INTERNATIONAL CONFERENCE

OF COMPUTATIONAL METHODS
IN SCIENCES AND ENGINEERING 2009
(ICCMSE 2009)

Rhodes, Greece 29 September – 04 October 2009

EDITORS
Theodore E. Simos
European Society of Computational Methods in Sciences
Engineering and Technology (ESCMSET)
European Academy of Sciences and Arts
King Saud University, Saudi Arabia
University of Peloponnese, Greece

George Maroulis
University of Patras, Patras, Greece

All papers have been peer reviewed.

SPONSORING ORGANIZATION
European Society of Computational Methods in Sciences, Engineering and Technology (ESCMSET)

Melville, New York, 2012

AIP | CONFERENCE PROCEEDINGS 1504
Editors

Theodore E. Simos
Laboratory of Computational Sciences
Department of Computer Science and Technology
Faculty of Sciences and Technology
University of Peloponnese
Greece
E-mail: tsimos.conf@gmail.com
George Maroulis
Department of Chemistry
University of Patras
GR-26500 Patras
Greece
E-mail: maroulis@upatras.gr

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 AIP Conference Proceedings, Volume 1504
International Conference of Computational Methods in Sciences and Engineering 2009
(ICCMSE 2009)

Table of Contents

Preface: Lectures Presented at the International Conference on Computational Methods in

Science and Engineering (Rhodes, Greece, 29 September - 4 October, 2009)
George Maroulis and Theodore Simos 1

European Society of Computational Methods in Sciences, Engineering and Technology 3

(ESCMSET)

PLENARY AND INVITED SPEAKERS

Variational definitions of orbital energies

Ernest R. Davidson 5

Rate of convergence of basis expansions in quantum chemistry

Werner Kutzelnigg 15

Nanoparticles and theory

Nadine Harris, Shuzhou Li, and George C. Schatz 31

Molecular modeling and the violation of linear scaling principles

Paul G. Mezey 43

Calculation of the vibrational contribution to electronic properties

Bernard Kirtman 50

Theory of chemical bonds in metalloenzymes - Manganese oxides clusters in the oxygen evolution
center -
K. Yamaguchi, M. Shoji, T. Saito, H. Isobe, S. Yamada, S. Nishihara, T. Kawakami, Y. Kitagawa,
S. Yamanaka, and M. Okumura 63

Efficient quantum chemical valence-only treatments of lanthanide and actinide systems

Michael Dolg 80

Range-dependent adiabatic connections

A. M. Teale, S. Coriani, and T. Helgaker 92

Collision-induced dipoles and polarizabilities of pairs of hydrogen molecules: Ab initio

calculations and results from spherical tensor analysis
Xiaoping Li, James F. Harrison, Magnus Gustafsson, Fei Wang, Martin Abel, Lothar Frommhold,
and Katharine L. C. Hunt 100

v
One- and two-photon absorptions in open-shell singlet systems
Masayoshi Nakano, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Takashi Kubo, Kenji
Kamada, Koji Ohta, Benoît Champagne, and Edith Botek 136

Hartree-Fock via variational coupled cluster theory: An alternative way to diagonalization free
algorithm
Ján Šimunek and Jozef Noga 143

Vibrational treatment from a variation-perturbation scheme: The VCI-P method. Application to

the glycolaldehyde
Philippe Carbonniere and Claude Pouchan 152

Analysis of the structure, bonding, aromaticity and existence of possible bond-stretch isomerism
in trigonal anionic metal clusters, X3− ( X = Be,Mg,Ca)
Santanab Giri, Arindam Chakraborty, Soma Duley, Gabriel Merino, Venkatesan Subramanian, and
Pratim Kumar Chattaraj 160

Elongation method for linear scaling

Feng Long Gu and Yuriko Aoki 167

Can long-range collision-induced properties be modeled semi-classically?

