repulsion integrals (ERI) are recomputed each time when needed, a lot of progress has been made in the area of efficient ERI calculations. Majority of current methods for ERI computation employ the set of recurrence relations to construct the final quantities from (ss|ss)-type integrals proceeding through some number of intermediate steps and auxiliary integrals. In this paper we will discuss some techniques that optimize the way such recursions are employed in actual ERI generation algorithms. In applications presented here we will refer to two typical classes of algorithms. One of them concerns the evaluation of integrals over low contracted basis functions and the other is relevant for integrals over the basis functions of low angular momentum and high contraction degree.

LOW CONTRACTION CASE One of the most popular schemes used when basis functions with relatively low degree of contraction are present is the one proposed by Obara and Saika [1] and later modified by Head-Gordon and coworkers [2], and Lindh with coworkers [3]. For a given quartet of primitive functions it starts from the set of Boys functions FN which are used to calculate auxiliary s-type integrals (ss|ss)N : 5

ΘN000000000000 = (ss|ss)N =

2π 2 √ K xyz K xyz FN (αR2PQ ), pq p + q ab cd

(1)

where for primitive Gaussian functions with exponents equal a, b, c, d and centered on A, B,C, D respectively, relevant quantities are defined as follows: p q α Px XPQ xyz Kab

= a+b = c+d pq = p+q aAx + bBx = a+b = Px − Qx ab 2 = exp(− R ). a + b AB

(2)

Theoretical study of the reaction between NH2+ and CH3COOH Laura Largo, Pilar Redondo, Carmen Barrientos, Víctor M. Rayón, Antonio Largo Dpto. Química Física y Química Inorgánica, Universidad de Valladolid, 47005-Valladolid, España

ABSTRACT In recent years, the number of molecules detected in the interstellar medium has increased and it is expected that new molecules will be detected with the new instrumental techniques. The detection of aminoacids in interstellar medium is one of the main challenges for radioastronomers. Glycine is the simplest aminoacid and a tentative detection in space1, not confirmed2, was reported. In the present work we have carried out a theoretical study about possible processes the synthesis which could lead to precursors of glycine in the interstellar medium. In particular, we propose the reaction between NH2+ and CH3COOH as a possible process leading to precursors of glycine. We have carried out a thermodynamic analysis of the reaction products and we only find two exothermic channels leading to the products NH2CH2COOH+ (ionized glycine) and CH3COONH2+ respectively. In order to analyze their viability in the interstellar medium we have constructed the correponding potential energy surface [NC2O2H5]+, characterizing differents intermediates and transition states. We have employed second-order Möller-Plesset perturbation theory with the cc-pVTZ basis set for geometry optimizations and harmonic vibration frecuencies calculations. Electronic energies were refined at the CCSD(T)/aug-cc-pVTZ level.

REFERENCES 1. Y.J. Kuan, S.B. Charnley, H.C. Huang , W.L. Tseng, Z. Kisiel, Astrophys. J. 593, 848-867 (2003). 2. L.E. Snyder, F.J. Lovas, J.M. Hollis, D.N. Friedel, P.R. Jewell, A. Remijan, V.V. Ilyushin, E.A. Alekseev, S.F. Dyubko, Astrophys. J. 619, 914-930 (2005).

A Systematic Study of Cyanides and Isocyanides of First-Row Transition Metals P. Redondo1, V. M. Rayón1, H. Valdés2, C. Barrientos1, and A. Largo1 1

Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain 2 Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic

ABSTRACT In recent years, there has been a renewed interest from the experimental point of view in determining the molecular structure of simple metal cyanide species. Metal monocyanides are known to adopt different type of arrangements in the gas phase depending on the metal atom1-3: alkaline cyanides adopt a T-shape structure whereas alkaline earth elements prefer the linear isocyanide geometry. On the other hand, the observation of MgCN, MgNC, AlNC, NaCN, SiCN, and SiNC in the interstellar medium, have inspired the search for similar transition metal species. A theoretical study at uniform levels of theory along the first-row transition metal series might allow a detailed knowledge of the factors governing the molecular structure and properties of these compounds. The isomerization process has also been studied. In addition, a detailed analysis of the bonding has been carried out employing the topological analysis of the charge density and an energy decomposition analysis. The role of the covalent and electrostatic contributions to the metal-ligand bonding, as well as the importance of π bonding, are discussed. Optimized geometries and vibrational frequencies for the different M(CN) systems (M=Sc-Zn) have been obtained employing two different theoretical approaches: the density functional theory calculations, in particular B3LYP, and the QCISD level. For checking the adequacy of monoconfigurational theoretical methods we have carried out CASSCF optimizations followed by MRCI single-point calculations to improve the energy. In order to refine the electronic energy single-point calculations at the CCSD(T) level employing the 6-311+G(3df) basis set have been carried out. The general trend suggested by the theoretical calculations is that early transition metals (Sc-Fe), with the only exception of the Cr(CN) system, favor the isocyanide isomer, whereas late transition metals (Co-Zn) clearly prefer a cyanide arrangement. The preference for cyanides in the case of late transition metals (Co-Zn) is mainly due to electrostatic interactions. For the early transition metals the final preference for the cyanide or isocyanide conformation is the result of a delicate balance between the different contributions to the interaction energy.

REFERENCES 1. Sheridan, P.M.; Flory, M.A.; Ziurys, L.M. J. Chem. Phys. 2004, 121, 8360 and references therein. 2. Kingston, C.T.; Merer, A.J.; Varberg, T.D. J. Mol. Spectrosc. 2002, 215, 106. 3. Lie, J.; Dagdigian, P.J. J. Chem. Phys. 2001, 114, 2137.

Complexes of Fe2+ with CN− Ligands: A Theoretical Study of Cyanide vs. Isocyanide Competition V.M. Rayón1, H. Valdés2, P. Redondo1, C. Barrientos1, and A. Largo1 1

Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain 2 Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic

ABSTRACT The cyanide ion is one of the most important ligands in organometallic chemistry. Polycyanides of transition metals are within the most studied complexes in chemistry. One classical example is the [Fe(CN)6]4− ion with very important chemical applications. It is very well established that complexation of the Fe2+ cation with the six CN− ligands takes place through the carbon atom, that is, giving rise to the cyanide form. On the other hand, quite recently the mololigand compounds of first-row transition metals have been characterized, both experimentally and theoretically. Ziurys et al.1 have characterized the cyanides of Cu, Zn, Ni, and Co. However, in the case of iron, Lie and Dagdigian2 have detected through laser fluorescence excitation spectroscopy only the isocyanide isomer FeNC. From the theoretical side a recent systematic study of first-row transition metal cyanides and isocyanides has shown3 that late transition metals have a clear tendency to favour cyanide isomers, whereas for early transition metals the isocyanide isomer is slightly lower in energy. Iron is an intermediate case, and both isomers, cyanide and isocyanide, lie very close in energy although FeNC is slightly favoured. In the present work a theoretical study of the complexes formed by Fe2+ with n CN− ligands (n=1-6) has been carried out. The possibility of forming cyanides, isocyanides, as well as mixed complexes, has been taken into account. Optimized geometries and vibrational frequencies have been obtained at the B3LYP/6-311+G(d) level. Electronic energies have been refined through single-point CCSD(T)/6-311+G(d) calculations. In order to obtain more detailed information about the bonding in these compounds, an energy decomposition analysis has been carried out. Based on these studies the competition between cyanide and isocyanide complexation, as a function of the number of ligands, has been analyzed.

REFERENCES 1. P. M. Sheridan, M. A. Flory, and L. M. Ziurys, J. Chem. Phys. 121, 8360-8368 (2004). 2. J. Lie and P. J. Dagdigian, J. Chem. Phys. 114, 2137-2143 (2001). 3. V. M. Rayon, P. Redondo, H. Valdes, C. Barrientos, and A. Largo, J. Phys. Chem. A, in press.

Directional Aspects of Swift Ion Stopping in a ProtoBiological Molecule: Formaldehyde John R. Sabin,1,2 Remigio Cabrera Trujillo,3 L.T. Chadderton,4 N. Yngve Öhrn,1 and Erik Deumens1 1. Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611 USA 2. Institute for Physics and Chemistry, University of Southern Denmark, 5230 Odense, Denmark 3. Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico 4. Atomic and Molecular Physics Laboratory, Australian National University, Canberra, ACT0200, Australia

Abstract. The energy deposition (stopping) cross section for alpha particles (3He2+) on a formaldehyde molecule is calculated, using Electron Nuclear Dynamics, over the projectile energy range of 0.1 to 250 keV/amu. The differences with respect to the orientation of the target molecule with respect to the projectile beam, and the contributions from electronic, nuclear, and rovibrational stopping are discussed. Keywords: energy deposition, stopping power, directional dependence PACS: 34.50.Bw, 34.70.+e, 87.16.Ac, 87.17.Aa, 87.50.Gi

Coherent-States Dynamics: A Tribute to N. Yngve Öhrn Jorge A. Morales Department of Chemistry and Biochemistry, Texas Tech University, Box 41061 Lubbock, TX 79409-1061, USA Abstract. Inspired by Öhrn’s electron nuclear dynamics (END), a new coherent-states dynamics (CSD) to study chemical reactions is presented. CSD exploits basic properties of coherent states (CS) sets to represent the electrons and nuclei in a reactive system, and advances the concept of quasi-classical CS to formulate quantum/classical treatments. An original feature in CSD is its systematic employment of different types of CS to address specific chemical problems; some of those CS have been created by this author. In that context, END is revisited and some modifications are suggested. A full CSD procedure to calculate chemical reaction properties (e.g. differential cross sections) is also introduced in conjunction with semiclassical techniques. Results of simulations and properties calculations of the H+ + C2H4 and H+ + CO2 reactive systems at ELab = 30 eV are presented in comparison with experimental data. Current efforts in the CSD project (such as a CSD compute grid implementation and a CSD density-functional-theory formulation) are finally discussed. Keywords: Coherent-States Theory, Electron Nuclear Dynamics, Semiclassical Theory, Proton-Molecule Collisions PACS: 34.10.+x, 34.50.-s, 34.50.Ez, 34.70.+e, 82.20.Ej, 82.20.Fd, 82.20.Gk, 82.20.Ln, 82.20.Nk, 82.30.Fi

Highly Compact Wavefunctions for Four-Body Systems Frank E. Harris Department of Physics, University of Utah, Salt Lake City, UT 84112, USA Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA Abstract. Wavefunctions which are compact, but still quite accurate, are extremely valuable as tools for gaining understanding of quantum systems. This presentation reviews methods applicable to systems consisting of four or fewer particles, with an emphasis on expansions in basis functions that depend exponentially on all the interparticle distances. Applications to a variety of three and four-body systems are reviewed, and the virtues of these methods are illustrated, first by detailed studies we have carried out on threebody systems (the He isoelectronic series), and second, by work now in progress on a four-body system (the Li atom). It is shown (in computations that are still ongoing) that an expansion with as few as six exponential basis functions is capable of reproducing the nonrelativistic Li ground-state energy to within about 230 microhartrees of the exact value, an error far less than has been obtained for previously reported basis-set expansions of comparable length. Keywords: Compact wavefunctions, STO integrals, Few-electron systems PACS: 31.15.Ar, 31.25.Eb

Time-Dependent Molecular Reaction Dynamics Yngve Öhrn QTP, Departments of Chemistry and Physics, University of Florida, Gainesville, FL 32611-8435, USA Abstract. This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefficients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions. Keywords: time-dependent, dynamics, reaction, nonadiabatic, cross section

PACS: 34.50.-s, 34.10.+x, 82.20.-w

Interatomic (Intermolecular) Decay Processes in Clusters: Current Status and Outlook V. Averbukh, L. S. Cederbaum Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany Abstract. Since their theoretical prediction a decade ago, interatomic (intermolecular) Coulombic decay (ICD) and related processes have been in the focus of intensive theoretical and experimental research. The spectacular progress in this direction has been stimulated both by the fundamental importance of the new electronic decay phenomena and by the exciting possibility of their practical application, for example in spectroscopy. We review the current status of the research of interatomic (intermolecular) decay phenomena in clusters and discuss some perspectives of this new field. Keywords: Interatomic Coulombic decay, environmental effects on electronic decay PACS: 31.15.Ar, 31.50.Df, 31.70.Dk, 32.80.Dz, 36.40.-c

Quantum Chemistry and Non-Equilibrium Thermodynamics: Does Chaos Play a Role in Quantum Chemical Calculations? J.-M. André, M.-Cl. André, J.G. Fripiat and C. Lambert University of Namur, Laboratory for Applied Theoretical Chemistry 61, rue de Bruxelles, B-5000-Namur (Belgium) Abstract. The theory of solitons in polyacetylene chains is reviewed with the emphasis on the force that drives the phenomenon. Then, the origin of bifurcation schemes in non-equilibrium thermodynamics is summarized. Examples of bifurcations schemes and of chaotic behaviors in quantum chemical calculations are given. Keywords: bifurcation, deterministic chaos, soliton, electron transfer, instability PACS: 31.15.Ar, 05.45.Pq, 82.40.Bj, 82.40.Bj, 05.45.Yv

Relativity and Quantum Mechanics Erkki J. Brändas Department of Quantum Chemistry; Uppsala University, Box 518 S-751 20 Uppsala, Sweden Abstract. The old dilemma of quantum mechanics versus the theory of relativity is reconsidered via a first principles relativistically invariant theory. By analytic extension of quantum mechanics into the complex plane one may (i) include dynamical features such as time- and length-scales and (ii) examine the possibility and flexibility of so-called general Jordan block formations. The present viewpoint asks for a new perspective on the age-old problem of quantum mechanics versus the theory of relativity. To bring these ideas together, we will establish the relation with the Klein-Gordon-Dirac relativistic theory and confirm some dynamical features of both the special and the general relativity theory. Keywords: Klein-Gordon-, Dirac equation, particle-antiparticles, complex symmetry, non-positive metric, Jordan blocks, special- and general relativity. PACS: 03:30.+p, 03:65.pm, 31:30.Jv

Bands in Transition Metal Compounds A. Stoyanova*, C. de Graaf† and R. Broer* *

Theoretical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands † ICREA Researcher at the Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili, Marcel.l Domingo s/n, 43007 Tarragona, Spain

Abstract. A new method is presented for generating correlated many-electron bands for localized excited states, hole states and added-electron states in extended systems with strong electron correlation effects. The method allows for a rigorous treatment of the local electronic response that accompanies the excitation process. The energy bands are calculated with an ab initio manyelectron non-orthogonal tight-binding approach. The corresponding wave functions consist of optimized linear combinations of local many-electron basis functions. The many-electron basis is obtained from multiconfiguration wave functions for large embedded clusters. Each local state is expressed in terms of its own optimized orbitals set. To demonstrate the method we investigate the dependence of the energies of the lowest added-electron states in the perovskite CaMnO3. These states are important for understanding the interplay of conduction and magnetism in doped CaMnO3. Keywords: many-electron bands, localized states, electron-doped CaMnO3 PACS: 71.10.-w; 71.15.-m; 71.15.Nc; 71.15.Qe; 71.20.-b; 71.23.An

Oscillator Strengths And Related Properties Benoît Champagne Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix (FUNDP), rue de Bruxelles, 61, 5000 Namur, BELGIUM Abstract. Based on recent monographies by Yngve ÖHRN, the central role of transition dipole moments for determining molecular properties is highlighted. In particular, the focus is placed on oscillator strengths, polarizabilities, and hyperpolarizabilities. Keywords: oscillator strengths, transition dipole moments, excited states, polarizabilities and hyperpolarizabilities. PACS: 32.70.Cs, 33.15.Kr, 42.65.An

The Hartree-Fock-Heitler-London Method with Applications to First and Second Row Diatomic Hydrides and Homopolar Molecules Giorgina Corongiu* and Enrico Clementi† *

Dipartimento di Scienze Chimiche ed Ambientali, Università dell’Insubria, Via Lucini 3, Como I-22100, Italy † Via Carloni 38, Como, I-22100, Italy Abstract. The HF-HL (Hartree-Fock―Heitler-London) method for molecular calculation is reviewed. The original (simple) HF-HL method is extended to include ionic terms and to take account of the Coulomb hole; all these methods are applied to first and second row hydrides and homopolar molecules. Ground states and some excited states are examined. The results support the conclusion that HF-HL methods provide realistic molecular binding for ground and excited states, both for single-bond and for multiple-bond molecules. Keywords: Molecular binding energy, Hartree-Fock, Heitler-London, Correlation energy, Diatomic molecules, Hydrides. PACS: 31.10.+z, 31.15.Rh, 31.25.-v.

Ground State Energy Shift of He and He+ Close to a Surface: A Confinement Model Salvador A. Cruz*, Eugenio Ley-Koo† and Remigio Cabrera-Trujillo‡ *

Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, Apdo. Postal 55534, 09340, México City, México † Instituto de Física, Universidad Nacional Autónoma de México, Apdo. Postal 20364, 01000, México City, México ‡ Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apdo. Postal 48-3,62251 Cuernavaca, Morelos, México

Abstract. The model of an atom confined in a semi-infinite space with a plane boundary allows the variational evaluation of the ground-state energies and wavefunctions for He and He+ at different positions from the surface. The respective Born-Oppenheimer energy curves serve to model the ground-state energy shift for the elastic scattering channel in atom (ion)-surface interactions. Comparison with recent experimental evidence of an energy shift of the He ground-state as a function of distance from an aluminum surface is presented. Further validation of the model is analyzed taking as reference pilot calculations based on Electron Nuclear Dynamics for the elastic channel in He (He+)- benzene molecule interactions. Keywords: Quantum Confinement, Helium atom, Ground State, Elastic Channel . PACS: 31.15.-p , 31.15.Pf, 34.50.Dy

Calculating Spin-Spin Coupling Constants Udo Benedikt,* Alexander A. Auer,* Frank Jensen† * Department of Chemistry, Technische Universitet, Chemnitz, Germany † Department of Chemistry, Aarhus University, Aarhus, Denmark Abstract. We propose a series of basis sets for systematically reducing the basis set error for calculating nuclear spin-spin coupling constants. At the density functional level, the basis sets are derived from the previously proposed polarization consistent basis sets by augmentation with tight s-, p-, d- and f-functions. The optimum exponents for the tight functions can be derived by a variational procedure, and the optimum exponents are sufficiently regular that a standard set of tight functions can be derived. Preliminary results at the coupled cluster level suggest that a similar sequence of optimum basis sets can be derived from the correlation consistent basis sets by augmentation with tight functions. Keywords: Basis set, NMR, spin-spin coupling constants. PACS: 32.30.Dx

Methods Be Used To Improve Polarization Propagator Methods? Hans Jørgen Aagaard Jensen Department of Physics and Chemistry, University of Southern Denmark DK-5230 Odense M, Denmark Abstract. Calculations of Rydberg excitation energies with the second-order polarization propagator approximation (SOPPA) often produce results which are more in error than the random phase approximation (RPA), which formally is the first-order model. This is obviously because of cancellation of errors at the RPA level. On the other hand, valence excitation energies behave as expected, and they are systematically improved in SOPPA compared to RPA. Note that a Rydberg series is related to one of the ionization thresholds of the molecule, and it is thus obvious that a good description of the ionization limits is necessary in order to calculate good values for the Rydberg excitations. From perturbative electron propagator methods it is well-known that the second-order level is inadequate to obtain good ionization energies. It is also known from electron propagator methods that partial inclusion of higher-order terms can greatly improve the ionization energies. In this work it will be investigated if the lessons from electron propagator models can be used to improve to the calculation of Rydberg excitations in perturbative polarization propagator methods. Keywords: Electron Propagator, SOPPA, Second Order Polarization Propagator Approximation, Rydberg states. PACS: 31.10.+z, 31.15.Ar, 31.35.Md, 31.25.Jf, 32.20.-t

Three Quantum Leaps in the Development of Information Security Per Kaijser Moarstrasse 18, D-85737 Ismaning, Germany Abstract. This paper gives a coarse overview of the historical development of algorithms used for information security. It is shown that the development of these encryption algorithms has been made in small incremental steps for almost 2000 years until the latter part of the last century when three revolutionary inventions were made. The main properties of these new technologies, the public key encryption method, quantum cryptography and quantum computing are explained and demonstrates why they can be seen as quantum leaps in the development of information security. Keywords: Cryptography, Encryption Algorithms, Information Security, Quantum Computers, Quantum Cryptography. PACS: 03.67.Dd, 03.67.Lx.