Tadeusz Bancewicz 176

On the chemical enhancement in SERS

Lasse Jensen 182

Overview of finite difference Hartree-Fock method algorithm, implementation and application

J. Kobus 189

Atomic calculations for future technology and study of fundamental problems

M. S. Safronova 209

Relativistic Hamiltonians for chemistry

Trond Saue 219

Properties of halogen atoms related to the electrostatic origin of halogen bonding: Basic aspects
and some applications
Hajime Torii 228

A quantum chemistry approach to energies, structures, and spectroscopy of doped helium

clusters
R. Pérez de Tudela, D. López-Durán, M. P. de Lara-Castells, R. Prosmiti, O. Roncero, G. Delgado-
Barrio, F. A. Gianturco, J. Jellinek, and P. Villarreal 240

Vibrational multipolar analyses in isotropic media: Combining IR, Raman and hyper-Raman
spectroscopies
Vincent Rodriguez 254

Performance assessment of density functional methods with Gaussian and Slater basis sets using
7σ orbital momentum distributions of N2O
Feng Wang, Wenning Pang, and Patrick Duffy 266

vi
Electronic structure and optical properties of conjugated molecules: SAC-CI study
Masahiro Ehara, Biswajit Saha, Potjaman Poolmee, Malinee Promkatkaew, Supa Hannongbua,
Yun-peng Lu, and Hiroshi Nakatsuji 279

Giant diamagnetism in graphenes

Mikito Koshino, Yasunori Arimura, and Tsuneya Ando 291

The Renner effect in triatomic molecules

P. R. Bunker, W. P. Kraemer, Tsuneo Hirano, and Per Jensen 302

Detecting small effects in molecules by high-resolution spectroscopy: From nuclear hexadecapole

coupling to parity violation and the change of fundamental constants in space-time
Peter Schwerdtfeger 315

L'Oeuvre of Bernie Kirtman

Benoît Champagne, Feng Long Gu, Josep M. Luis, and Michael Springborg 320

On the additive version of the connectivity index

Sonja Nikolić, Nenad Trinajstić, and Sanja Ivaniš Turk 342

Phase field theory modeling of methane fluxes from exposed natural gas hydrate reservoirs
Pilvi-Helinä Kivelä, Khuram Baig, Muhammad Qasim, and Bjørn Kvamme 351

Various parallel and diversive aspects of the mathematical fluctuations theory with the related
standing issues
Metin Demiralp 364

A force-based large increment method for 2D continuum solids and the mesh convergence study
Danbing Long, Zaoyang Guo, Xila Liu, Sundararajan Natarajan, and Stéphane Bordas 377

Edge states in stacked nanographene

Kikuo Harigaya 388

Spin polarization and third-order nonlinear optical properties of open-shell singlet graphene
nanoflakes
Masayoshi Nakano, Kyohei Yoneda, Hiroshi Nagai, Takashi Kubo, Kenji Kamada, Koji Ohta,
Benoît Champagne, and Edith Botek 392

Theoretical consideration of singlet open-shell character of polyperiacenes using Clar's aromatic

sextet valence bond model and quantum chemical calculations
Akihiro Shimizu, Yasukazu Hirao, Takashi Kubo, Masayoshi Nakano, Edith Botek, and Benoît
Champagne 399

Electronic contributions to linear and nonlinear electric properties in fullerene-based molecular

systems
B. Skwara, O. Loboda, A. Avramopoulos, J.-M. Luis, H. Reis, and M. G. Papadopoulos 406

The effect of the vibrational contributions to the non-linear optical properties of small and
medium size molecules
Aggelos Avramopoulos, Heribert Reis, and Manthos G. Papadopoulos 414

vii
Pressure-induced critical influences on workpiece-tool thermal interaction in high speed dry
machining of titanium
H. A. Abdel-Aal and M. El Mansori 424

The boron connection: Roots (routes), grounds, horizons

Aristides D. Zdetsis 441

SESSION 1

Highlighted symposium in computational spectroscopy high precision calculations of molecular

energy levels and spectra
Philip Bunker and Peter Schwerdtfeger 453

Testing the time-invariance of fundamental constants using cold and not-so-cold molecules
Hendrick L. Bethlem, Paul Jansen, and Wim Ubachs 454

High-level ab initio calculations for (potential) interstellar anions: Structures, spectroscopic

properties and energetics
Peter Botschwina and Rainer Oswald 458

Parity violating effects in diatomic molecules and some group-theoretical considerations on

chirality in polyatomic molecules
Timur A. Isaev, Sophie Nahrwold, Yunlong Xiao, and Robert Berger 461