The Concept of Molecular Shape Response Quantified within Force Field Approach Alfred Karpfen* and Eugene S. Kryachko†¶ *

University of Vienna, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria † Department of Chemistry, Bat. B6c, University of Liege, Sart-Tilman, B-4000 Liege 1, Belgium ¶ Bogoliubov Institute for Theoretical Physics, Kiev, Ukraine

Abstract. We propose the concept of molecular structural or shape negative and positive response and develop it within the molecular force field ansatz using the graph theory. Keywords: Molecule, graph, vertex, edge, bond, interaction, response, spectacular bond, intramolecular coupling, hydrogen bonding PACS: 02.10.Ox; 31.10.+z; 31.15.Ar

Recent Developments in Quantum Monte Carlo: Methods and Applications Alan Aspuru-Guzik*, Brian Austin*†, Dominik Domin*, Peter T. A. Galek‡, Nicholas Handy‡, Rajendra Prasad*†, Romelia Salomon-Ferrer*†, Naoto Umezawa¶, and William A. Lester, Jr. *† *Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California Berkeley, CA 94720-1460, USA †

Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ‡

¶

Department of Chemistry, University of Cambridge, CB2 1EW United Kingdom

National Institute for Materials Science, Nanomaterials Laboratory, Namiki 1-1, Tsukuba, Ibaraki, 305-0044, Japan

Abstract. The quantum Monte Carlo method in the diffusion Monte Carlo form has become recognized for its capability of describing the electronic structure of atomic, molecular and condensed matter systems to high accuracy.* This talk will briefly outline the method with emphasis on recent developments connected with trial function construction, linear scaling, and applications to selected systems.

The Science of Yngve Öhrn Jan Linderberg Department of Chemistry, Aarhus University Langelandsgade 140, DK-8000 Aarhus C Abstract. Emphasis is directed in this paper towards the accomplishments by Yngve Öhrn in theory of molecular reactions with his Electron Nuclear Dynamics time-dependent formulation and its competent implementation to a manageable and versatile tool. Keywords: time dependence, reactive scattering. PACS: 34.10

First Principles Dynamics of Photoexcited DNA and RNA Bases Hanneli R. Hudock, Benjamin G. Levine, Alexis L. Thompson, and Todd J. Martinez Department of Chemistry, Beckman Institute, and Center for Biophysics and Computational Biology University of Illinois, Urbana, Illinois 61801 Abstract. The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multi-component decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S2 electronic state is responsible for the first step which occurs on a femtosecond timescale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S2/S1 conical intersection is responsible for the picosecond decay. Keywords: Femtosecond, DNA, Internal Conversion, Ab Initio Molecular Dynamics, Time-Resolved Photoelectron Spectroscopy PACS: 31.50.Df, 31.50.Gh, 31.70.Hq, 32.80.Fb, 33.50.Hv

Local Complex Potential Based Time Dependent Wave Packet Approach to Calculation of Vibrational Excitation Cross-sections in e-N2, e-H2 and e-CO Scattering Manabendra Sarma, Raman K. Singh, and Manoj K. Mishra Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076, India

Abstract. Vibrational excitation cross–sections σ n ← m ( E ) in resonant e–N2, e–CO and e–H2 scattering are calculated from transition matrix elements Tn ← m ( E ) obtained using Fourier transform of the cross correlation function φ n ( R) ψ m ( R, t )

where ψ m ( R, t ) ; e

− iH

A−

φm ( R) . Time evolution under the influence of the resonance anionic Hamiltonian

( R)t / h

H A − ( A = N / CO / H ) is effected using Lanczos and fast Fourier transforms and the target (A) vibrational −

− 2

− 2

eigenfunctions φ m ( R) and φ n ( R) are calculated using Fourier grid Hamiltonian method applied to PE curve of the neutral target. The resulting vibrational excitation cross-section profiles provide reasonable agreement with experimental results and the cross correlation functions offer an unequivocal differentiation between the boomerang and impulse models. Keywords: Electron scattering; shape resonance; vibrational excitation; time dependent wave packet (TDWP) PACS: 34.80.-i

Accurate Dissociation Energies of He2 and Be2 Calculated by MRCI Method Alexander V. Mitin Center for Environmental Kinetics Analysis, The Pennsylvania State University, 2217 EES Building, University Park, PA 16802 Abstract. The dissociation energies of He2 and Be2 have been calculated by extrapolating to the infinite basis of the BSSE corrected MRCI total energies obtained with large finite Gaussian basis sets and pseudo-natural molecular orbitals. The calculated He2 dissociation energy of 11.0012 K is in excellent agreement with the value of 10.998±0.005 obtained recently by the quantum Monte Carlo method. The dissociation energy of 796 cm-1 of Be2 is in a good agreement with the experimental value of 790±30 cm-1. Keywords: Ab initio calculations, diatomic molecules, dissociation energy. PACS: 31.10.+z; 31.15.Ar; 31.25.Nj

Non-Adiabatic Effects in Electron Tunneling in Molecular Junctions Vladimiro Mujica*,†, Thorsten Hansen* and Mark A. Ratner* * Northwestern University, Department of Chemistry, 2145 Sheridan Road, Evanston, IL 60208-3113, U.S.A. † Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439-4731, U.S.A. Abstract. Most models on electron transport in molecular junctions implicitly assume that there is only one potential energy surface (PES) involved in transport. The current and/or the voltage across the junction may invalidate this assumption in a number of important situations. We recently developed a model for the description of STM-induced unimolecular surface reactions as an electronic cotunneling process that takes explicitly into account the possibility of coupling of two PES via the interaction between the molecule and the electrode as described by the self-energy. In this contribution we extend our model in the framework of a theory of nonadiabatic tunneling developed by Zhu and Lin. Our results may be of importance in the context and current and voltage-induced processes in nano-junctions and also on a more fundamental level to broaden our understanding of the relationship between molecular conductance and electron transfer reactions. Keywords: electron transport, non-adiabatic, molecular junctions PACS: 73.23.-b

Electron Propagator Theory and the Development of Chemical Intuition J. V. Ortiz Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, U. S. A. Abstract. Electron propagator theory is the foundation of a many-body, ab initio approach to the prediction of electron binding energies and ground-state properties of molecules, but it also produces one-electron interpretations of electronic structure that are as succinct as those that emerge from qualitative molecular orbital theory. Practical approximations that are implemented in efficient algorithms enable the scope of applications of electron propagator theory to rival those of elementary correlation and self-consistent field methods. Studies of nucleotides, metal-oxide clusters and double Rydberg anions illustrate the ability of electron propagator theory to produce predictive calculations and convincing assignments on photoelectron spectra of unusual species and to introduce novel, qualitative concepts of chemical bonding. Keywords: Electron propagator, nucleotides, metal-oxide clusters, double Rydberg anions PACS: 31.10.+z

Recent Results in Quantum Chemical Kinetics from High Resolution Spectroscopy Martin Quack ETH Zürich, Physical Chemistry, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland [email protected], web: www.ir.ethz.ch Abstract. We outline the approach of our group to derive intramolecular kinetic primary processes from high resolution spectroscopy. We then review recent results on intramolecular vibrational redistribution (IVR) and on tunneling processes. Examples are the quantum dynamics of the C–H-chromophore in organic molecules, hydrogen bond dynamics in (HF)2 and stereomutation dynamics in H2O2 and related chiral molecules. We finally discuss the time scales for these and further processes which range from 10 fs to more than seconds in terms of successive symmetry breakings, leading to the question of nuclear spin symmetry and parity violation as well as the question of CPT symmetry. Keywords: High resolution spectroscopy, kinetics, quantum dynamics, infrared, isotopes, symmetry. PACS: 33.20.-t, 39.30.+w, 78.47.+p, 82.20.-w.

How Do Low-energy (0.1-2 eV) Electrons Cause DNA Strand Breaks? Jack Simons Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA Abstract. We overview our recent theoretical predictions and the innovative experimental findings that inspired us concerning the mechanisms by which very low-energy (0.1-2 eV) free electrons attach to DNA and cause strong (ca. 4 eV) covalent bonds to break causing so-called single strand breaks. Our primary conclusions are that (i) attachment of electrons in the above energy range to base π* orbitals is more likely that attachment elsewhere and (ii) attachment to base π* orbitals most likely results in cleavage of sugar-phosphate C-O σ bonds. Later experimental findings that confirmed our predictions about the nature of the electron attachment event and about which bonds break when strand breaks form are also discussed. The proposed mechanism of strand break formation by low-energy electrons involves an interesting through-bond electron transfer process. Keywords: DNA damage, strand breaks, metastable anions. PACS: 31.50-x, 34.80.Lx, 87.50 –a, 87.14.Gg

Enormous Isotope Effects on Charge Transfer in Slow Collisions of He2+ with H, D, and T N. Stolterfoht*†, R. Cabrera-Trujillo*,¶, Y. Öhrn*, E.Deumens*, R. Hoekstra‡, and J. R. Sabin*,§ *

Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville FL 32611-8435, USA † Hahn-Meitner Institut, Glienickerstraße 100, D-14109 Berlin, Germany ¶ Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos, 62210, México ‡ KVI Atomic Physics, Rijksuniversiteit Groningen, NL 9747 AA Groningen, Netherlands § Institute for Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark Abstract. Probabilities and cross sections for charge transfer by He2+ impact on atomic hydrogen (H), deuterium (D), and tritium (T) at low collision energies are calculated using the END approach. Differences by orders of magnitude are observed between the cross sections for H, D, and T. A method is introduced to separate the contributions of charge transfer mechanisms due to radial and rotational coupling. The large differences observed for H, D, and T are attributed to isotope effects in the rotational coupling mechanism. Keywords: slow collisions, charge transfer, isotope effect, rotational coupling. PACS: 34.50.Fa, 32.80.Fb

Long-Distance Electron Transfer Coupled to Proton Pumping and Energy Transduction in Biological Systems: A Semiempirical First-Principles Approach Xuehe Zheng*, Ngan M. Ly* and Alexei A. Stuchebrukhov† * Department of Chemistry and Center for Macromolecular Modeling and Materials Design, California State Polytechnic University, Pomona, California 91768 † Department of Chemistry, University of California, Davis, California 95616

Abstract. The first-principles method of electron tunneling currents for electron transfer was previously used to compute the electron coupling matrix in the Marcus theory as well as the tunneling pathway at the extended Huckel level of theory of electronic structure for the redox centers in some living systems such as cytochrome c oxidase. We present here the work in recent development of electron tunneling currents theory that implements in its formalism the inherent systematic ZDO approximation used in ZINDO/S quantum chemical model of electronic structure. Together with the molecular orbitals so calculated semiempirically we develop an approach that is consistent in its approximation, more accurate than the previous methodology and particularly applicable to large biological systems which cannot yet be fully treated ab initio. We calibrate this approach with ab initio results for a small model system of protein, the donor-bridge-acceptor complex of (His)2 (Met)Cu+ -(Cys)-(Gly5)-(His)Ru3+bpy5Im, and make predictive calculations for the real biological electron transfer systems of His126 Ru-modified blue copper protein Pseudomonas aeruginosa azurin and cytochrome c oxidase. Furthermore, the coupling between electron transfer and energy transfer is demonstrated with the thermal motion in protein dynamics for the case of DNA repair by photolyase. Continuing work is underway on the newly crystallized structure of NADH dehydrogenase, the electron entrance to the cellular electron transport respiratory chain. Combining both the rigor of tunneling currents theory and the expedience of ZINDO/S quantum chemical model our approach offers a useful computational method for long-distance electron transfer in biological systems. Keywords: Electron Transfer, Tunneling Currents, ZINDO/S. NADH Dehydrogenase, Cytochrome c Oxidase, DNA repair. PACS: 31.15.Ct 31.15.Qg 32.50.+d 33.20.Kf 33.20.Tp 33.50.Dq

Molecular Photoionization Cross-Sections by Application of Stieltjes Imaging to Lanczos Pseudospectra K. Gokhberg, V. Averbukh, V. Vysotskiy, L. S. Cederbaum Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany

Abstract. Stieltjes imaging technique is widely used for ab initio computation of photoionization cross-sections and decay widths. The main problem hampering the application of the standard Stieltjes imaging algorithms in conjunction with high-level ab initio methods to polyatomic molecules is the requirement of full diagonalization of excessively large Hamiltonian matrices. Here we show that the full diagonalization bottleneck can be overcome by applying the Stieltjes imaging procedure to Lanczos pseudospectrum of the molecular Hamiltonian. The new technique is applied to calculation of the total photoionization cross-section of benzene within an ab initio approach explicitly taking into account single and double electronic excitations. A good agreement with the experimental cross-section is obtained. Keywords: Stieltjes imaging, Lanczos diagonalization PACS: 33.80.Eh, 31.15.Ar

Fourier Representation Methods for Møller-Plesset PerturbationTheory in One-Dimensionally Periodic Systems J. G. Fripiat*, J. Delhalle*, Frank E. Harris†,¶ * Département de Chimie, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles, 61, Namur, Belgium † Department of Physics, University of Utah, Salt Lake City, UT 84112, USA ¶ Quantum Theory Project, University of Florida, P.O. Box 118435, Gainesville, FL 32611, USA

Abstract. Ab initio studies of one-dimensionally periodic systems are advantageously carried out by methods that employ Fourier representations and the Ewald method for accelerating the lattice sums. This communication describes the first investigation in which these techniques have been applied at the Møller-Plesset level of perturbation theory, MBPT(2). Second-order corrections to the restricted Hartree-Fock energy and energy bands are reported for H2, Be, and LiH chains, and these results are compared to direct-space extended-system and oligomer computations. The methods described herein exhibit improved convergence relative to the other methods to which they are compared. Keywords: electronic structure of polymers, Fourier methods, Ewald method, Møller-Plesset theory, one-dimensionally periodic systems, band structure of polymers PACS: 71.15.-m, 71.15.Dx, 71.20.Rv

Explicit Electron Correlation by a Combined Use of Gaussian-Type Orbitals and Gaussian-Type Geminals Pål Dahle*,†, Trygve Helgaker†, Dan Jonsson¶, Peter R. Taylor‡ †

*Norwegian Computing Center, Gaustadalléen 23, N-0314 Oslo, Norway Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Norway ¶ Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden ‡ Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK

Abstract. In MP2-GGn theory, the second-order Møller--Plesset (MP2) energy is recovered by a combined Gaussianorbital---Gaussian-geminal (GG) expansion of the first-order wave function. While the restriction of geminals to doubly occupied orbital pairs (MP2-GG0) provides a modest improvement on standard MP2 theory, their inclusion also in all singly-excited (MP2-GG1) and doubly-excited (MP2-GG2) pairs recovers essentially all of the correlation energy in small (double- and triple-zeta) basis sets. For several small systems, our MP2-GGn energies represent the best MP2 energies reported in the literature. Keywords: explicit electron correlation, Gaussian-type geminals, Møller-Plesset theory

PACS: 31.15.Md, 31.25.-v

Trial Wavefunctions for Quantum Monte Carlo Simulations with Numerically Stable Analytical Gradients over Exponential Type Orbitals Philip E Hoggan LASMEA, UMR CNRS 6602, University Blaise Pascal, 24 Avenue des Landais, Clermont-Ferrand, France

Abstract. High quality quantum Monte-Carlo calculations require good trial wavefunctions. This is particularly true of the most accurate fixed node Monte Carlo approach. This need is satisfied by Sturmian functions which possess suitable nodal behavior. These functions are exponential type orbitals (ETOs) with the required long-range analytical behavior for molecular wavefunctions. Hydrogen-like atomic orbitals are a (familiar but restricted) special case of Sturmians. Quantum Monte Carlo simulations requires correlated wavefunctions which are usually obtained by optimizing the trial wavefunction with an explicitly correlated Jastrow factor with the inter-particle distance as variable. Sturmians are also good starting points for the construction of geminal trial functions that explicitly include inter-particle (electron-electron) distances. These Sturmian geminals are functions of the electron-electron vector. This paper discusses the use of Sturmians (as a function of the usual electron position vector) and in particular the evaluation of molecular integrals in a Sturmian basis. Their analytical computation can be pursued by techniques that include symbolic computation methods. These ideas have been used to construct an improved Slater-Type Orbital Package (STOP) for the evaluation of threeand four-center molecular integrals that are needed to perform meaningful molecular calculations. Keywords: analytical Coulomb potential, Coulomb Sturmians, Spectral forms, explicit correlation PACS: 31.90.+s

Vector Potential Approach for Response of Infinite Periodic Systems to Electric Fields Bernard Kirtman*, Michael Springborg† *

Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, U.S.A. † Physical and Theoretical Chemistry, University of Saarland, 66123 Saarbrücken, Germany

Abstract. A detailed study of the vector potential approach (VPA) for the response of periodic systems to a finite electric field is carried out using a parameterized model self-consistent field (SCF) polymer Hamiltonian. Specific issues discussed include "smoothing" of crystal orbitals, convergence and accuracy of SCF solutions as a function of field and number of k points, Zener tunneling, field-dependent band structure, determination of (non)linear susceptibilities, and nuclear relaxation. Keywords: polarization, electrostatic fields, periodic systems, structural properties, electronic properties PACS: 36.20.-r, 71.15.-m, 77.22.Ej, 78.20.Bh

Chirped Pulse Adiabatic Passage in CARS for Imaging of Biological Structure and Dynamics Svetlana A. Malinovskaya Department of Physics & Engineering Physics, Stevens Institute of Technology, Hoboken, NJ 07030, USA

Abstract. We propose the adiabatic passage control scheme implementing chirped femtosecond laser pulses to maximize coherence in a predetermined molecular vibrational mode using two-photon Raman transitions. We investigate vibrational energy relaxation and collisional dephasing as factors of coherence loss, and demonstrate the possibility for preventing decoherence by the chirped pulse train. The proposed method may be used to advance noninvasive biological imaging techniques. Keywords: stimulated Raman spectroscopy, coherent control, chirped pulse adiabatic passage, decoherence PACS: 32.80.Qk,42.65.Dr,42.65.Re

Two-Photon Cross-Sections of Photosensitizers in Vacuum, in Solution and within Proteins M. Rehman*, L. Olsen†, K. V. Mikkelsen* * †

Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark

Abstract. Molecular response theory is utilized for calculating two-photon cross-sections of photosensitizers in vacuum, in solution and within proteins. Keywords: photosensitizers, molecular oxygen, photodynamic therapy, molecular response theory, two-photon crosssections PACS: 31.15.Ew,31.70.Dk,33.80.Wz

Quasiparticle and Optical Excitations in Solid Ne and Ar: GW and BSE Approximations Charles H. Patterson, S. Galamić-Mulaomerović School of Physics, Trinity College Dublin, Dublin 2, Ireland

Abstract. The GW approximation and the Bethe-Salpeter equation (BSE) have been used to calculate quasiparticle and optical excitations in solid Ne and Ar. Absolute positions of quasiparticle and quasihole energies are found to be in very good agreement with experimental values. Binding energies of Frenkel excitons for these systems calculated using the BSE are also in good agreement with experiment. Splitting of excitons into longitudinal and transverse modes is calculated and found to be approximately twice the experimentally measured value. Keywords: Solid Ne, Solid Ar, rare gases, Frenkel excitons PACS: 71.30.+h, 72.25.Ba, 71.45.Lr

Why Does Controlling Quantum Phenomena Appear Easy to Achieve? Herschel Rabitz Princeton University, Frick Laboratory, Princeton, NJ 08544, USA

Abstract. The introduction of optimal control theory and associated optimal control experiments have produced many successful results for manipulating quantum systems including those of high complexity. This paper discusses the reason for this attractive behavior, revealing that the search space landscape for maximizing the probability of making a quantum transition has no false extrema. Although real systems may not be fully controllable, this result provides the basis to explain the generally successful findings from quantum optimal control simulations and experiments, as well as provides a very positive projection of the future for the field. Keywords: quantum dynamics and control PACS: 42.50.-p, 42.55.-f, 42.62.-b

Response to Geometric Distortions from Atom-Based Relativistic Projection on Electronic States Alexei V. Matveev, Notker Rösch Department Chemie, Theoretische Chemie, Technische Universität München, 85748 Garching, Germany

Abstract. We suggest a quasi-relativistic model for molecular electronic structure calculations obtained by an atomic ansatz for the relativistic projection transformation. With such a choice, the projection transformation becomes both transferable and independent of the geometry. The formulation is flexible with regard to the choice of the projection transformation. We employ the free-particle Foldy--Wouthuysen and the Douglas—Kroll second-order variants for the projection coefficients. First results for the diatomic molecules AuH, AuCl, and Au2 and two structural isomers of Ir4 suggest the new approximate method as an efficient and accurate replacement for the conventional transformation. Keywords: Douglas--Kroll--Hess method, linear response, energy gradients, LCAO PACS: 03.65.Pm, 31.15.Ew, 31.30.Jv, 31.15.Md, 31.15.-p

Limitations of Racah-Wigner Algebra in Sn-Invariant Theoretic Modelling of NMR Spin Dynamics via Dual Tensorial Sets F. P. Temme Department of Chemistry, Queen's University, Kingston-ON K7L 3N6, Canada Abstract. Augmented quasiparticle (QP) mapping techniques for indistinguishable point sets, based on (Liouvillian tensorial) democratic recoupling (DR), are shown to induce a full 1:1 invariant-labelling of the underlying (disjoint) projective mapping subspaces. This theoretical simple reducibility SR-driven view of dual group algebras underlies certain parallel limitations of Jucys graph recoupling and (in consequence) standard Racah-Wigner (R-W) algebras for tensorial point sets once it is applied to indistinguishable point sets. The explicit invariants (for labelling of all disjoint carrier subspaces) and their cardinality are central to automorphic dual (symmetry) tensorial formalisms, because they provide the essential quantal-completeness condition for DR Liouvillian tensorial sets. By drawing on augmented-QP properties [2002, Int. J. Quantum Chem. 89, 429; 1993, Physica A 198 245]---beyond the classic Hilbert boson-pattern overview of Louck \& Biedenharn [1979, Permutation group in physics ..,Springer] of simple carrier space projective mapping---a definitive theoretical basis is derived for Atiyah and Sutcliffe's recent assertions [2002, Proc. Roy. Soc., Lond. A 458, 1089], concerning the specific limitations of graph recoupling theory to distinct point sets. Direct insight is obtained into the central question of why general index `n' matrix formulations of multi-invariant DR tensorial set-based, (automorphic) spin problems are not amenable to analytic treatment---even utilising indirect Lévi-Civitá-based cycliccommutation (R-W) approaches, e.g. of [ Lévy-Leblond, Lévy-Nahas, 1965, J. Math. Phys. 6, 1372], unless the tensorial system is constrained to a mono-invariant form. The importance of this (DR) tensorial-set work comes from its focus on the specialised nature of indistinguishable point sets in (multi)invariant theoretic views of quantum dynamical spin physics. Keywords: spin physics; democratic recoupled tensorial sets; Sn invariants-modified group actions & mappings; Liouvillian disjoint projective subspaces; NMR spin dynamics; indistinguishable DR point sets PACS: 02.10 -De; 02.10 -v/x; 82.56b/Dj

Cross Sections for C+ and O+ Production in the Collision of CO2+ Ions with Atomic He Olmo González*, Manuel Combes†, Cristian Gleason¶, G. Hinojosa‡, R. Cabrera-Trujillo¶,** *

Facultad de Ciencias, Universidad Nacional Autónoma de México, México DF, C.P. 04510, México Ecole Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France ¶ Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos, 62209, México ‡ Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Ap. Postal 48-3, Cuernavaca, Morelos, 62251, México ** Physics Department, University of Florida, Gainesville, FL, 32611, USA †

Abstract. From the theoretical point of view, the problem of the dissociation of molecules induced by collisions is complex due to the coupling of the electronic and nuclear degrees of freedom, thus few theoretical approach exist that can compare directly with experiment. In this work an experimental and theoretical study of the total cross section for fragmentation of CO2+ ions into the C+ and O+ product channels induced by collisions with atomic He for projectile energies from 1 to 10 keV is presented. Our preliminary results show that the cross section for the C+ fragment is higher than the cross section for O+ fragment and both grow monotonically, although our theoretical results show larger cross sections at low projectile energies. Keywords: Molecular fragmentation, cross section, electron nuclear dynamics PACS: 34.50.-s, 34.50.Lf

Electron-Correlation Effects in Metals from First Principles: a Multi-Reference Incremental Scheme Elena Voloshina, Beate Paulus Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Straße 38, 01187 Dresden, Germany Abstract. In order to apply ab initio wavefunction-based correlation methods to metals, it is desirable to split the calculation into a mean-field part and a correlation part. Whereas the mean-field part (here Hartree-Fock) is performed in the extended periodic system, it is necessary to use for the correlation part local wavefunction based correlation methods (e.g. incremental scheme) in finite fragments of the solid. The recently proposed embedding scheme makes it possible to apply method of increments to metallic systems, which require special treatment because of several distinct features, i.e. charge screening and partially filled conduction bands. Another problem can bring difficulties in description of metallic systems: The quasi-degenerate bands presenting at the Fermi level makes questionable the application of a singlereference correlation methods. Keywords: Ab initio calculations, Electron correlations, Method of increments, Metals PACS: 71.15.-m, 31.15.Ar, 31.25.-v, 71.20.Dg

Similarities and Differences Between Silicon and Carbon Nanostructures: Theoretical Predictions Aristides D. Zdetsis Department of Physics, University of Patras GR-26500 Patras, Greece Abstract. It is illustrated by ab initio calculations based on density functional (DFT/B3LYP), that very stable high symmetry “fullerenes” of the form SinHn, can be formed with large HOMO-LUMO and optical gaps. Results are presented for n=20, 60 for which the corresponding polysilane cages (“fullerenes”) are fully analogous to their well known carbon counterparts, dodecahedrane, and fullerane. The search for flat aromatic silicon structures analogous to benzene (C6H6) leads to a planar Si6Li6 structure which is both stable and aromatic, sharing several key characteristics with benzene. Results for silicon nanowires, and silicon and carbon clusters are also used for comparison Keywords: Silicon Nanostructures, Carbon Nanostructures , Fullerenes, Aromaticity PACS: 61.46.Hk 31.90.+s 36.20.-r 81.05.Tp 72.80.Rj

Codoping goes Nano: Structural and Optical Properties of Boron and Phosphorus Codoped Silicon Nanocrystals Rita Magri1, F. Iori1, E. Degoli2, O. Pulci3, and S. Ossicini2 1

CNR-CNISM and Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy 2 CNR-INFM-S3and DISMI, Università di Modena e Reggio Emilia, Via G. Amendola 2, 42100 Reggio Emilia, Italy 3 ETSF and CNR-INFM, Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Roma, Italy Abstract. Doping control at the nanoscale can be used to modify optical and electronic properties thus inducing interesting effects that cannot be observed in pure systems. By using Density Functional Theory, Silicon Nanocrystals (Si-nc) of different size (diameter ranging from 1.1 nm to 1.8 nm) have been studied localizing impurities at different substitutional sites and calculating the impurity formation energies. Starting from hydrogen terminated silicon Si-nc, we found that codoping is always energetically favored with respect to a single B- or P-doping and that the two impurities tend to occupy nearest neighbor sites near the surface. The formation energy depends on the distance between the two impurities. The codoped Si-nc present bandedge states localized on the impurities which are responsible for a red-shift of the absorption threshold with respect to that of pure undoped Si nanocrystals. Concerning the emission spectra, we find a Stokes shift of the photoluminescence to a lower energy with respect to the absorption edge due to the nanocrystal (nc) structural relaxation after the creation of the electron-hole pair. We have calculated the absorption and emission spectra going beyond a single-particle approach showing the important role played by the many-body effects. The presence of electronic quasi-direct optical transitions between the donor and acceptor states within the band-gap makes it possible to engineer the optical properties of Si-nc. Keywords: Semiconductor nanostructure, Quantum Dots, Optical Absorption and Emission, Doping PACS numbers: 73.22-f, 71.15-m, 78.55.-m; 78.20.-e.

Ab-initio Investigations of Surface Electronic Structure and Metal-Hydrogen Interaction in Titanium- and PalladiumBased Alloys Svetlana E. Kulkova*†, Sergey S. Kulkov*, Sergey V. Eremeev* and Dmitry I. Bazhanov+ *Laboratory of Theory of Non-Equilibrium States, Institute of Strength Physics and Materials Science SB RAS, pr. Akademichesky 2/1, 634021 Tomsk, Russia † Physical Faculty, Tomsk State University, pr. Lenina 36, 634050 Tomsk, Russia + Physical Faculty, Moscow State University, Leninskie Gori 1/2, 119992 Moscow, Russia Abstract. We report ab initio investigation of the adsorption (absorption) of atomic hydrogen on low-index surfaces, at symmetrical tilt grain boundaries and in the bulk for a series of titanium- and palladium-based alloys. The chemical bonding of hydrogen with transition metals is analyzed with respect to the surface composition and its orientation. The correlations between the absorption energy of hydrogen in bulk palladium alloys with 3d-5d elements and their electronic structure are discussed. A microscopic explanation of the local surface reactivity in the transition metal alloys is given. It was also shown that H atoms induce the weakening of the grain boundary cohesion in investigated materials. Keywords: Transition metals and alloys; Electronic band structure; Thin films; Grain boundaries. PACS: 71.20.Be; 73.20.At; 73.20.-r; 68.35.-p

Pressure Driven Phase Transitions of Ferroelectric KNBO3: A Hybrid Functional Approach. Ph. Baranek* EDF R&D – MMC, BP. 46., Avenue des Renardières, 77818 Moret-sur-Loing Cedex, France Abstract. Pressure driven phase transitions of ferroelectric KNbO3 are investigated at the hybrid functional level using a periodic single cell simulation. The hybrid functional combines Hartree-Fock and PBE approximations. The calculated equations of state are in good agreement with experimental data. The pressure induced dynamics of the Γ-TO modes is investigated; the softening of an optical phonon is observed. The cubic, tetragonal and orthorhombic phases are characterised by a soft mode describing the Nb displacement relative to the O octahedral. The local-structure of KNbO3 is rhombohedral in the explored pressure interval; the other structures correspond to metastable average configurations of the system. Pressure effects and phases transitions are analysed in terms of evolution of the spontaneous polarization and of the Nb-O bond population. It is found that the phase stabilities involve principally the Nb displacement relative to the O octahedral due to an increase of the Nb-O hybridization when pressure is decreasing. The described dynamic of the phase transitions is compatible with a soft-mode scenario of displacive transitions. Keywords: KNbO3, perovskite; ferroelectricity, phase transitions under pressure, phonons dynamic, ab initio modeling, Hartree-Fock, Density Functional Theory, hybrid functionals. PACS: 31.10.+z, 31.15.Ar, 31.15.Ew, 31.50.-x, 71.15.-m, 71.15.-Mb, 71.15.-Nc, 77.80.Bh, 77.84.Dy

Electronic Structure and Vibrational Spectra of Magnetite Charles H. Patterson and Andrew D. Rowan School of Physics,Trinity College Dublin,Dublin 2,Ireland Abstract. The electronic structure, crystal structure and infra-red conductivity of magnetite have been calculated using hybrid density functional methods. The crystal structure was calculated using a conjugate gradient method and atomic coordinates were obtained while freezing lattice parameters at experimental values or by simultaneously allowing lattice parameters and atomic coordinates to relax. Atomic coordinates obtained when lattice parameters were frozen at experimental values are in excellent agreement with values from x-ray and neutron scattering data. The best agreement with experiment is obtained when a B3LYP hybrid functional is used. Phonon modes at the ℘ point of the Brillouin zone were calculated using a frozen phonon method. All computed phonon eigenfrequencies were real when experimental lattice parameters were used, but when phonons were calculated using the fully relaxed structure there was one imaginary phonon frequency. When frequencies from the calculation which used experimental lattice parameters are rescaled, there is agreement between the low temperature infra-red conductivity predicted using these phonon modes and experiment. Keywords: Magnetite,charge order,Verwey transition,spintronics PACS: 71.30.+h, 72.25.Ba, 71.45.Lr

High-stability finite-length silicon nanowires: A real space theoretical study E. N. Koukaras, A. D. Zdetsis* and C. S. Garoufalis Department of Physics, University of Patras GR-26500 Patras, Greece Abstract. We demonstrate by real-space density functional calculations that unreconstructed low-stability finite size hydrogenated silicon nanowires could bend through relaxation under the influence of internal strains, contrary to highstability “magic” nanowires. The strains and the resulting bending depend on the distribution and orientation of silicon dihydrides on the nanowire’s surface. This and other related effects cannot be accounted for by the usual k-space supercell techniques. We also demonstrate that reconstructed (2x1) nanowires, although bend they are practically as stable as the “magic” unreconstructed nanowires. Our calculations are in full agreement with the experimental work of Ma et al. [Science 299, 1874, (2003)]. Keywords: Nanowires, nanostructures, silicon PACS: 61.46.−w, 61.46.Fg, 68.65.La

Investigation Of The Electronic Structure And Magnetic Properties Of Heusler Half-Metallic Alloys At Surfaces And Interfaces S.V. Eremeev, S.E. Kulkova, I.Yu. Smolin 1

Institute of Strength Physics and Materials Science SB RAS, pr. Akademichesky 2/1, Tomsk, 634021, Russia 2 Tomsk State University, pr. Lenina 36, Tomsk, 634050, Russia

Abstract. The electronic and magnetic properties of different contacts between the half-metallic Heusler alloys NiMnSb, Co2MnSi and the semiconductors GaAs and InP were calculated using density functional theory methods. The calculated interface and surface electronic structures allow to understand the origin of states within the gap for minority electrons and to establish the mechanisms which can keep high spin polarization at the surface and interfaces. The influence of structural defects on the spin polarization at the Fermi level is also discussed. Keywords: Electronic band structure; Magnetic properties; Thin films; Surface; Interface PACS: 73.20.At; 73.20.-r; 75.70.-i

Theoretical Study of Sulphur Interaction with Ceria Ph. Baranek1*, L. Gauthier2 and M. Marrony2 1

EDF R&D – MMC, BP. 46., Avenue des Renardières, 77818 Moret-sur-Loing Cedex, France European Institute for Energy Research (EIfER), Emmy-Noether Strasse 11, 76131 Karlsruhe, Germany

2

Abstract. Sulphur-containing molecules are responsible for the poisoning of catalysts used in many chemical processes such as fuel processing for hydrogen production and for fuel cells. An option which would constitute a breakthrough in this field would be to developed sulphur tolerant catalysts. Ceria (CeO2) is an important ceramic material exploited in a wide range of applications such as solid oxide fuel cells. Then it is important to understand its surface catalytic properties. The adsorption of S, H2S and other S-containing compounds on different surfaces of ceria are investigated at the ab initio quantum mechanical level, by using the periodic CRYSTAL06 code. In this extended abstract, we focus on the S adsorption on the stoichiometric (111), (110) and (100) surfaces of ceria. The equilibrium lattice parameters of CeO2, surfaces stabilities, and S adsorption energies have been evaluated. The calculations have been performed at the HartreeFock (HF), density functional theory (DFT) and hybrid levels. A good agreement between calculated, and, other theoretical and experimental various properties has been found with hybrid approximations. The role of f orbitals of Ce is commented. Keywords: ceria, sulphur, surface, catalysis, adsorption, ab initio modeling, Hartree-Fock, Density Functional Theory, hybrid functionals. PACS: 31.10.+z, 31.15.Ar, 31.15.Ew, 31.50.-x, 61.66.Fn, 61.50.Lt, 68.35.Bs, 68.35.Dv, 68.35.Md, 68.43.Bc, 68.43.Fg

Is Aromaticity and Fluxionality The Key To Magicity Of Si6 Cluster? Aristides D. Zdetsis Replac Department of Physics, university of Patras, 26500 Patras, Greece,

Abstract. It is illustrated by high level ab initio calculations that the strange and controversial structure of the ground state and the low-lying excited states of the magic Si6 cluster as well as the structure of its ions can be understood in terms of fluxional and strange aromatic behavior, which are established on the basis of well known fluxionality and aromaticity criteria. This interpretation resolves the existing controversies and fully explains the known experimental results. Keywords: Clusters, Silicon, Structure, Aromaticity, Fluxionality PACS: 31.10.+z, 31.30.Gs, 36.40.-c, 82.30.Qt, 71.24.+q

I How T-cells ‘see’ antigen: A crossroad of the physical, life and engineering sciences Arup Chakraborty Dept. of Chemical Eng., MIT, Cambridge, MA 02139, USA; [email protected] Abstract. Do not replace the word “abstract,” but do replace the rest of this text. If you must insert a hard line break, please use Shift+Enter rather than just tapping your "Enter" key. You may want to print this page and refer to it as a style sample before you begin working on your paper. Keywords: Enter Keywords here. PACS: Replace this text with PACS numbers; choose from this list: http://www.aip.org/pacs/index.html

Equation-of-State Model for Temperature-Responsive Polymers with Tunable Response onset E. Manias* and Alexei M. Kisselev+ *

Dept. of Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA: [email protected] + Dept. of Physics, , Pennsylvania State University, University Park, PA 16802, USA Abstract. The phase behavior of aqueous solutions of temperature-responsive (ethylene oxide)/ethylene copolymers with tunable lower critical solution temperatures (LCST) is explored using an equation of state approach. The LCST in water of these polymers is tailored by their chemical composition, specifically by the balance of hydrophilic to hydrophobic groups in the polymer. The general formalism of the lattice-fluid with hydrogen-bonding theory, adjusted here to account for multiple types of hydrogen bonds, is employed, and the theoretical predictions are compared with experimental systems. The developed theoretical model is shown to be effective in describing the phase behavior of these systems, and the model parameters seem to be transferable between different homologous copolymer series. Keywords: Equation-of-State Theory; Smart Polymers; Temperature-Responsive Polymers. PACS: 82.60.Lf; 83.80.Rs; 82.35.Jk.