The 'MULTIMODE' approach to ro-vibrational spectroscopy

Stuart Carter, Joel M. Bowman, and Amit R. Sharma 465

The Renner effect in triatomic molecules

P. R. Bunker, W. P. Kraemer, Tsuneo Hirano, and Per Jensen 467

Rovibrational spectra of molecules in small helium clusters

Xiao-Gang Wang and Tucker Carrington Jr. 480

The Jahn-Teller effect and spin-orbit coupling in alkali trimers: Spectroscopic experiments and
ab initio calculations
Andreas Hauser, Carlo Callegari, and Wolfgang E. Ernst 483

Infrared spectroscopic and ab-initio studies of the benzene dimer

Undine Erlekam, Gerard Meijer, and Gert von Helden 487

Rotation-vibration energy level cluster formation in three- and four-atomic molecules

Sergei N. Yurchenko, Walter Thiel, and Per Jensen 491

Determination of the ionization and dissociation energies of H 2 and He2

Jinjun Liu, Daniel Sprecher, Frédéric Merkt, Edcel J. Salumbides, and Wim Ubachs 495

viii
Fully relativistic calculations of NMR and EPR parameters in the framework of the matrix
Dirac-Kohn-Sham equation
Michal Repiský, Stanislav Komorovský, Vladimir G. Malkin, and Olga L. Malkina 499

Detecting small effects in molecules by high-resolution spectroscopy: From nuclear hexadecapole

coupling to parity violation and the change of fundamental constants in space-time
Peter Schwerdtfeger 503

Theory and spectroscopy for ultracold KRb molecules

William C. Stwalley 509

Rovibrational and tunneling states of the benzene dimer; an ab initio study

Ad van der Avoird, Rob van Harrevelt, Claude Leforestier, Rafał Podeszwa, Krzysztof Szalewicz,
P. R. Bunker, Gert von Helden, Melanie Schnell, and Gerard Meijer 512

Simulating ionization spectra for small biomolecules in inner and valence shells
Feng Wang 516

SESSION 2

L'Oeuvre of Bernie Kirtman

Benoît Champagne, Feng Long Gu, Josep M. Luis, and Michael Springborg 522

Efficient algorithm for computing orbital energies within elongation method

Oleksandr Loboda, Feng Long Gu, Anna V. Pomogaeva, Marcin Makowski, and Yuriko Aoki 544

Theoretical model for infrared spectra of hydrogen- bonded 2,4-dithiouracil crystal

Marek J. Wójcik, Jacek Kwiendacz, and Marek Boczar 548

Experimental and theoretical investigations of reference molecules for nonlinear optics: The
example of acetonitrile
Elena Bogdan, Vincent Rodriguez, Frédéric Castet, Laurent Ducasse, Aurélie Plaquet, and Benoît
Champagne 555

Second-order nonlinear optical responses of flexible pyridine-pyrimidine foldamers

Frédéric Castet, Raphaël Méreau, Edith Botek, and Benoît Champagne 559

Band structure of polymer extracted from oligomer calculations by elongation method and its
applications to nanosystems
Anna Pomogaeva, Michael Springborg, Bernard Kirtman, Feng Long Gu, and Yuriko Aoki 563

On the dependence of bulk properties on surfaces

Michael Springborg, Bernard Kirtman, and Violina Tevekeliyska 567

Determining the size dependence of structural properties of clusters

Yi Dong and Michael Springborg 573

On the reliability of the maximum hardness and minimum polarizability principles in nontotally
symmetric vibrations
M. Solà, J. M. Luis, and M. Torrent-Sucarrat 578

ix
Generalized Van Vleck perturbation theory study of chlorine monoxide
Timothy J. Dudley, Jesse J. Howard, and Mark R. Hoffmann 582

A hierarchy for additive models of polarizability

Ajit J. Thakkar 586

A quantum chemical approach to the molecular conductance problem

Augusto César L. Moreira and Celso P. de Melo 590

Coupled perturbed HF/KS calculation of the dielectric constant of crystalline systems. The case
of six members of the garnet family
A. Meyer, M. Ferrero, L. Valenzano, C. M. Zicovich-Wilson, R. Orlando, and R. Dovesi 593