Theoretical study of adsorption of star-polymers by mean field theory Georgios Kritikos and Andreas F. Terzis Depart. of Physics, School of Natural Sciences, University of Patras, GR-26504, Patras, GREECE: [email protected] Abstract. In this work we present an investigation of star-like polymers in various architectures with the use of a recently developed numerical self-consistent mean field theory. The polymers have been previously studied experimentally and the comparison of the adsorption data with the findings of our method shows excellent agreement. The volume fraction and details about the inner structure of the formed brushes indicate that as the number of branches is increased the number of adsorbed polymers is significantly reduced. Mixtures of different kind of star polymers show interesting behavior as the more branched polymers try to develop in the outer region of brush. We also show information about the distribution of the free ends. Keywords: Star polymers, polymer brush, self-consistent mean field method. PACS: 61.25.Hq; 68.47.Mn.

Odd Electrons of Nanomaterials. A New Approach to Computational Chemical Engineering Elena F.Sheka Research Department, Peoples` Friendship University of the Russian Federation, Moscow, 117198 Russia [email protected] Abstract. A unified theoretical and/or computational odd-electrons approach is suggested to nanomaterials making possible their consideration on the same conceptual basis as well as on the same computational footing. The current paper presents the grounds of the approach that was successfully applied to the chemistry of fullerenes, carbon single-walled nanotubes, surface science of silicon crystal as well as to the molecular magnetism of both molecular crystals composed of nanosize transitional metal complexes and solid polymerized fullerenes. Keywords: odd electrons, Hartree-Fock approach, effectively unpaired electrons, chemical bonding, chemical susceptibility. PACS: 03.67.Lx; 31.10.+z ; 31.15.Ct; 81.05.Tp; 81.07.Bc.

On the Validity of the Geometric Rule in Multi-component Diffusion George D. Verros Department of Electrical Engineering,Technological & Educational Institute (TEI) of Lamia 35100 Lamia, GREECE: e-mail: [email protected] Abstract. In the present work the validity of the geometric rule for multi-component diffusion is re-examined by using sound principles of non-equilibrium thermodynamics. It is shown that the geometric rule satisfies both the nonequilibrium thermodynamics postulates (Linearity Postulate, Quasi Equilibrium Postulate and Onsager Reciprocal Relations) as well as the uniqueness criterion of the resistance coefficients. The computational aspects of the geometric rule are examined in detail by studying the evaporation process from non-solvent/solvent/polymer systems which are widely used in membrane & coating manufacture. The results of this work indicate that the geometric rule could be used to develop advanced computational models for physical and industrial multi-component diffusion processes. Keywords: Multi-component Diffusion, Non Equilibrium Thermodynamics, Onsager Reciprocal Relations. PACS: 0570Ln ; 6610Cb ; 8715Vv ; 44

II

Conformational Properties Of Dendritic Homopolymers With Interacting Branching Points Pavlos Efthymiopoulos, Marios Kosmas Chemistry Department, University of Ioannina, 45110 Ioannina, Greece: [email protected] Abstract. A microscopic model is used to determine analytically the macroscopic conformational properties of dendritic polymers with interactive branching points. Three mean square distances are calculated which determine the extension of the k generation from the origin, the sizes of the branches in each generation and the average distances between symmetrical points on different dendrons. Based on these distances the dependence on the microscopic characteristics of the dendritic polymer of the positions of the terminal groups and the average angles which describe the entrances and the vacancies to the dendritic polymer are given. Keywords: Conformational properties, dendritic homopolmers, branching points. PACS: 05.20.-y; 36.20.-r; 36.20.Ey; 61.25.Hq.

Conformational Transitions of a Model Polymeric System near Attractive Surfaces: A Monte Carlo Study A.N. Rissanou*,+, S.H. Anastasiadis*,#, I.A. Bitsanis* *

Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, GR-711 10 Heraklion, Greece; [email protected] + Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos” GR-153 10, Aghia Paraskevi Attikis, Greece # Department of Chemical Engineering, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece Abstract: We study the conformational transitions of polymer chains near attractive surfaces using Monte Carlo simulations on a simple cubic lattice. The shape of the adsorbed chain is studied as a function of the molecular weight, solvent quality and surface energy. The competition between two transitions induced by varying solvent conditions and the existence of an attractive wall results in various shapes of the adsorbate. Keywords: computer modeling; Monte Carlo simulations; adsorbate shape; surface energy PACS: 82.70.Dd, 36.20.Kd, 68.43.–h, 61.25.Hq

Clustering of Proteins embedded in Lipid Bilayers: a Monte Carlo Study Marianna Yiannourakou*+, Luca Marsella*, Frédérick de Meyer* and Berend Smit* *

Centre Europeén de Calcul Atomique et Moleculaire, 46 Allée d’Italie 69364 Lyon, France Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”,GR-153 10, Aghia Paraskevi Attikis, Greece; [email protected]

+

Abstract. The clustering behavior of peptides embedded in a lipid bilayer is extensively studied using a twodimensional coarse-grained model under different conditions of hydrophobic mismatch. We observe the formation of stable clusters of peptides with size exhibiting an upper limit. This result accounts for a natural tendency of peptides to aggregate, responding to the perturbation induced in the membrane, confirming previous experimental and computational findings. Keywords: Membrane, bilayer, proteins, peptides, lipids, hydrophobic mismatch, clusters PACS: 87.14.Cc, 87.14Ee, 87.15.Aa

III Computer Design of Copolymers with Desired Functionalities: Microphase Separation in Diblock Copolymers with Amphiphilic Block Alexei R. Khokhlov*,#, Yury A. Kriksin†, Igor Ya. Erukhimovich‡, and Pavel G. Khalatur#,‡ *Physics Department, Moscow State University, Moscow 119899, Russia; [email protected] # Department of Polymer Science, University of Ulm, Ulm D-89069, Germany † Institute for Mathematical Modeling, Russian Academy of Sciences, Moscow 125047, Russia ‡ Institute of Organoelement Compounds, Russian Academy of Science, Moscow 119991, Russia Abstract. Using the mesoscale simulation techniques, self-consistent field (SCF) method and dissipative particle dynamics (DPD), we study microphase separation in the melt of amphiphilic/nonpolar diblock copolymers. It is shown that the phase diagram for the melt of diblock copolymers with an amphiphilic block can be significantly different from that known for the conventional model of a diblock copolymer. In particular, we find that longer nonpolar blocks may be assembled in micelles separated by a matrix of shorter amphiphilic blocks. The physical reason behind this is connected with the surface activity of amphiphilic monomer units, which forces them to be located in the regions of maximum concentration gradient. In the limit of significant amphiphilicity (surface activity), the resulting morphology corresponds to thin channels and slits of amphiphilic units penetrating through the matrix of a major nonpolar component. Keywords: Molecular design, microphase separation, amphiphilic PACS: 82.35Jk, 81.16Fg, 61.43Bn

Phase Equilibrium of Colloid Systems with Particle Size Dispersity: A Monte Carlo Study Marianna Yiannourakou+, Ioannis Bitsanis*, Ioannis Economou+ +

Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”,GR-153 10, Aghia Paraskevi Attikis, Greece * Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, GR-711 10 Heraklion, Greece; [email protected]

Abstract. We have studied the solid-fluid coexistence for systems of polydisperse soft spheres with near-Gaussian diameter distributions that interact via an inverse power potential, the softness of which is being tuned. The study employs simulation in the isobaric semigrand ensemble. Gibbs-Duhem integration is used to trace the coexistence pressure as a function of the variance of the imposed activity distribution. Both the fluid-solid coexistence densities and volume fractions are monotonically increasing functions of the polydispersity s, which is given in terms of the standard deviation in the particle diameter distribution function. We observe a terminal polydispersity, i.e. a polydispersity above which there can be no fluid-solid coexistence. At the terminus, polydispersity increases from 5.8% to 6.1% to 6.4% and to 6.7% for the solid phase as the softness parameter n, takes on smaller values: from 100 to 50 to 12 and to 10 respectively. Keywords: colloids, polydispersity, phase coexistence, soft spheres PACS: 05.10.Ln, 82.60.Qr

Physico-chemical Characteristics of Thermopylae Natural Hot Water Springs in Central Greece: Chemical Geothermometry G. D. Verrosa,*, T. Latsosa, K. E. Anagnostoua, P. Avlakiotisa, C. Chaikalisa, C. Lioliosa, D. Antonioua, S. Kotsopoulosb and P. Arsenosc a

Department of Electrical Engineering, Technological & Educational Institute (TEI) of Lamia 35100 Lamia, GREECE, *e-mail : [email protected] b School of Electrical & Computer Engineering (E.C.E.), University of Patras 26500 Patras, GREECE c

Technological & Educational Institute (TEI) of Piraeus 12244 Aegaleo, GREECE

Abstract. In this work, the temperature of the subsurface reservoir in the Thermopylae natural hot water springs in Central Greece is estimated using chemical geothermometry. For this purpose, a novel computational methodology is proposed. This methodology is based on the selection of the minerals which might be in equilibrium with the subsurface water in the reservoir. The selection of minerals is achieved by comparing for a given tempearture the well established equilibrium constants of various minerals with the estimated values from the water chemical analysis. Finally, an optimization techique was applied to estimate the optimal temperature of the water in the reservoir by minimizing the deviation from equilibrium. The estimated temperature for the Thermopylae reservoir was in satisfactory agreement with experimental findings from geological exploration. Keywords: Geothermy, Geochemistry, Chemical Equilibria PACS: 91.35.Dc, 92.40.Bc, 82.60.Hc

Modeling the Viscosity of Aluminosilicate Melts Sergei A. Decterov, A. Nicholas Grundy, In-Ho Jung and Arthur D. Pelton Centre de Recherche en Calcul Thermochimique, Département de génie chimique, École Polytechnique de Montréal, Canada :[email protected] Abstract. Silicate systems are of fundamental importance for many metallurgical processes, for the glass industry and also for many aspects of geology. In addition to the phase relations, there are many properties of the liquid phase such as molar volume, surface tension, absorption coefficient, thermal conductivity and viscosity that are important for understanding, simulating and modeling processes involving silicate liquids. Over the past several years, through critical evaluation of all available thermodynamic and phase equilibrium data, we have developed a quantitative thermodynamic description of multicomponent silicate melts using the Modified Quasichemical Model for short-range ordering. We find that the local structure of the liquid, in terms of the bridging behavior of oxygen, calculated using our thermodynamic description allows us to link the viscosity and the thermodynamics of the silicate liquid. We can thus simultaneously calculate phase relations, thermodynamics and viscosity of the liquid over a wide composition and temperature range. In the present work we outline the viscosity model using selected binary and ternary systems as examples. The model has successfully been applied to melts in the multicomponent Na2O-K2O-MgO-CaO-MnO-FeO-ZnO-PbO-Al2O3-SiO2 system and more elements are currently being added to the database. Keywords: Viscosity, Thermodynamic Modeling, Silicate. PACS: 66.20

Molecular Modeling of Polydimethylsiloxane Mixtures Zoi A. Macrodimitri and Ioannis G. Economou Molecular Thermodynamics and Modeling of Materials Laboratory, Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, GR-153 10 Aghia Paraskevi, Attikis, Greece * corresponding author: [email protected]

Abstract. The thermodynamic properties and microscopic structure of PDMS are examined using Molecular Dynamics. A force field is developed that focuses on the accurate representation of polymer melt density over a wide temperature range at ambient pressure. The force field is also used for melt density prediction at high pressures. Model predictions and experimental data are in good agreement in all cases. Subsequently, the solubility of n-alkanes, n-perfluoroalkanes, noble and light gases in PDMS at various temperatures is calculated using the Widom test particle insertion technique. Accurate force fields are used for the solute molecules. Results agree very well with available experimental data, with the exception of CF4. MD runs at 300 K are further used for the calculation of diffusion coefficients of light gases and nalkanes in PDMS. Calculations for the lighter gases are in good agreement with limited experimental data available from the literature while for the alkanes the deviation is higher. Keywords: Molecular Dynamics, polymers, solubility, diffusion.

PACS: 64.75.+g, 66.10.Cb

Computational Modelling of Amperometric Enzyme Electrodes with Selective and Perforated Membranes Romas Baronas*†, Feliksas Ivanauskas*† and Juozas Kulys** *

Faculty of Mathematics and Informatics, Vilnius University, Naugarduko 24, 03225 Vilnius, Lithuania † Institute of Mathematics and Informatics, Akademijos 4, 08663 Vilnius, Lithuania ** Vilnius Gediminas Technical University, Sauletekio al. 11, 10223, Vilnius, Lithuania

Abstract. A two-dimensional-in-space mathematical model of an analytical system based on an amperometric enzyme electrode with selective and perforated membranes has been proposed and analyzed. The model involves the geometry of perforated holes partially or fully filled with an enzyme. The mathematical model is based on the reaction-diffusion equations containing a nonlinear term related to the enzymatic reaction subject to Michaelis-Menten kinetics. Using numerical simulation, the influence of the geometry of the membranes and of the enzyme region on the response of the enzyme electrode was investigated. The numerical simulation was carried out using the finite difference technique. Keywords: Modelling, simulation, reaction-diffusion, enzyme electrode, perforated membrane PACS: 82.20.Wt, 82.39.Fk, 82.45.Fk, 82.45.Mp, 82.47.Rs

A Unifying View of Computational Electrochemistry L. K. Bieniasz Department of Electrochemical Oxidation of Gaseous Fuels, Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Zagrody 13, 30-318 Cracow, Poland Abstract. The current state of development of Computational Electrochemistry is briefly discussed, and a unifying view of the field is proposed, with the aim of stimulating a communication between, and unity of, computationally oriented electrochemists involved in diverse kinds of computations. The most recent work of the author, pertaining to the field, is also reviewed. Keywords: computational electrochemistry, computer experiments, digital simulation, continuum electrochemical theory, quantum electrochemistry PACS: 02.70.Bf, 31., 07.05Kf, 07.05.Tp, 82.45Fk, 82.80.Fk

Turing instability in an electrodeposition morphogenesis model: an analytical, numerical and experimental study Benedetto Bozzini*, Deborah Lacitignola† and Ivonne Sgura1** *

Dipartimento di Ingegneria dell’Innovazione, Università di Lecce, Via per Monteroni, 73100 Lecce, Italy † Dipartimento di Matematica, Università di Lecce, Via per Arnesano, 73100 Lecce, Italy ** Dipartimento di Matematica, Università di Lecce, Via per Arnesano, 73100 Lecce, Italy Emails: {benedetto.bozzini,deborah.lacitignola,ivonne.sgura}@unile.it

Abstract. In the present paper we shall focus on the coupling between surface morphology and surface composition, as a means of understanding the formation of morphological patterns found in electrodeposition (ECD) and, prospectively, as a control strategy of ECD morphology based on manipulations of the surface chemistry (in terms of additive adsorption at the growing cathode). The relevant mathematical background is that of reaction-diffusion systems: the discussion will be restricted to the case of a single reaction-diffusion equation for one chemical species adsorbed at the surface of the growing cathode and source terms for both the "chemical" and the "morphological" equations of a simple form. We investigate on the dynamics and we show the arising of spatial patterns induced by diffusion which qualitatively match results found in the experiments. Keywords: Morphological Patterns in Electrodeposition, Turing Instability, Finite Element Method PACS: 81.07.b, 82.45.Yz, 81.07.Nb,02.30.Jr

1

Corresponding author

Using Digital Simulation to Study Hydroquinone Oxidation on Porous Electrodes by Cyclic Voltammetry R.H. Carvalho, M.A.N.D.A. Lemos*, F. Lemos and F. Ramôa Ribeiro IBB-Institute for Biotechnology and Bioengineering, Centre for Chemical and Biological Engineering, Instituto Superior Técnico, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal Abstract. Digital simulation is a very useful tool to understand dynamic electrochemical processes. Composite porous electrodes, comprising a micro-porous material provide electrodes with very high effective areas and can also make use of the molecular sieving properties of some of these materials, like zeolites. Porous electrodes also raise some difficulties for the analysis of their behaviour, due to internal diffusion/adsorption processes and high ohmic-drops. In this paper we have applied digital simulation to analyse the cyclic voltammetric behaviour of a zeolite/graphite composite electrode used in the electro-oxidation of phenolic compounds. Keywords: Digital Simulation, Method-of-Lines, Cyclic Voltammetry, Porous Electrodes, Phenolic Compounds. PACS: 82.45.Fk, 82.45.-h, 68.43.Jk

An Ab-Initio Theoretical Study Of The Electrochemical Grafting Process Of Alkynil(aryl)iodonium Salts On Glassy Carbon Surfaces Kim Daasbjerg*, Umberto Del Pennino†, Valentina De Renzi†, Claudio Fontanesi¶, Francesca Parenti¶ and Augusto Rastelli¶ *

Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, DENMARK. † Department of Physics, University of Modena, Via Campi 213/A, 41100 Modena, ITALY. ¶ Department of Chemistry, University of Modena, Via Campi 183, 41100 Modena, ITALY.

Abstract. The behaviour of alkynil(aryl)iodonium salts upon electrochemical reduction, on glassy carbon electrodes, is here studied by comparing both theoretical and experimental results. In particular, experimental results are obtained by means of cyclic voltammetry and chronocoulometric measurements as well as by collecting XPS spectra, while the standard electrode potential and different dissociation paths (I-C, arylic, compared to the I-C, alkynil, bond cleavage) have been characterized theoretically at the B3LYP/3-21g** level of the theory (the solvation free Gibbs energy of the cation and of the neutral radical species have been calculated by using the CPCM method). Keywords: Ab-Initio, DFT, Solvation, Iodonium Salt. PACS: Category 31.15Ar: Ab initio calculations

Numerical Method and Analysis of Consistency for Electrodiffusion Problem R. Filipek1, K. Szyszkiewicz1,2, M. Danielewski1 and A. Lewenstam1,3 1

Faculty of Materials Science and Ceramics, Interdisciplinary Centre of Materials Modeling, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Kraków, Poland 2 Faculty of Computer Sciences, WSB-NLU, Zielona 27, 33-300 Nowy S cz, Poland 3 Department of Chemistry, Åbo Akademi UniVersity, Biskopsgatan 8, 20500 Åbo/Turku, Finland Abstract. Numerical procedure based on method of lines for time-dependent electrodiffusion transport is developed. Finite difference space discretization with suitably selected weights based on a non-uniform grid is applied. Consistency of this method and the method put forward by Brumleve and Buck are analyzed and compared. The resulting stiff system of ODEs is effectively solved using the Radau IIa integrator. The applications to selected electrochemical systems: liquid junction, bi-ionic case and fused salts have been tested. Results for ion-selective electrodes are demonstrated. Keywords: electrodiffusion, ion transport, Nernst-Planck-Poisson, method of lines, consistency, ion selective electrodes PACS: 82.45.–h, 82.45.Rr, 82.47.Rs, 82.45.Mp

Signal Processing in DP and NP Voltammetry by Means of a Dedicated Mother Wavelet M. Jakubowska, B. Ba , E. Niewiara, W. Reczy ski and W.W. Kubiak Faculty of Materials Science and Ceramics, AGH University of Science and Technology al. Mickiewicza 30, 30-059 Kraków, Poland Abstract. In the paper the new signal processing method which utilizes the continuous wavelet transform and especially defined a dedicated mother wavelet is proposed. In the definition knowledge of the ideal signal shape in the considered problem is used. The application of this algorithm in transformation of curves recorded by means of differential pulse voltammetry (DPV) and normal pulse voltammetry (NPV) is described. Transformation of the signals, elimination of noise, baseline correction and separation of overlapping data can be achieved in one step by means of the proposed procedure. Due to linearity of wavelet transform (WT) the whole process of quantitative determination of analyte may be realized in the wavelet coefficients space. Keywords: continuous wavelet transform, dedicated mother wavelet, DPV, NPV, signal processing. PACS: 82.45.Rr

Computational Study of the Interactions Between Electrochemically-Generated 1,4-Dinitrobenzene Dianion and Substituted Imidazolium Ions Yusuke Minami and Albert J. Fry Chemistry Department, Wesleyan University, Middletown, CT 06459 Abstract. Density functional quantum chemical methods are used to predict the structure of the adducts of electrochemically generated dinitrobenzene dianions with substituted imidazolium ions. One of the oxygen atoms of 1,4dinitrobenzene dianion abstracts the C-2 proton from 1,3-dimethylimidazolium ion, whereas 1,2,3-trimethylimidazolium ion, in which proton transfer is inhibited, stacks in a plane parallel to and above that of the dianion. Keywords: Ion-pairing; dianions, imidazolium ions. PACS: 82.30.Rs, 31.15.Ew, 82.20.Wt, 82.45.Hk

Quantum Chemical Study Of Cl– Anion Adsorption On LowIndex Faces Of Cu, Ag And Au From Aqueous Solutions I. Nechaev, A. Vvedenskii and S. Grushevskaya Voronezh State University, Universitetskaya pl. 1, Voronezh, 394006 RUSSIA Abstract. Chloride anion chemisorption on (001), (011) and (111) faces of Cu, Ag and Au has been studied using the cluster model approximation. The calculations were performed in the framework of the Density Functional Theory (B3LYP). The solvation effects were taken into account with Polarizable Continuum model (COSMO) and supermolecular approach. The combined molecular-continuum model was also used. Results indicate that adsorption of Cl– from aqueous solutions occurs with sufficient lower energetic effect against vacuum adsorption. Adsorption energy decreases in row: (011)≈(001)>(111). Keywords: ab initio calculations, chloride anion chemisorption. PACS: 31.15.Ar

Electronic Structure Of Five-Atomic Thickness Cu, Ag, Au And Pd Films With Adsorbed Chloride Anion I. Nechaev, V. Sokova, A. Vvedenskii and S. Grushevskaya Voronezh State University, Universitetskaya pl. 1, Voronezh, 394006 RUSSIA Abstract. The quantum chemical ab-initio electronic structure calculations of the statistically completely ordered Cu, Ag, Au and Pd (001) and (011) films with adsorbed chloride anion have been done using the Density Functional Theory in the framework of the linearized augmented plane-wave (LAPW) model in “muffin-tin” approach. Differential and integral density of states (DOS), valence bandwidth (Eval), work function (W) and X-ray emission and photoelectron spectra were calculated. It was established that Eval increases for 5.5-6 eV with full surface coverage (Θ=1) while W decreases its value for 4-5.5 eV. Keywords: ab initio calculations, electronic structure. PACS: 31.15.Ar

Use of Factor Analysis in Multi-Electron Spectroelectrochemistry Michael D. Ryan and Robert L. Keesey Marquette University, Chemistry Dept., PO Box 1881, Milwaukee, WI 53092 USA Abstract. Spectroelectrochemistry and voltammetry contain both unique and complementary information. For multielectron transfers, information on each electron exchange is only directly accessible in the voltammetric data if the potentials are well separated so that two distinct waves can be observed. If the E°’s are close together, the voltammetric data will contain the sum of the two exchanges which can only be deconvoluted by modeling the system and solving the appropriate equations. On the other hand, the spectroscopic data contains direct information on each electron exchange even when the E°’s are close together. Unfortunately, this information cannot be readily extracted if the intermediate oxidation state does not have a potential region where it is the dominant species. Chemometric methods such as factor analysis though can be used to deduce the spectra of each species even if they don’t dominate in any potential region. Initial work on the application of factor analysis to spectroelectrochemistry has been reported. Traditional methods of electroanalytical analysis are based on models that relate the concentration of electroactive materials to electrode potentials and solution concentrations. The model and parameters are adjusted to obtain the best fit to a model. Chemometric methods such as factor analysis allow the experimenter to determine solution concentrations without knowledge of the precise electrochemical mechanism. The utility of this approach will be demonstrated by the study of a protein, E. coli sulfite reductase hemoprotein, which is capable of transferring two-electrons and the ∆E° values are less than 100 mV, causing the waves to overlap. With these methods more detailed information on the electron transfer rate and associated kinetics processes can be more clearly identified. Keywords: spectroelectrochemistry, factor analysis, voltammetry, sulfite reductase, E. coli, electron transfer kinetics PACS: 82.45.Rr

Nonlinear Boundary Conditions In Simulations Of Electrochemical Experiments Using The Boundary Element Method. Markus Träuble, Carolina Nunes Kirchner and Gunther Wittstock Center of Interface Science (CIS), Faculty of Mathematics and Sciences, Department of Chemistry (FB9) and Institute of Chemistry and Biology of the Marine Environment (ICBM) Carl Von Ossietzky University of Oldenburg, D-26111 Oldenburg, Germany Abstract. The use of the boundary element method (BEM) in simulating steady-state experiments of scanning electrochemical microscopy in feedback mode and in generation-collection mode using complex three dimensional geometries has been shown in previous papers. In the context of generation-collection mode experiments, catalytic reaction mechanisms of immobilized enzymes are of great interest. Due to the catalytic reaction behaviour, which can be described by nonlinear Michaelis-Menten kinetics, the modelling of such systems results in solving a diffusion equation with nonlinear boundary conditions. In this article it is described how such nonlinear reaction mechanisms can be treated with the BEM. Keywords: boundary element method (BEM), scanning electrochemical microscopy (SECM), nonlinear boundary condition, enzymatic modified surface. PACS: 47.11.Hj

Inclusion of additional coordination sphere into clustermodel redox potential calculations Merle Uudsemaa and Toomas Tamm Department of Chemistry, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia Abstract. Combination of cluster model for the inner solvation spheres with dielectric continuum solvation model for the bulk solvent has previously yielded good accuracy for prediction of redox potentials of transition metal cations. The influence of adding a third solvation sphere to the cluster on the accuracy of calculated redox potential is explored in this work. It is found that the accuracy is not improved which leads to the conclusion that apparent accuracy of previous models is based on compensation of errors. Keywords: computational electrochemistry, cluster, density-functional theory, continuum solvation PACS: 31.70.Dk, 31.15.Ew, 33.15.Ry, 82.45.-h, 92.20.cj

Numerical simulation of mass transport in electrochemical systems based on the mean spherical approximation S. Van Damme and J. Deconinck Computational Electrochemistry Group, ETEC, Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels [email protected] Abstract. The mean spherical approximation is used to compute the activity coefficients and the Onsager coefficients in the mass transport equations. Numerical simulation of limiting current densities for aqueous CuSO4 solutions is performed with this transport model and with “ideal” transport models. The results are compared with reported limiting current densities. Keywords: mean spherical approximation, mass transport, finite element PACS: 82.45, 02.70, 05.20

CASSCF Calculations For Excited States Of Large Molecules: Choosing When To Use The RASSCF, ONIOM And MMVB Approximations Michael J. BearparkA, Francois OgliaroB, Thom VrevenC, Martial Boggio-PasquaA, Michael J. FrischC, Susan M. LarkinA, and Michael A. RobbA A

Department of Chemistry, Imperial College London, London SW7 2AZ, UK Equipe de Chimie et Biochimie Théoriques, UMR 7565 – CNRS, Université Henri Poincaré, Nancy 1, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France C Gaussian, Inc., 340 Quinnipiac St Bldg 40, Wallingford, CT 06492 USA

B

Abstract. We compare and contrast the RASSCF, ONIOM and MMVB electronic structure methods for calculating relaxation paths on potential energy surfaces of the excited states of large molecules, and for locating any resulting conical intersections at which nonadiabatic decay can take place. Each method is treated as an approximation to CASSCF, which we choose as our reference level of theory, but which becomes prohibitively expensive computationally for large molecules. Both MMVB and ONIOM are hybrid computational methods – combining different levels of theory in an energy plus derivatives calculation at a particular molecular geometry – but they differ fundamentally in that MMVB is a hybrid-atom method, whereas ONIOM is a hybrid-molecule method. We explain this distinction through representative applications, and show that each method is more appropriate for a particular type of photochemical problem. Keywords: QM/MM, excited states, CASSCF, RASSCF, ONIOM, MMVB

Benign And Degrading Excited-State Processes Of DNA Nucleobases And Their Derivatives Lluís Blancafort,A David Asturiol,A Annapaola Migani,A Monika Kobyłecka,B and Janusz RakB A

Institut de Química Computacional, Departament de Química, Universitat de Girona, 17071 Girona, Spain B Department of Chemistry, UnivVersity of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland

Abstract. The photochemically induced dimerization of thymine and the photodecomposition of 5-bromouracil are investigated using the CASSCF (complete active space self-consistent field) and CASPT2 (complete active space second order perturbation) methodologies, where excited state reaction paths are calculated with CASSCF, and the energies refined with CASPT2. The studies focus on the central role of conical intersections for the ultrafast decay and the reactivity. Keywords: Excited-state potential energy surfaces, ultrafast decay, photoreactivity, DNA nucleobases, CASSCF and CASPT2. PACS: 31.15.Ar, 31.25.Qm, 31.50.Df, 31.50.Gh, 82.20.Kh.

Molecular Structure And Function Probed By High-Resolution Spectroscopy Wybren Jan Buma*, Mattijs de Groot, and Anouk M. Rijs Van’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands. Abstract. Understanding, using, and predicting the macroscopic properties of photoresponsive materials employed in technology and nature increasingly centers on the question what their photophysical and photochemical properties are at the molecular level, and how these properties can be addressed and influenced in a controllable way. High-resolution spectroscopy can in principle provide such a detailed picture of the electronic structure and dynamics of excited states, but requires at the same time often the development of novel experimental techniques to meet current demands on the size of the systems that can be studied and the level of detail. Furthermore, a multidisciplinary approach in which quantumchemical calculations play a prominent role is necessary to fully take advantage of the experimental results. Keywords: Fluorescence spectroscopy; Resonance enhanced multiphoton ionization spectroscopy; Excited-state photoelectron spectroscopy; Laser desorption; Quantumchemical simulations of vibronic spectra; Electronic coupling; Mechanically-interlocked molecular systems PACS: 31.50.Bc, 31.50.Df, 33.20.-t, 33.50.-j, 33.60.-q, 33.80.Rv, 34.50.Gb

Molecular Simulation Studies Of Proteins Involved In Parkinson’s Disease Paolo Carloni International School for Advanced Studies, INFM-CNR Democritos Center for Atomoistc Simulationi and Italian Institute of Technology-SISSA Unit, Via Beirut 2-4 34100 Trieste, Italy Abstract. This contribution describes two recent computational studies related to proteins involved in Parkinson's Disease (PD). The first focuses on the interplay between dopamine and α-synuclein (AS), which plays a central role in PD (unpublished results). The second deals with the protein DJ-1, whose mutations are present in patients suffering from familiar PD. Computational methods are used to investigate the relationship between such mutations and the protein oligomeric state, which may be important for the progression of the disease.

The Role Of Intersection Space Segments In Photochemical Reactions Obis Castaño,§ Unai Sancho, § Marco Garavelli,¤ Massimo Olivucci† and Luis Manuel Frutos,§,‡ §

Departamento de Química Física, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid (Spain). Dipartimento di Chimica ‘G. Ciamician’, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy † Dipartimento di Chimica Organica, Università di Siena, Via Aldo Moro, 53100 Siena, Italy. and Chemistry Department, Bowling Green State University, Bowling Green, OH 43403, USA ‡ Technical University of Munich, 85747 Garching (Germany) ¤

Abstract. We analyze here the role of the intersection space in the photochemistry of some organic compounds and how the topological properties of this space affect the mechanism of the photochemical reaction. This mechanism is related to the accessibility of different reaction paths in the relaxation in the ground state once the system reaches the intersection space (i.e. a conical intersection). It is proved that sometimes, even in the photochemistry of small organic molecules, the complete analysis of the intersection space is necessary for the correct computational prediction of the chemical mechanism and the formed photoproducts underlying the photoinduced reaction. Keywords: Conical Intersections, Intersection Space, Theoretical Photochemistry, CASSCF, CASPT2, diabatic transition, diene phtochemistry. PACS: 31.50.Gh; 31.15.Ne; 31.50.Df; 33.20.Lg

Protein Conformational Plasticity: The “Off-On” Switching Movement In Cdk5 Andrea Cavalli,A Anna Berteotti,B Davide Branduardi,B Francesco L. Gervasio,B Maurizio Recanatini,A Michele ParrinelloB A

Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy – [email protected]

B

Computational Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland

Abstract. Cyclin-dependent kinases (CDKs) are mostly known for their role in the cell cycle regulation. The activation mechanism of all CDKs involves the association with a regulatory protein, generally a cyclin, that binds to the kinase unit and stabilizes a catalytically active conformation. Active and inactive conformations of CDKs are characterized by the different spatial localization of two typical elements, namely the activation loop and an -helix, whose amino-acid composition varies throughout the family.

The Calculation Of The Correlation Energy In Ground And Excited States: The N–Electron Valence State Perturbation Theory Approach Renzo Cimiraglia Dipartimento di Chimica, Università di Ferrara, Via Borsari 46, I–44100 Ferrara, Italy Abstract. NEVPT (“n–electron valence state perturbation theory”) is a form of multireference perturbation theory which is characterized by a partially bielectronic zero order Hamiltonian. Such a choice ensures important properties such as size consistence and absence of the notorious intruder state problem. Recent progress in the development of NEVPT has concerned a) the construction of a quasi–degenerate formulation, b) the implementation of the third order code. In this contribution two significant applications are shown: a) the study of the ground state of the dimers of group 6 transition metals (Cr2, Mo2, W2 and CrMo), b) the calculation of the vertical spectrum of the biologically interesting molecule free base porphin. Keywords: multireference perturbation theory, NEVPT, transition metal dimers, free base porphin PACS: 31.10.+z, 31.15.Ar

Artificial Molecular Devices And Machines Driven By Light Monica Semeraro, Serena Silvi, and Alberto Credi* Dipartimento di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy Abstract. Light-induced processes are at the basis of fundamental natural phenomena as well as of a variety of applications. Since the functions that can arise from the interaction between light and matter depend on the degree of complexity and organization of the receiving ‘matter’, the research on these processes has progressively moved from molecular to supramolecular (multicomponent) systems, thereby originating the field of supramolecular photochemistry. In this context, examples of photochemical molecular devices and machines – that is, multicomponent chemical systems capable to perform specific functions under light stimulation – have been developed. Here we describe two recent examples of such systems based on pseudorotaxane and rotaxane species. These studies are of interest not only for the growth of nanoscience, but also for increasing the basic understanding and testing current theoretical treatments of photoinduced processes. Keywords: Binary Logic, Catenane, Luminescence, Photochemistry, Rotaxane, Supramolecular Chemistry PACS: 33.15.Bh, 33.20.Kf, 33.50.-j, 36.20.Kd, 81.07.Nb, 85.85.+j

Vertical Singlet Excitations On Adenine Dimer: A Time Dependent Density Functional Study Carlos E. Crespo-Hernández*,§ and Christopher N. J. Marai§1 *

Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106 USA § Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 USA Abstract. The condense phase, excited state dynamics of the adenylyl(3’→5’)adenine (ApA) dinucleotide has been previously studied using transient absorption spectroscopy with femtosecond time resolution (Crespo-Hernández et al. Chem. Rev. 104, 1977-2019 (2004)). An ultrafast and a long-lived component were observed with time constants of < 1 ps and 60 ± 16 ps, respectively. Comparison of the time constants measured for the dinucleotide with that for the adenine nucleotide suggested that the fast component observed in ApA could be assigned to monomer dynamics. The long-lived component observed in ApA was assigned to an excimer state that originates from a fraction of base stacked conformations present at the time of excitation. In this contribution, supermolecule calculations using the time dependent implementation of density functional theory is used to provide more insights on the origin of the initial Franck-Condon excitations. Monomer-like, localized excitations are observed for conformations having negligible base stacking interactions, whereas delocalized excitations are predicted for conformations with significant vertical base-base overlap. Keywords: Time-dependent density functional theory, single excited states, DNA photophysics, supermolecule calculations, molecular dimers.

1

Fellow of the Research Experiences for Undergraduates Program (REU 2004), NSF.

Agile Modelling Of Cellular Signaling Vincent Danos Plectix Biosystems, CNRS, Université Paris-Diderot Abstract. We illustrate with a simple example how using a rule-based approach to the modelling of cellular signalling allows for quickly putting together models (ease of expression), and quickly modifying them (ease of variation). Keywords: Stochastic simulation; Gillespie algorithm; Rule-based modelling; kappa-calculus PACS: 82.20.Fd

Ab Initio Molecular Dynamics Simulations Of Reactivity In Complex Systems Filippo De Angelis and Simona Fantacci Istituto CNR di Scienze e Tecnologie Molecolari, Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06123, Perugia, Italy. Abstract. We present a review of our recent activity in the field of ab initio molecular dynamics of chemical reactivity in complex systems and environments. We use a computational strategy based on a combination of codes and techniques rooted in the Density Functional Theory to unravel the hitherto inaccessible details of the reaction dynamics in several system of interest in various fields, spanning from organic to bio-inorganic and organometallic reactivity. The systems investigated here are complex because of: i) the large number of atoms they are made of; ii) the intermolecular interactions arising from the presence of transition metal centers; and iii) the environment (solution or protein) in which they are investigated. Keywords: Car-Parrinello molecular dynamics, Density Functional Theory, Chemical Reactivity. PACS: 31; 31.15.Qg; 31.50.-x

Kinetic And Spectroscopic Investigations By Ultrafast Absorption And Emission Techniques Fausto Elisei, Arianna Barbafina, Benedetta Carlotti and Loredana Latterini Dipartimento di Chimica and Centro Eccellenza Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy Abstract. Femtosecond time-resolved absorption and fluorescence spectroscopy have been used to probe the excitedstate reaction of the antimalarial quinacrine (QC) in order to obtain a better understanding of the excited states of the molecule. All the measurements were performed by using 40 fs visible pump pulses with a centre wavelength of 400 nm in buffered solutions at different pHs. The excitation at 400 nm reveals the presence in buffered solution of three different decay times both in absorption and emission experiments while in water (pH=5.5) a fourth short component of about 1ps was also detected. These components were interpreted in terms of the reactivity of different protonated species of QC, in the singlet excited state. Keywords: femtosecond, pump-probe absorption, upconverted fluorescence, proton transfer, pH effect, quinacrine.