Exciton effects in boron-nitride (BN) nanotubes

Kikuo Harigaya 597

The applicability of the HSAB principle

Miquel Torrent-Sucarrat 601

Insight and progress in density functional theory

Weitao Yang, Paula Mori-Sanchez, and Aron J. Cohen 605

Nonlinear optical properties and large amplitude anharmonic vibrational motions

Josep M. Luis, Heribert Reis, Manthos Papadopoulos, and Bernard Kirtman 607

Anharmonic vibrational analysis of water at CCSD(T) level: Comparison of traditional and

explicitly correlated methods
Kalju Kahn, Bernard Kirtman, Jozef Noga, and Seiichiro Ten-no 611

The effect of the vibrational contributions to the non-linear optical properties of small and
medium size molecules
Aggelos Avramopoulos, Heribert Reis, and Manthos G. Papadopoulos 616

Implementation of a vector potential method in an ab initio Hartree-Fock code

Violina Tevekeliyska, Michael Springborg, Benoît Champagne, and Bernard Kirtman 627

Linear and nonlinear second order susceptibilities of molecular crystals

Edith Botek, Benoît Champagne, Małgorzata Olejniczak, and Magdalena Pecul 631

Polarizability and charge density distribution in crystalline urea

Mauro Ferrero, Bartolomeo Civalleri, and Michel Rérat 635

A general toolbox for the calculation of higher-order molecular properties using SCF wave
functions at the one-, two- and four-component levels of theory
Kenneth Ruud, Radovan Bast, Bin Gao, Andreas J. Thorvaldsen, Ulf Ekström, and Lucas Visscher 639

x
Prediction of the linear and nonlinear electric susceptibilities of 3-methyl-4-nitropyridine-N-
oxyde (POM) and meta-nitroaniline (mNA) crystals with account of electronic and molecular
vibrational contributions
Heribert Reis and Josep M. Luis 643

Generalized elongation method: From one-dimension to three-dimension

Yuriko Aoki and Feng Long Gu 647

Long-range-corrected UDFT study on second hyperpolarizabilities of open-shell singlet systems

Ryohei Kishi, Sean Bonness, Kyohei Yoneda, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoît
Champagne, Edith Botek, Takao Tsuneda, and Masayoshi Nakano 651

Critical assessment of density functional theory for computing vibrational (hyper)polarizabilities

R. Zaleśny, I. W. Bulik, M. Mikołajczyk, W. Bartkowiak, J. M. Luis, B. Kirtman, A.
Avramopoulos, and M. G. Papadopoulos 655

SESSION 3

Computational quantum chemistry

George Maroulis 659

Global search algorithm of minima exploration to find low lying isomers of clusters in which
spheroidal generation and raking optimization appear as an original process
Rémi Marchal, Philippe Carbonnière, and Claude Pouchan 660

One-electron pseudopotential investigation of the RbAr and FrAr van der Waals systems
J. Dhiflaoui and H. Berriche 664

A theoretical investigation of the low-lying 1Σ+ states of the beryllium hydride ion BeH+
M. Farjallah, C. Ghanmi, and H. Berriche 670

Theoretical study and formation prediction of the ultra-cold molecule RbLi

I. Jendoubi, H. Berriche, and H. Ben Ouada 675

Is there any connection between the (Hyper) polarizabilities of the ground state structures of
clusters and those of their low lying isomers? A case study of aluminum doped silicon clusters
P. Karamanis, R. Marchal, P. Carbonnierre, and C. Pouchan 679

Theoretical study of Si20Li20 cage cluster

Aristides D. Zdetsis and Emmanuel N. Koukaras 683

Oxidation reactions of H2O and N2O with Si clusters: A first-principles study

Bao-Xing Li, Xiao-Jun Ren, and Yi-Feng Xu 687

Oscillatory and rotatory exciton recurrence motions in double-ring molecular aggregates

controlled by two-mode circular-polarized laser field
Takuya Minami, Kyohei Yoneda, Ryohei Kishi, and Masayoshi Nakano 691

xi
A comparison of density functional theory and coupled cluster methods for the calculation of
electric dipole polarizability gradients of methane
Ivana Paidarová and Stephan P. A. Sauer 695