Simulation Of Proton Transfer Processes And Excited-State Properties In Proteins With QM/MM Methods M. Elstner*,†, M. Hoffmann** and M. Wanko** Physical and Theoretical Chemistry, Technical University of Braunschweig, D-38106 Braunschweig, Germany † Dept. of Molecular Biophysics, German Cancer Research Center, D-69115 Heidelberg, Germany ** BCCMS, Universität Bremen, D-28359 Bremen, Germany

*

Abstract. Simulations of chemical reactions in biological systems have to face the problems of complexity and long time scales. This often requires the use of a multitude of methods in an integrated (quantum mechanical/molecular mechanical, or other multi-scale approaches) or in a sequential way (e.g., using different levels of theory for determining structures and energies). In this article, we brie_y describe some of our efforts to treat proton-transfer reactions and excited-state properties of proteins applying and assessing such combined approaches. Keywords: retinal, rhodopsin, bacterio-rhodopsin, pharaonis phoborhodopsin, proton transfer, polarization, QM/MM, excited states, opsin shift, multi-reference con_guration interaction PACS: 87.14.Ee 87.15.-v 87.15.Aa 87.15.He 87.15.Mi 87.16.Ac 87.16.Uv 87.16.Xa 87.17.Aa 87.18.Bb 87.50.Hj 31.15.Ar 31.15.Ct 31.15.Ew 31.25.-v 31.50.Df 31.70.Dk 33.20.Kf

Structural Order In Water: Comparison Between The Spectral Analysis Of Raman Data And Molecular Dynamics Results N. Faginas Lago_, M. Paolantoni_, A. Laganá_ and M. Alberti† _Department †Department

of Chemistry, University of Perugia, Italy of Chemistry, University of Barcelona, Spain

Abstract. We utilize molecular dynamics calculations performed using the DL_POLY suite of programs to test the validity of two popular water interaction models and to better understand the structural order of its liquid phase by comparing calculated properties with the Raman spectrum. Keywords: Structural order, Raman Spectrum, Molecular Dynamics, model potentials PACS: 61.25.EM

Reachability Analysis Of Biological Signalling Pathways By Abstract Interpretation Jérôme Feret1,2 École Normale Supérieure 45, rue d’Ulm 75 005 Paris, FRANCE Abstract. Agent-based formal languages can be used to describe biological signalling networks. As for any language, this process is error prone. Thus we require static analysis tools to check whether the formal description of models matches with what the programmer (or the biologist) has in mind. However, biological networks involve a large number of nonisomorphic complexes (i.e. the number of non-isomorphic ways in which agents can connect), as a consequence static analyses must cope with this combinatorial blow up. We use the abstract interpretation framework, which is a theory of semantics approximation, to design an abstraction of the set of reachable complexes. This abstraction is both accurate and efficient. Then we show several applications. First, we use this abstraction to detect some bugs such as dead reactions (reactions that can never be triggered) and conflicting rules (distinct rules that compute the same thing). Our analysis also predicts whether two sites may bind in any context, or if this binding is controlled by other sites. Keywords: Biological signalling pathways, k-calculus, reachable complexes, abstract interpretation.

New Computational Approaches In The Study Of Nonvertical Triplet Energy Transfer Luis Manuel Frutos,§,‡ A. Ulises Acuña† and Obis Castaño§ §

†

University of Alcalá, Alcalá de Henares, 28871 Madrid (Spain). Instituto de Química Física "Rocasolano", C.S.I.C., 28006 Madrid (Spain) ‡ Technical University of Munich, 85747 Garching (Germany)

Abstract. We have recently developed some new theoretical methods for the study of the nonvertical triplet energy transfer. These methods are based on the accurate description of the potential energy surfaces of the acceptor molecule for the electronic states (singlet ground and triplet excited) involved in the process. We show a brief overview of these theoretical tools and how they are implemented, and we apply them to the study of some prototypical nonvertical acceptors as cis- and trans-stilbene. It is shown that in trans-stilbene, the role of the stretching modes is dominant in its triplet quenching activity even for large endothermic reactions, in contrast with the classical discussion of this behavior in terms of phenyl-vinyl and central bond torsional modes. This methodology constitutes a new potential computational tool for designing new triplet quenchers. Keywords: Nonvertical triplet energy transfer. Stilbenes. PACS: 31.50.-x; 31.50.Gh; 31.50.Df; 31.50.Bc

Branching And Momentum Effects In Photochemistry Werner Fuß Max-Planck-Institut für Quantenoptik, D-85748 Garching, Germany Abstract. The decision on the fate of the reaction (branching of the path) is sometimes not only taken at the last conical intersection, but the Franck-Condon region can also contribute. Consideration of simple properties such as the slopes of the potential surfaces can explain effects such as the principle of least motion or the torquoselectivity without invoking ad-hoc electronic effects. The lack of stereospecificity of cyclobutene ring opening and the wavelength dependence of photochemical reactions of alkylated olefins and cyclobutenes can similarly be explained, if one assumes in addition that the momentum is conserved over a certain time. Keywords: Kasha rule, dynamic effects, carbene formation, pericyclic photochemical reactions, stereospecificity, wavelength dependence PACS: 82.20.-w, 82.20.Gk, 82.20.Hf, 82.20.Kh, 82.30.Qt, 82.50.-m

Towards The Understanding Of The Excited State Dynamics Of Nucleic Acids: Solvent And Stacking Effect On The Photophysical Behavior Of Nucleobases Fabrizio SantoroA, T. GustavssonB, Sandro LamiA, Vincenzo BaroneC and Roberto ImprotaC,D A

Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy B Laboratoire Francis Perrin, - CNRS URA 2453, CEA Saclay, F-91191 Gif-sur, Yvette, France C Dipartimento di Chimica and INSTM, Universita Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy D Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, I-80134 Napoli, Italy Abstract. This contribution describes the results of some recent studies concerning the excited state behavior of nucleic acid bases, where solvent and stacking effect are included. Our computational approach is based on PBE0 and TD-PBE0 geometry optimizations, while bulk solvent effects are taken into account by the Polarizable Continuum Model, with the possible inclusion of the solvent molecules of the first solvation shell. This approach provides accurate absorption and emission spectra both for pyrimidine and purine bases and is able to explain solvent effect on the excited state lifetimes of uracil-like molecules. Solvent indeed modulates the accessibility of an extra decay channel for the bright excited state, involving an underlying dark state. The effect of base stacking, investigated on 9-methyl-adenine stacked dimers and trimers, on the absorption and emission spectra is also fully reproduced by our calculations. Although light absorption leads to a state (SB) delocalized over different adenine molecules, excited state geometry optimization indicates that afterward it evolves into a state where the excitation is localized on a single base. Analysis of the excited state potential energy surfaces shows that SB can easily decay into the lowest energy excited state (SCT). SCT is a dark excimer produced by inter-monomer charge transfer between two stacked bases. Keywords: excited state, nucleic acids, solvation, spectroscopy, time-dependent density functional theory PACS: 01.30.Cc, 31.50.Df, 31.70.Hq, 31.70.Dk, 36.20.Kd

The Determinant Of Light-Energy And Light-Signal Conversion In Rhodopsins Hideki Kandori Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan Abstract. Rhodopsins can convert light into either chemical energy or signal. It is therefore reasonable to postulate the existence of specific structures for each function. Nevertheless, X-ray crystallographic structures showed similar protein architectures for microbial rhodopsins of both functional classes. But then, the question is how is each function achieved? We have studied protein structural changes in the functional processes of rhodopsins by means of Fourier-transform infrared (FTIR) spectroscopy. In particular, highly accurate spectral detection of the light-minus-dark difference spectra enabled us to observe hydrogen-bonding alterations from the analysis of X-H and X-D stretching vibrations [3]. We show that the mechanism of light-energy storage appears to be different between light-energy and light-signal conversions, though their structures are very similar. Destabilization of water-containing hydrogen-bonding network is crucial for the light-energy storage of proton pump. In contrast, steric constraint is important for the light-energy storage of light sensor. Keywords: FTIR spectroscopy, water molecule, proton pump, rhodopsin, membrane protein, photoisomerization, lightinduced PACS: 87.14.Ee, 87.16.Uv, 87.15.-v

An Exact And Scalable Stochastic Simulation Algorithm Jean Krivine Computer Science Laboratory (LIX), École Polytechnique, Palaiseau, France Abstract. We present a scalable and dimension-insensitive simulation algorithm in which dimensionality is taken care of by not enumerating the agents’ configurations; scalability is obtained by storing all potential events. This results in a simulation event cost which is purely logarithmic in the static measure of the rule set (number and size of rules) and opens the way for an implementation which can handle systems which are both large and high-dimensional. Keywords: Stochastic simulation;Gillespie algorithm;Rule based modeling;kappa-calculus PACS: 82.20.Fd

A Calculus For Modelling, Simulating And Analysing Compartmentilized Biological Systems Radu Mardare and Adaoha Ihekwaba Microsoft Research-University of Trento Centre for Computational and Systems Biology Trento, Italy Abstract. This paper introduces Process Calculus, a special modeling language designed for encoding and calculating the behaviors of compartmentilized biological systems. The formalism combines, in a unified framework, two successful computational paradigms - process algebras and membrane systems. The goal of Protein Calculus is to provide a formal tool for transforming collected information from in vivo experiments into coded definition of the different types of proteins, complexes of proteins, and membrane-organized systems of such entities. Using this encoded information as input, our calculus computes, in silico, the possible behaviors of a living system. Keywords: biological systems, modeling languages, process algebra, membrane systems

Functional Molecular Materials: Modelling Structure, Optical Properties, Intermolecular Interactions. Fabrizia Negri Università di Bologna, Dipartimento di Chimica “G. Ciamician” and INSTM UdR Bologna, Via F. Selmi 2, I-40126 Bologna, Italy e-mail: [email protected]. Abstract. In the past few years we have investigated structural, electric and photo-physical properties of several molecular systems forming the building blocks of functional molecular materials, and we paid increasing attention to the effects that condensed phase and structured environments can have on the properties of the material. Here we present an overview of our most recent achievements concerning the modelling of properties of several classes of organic functional molecules. The results presented comprise the prediction of optical properties of 2D and 3D carbon rich materials (models for defected graphite, hetero-fullerenes), studies on reactivity, dynamics and aggregation of polyphenylene dendrimers including their ability to encapsulate gas molecules, predictions of photo-physical properties of molecular switches, linear, non-linear electric responses and optical properties of polar chromophores and dyes for organic electric memory devices. Keywords: Quantum-chemical calculations, Molecular dynamics, Electric properties, Electronic spectra, Functional chromophores, Molecular materials. PACS: 01.30.Cc, 31.15.Ar, 31.15.Ew, 31.70.Dk, 36.20.Kd

An Ab Initio Study Of Decay Mechanism Of Adenine: The Facile Path Of The Amino NH Bond Cleavage Irene ContiA, Marco GaravelliA and Giorgio OrlandiA A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy

Abstract. A comprehensive study of the radiationless decay processes of the lowest excited singlet states in the isolated 9H-Adenine has been performed at the CASPT2//CASSCF level. The minimum energy paths of the La, Lb and nπ* singlet states along different skeletal distortions have been computed and the Conical Intersections (CIs) involving these states have been determined. The fast deactivation path of La along a skeletal deformation, which leads to a S0/La CI, as previously discussed, is confirmed. Moreover, low-lying CIs between S0 and πσ* singlet states have been characterized, where σ* is the antibonding orbital localized on a N-H bond of the amino (πσNH2*) or of the azine group (πσN9H*). We have found that the repulsive πσNH2* state associated with an amino N-H bond can be populated through a barrierless way. Therefore, the decay path shows a bifurcation leading to two possible ways of radiationless deactivation: on one hand a non-photochemical decay through the S0/La or S0/nπ* CIs and on the other hand a photochemical process via the possible access to the S0/πσNH2* CI that produces N-H cleavage. In this way, we can explain the H atom loss found upon UV excitation. We have considered also the decay of higher energy bright states. We have found that these states can decay also by converting to the repulsive πσN9H* state associated with the azine NH bond. This new channel suggests an increase of H-atom photoproduction yield by excitating Adenine with lower wavelength radiations. The study of the decay processes of an Adenine molecule in the double strand d(A)10·d(T)10 in water solvent is currently underway: Adenine is treated by the Quantum Mechanical (QM) approach and the remaining molecules are described at the Molecular Mechanics (MM) level. We use the COBRAMM program that is a tunable QM/MM approach to complex molecular architectures developed by our research group. Keywords: adenine photochemistry, DNA properties, conical intersections, multiconfigurational wave function methods, ultrafast decay, N-H dissociation, QM/MM.

Iridium Complexes With Terdentate Ligands: Cyclometalated Vs. Polypyridine Analogues; Hybrid Vs. “Pure” DFT. Marcella Ravaglia*, Marco Garavelli‡, Matthew Polson*†, and Franco Scandola* *

Dipartimento di Chimica, Università di Ferrara, INSTM, UdR Ferrara, 44100 Ferrara, Italy. ‡ Dipartimento di Chimica “G. Ciamician”, 40126 Bologna, Italy. † Present address: Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand. Abstract. The present investigation has a twofold aim. In the first place, the ground-state spectroscopic features of three IrIII polypyridyl complexes were studied by computational means, in order to elucidate the nature of their UV-visible spectra and electrochemical behaviour. Coincidentally, the limited but variegated set of molecules was employed to analyse how different exchange-correlation functionals model the properties of interest in the presence of transition metal atoms. These iridium complexes involve various terdentate ligands: a N^N^N bonded ttpy derivative (ttpy = 4'-tolyl2:2',6':2"-terpyridine), a C^N^C bonded dppy derivative (dppy = 2,6-diphenyl-pyridine), a C^N^N pbp derivative (pbp = 6-phenyl-2:2'-bipyridine). The axially-symmetric -homoleptic or heteroleptic- arrangement gives the low-lying excited states of these molecules a unique directional nature. Analysis of the electronic transitions calculated by first-principle method based on time-dependent density functional theory (TDDFT) gives insight on their steady-state visible absorption bands. The comparison of generalised-gradient approximation (GGA) functionals (BLYP and G96LYP) with hybrid GGA functionals (B3LYP and PBE0) values the consequences of the nonlocal Hartree–Fock exchange embedded in the latter. Keywords: Iridium complexes photophysics, UV-Vis spectroscopy, Density-functional theory, Time-dependent DFT. PACS: 31.10.+z. 31.15.Ew. 33.70.-w.

Primary Events In Retinal Proteins Revealed By Ultrafast Spectroscopy O. Bismuth1, A. Kahan1, N. Friedman2, M. Sheves2, and S. Ruhman1 1

Department of Physical Chemistry and the Farkas center for light induced processes, Hebrew University, Jerusalem 91904, Israel. 2 Department of Organic Chemistry, Weizmann Institute, Rehovot 76100, Israel. E-mail: [email protected]. Abstract. Bacteriorhodopsin (BR) is a light energized proton pump, embedded in the purple membrane of the photosynthetic Halobacterium. The absorbing chromophore is a retinal molecule covalently linked to the protein. Early in the BR photocycle, the retinal selectively isomerizes from all-trans to the 13-cis form, and the protein undergoes a series of structural changes leading to ejection of one proton from the cytoplasm. Previous studies have demonstrated that photon absorption leads to the appearance of a fluorescent state coined (I460) exhibiting stimulated emission and excited state absorption bands peaking at 850 and 460 nm respectively. These features decay concertedly within ~1 psec, to form a red shifted intermediate coined “J”, thought to be in the ground electronic state. Fundamental questions concerning excited state dynamics in BR remain unresolved. Resonance Raman spectroscopy shows that numerous retinal degrees of freedom are activated by BR photoexcitation aside from double bond torsion – particularly double bond stretches. Mounting evidence suggests that the decay of I460 reflects the stage of retinal isomerization / internal conversion (IC), yet remarkably it is accompanied by negligible spectral evolution, and the contours of transient absorption changes reveal little of the underlying structural changes. Vibrational spectroscopies such as transient Raman or IR can provide multimode structural information concerning short lived intermediates, but in the case of BR have not clarified the questions above. An alternative based upon stimulated Raman probing with ultrafast time resolution has been employed to study excited state dynamics in retinal proteins. Here early photoinduced BR dynamics are covered with impulsive vibrational spectroscopy (IVS). The wave packets formed along the active vibrations in both the ground and excited states evolve and can be read out as modulations in probe transmission, and through their delineation, excited state dynamics can be deduced. Low frequency spectral modulations (~160 cm-1) observed in I460 stimulated emission have been assigned to excited state coherent torsions. However, coverage of all relevant frequencies requires sub 10 fsec time resolution. Two previous studies by Shank, Mathies, and coworkers and more recently by the Kobayashi lab have led to conflicting interpretations concerning the source of modulation. Here we investigate BR and its isolated chromophore the retinal protonated Schiff base (RPSB) with ~6 fsec IVS to separate S0 and S1 coherences, and from them understand photon energy storage in BR.

Quantum Dynamics Of Ultrafast Photoinduced Processes In Biological Molecules Fabrizio SantoroA, Vincenzo BaroneB, Roberto ImprotaB,C, Alessandro LamiA, and Massimo OlivucciD,E A

Istituto per i Processi Chimico-Fisici del CNR, Area della Ricerca del CNR, Via G. Moruzzi 1,56124 Pisa, Italy Dipartimento di Chimica, Università Federico II di Napoli, Complesso Universitario Monte S. Angelo, Via Cintia, 11, 80126 Napoli, Italy C Istituto di Biostrutture eBioimmagini del CNR, Via Mezzocannone 6, 80134 Napoli, Italy D Dipartimento di Chimica dell’Università di Siena, via A. Moro 2, I-53100 Siena, Italy, E Centro per lo Studio dei Sistemi Complessi, Via Tommaso Pendola 37, I-53100 Siena, Italy

B

Abstract. We present different examples where a quantum dynamical approach to photoinduced processes can reveal features and give answers not available only on the ground of static computations of the potential energy surfaces (PES). We face with different processes of great biological relevance and namely the retinal photoisomerization and the internal conversion in monomers and dimers of DNA nucleobases. Depending on the case, we compute dynamics on a single or on coupled excited electronic states, with PES obtained by first-principle calculations or provided by model Hamiltonians. Keywords: Nonadiabatic quantum dynamics, photoisomerization, photodeactivation, nonradiative transitions, retinal, uracil, 5fluoro-uracil, adenite dimers. PACS: 01.30.Cc, 31.50.Df, 31.50.Gh, 31.70.Hq, 31.15.Ar, 31.15.Ew

Bioexcimers As Precursors Of Charge Transfer And Reactivity In Photobiology Luis Serrano-Andrés,†,* Manuela Merchán,† Daniel Roca-Sanjuán,† Gloria OlasoGonzález,† Mercedes Rubio‡ †

Instituto de Ciencia Molecular, Universitat de València Apartado de Correos 22085, ES-46071 Valencia, Spain, and ‡ Fundació General, Universitat de València, Plaza del Patriarca, 4, 1, ES-46002 Valencia, Spain [email protected]

Abstract. Accurate CASPT2//CASSCF calculations show that π-stacked interactions in different biochromophores such as DNA nucleobases or porphyrin-quinone pairs yield excimer-like situations which behave as precursors of processes like charge transfer or photoreactivity. Examples are the transfer of charge between a reduced pheophytin and an accepting quinone molecule, process that trigger the sequence of electron transfer phenomena in photosynthetic photosystem II, the electron transfer between adjacent DNA nucleobases in a strand of oligonucleotides, and the photodimerization taking place in cytosine pairs leading to cyclobutanecytosine mutants. These processes take place through nonadiabatic photochemical mechanisms whose evolution is determined by the presence and accessibility of conical intersections and other surface crossings between different electronic states. Keywords: Bioexcimer; CASPT2: Conical Intersection; DNA photochemistry PACS: 31.10.+z; 31.15.Ar; 31.25.Qm; 31.50.Df; 31.50.Gh; 33.50.-j; 34.70.+e

FTIR Studies Of Internal Water Molecules Of Bacteriorhodopsin: Structural Analysis Of Halide-Bound D85S And D212N Mutants In The Schiff Base Region Mikihiro Shibata and Hideki Kandori Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan Abstract. Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of Cl- brings different effects for pumping functions in mutants at D85 and D212 position. While Cl--bound D85T and D85S pump Cl, photovoltage measurements suggested that Cl--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed. Keywords: FTIR spectroscopy, water molecule, ion-pump, rhodopsin, membrane protein, photo isomerization, lightinduced PACS: 87.14.Ee, 87.16.Uv, 87.15.-v

Flavin Charge Transfer Transitions Assist DNA Photolyase Electron Transfer Spiros S. SkourtisA,*, Tatiana PrytkovaB and David N. BeratanB,* A

Department of Physics, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708,,USA

B

Abstract. This contribution describes molecular dynamics, semi-empirical and ab-initio studies of the primary photoinduced electron transfer reaction in DNA photolyase. DNA photolyases are FADH --containing proteins that repair UVdamaged DNA by photo-induced electron transfer. A DNA photolyase recognizes and binds to cyclobutatne pyrimidine dimer lesions of DNA. The protein repairs a bound lesion by transferring an electron to the lesion from FADH-, upon photo-excitation of FADH- with 350-450 nm light. We compute the lowest singlet excited states of FADH - in DNA photolyase using INDO/S configuration interaction, time-dependent density-functional, and time-dependent Hartree-Fock methods. The calculations identify the lowest singlet excited state of FADH- that is populated after photo-excitation and that acts as the electron donor. For this donor state we compute conformationally-averaged tunneling matrix elements to empty electron- acceptor states of a thymine dimer bound to photolyase. The conformational averaging involves different FADH- - thymine dimer confromations obtained from molecular dynamics simulations of the solvated protein with a thymine dimer docked in its active site. The tunneling matrix element computations use INDO/S-level Green’s function, energy splitting, and Generalized Mulliken-Hush methods. These calculations indicate that photo-excitation of FADHcauses a π  π* charge-transfer transition that shifts electron density to the side of the flavin isoalloxazine ring that is adjacent to the docked thymine dimer. This shift in electron density enhances the FADH - - to - dimer electronic coupling, thus inducing rapid electron transfer. Keywords: DNA photolyase, DNA repair, photo-induced electron transfer, charge-transfer transitions, flavins. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

Protein Induced Torsion Of The Retinal Chromophore And How It Affects The Photochemistry Of Rhopdopsin Oliver Weingart and Volker Buss Theoretische Chemie, Universität Duisburg-Essen, Universitätsstr.2 D-45141 Essen, Germany Abstract. The influence of protein induced chromophore deformations on reaction timescale and quantum yield is investigated using ab initio molecular dynamics in vacuo on four and five double bond models of the retinal chromophore. The opposite twist of the C11=C12 and the C12-C13 bonds appears to be the prerequisite for the highly stereoselective and efficient cis-trans photodynamics of the retinal chromophore in the binding pocket of rhodopsin. The formation of the photoproduct is determined by the phase of the hydrogen out-of-plane mode of the 11-cis double bond. Keywords: Retinal, Rhodopsin, Molecular Dynamics, excited states, photochemistry. PACS: 31.15.Ar

Computer Simulation of Liquid Crystal Materials: From Generic to Specifically Decorated Molecular Models Claudio Zannoni Dipartimento di Chimica Fisica e Inorganica and INSTM, Università, viale Risorgimento 4, 40136 Bologna, Italy Abstract. In this paper we discuss the state of the art of modelling of liquid crystals at molecular resolution level, showing their evolution from simple uniaxial to more complex mono-site and multi-site models. We then introduce “decorated” models, where specific molecular details, e.g. electrostatic charge distributions are added to allow the computer simulation of more realistic and more specific features and briefly show some of their applications. Keywords: Liquid Crystals, Computer Simulations. PACS: 61.30.-v, 61.30.Cz, 61.20.Ja

Compositional Vs. Monolithical Modeling Of Nano Devices Gianluigi Zavattaro Dipartimento di Scienze dell’Informazione, Università di Bologna, Mura A. Zamboni, 7, 40127 Bologna, Italy Abstract. The nanok calculus has been recently introduced in [1] as a tool for the modeling and simulation of the behaviour of nano devices. Its basic components are molecules specified in terms of an interface and a set of fields. The interface is used to represent the bonds between the specified molecule and the other molecules in the nano device. The fields, on the other hand, describe the internal state of the molecule. The dynamics is modeled by means of reactions defined in terms of rewriting rules applied to pairs of abstractly specified molecules. In this paper we discuss the comparison between the nanok specification and the traditional specification of a two-station rotaxane [2], a versatile molecular shuttle currently used as a building block for more complex nano devices. Keywords: Process calculi, nano devices, compositional modeling.

Towards Understanding Different Spatial And Temporal Scales Francesco Zerbetto Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy, Email: [email protected] Abstract. Through the illustration of five examples of recent work, I try to show the interplay that exists between the macroscopic description of the physical chemistry properties and dynamics of molecules and the insight that can be obtained by atomistic simulations. The difficulties and problems of bridging the gaps between the different scales with atomistic simulations are highlighted with the general intent of trying to assess at which point in time or in space the continuum or engineering type of treatment switches to the discrete level. Keywords: Dynamics, continuum models, atomistic simulations, Rayleigh Plesset, Poisson, membrane channels, ion transport, proteins, mechanochemistry, gelation, hydrophobicity, carbon nanotubes, confinement. PACS: 41.20.Cv, 47.11.Mn, 47.55.D-, 61.46.Fg, 82.37.Gk, 82.70.Gg, 87.14.Ee.

COBRAMM (Part 1): A Tunable QM/MM Approach To Chemical Reactivity, Structure And Physico-Chemical Properties Prediction Piero AltoèA,B, Marco StentaC, Andrea BottoniA and Marco GaravelliA A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy B INSTM, UdR Bologna c Dipartimento di Chimica“A. Mangini“, Universita’ di Bologna, Via San Giacomo, 11, 40126 Bologna, Italy Abstract. This contribution describes a new implementation of a general hybrid approach with a modular structure (called COBRAMM: Computations at Bologna Relating Ab-initio and Molecular Mechanic Methods) that is able to integrate some specialized programs and acts as a flexible computational environment, thus increasing the flexibility/efficiency of both QM, and MM, and QM/MM calculations. Specifically, QM/MM ground and excited states geometry optimizations, frequency calculations, conical intersection searches and adiabatic/non-adiabatic molecular dynamics can be performed on a large molecular system, that can be split up to three different layers corresponding to different levels of accuracy. Keywords: QM/MM, COBRAMM, ab-initio, multiple layer, electrostatic embedding. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

Rhodopsin And GFP Chromophores: QM/MM Absorption Spectra In Solvent And Protein Piero AltoèA,B, Marco StentaC and Marco GaravelliA A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy B INSTM, UdR Bologna C Dipartimento di Chimica“A. Mangini“, Universita’ di Bologna, Via San Giacomo, 11, 40126 Bologna, Italy Abstract. This work presents a QM/MM investigation of the spectral properties of the 11-cis-retinal and the GFP chromophore in polar solvents and protein. The results of the computations are in surprising agreement with the experimental values indicating the accuracy of our computational approach. In addition it has been demonstrated the key role of the solvent to create a “virtual conter-ion”. This effect is due to the reorientation (i.e. polarization) of the polar solvent close to the chromophore: the polarized permanent dipoles of the solvent act similarly to the counter ion, stabilizing the ground state respect to the charge transfer excited state. Keywords: QM/MM, solvation, spectroscopy, retinal, GFP. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

The CIS-TRANS Photoisomerization Of The Phytochromobilin Giulia C. De FuscoB, Piero AltoèA,C and Marco GaravelliA A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy B Department of Chemistry, Imperial College London, South Kensington, LONDON, SW7 2AZ, UK C INSTM, UdR Bologna

Abstract. This work presents the results of the computational studies for the photochemical activity of phytochromobilin in vacuo with particular attention to the isomerization of the exocyclic double bonds. The spectroscopic state has been characterized and fully unconstrained optimizations on S1 have been performed to investigate the possible deactivation paths. In fact, while in the protein the mechanism involve the rotation of the C15-C16 bond only, in isolated conditions (i.e. solvent or vacuo) several possible competing photoisomerization paths have been unveiled, which could recover the system to the ground state. Keywords: phytochrome, phytochromobilin, ab-initio, photoisomerization. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

Computational QM/MM Study Of The Reaction Mechanism Of Human Glutathione S-Transferase A3-3 Matteo CalvaresiA, Marco Stenta B, Piero AltoèA, Andrea BottoniA, Marco GaravelliA and Domenico SpinelliB A

Dipartimento di Chimica “G. Ciamician”, via Selmi 2, I-40126 Bologna, Italy Dipartimento di Chimica Organica “A. Mangini”, via San Giacomo 11, I-40126 Bologna, Italy

B

Abstract. Human Glutathione S-Transferase A3-3(hGSTA3-3) is the most efficient human steroid double-bond isomerase enzyme. It catalyzes the double bond isomerization of Δ5-androstene–3,17–dione (Δ5-AD) and Δ5-pregnene– 3,20–dione (Δ5-PD). The isomerization products are the precursors of the steroid hormones testosterone and progesterone. We have carried out a QM/MM study to elucidate some interesting aspects of the enzyme catalytic mechanism. In particular, we have analyzed either a concerted or a stepwise reaction path. Moreover, we have attempted to rationalize the electrostatic effects on the catalytic activity of the residues surrounding the active site. Specifically, we have performed a “finger print” analysis to determine the electrostatic contribution of each aminoacid residue to the global electrostatic term, thus ranking the effect of the various aminoacids in the course of the reaction. In this way, we have highlighted the most important terms affecting the stabilization-destabilization of the enzyme. Keywords: QM/MM, isomerase, Glutathione S-Transferase A3-3, catalytic mechanism , enzymatic processes, fingerprint analysis PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

Azobenzene Cis-Trans Photoisomerization Mechanism: Characterization Of The Decay Ways From The Lowest ππ* Absorbing Singlet State Irene ContiA, Marco GaravelliA and Giorgio OrlandiA A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy

Abstract. In this paper, we analyze the photoisomerization processes of azobenzene after its excitation in the bright S(ππ*). By state of the art/ ab initio/ Complete Active Space calculations followed by perturbative corrections (CASPT2//CASSCF) we have identified the critical structures, the Minimum Energy Paths originating on the bright S(ππ*) and on other relevant excited states including the state S1(nπ*). The seams of conical intersections that are important in guiding the photoreaction are determined. We aim at establishing the mechanism of decay and of photoisomerization for the S(ππ*) state and at explaining the difference between the quantum yields found for the two lowest energy S1(nπ*) and S(ππ*) excited states. We found that an excited state based on the πN=NπN=N→π*N=Nπ*N=N configuration is a photoreaction intermediate that plays a very important role in the decay the bright S(ππ*). This doubly excited state, by driving the photoisomerization along the torsion path and by inducing a fast internal conversion to the S1(nπ*) occurring in a variety of geometries, explains all the most important features of the S(ππ*) azobenzene photoisomerization. Keywords: azobenzene, excited electronic states, photoisomerization, multiconfigurational wave function methods, conical intersections.

Heteroaromatic Chromophores: Structure, Electric Properties, Condensed Phase And Aggregation Effects. A Combined Experimental And Theoretical Study. Stefano Ellia, Andrea Magrìa, Elisa Venturinia, Fabrizia Negria , Alessandro Abbottob, Luca Bellottob, Anna Painellic, Cristina Sissac, Francesca Terenzianic a

b

Università di Bologna, Dipartimento di Chimica “G. Ciamician” and INSTM UdR Bologna, Via F. Selmi 2, I40126 Bologna, Italy.

Università di Milano-Bicocca, Dipartimento di Scienza dei Materiali and INSTM UdR Milano-Bicocca, Via Cozzi 53, I-20125 Milano, Italy. b

Università di Parma, Dipartimento di Chimica GIAF and INSTM UdR Parma, Parco Area delle Scienze 17/a, I43100 Parma, Italy Abstract.. We present a combined computational and experimental study on structural and electric properties of recently synthesized heteroaromatic dyes and their simple aggregates. Ab initio and density functional theory calculations are carried out to investigate ground state and excited state properties along with their modulation induced by the solvent described with the implicit solvent polarizable continuum model. The results are compared with experimental data concerning spectroscopic studies. Electronic and vibrational contributions to the first hyperpolarizability and condensed phase effects on these properties are also evaluated for single or selected dimeric chromophore structures. Intermolecular interactions are evaluated both at correlated ab initio level and with simplified atomistic models employing molecular mechanics force fields parametrized, as regard electrostatic interactions, on the basis of ab initio computed partial atomic charges. Specific chromophore orientations are considered and the results of the two procedures are compared. Keywords: Quantum-chemical calculations, Molecular mechanics, Hyperpolarizabilities, Electronic spectra, Functional chromophores, Molecular materials. PACS: 01.30.Cc, 31.15.Ar, 31.15.Ew, 31.70.Dk, 36.20.Kd

Three-Layer ONIOM Studies Of Rhodopsin In The Dark State: Shedding Light On The Protonation State Of Glu-181 Katherine F. Hall1, Thom Vreven2, Michael J. Frisch2, and Michael J. Bearpark1. (1) Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom, [email protected], (2) Gaussian, Inc., Wallingford, CT 06492, USA. Abstract. We used a new three-layer ONIOM(QM:QM:MM) scheme to probe the protonation state of the Glu-181 residue in the binding pocket of the dark-adapted state of Rhodopsin. Recent experimental evidence has led to conflicting conclusions about the protonation of Glu-181, which has important consequences for the proposed “counterion-switch” mechanism: In particular, the possible role of a proton transfer from Glu-181 to the primary Glu-113 counterion in destabilizing the salt bridge with the retinal protonated Schiff base to form the active meta-II state. By incorporating the interaction of retinal with important binding pocket residues at the QM level, we can calculate accurate structural, NMR, vibrational, and electronic absorption data for charged and neutral Glu-181 models of the dark state of the wild type, and of the E181Q mutant. Comparison of our new results with experiment gives valuable insight into the reliability of experimental methods in determining the protonation state of Glu-181.

Ultrafast Electron Transfer in Photosynthesis: Reduced Pheophytin and Quinone Interaction Mediated by Conical Intersections Gloria Olaso-González†,*, Manuela Merchán†, Luis Serrano-Andrés† †

Instituto de Ciencia Molecular, Universitat de València. Apartado de Correos 22085, ES-46071 Valencia, Spain,

Abstract. The mechanism of electron transfer (ET) from reduced pheophytin (Pheo-) to the primary stable photosynthetic acceptor, a quinone (Q) molecule, is addressed by using high-level ab initio computations and realistic molecular models. The results reveal that the ET process involving the (Pheo-+Q) and (Pheo+Q-) oxidation states can be essentially seen as an ultrafast radiationless transition between the two hypersurfaces taking place via conical intersections (CIs) and it is favoured when the topology of the interacting moieties make possible some overlap between the lowest occupied molecular orbitals (LUMO) of the two systems. Thus, it is anticipated that large scale motions, which are difficult to monitor experimentally, may actually occur in the photosynthetic reaction centers of bacteria, algae, and higher plants, to fulfil the observed ultrafast ET processes. Keywords: Conical Intersection, Electron Transfer, Pheophytin, Photosynthesis, Quinone. PACS: 31.10.+z; 31.15.Ar; 31.25.Qm; 31.50.Df; 31.50.Gh; 33.50.-j; 34.70.+e

Toward An Understanding Of The Spectral Tuning In Rhodopsin Gloria Olaso-GonzálezA, Gaia TomaselloB, Piero AltoèB, Marco StentaC, Luis Serrano-AndrésA, Manuela MerchánA and Marco GaravelliB A

Instituto de Ciencia Molecular, Universitat de València Apartado de Correos 22085, ES-46071 Valencia, Spain, B Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy C Dipartimento di Chimica“A. Mangini“, Universita’ di Bologna, Via San Giacomo, 11, 40126 Bologna, Italy Abstract. The contribution to the spectral tuning of the main residues in the Rhodopsine protein is being evaluated by employing high level ab initio quantum chemistry tools and the new Reverse Finger Print (RFP) technique. Keywords: Rhodopsin, spectral tuning, visual pigments, Reverse Finger Print.