Unraveling interactions in large complex systems using quantum chemistry interpretative

techniques and new generation polarizable force fields
R. Chaudret, B. de Courcy, A. Marjolin, M.-C. van Severen, P. Y. Ren, J. C. Wu, O. Parisel, and J.-
P. Piquemal 699

A new DFT functional based on spin-states and SN2 barriers

M. Swart, M. Solà, and F. M. Bickelhaupt 703

SESSION 4

Prefaces of the symposia on mathematical chemistry

Sonja Nikolić 707

A new approach to a century-old problem: Henri-Michaelis-Menten enzyme kinetics

Mário N. Berberan-Santos 711

Density gradient quantum similarity

Ramon Carbó-Dorca and Luz Dary Mercado 716

Adaptive modelling of structured molecular representations for toxicity prediction

Carlo Bertinetto, Celia Duce, Alessio Micheli, Roberto Solaro, and Maria Rosaria Tiné 721

Discrete skeletons of continua in the universal molecule model

Paul G. Mezey 725

Fold and sequence independent protein binding sites prediction algorithm

Dušanka Janežič, Janez Konc, Joanna Trykowska Konc, Matej Penca, and Matej Janežič 729

Comparative numerical study on the optimal vulcanization of rubber compounds through

traditional curing and microwaves
Gabriele Milani and Federico Milani 733

Analysis of randomly shaped puzzle-fragment-particles via their chord length distribution

Wilfried Gille 737

Quantum chemical studies on binding energy in some positronic complexes

H. Chojnacki 742

A metalanguage for thermodynamics

Lionello Pogliani 746

Chemistry as mathematical system - Involutory forms of molecules and their genetic codes
Lech P. Schulz 750

xii
 SESSION 5

Symposium on natural gas hydrates: A future climate bomb or a valuable source of energy?
Opportunities and challenges for the computational physics community
Bjorn Kvamme 754

Modeling trapping mechanism for PCB adsorption on activated carbon

Bjørnar Jensen, Bjørn Kvamme, Tatyana Kuznetsova, and Åge Oterhals 755

Properties of aging FeCl2 clusters grown in supercritical water investigated by molecular

dynamics simulations
Norbert Lümmen and Bjørn Kvamme 759

An alternative for carbon dioxide emission mitigation: In situ methane hydrate conversion
Tatiana Kuznetsova, Bjørn Kvamme, and Kathryn Morrissey 772

Molecular dynamics simulations of methane hydrate pre-nucleation phenomena and the effect of
PVCap kinetic inhibitor
Tatiana Kuznetsova, Bjørn Kvamme, and Archana Parmar 776

Molecular dynamics studies of water deposition on hematite surfaces

Bjørn Kvamme, Tatiana Kuznetsova, and Martin Haynes 780

SESSION 6

Symposium: Recent developments in numerical schemes for Hilbert space related issues in
science and engineering
Metin Demiralp 784

Representing potential energy surfaces with neural networks and high dimensional model
representations
Sergei Manzhos and Tucker Carrington 785

Self-consistent fluctuation expansion and its application to numerical integration

Coşar Gözükirmizi and Metin Demiralp 788

Fluctuation free matrix representation based random data partitioning through HDMR
M. Alper Tunga and Metin Demiralp 792

Support function influences on the univariance of the enhanced multivariance product

representation
Burcu Tunga and Metin Demiralp 796

Taylor series based integration with the fluctuation freely approximated remainder over gauss
wave type basis functions
Süha Tuna, N. A. Baykara, and Metin Demiralp 800

Optimal control equations for the one dimensional quantum harmonic oscillator under the
influence of external dipole effects
Muzaffer Ayvaz and Metin Demiralp 804

xiii
Fluctuation studies in the infinite interval matrix representations of operator products and their
decompositions
N. A. Baykara, Ercan Gürvit, and Metin Demiralp 808

Fluctuation studies on the finite interval matrix representations of operator products and their
decompositions
Ercan Gürvit, N. A. Baykara, and Metin Demiralp 812

Taylor series expansion with the fluctuation freely approximated remainder over gauss wave
type basis functions
Caner Gülpinar, Meseret Tuba Gülpinar, and Metin Demiralp 816

Exponentially supported polynomial basis set using fluctuation free integration in the Taylor
expansion remainder term evaluation
Meseret Tuba Gülpinar, Caner Gülpinar, and Metin Demiralp 820