COBRAMM (Part 2): An Overview On Some Computational Details; Geometry Optimization, Frequency Calculation, Analysis Of The Results. Marco StentaA, Piero AltoèB, Andrea BottoniB and Marco GaravelliB A

Dipartimento di Chimica“A. Mangini“, Universita’ di Bologna, Via San Giacomo, 11, 40126 Bologna, Italy B Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy

Abstract. This contribution illustrates some features of a new of a newly implemented general hybrid approach. This method, included in the COBRAMM (Computations at Bologna Relating Ab-initio and Molecular Mechanic Methods) suite of programs, has a modular structure that integrates some specialized programs and represents a flexible computational environment that increases the flexibility/efficiency of QM, and MM, and QM/MM calculations. Here we describe some aspects of the geometry optimization procedure and explain some approximations used in the frequency computation. Moreover we present two analysis procedures that allow to rank the contribution of the various aminoacid residues of an enzyme in determining the catalytic mechanism and the shape of a Potential Energy Surface (PES). Keywords: QM/MM, reaction mechanisms, geometry optimization, frequency calculation, electrostatic catalysis. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

The Catalytic Activity Of Diaminopimelate Epimerase: A QM/MM Study. Marco StentaB, Matteo CalvaresiA, Piero AltoèA, Domenico SpinelliB, Marco GaravelliA and Andrea BottoniA A

Dipartimento di Chimica “G. Ciamician”, via Selmi 2, I-40126 Bologna, Italy Dipartimento di Chimica Organica “A. Mangini”, via San Giacomo 11, I-40126 Bologna, Italy

B

Abstract. A QM/MM study has been carried out to clarify the catalytic mechanism of the enzyme diaminopimelate (DAP) epimerase. In particular the potential energy surface (PES) for the stereo-inversion of the distal Cα of the substrate has been has been investigated. The nature of the critical points located on the PES has been checked by numerical frequencies calculations. The role of the various aminoacid residues in the catalysis has been elucidated using a recently developed analysis method. Keywords: QM/MM, reaction mechanisms, diaminopimelate epimerase, DFT, enzymatic processes. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

The Catalytic Activity Of Proline Racemase: A QM/MM Study. Marco Stenta,B Matteo Calvaresi,A Piero Altoè,A Domenico Spinelli,B Marco Garavelli,A and Andrea BottoniA A

Dipartimento di Chimica ''G. Ciamician'', via Selmi 2, I-40126 Bologna, Italy Dipartimento di Chimica Organica'‘A. Mangini'', via San Giacomo 11, I-40126 Bologna, Italy

B

Abstract. The catalytic activity of an interesting enzyme (involved in the life cycle of the Trypanosoma Cruzi eucariotic parasite) has been elucidated by mean of a QM/MM study. The reaction mechanism of the stereo-inversion of the substrate has been studied by characterizing the associated PES. The nature of the found critical point has been checked by means of numerical frequencies calculations. The role of the various residues in the catalysis has been pointed out Keywords: QM/MM, reaction mechanisms, proline racemase, Tripanosoma Cruzi, DFT, enzymatic processes. PACS: 01.30.Cc, 31.50.Bc, 31.50.Df, 31.50.Gh, 36.20.Kd

Ab Initio Investigation To Model Stilbene Photo-Physical Properties By Combining CC2 Topological Investigation And CASPT2 Energy Corrections Gaia Tomasello, Piero Altoè, Marco Garavelli, Giorgio Orlandi A

Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy

Abstract Stilbene photoexcitation and consequent decay to the ground state has been investigated by mapping the Minimum Energy Path (MEP) from S1 spectroscopic state triggering an almost barrierless reaction pathway to an S1/S0 degenerate region. The particular influence of the σ-π excitation on the S1 wave function, dominated by a π→π* character, reveals how the non-dynamical correlation energy was important to correctly describe the excited state behaviour and the topological aspect of its potential energy surface. Several strategies of calculations, by using CASSCF//CASPT2 methods, were performed trying to improve the photochemical description nowadays known. Both symmetry and non symmetry preserving computations were performed; systematically was concluded that, because of the limit of CASSCF description enables only to introduce the correlation effect such as the ones due to σ-π excitations, CASSCF and CASPT2 topologies are probably often not in agreement. Thus CC2 methodology was adopted o optimize the S1 geometries and obtain reasonable structures for the minima. Two S1/S0 accessible conical intersections featured by pyramidalized carbons were located on the first excited state explaining the ultrafast radiationless decay to the ground state and the photoproducts observed within the timescale of ps. Keywords: Stilbene, stilbenoid compounds, reaction pathway, Minimum Energy Path, spectroscopy, electronic excited state, dynamical and non dynamical correlation, multiconfigurational methods, perturbation correction, ultrafast radiationless process, pyramidalized carbons, conical intersection.

Retinal Photoisomerization In Rhodopsin: Electrostatic And Steric Catalysis Gaia Tomasello, Piero Altoè, Marco Stenta, Gloria Olaso-González, Marco Garavelli, Giorgio Orlandi Dipartimento di Chimica ’G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy Dipartimento di Chimica“A. Mangini“, Universita’ di Bologna, Via San Giacomo, 11, 40126 Bologna, Italy Instituto de Ciencia Molecular, Universitat de València Apartado de Correos 22085, ES-46071 Valencia, Spain, Abstract. Excited state QM(CASPT2//CASSCF)/MM(GAFF) calculations, by our recently developed code COBRAMM (Computations at Bologna Relating Ab-initio and Molecular Mechanic Methods), were carried out in rhodopsin to investigate on the steric and electrostatic effects in retinal photoisomerization catalysis due to the β-ionone ring and glutammate 181 (GLU 181), respectively. The excited state photoisomerization channel has been mapped and a new christallographyc structure (2.2 Å resolution) has been used for this purpose. Two different set-ups have been used to evaluate the electrostatic effects of GLU 181 (which is very close to the central double bond of the chromophore): the first with a neutral GLU 181 (as commonly accepted), the second with a negatively charged (i.e. deprotonated) GLU 181 (as very recent experimental findings seem to suggest)12. On the other hand, β-ionone ring steric effects were evaluated by calculating the photoisomerization path of a modified chromophore, where the ring double bond has been saturated. Spectroscopic properties were calculated and compared with the available experimental data. Keywords: Retinal, Rhodopsin, primary event, photoisomerization, ultrafast photochemistry, electrostatic catalysis, steric catalysis, vision process, proteic environment, QM/MM methods.

Quantum Communication and Entanglement Distribution Through Spin Chains and Allied Systems Sougato Bose Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom Abstract. I will start with a brief introduction to the use of a spin chains for quantum communications. Following this, I will describe some methods to perfect these communications using certain reasonable strategies when one uses chains in their ferromagnetic ground state. I will then briefly point out the use of antiferromagnetic spin chains for the same purpose. Next, I will discuss the use of a bosons hopping freely in a one-dimensional lattice to generate entanglement between its ends. I will also describe the generation of entanglement from the ground state of a chain of qudits coupled by purely exchange interactions.

Quantum Control and Entanglement of Two Electrons in a Double Quantum Dot Structure John Boviatsis and Evangelos Voutsinas Technological and Educational Institute of Patras, Patras 26334, Greece Abstract. The interaction of two electrons in a double quantum dot structure with an electromagnetic field is studied. Using proper approximations we obtain analytical solutions for the time evolution of the probabilities in the several quantum states and present conditions for the creation of maximally entangled two-electron states. Acknowledgements: The authors acknowledge financial support by the “Archimedes-EPEAEK II Research Programme” co-funded by the European Social Fund and National Resources.

Quantum Phase Transitions in Coupled Arrays of Cavities F. G. S. L. Brandão1,2, M. J. Hartmann1,2 and M. B. Plenio1,2 1

IMS, Imperial College London, 53 Prince's Gate Exhib. Rd, London SW7 2PG, UK 2 QOLS, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK

Abstract. Recent experimental progress in cavity quantum-electrodynamics has lead to the fabrication of arrays of coupled cavities, which could be employed to create strongly correlated many-body systems, when operated in the strong coupling regime. In this work, we show that two models of interest to both, condensed matter physics and quantum information science, namely the Bose-Hubbard model and the anisotropic Heisenberg model (XYZ-model), could be realized in such systems with present or near future experimental capabilities. We also discuss the feasibility of realizing a Mott-insulator of photons in such systems. Crucial for this proposal is the possibility of creating very strong photonic Kerr nonlinearities, several orders of magnitude larger than previously considered feasible. We show how this could be achieved with the setting based on electromagnetically induced transparency and with a new scheme, which is experimentally less demanding than the former.

A Simple Control Switch Model for Quantum Computation K. Ch. Chatzisavvas1, C. Daskaloyannis2 and S. G. Schirmer3 1

Department of Theoretical Physics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece 2 Mathematics Department, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece 3 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK

Abstract. A simple control switch model can be used to perform exact computation in a finite amount of time. It is based on the equivalence of the notion of universality in quantum computation with the notion of controllability in control theory and focuses to the ability of a physical system to act as a quantum computer using only its natural available interactions. The control switch model is a different approach from the conventional circuit model of quantum computation and it is applicable to various physical systems even if the available systems Hamiltonians are not orthogonal. Analytical results for the case of the SU(2) are also presented using a complete analytical algorithm.

The Study Of The Nuclear Motion In D2+ Molecular Ion By Using The Harmonic Spectra R. Daniele∗§, G. Castiglia∗§, P. P. Corso∗§, E. Fiordilino∗§, F. Morales#§, G. Orlando∗§ and F. Persico∗§ * Dipartimento di Scienze Fisiche ed Astronomiche, Via Archirafi 36, 90123 Palermo, Italy. # Dipartimento di Fisica e Tecnologie Relative, Viale delle Scienze, 90128 Palermo, Italy. § Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, via della Vasca Navale 84, 00146 Roma, Italy

Abstract. In this paper we show how it is possible to investigate the nuclei dynamics of a D2+ molecular ion by using the high harmonic generation spectra emitted by the system when subjected to an intense laser field. In particular, the emitted spectra contains, in addition to the usual odd harmonic peaks, additional satellite peaks whose frequency spacing is equal to the vibrational frequency of the nuclei.

Quantum Control of Interacting Multiatom Systems Jörg Evers, Martin Kiffner and Christoph H. Keitel Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, Heidelberg, Germany Abstract. Control schemes in dipole-dipole interacting two-particle systems are discussed. In contrast to single-particle systems, in such collective systems vacuum-induced dipole-dipole interactions can couple transitions regardless of the orientation of the two involved dipole moments. We show that these couplings gives rise to a significant modification of the system properties, and demonstrate how they can be exploited to alter the system dynamics. In particular, we discuss a setup where the long-time dynamics crucially depends on the relative position of the two atoms, and demonstrate that such systems are a promising candidate for the realization of a multidimensional decoherence free subspace.

Cavity QED Schemes for Controlled Creation of Entanglement Between Distant Atoms Zbigniew Ficek Department of Physics, School of Physical Sciences, The University of Queensland, Brisbane, Australia 4072 Abstract. We analyse the commonly used adiabatic techniques in the atom-cavity field interaction to controllably entangle two distant atoms trapped inside a single-mode optical cavity. Two techniques are considered: the first involves a highly detuned cavity from the atomic transition frequencies, and the second involves a near resonant but strongly damped cavity. We show that both, the detuning and the cavity damping are needed to obtain the master equation of the collectively interacting atoms. We analyse the feasibility of the adiabatic techniques in creation of a long living entanglement and find that the cavity damping is more robust for generation of a stationary entanglement between the atoms. The dependence of the stationary entanglement on number of excitations in the system and strengths of the couplings of the atoms to the cavity mode is also discussed.

Dressed rf Trapping Barry M. Garraway Department of Physics and Astronomy, University of Sussex, Falmer, Brighton, BN1 9QH, United Kingdom Abstract. Dressed rf trapping is a new technique [1] for the trapping and control of cold atoms. For some time it has been possible to trap neutral atoms in optical dipole traps or in magnetic traps, but the application of rf with variable frequency and detuning offers new versatility in atom trapping. The technique relies on the transfer of atoms from a static magnetic trap to a dressed trap where combinations of static and dynamic magnetic fields are involved. If atoms are correctly loaded into the dressed trap then in the first instance they are localised to a region of rf resonance. However, the action of gravity modifies this scenario. In this talk we discuss and illustrate the trapping process and leakage from the dressed trap. 1.

O. Zobay and B. M. Garraway, Phys. Rev. Lett. 86, 1195 (2001); Phys. Rev. A 69, 023605 (2004).

Coherent Control of Extreme Nonlinear Optical Properties of Quantum System via Ultrashort Laser Pulses Shangqing Gong, Keyu Xia and Yueping Niu State Key Laboratory of High Field Laser Physics, ShanghaiInstitute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China 201800 Abstract. We investigate the extreme nonlinear optical properties of quantum system driven by ultrashort laser pulses by solving the one and two dimensional, full-wave Maxwell-Bloch coupled equations. We find that the near-dipole-dipole (NDD) interactions have a crucial influence on the absolute phase of few-cycle laser pulses. The difference of the absolute phase between the cases with and without NDD effects can go up to π. Moreover, a novel ultrafast transient population grating induced by a two-dimensional, ultrashort dipole soliton is demonstrated. The number of lines and the period of the grating can be controlled by the beam waist and the area of the pulse.

Laser Control of Wavepacket Photodissociation and Photoisomerization Dynamics in Isolated Molecules Leticia González1, Tamás Rozgonyi2, David Ambrosek1 and Guillermo PérezHernández1 1

Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany 2 Institute of Structural Chemistry, Chemical Research Center, Hungarian Academy of Sciences, 1025 Budapest, Pusztaszeri út 59-67, Hungary

Abstract. Control of time-dependent wavepackets in the frame of unimolecular reactions is described. The shown applications include photodissociation and photoisomerization dynamics in three isolated systems.

Control of Atomic and Molecular Processes by Designed External Fields: From Adiabatic to Ultrashort Pulse Strategies S. Guérin Institut Carnot de Bourgogne UMR 5209 CNRS, Université deBourgogne, B.P. 47870, 21078 DIJON Cedex, France Abstract. I present tools and strategies for the control of atomic and molecular processes by external fields, such as laser and cavity fields, with parameters specifically designed to achieve particular goals. Applications to selective population transfer, control of atomic deflection, tunneling effect, alignment of molecules, and quantum information processing are addressed.

Electronic Structure of Few-electron Quantum Dot Molecules V. Popsueva1, J. P. Hansen1 and J. Caillat2 1

2

Institute of Physics and Technology, Allegaten 55, 5007 Bergen, Norway Laboratoire de Chimie Physique-Matière et Rayonnement, Université Pierre et Marie Curie, 11, rue Pierre et Marie Curie, F 75231 Paris Cedex 05, France

Abstract. We present a study of strongly correlated few-electron quantum dots, exploring the spectra of various few-electron quantum dot molecules: a double (diatomic) structure a quadruple two-electron quantum dot, and a three-electron double dot. Electron energy spectra are computed for different values of dot separation. All spectra show clear band structures and can be understood from asymptotical properties of the system.

Controllable Atom Localization in Four-level Atomic Systems Luling Jin, Shiqi Jin and Shangqing Gong State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, CAS, Shanghai, 201800 Abstract. We propose controllable atom localization schemes for four-level atomic systems. In the alkaline earth atomic system we give the analytical expressions of the localization peak positions as well as the widths versus the parameters of the optical fields. We show that the probability of finding the atom at a particular position can be increased from 1/4 to 1/3 or 1/2 by adjusting the detuning of the probe field and the Rabi frequencies of the optical fields. Furthermore, the localization precision can be dramatically enhanced by increasing the intensity of the standing-wave field. In the ladder-type system, we use two standing-wave fields and find that the detecting probability can be increased to 1/2 by adjusting the Rabi frequencies of the standing-wave fields.

High-energy Quantum Dynamics in Ultra-intense Laser Pulses Carsten Müller, Guido R. Mocken, Karen Z. Hatsagortsyan and Christoph H. Keitel Max-Planck-Institute for Nuclear Physics, Saupfercheckweg 1, D-69117 Heidelberg, Germany Abstract. Relativistic quantum dynamics and high-energy reactions of electrons and positrons in strong laser fields are studied by theoretical means. The laser-driven phenomena addressed comprise propagation of an electronic wave packet, microscopic electron-positron collisions, and muon pair creation from a positronium atom. By way of these examples we demonstrate a variety of computational methods employed in this field of theoretical physics and discuss their respective applicability ranges.

Tomographic Imaging of Molecular Orbitals in Length and Velocity Form Elmar V. van der Zwan and Manfred Lein Institute for Physics, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel,Germany Abstract. Recently Itatani et al. [Nature 432, 876 (2004)] introduced the new concept of molecular orbital tomography, where high harmonic generation (HHG) is used to image electronic wave functions. We describe an alternative reconstruction form, using momentum instead of dipole matrix elements for the electron recombination step in HHG. We show that using this velocity-form reconstruction, one obtains better results than using the original length-form reconstruction. We provide numerical evidence for our claim that one has to resort to extremely short pulses to perform the reconstruction for an orbital with arbitrary symmetry. The numerical evidence is based on the exact solution of the time-dependent Schrödinger equation for 2D model systems to simulate the experiment. Furthermore we show that in the case of cylindrically symmetric orbitals, such as the N2 orbital that was reconstructed in the original work, one can obtain the full 3D wave function and not only a 2D projection of it.

Ab Initio Many-Electron Calculation Of Hyperfast TimeResolved Coherent Excitation And Decay Of Polyelectronic Atoms Cleanthes A. Nicolaides1,2, Theodoros Mercouris1 and Yannis Komninos1 1

Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vasileos Constantinou Avenue, Athens, 11635 Greece 2 Physics Department, National Technical University, Athens, Greece

Abstract. The theoretical quantitative understanding of time-resolved processes of coherent excitation and decay in polyelectronic atoms, induced by hypershort electromagnetic pulses, is a prerequisite for their possible control. We review key elements of an approach to the ab initio determination of perturbative as well as of nonperturbative solutions of the time-dependent Schrödinger equation describing such processes. The essential element of this approach is the development of formalism and methods that utilize physically relevant state-specific wavefunctions of stationary states of the discrete and the continuous spectrum.

Laser Control of Photoassociation in Reaction O + H

→

OH

Kiyoshi Nishikawa, Kimikazu Sugimori1, and Hidemi Nagao Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan 1 Kinjo University, Kasama,Hakusan, 924-8511, Japan Abstract. In this work, we simulate the laser-induced photoassociation of the collision reaction O + H to generate the OH molecule. The photoassociation process involves the continuum-discrete transition, and the initial wavepacket corresponding to the collision pair is generally given by a superposition of continuum state. By numerically solving the time-dependent Schrödinger equation (TDSE) with split operator method (SOM), we can take into account implicitly but completely for the continuum state in the photoassociation process. In our simulation, we find interestingly the above threshold dissociation (ATD) spectrum due to the continuum-continuum transition as well as the target bound states by the photoassociation. In order to analyze the continuum state involved, we show the effective method by means of the quasicontinuum state on the Morse potential obtained by numerically diagonalizing the total system.

Implementation of a Hadamard Gate using laser light on a Phosphorus doped Si device D. Ntalaperas1,2 and N. Konofaos3 1

Computer Engineering and Informatics Department, University of Patras, Patras, Greece 2 Research Academic Computer Technology Institute, Patras, Greece 3 Department of Information and Communication Systems Engineering, University of the Aegean, Karlovassi, Samos, Greece Abstract. The dynamics of a single qubit, encoded in the charge states of a singly ionized phosphorus atom embedded in silicon bulk material are studied. For the simulation of the system a suitably modified version of the MATLAB package SCHRODINGER was used. Preliminary results were in agreement with previously published work regarding single qubit rotations. For the Hadamard Gate, the duration of the pulse T was computed as a function of input parameters the results produced outputs of the order of 9x10-10 sec.

Controlled Population Transfer in a Double Quantum Dot System Antonios Fountoulakis1, Andreas F. Terzis1 and Emmanuel Paspalakis2 1

2

Physics Department, School of Natural Sciences, University of Patras, Patras 265 04, Greece Materials Science Department, School of Natural Sciences, University of Patras, Patras 265 04, Greece

Abstract. We study the potential for controlled population transfer between the ground states of two anharmonic coupled quantum dots. We propose a method based on the interaction of the quantum dot structure with external electromagnetic fields. The interaction of the quantum dot system with the electromagnetic fields is studied with the use of the time-dependent Schrödinger equation. We present numerical results for an asymmetric quantum dot structure. Acknowledgements: We thank the European Social Fund (ESF), Operational Program for Educational and Vocational Training II (EPEAEK II), and particularly the Program PYTHAGORAS II, for funding this work.

Parametric Four-Wave Mixing in Low Atomic Densities of Potassium Vapor D. Pentaris1, N. Merlemis1, A. Lyras2 and T. Efthimiopoulos1 1 2

Laser Physics Laboratory, Physics Department, University of Patras, Rio, GR-26500, Greece Atomic & Mol. Physics Lab., Dept. of Physics, Univ. of Ioannina, GR-45110 Ioannina, Greece

Abstract. We study the generation of radiation at the 5P3/2-4S1/2 transition of potassium vapor under excitation of the 4S1/2-6S1/2 two-photon resonance. The model consists of the coupled Maxwell-Bloch equations for a four-level configuration of Potassium atom including states 4S, 4P, 5P and 6S, which is numerically solved. Previous experimental studies have shown the emission of Parametric Four-Wave Mixing (PFWM) radiation near the 5P3/2-4S1/2 transition at low vapor pressures (P