Basic components in fluctuation free integration of highly oscillatory functions

Sevda Üsküplü and Metin Demiralp 824

Data completion via combined and optimized small scale high dimensional model representation
Evrim Korkmaz and Metin Demiralp 828

Adaptive wavelet methods - Matrix-vector multiplication

Dana Černá and Václav Finěk 832

Dimensionality reduction and approximation via space extension and multilinear array
decomposition
Metin Demiralp and Emre Demiralp 837

SESSION 7

Electron spin resonance spectra of nitroxyl radicals

Edith Botek, Natalia Zarycz, Benoît Champagne, Valérie Sciannaméa, and Christophe Detrembleur 841

Theoretical aspects on the evaluation and interpretation of the third-order nonlinear optical
properties of diradical compounds
Benoît Champagne, Edith Botek, Akihiro Shimizu, Takashi Kubo, Kenji Kamada, Koji Ohta,
Ryohei Kishi, Hitoshi Fukui, Hideaki Takahashi, and Masayoshi Nakano 844

Electronic structure and optical properties of conjugated molecules: SAC-CI study

Masahiro Ehara, Lu Yun-peng, Malinee Promkatkaew, and Supa Hannongbua 848

Second hyperpolarizabilities of singlet diradical compounds and their radical ions

Hitoshi Fukui, Kyohei Yoneda, Edith Botek, Benoît Champagne, and Masayoshi Nakano 852

Magnetic shielding in carbon nanotube

Nobuhisa Miyake, Daisuke Yamaki, and Masahiko Hada 856

xiv
Edge states in stacked nanographene
Kikuo Harigaya 860

Synthesis and electronic structure of bisanthene: A small molecular-sized graphene with zigzag
edges
Yasukazu Hirao, Akihito Konishi, Kouzou Matsumoto, Hiroyuki Kurata, and Takashi Kubo 863

Spin-orbit effects in graphene p - n junction

A. Yamakage, K.-I. Imura, J. Cayssol, and Y. Kuramoto 867

Z2-classification of localization properties in graphene

Ken-Ichiro Imura, Yoshio Kuramoto, and Kentaro Nomura 871

Broken-symmetry MO-CI quantum master equation approach to exciton dynamics in open-shell

singlet systems
Ryohei Kishi, Takuya Minami, Kyohei Yoneda, and Masayoshi Nakano 875

Vibrational frequency without spin contamination error - Approximately spin projected force
constant -
Y. Kitagawa, T. Saito, Y. Kataoka, Y. Nakanishi, T. Matsui, T. Kawakami, M. Okumura, and K.
Yamaguchi 879

Singlet open-shell character of conjugated Kekulé molecules

Takashi Kubo, Mitsuya Aoba, Akihiro Shimizu, Yasukazu Hirao, Kozo Matsumoto, Hiroyuki
Kurata, and Masayoshi Nakano 883

Coronene-transition metal complex: View from quantum chemistry and statistical mechanics
Hirofumi Sato, Chisa Kikumori, and Shigeyoshi Sakaki 887

I-V characteristics of several modified DNA bases

Y. Shigeta, T. Matsui, Y. Nakanishi, Y. Kitagawa, and M. Okumura 891

Multi-paradigm simulation at nanoscale: Methodology and application to functional carbon

material
Haibin Su 895

Electron donor solvent effects on the (Hyper) polarizabilities of a solute presenting singlet
diradical character
Hideaki Takahashi, Kazuki Kubota, Hitoshi Fukui, Sean Bonness, Kyohei Yoneda, Ryohei Kishi,
Takashi Kubo, Kenji Kamada, Koji Ohta, Benoît Champagne, Edith Botek, and Masayoshi Nakano 899

A multiconfigurational density functional theory

Takao Tsuneda 903

Electronic transport of graphene nanoribbons: Effect of edges and geometry

Katsunori Wakabayashi 907

Quantum-chemical analysis of paramagnetic 13C NMR shifts of iron-bound cyanide ions in heme-
protein environments
Daisuke Yamaki and Masahiko Hada 912

xv
Locality and nonlocality of electronic structures of molecular systems: Toward QM/MM and
QM/QM approaches
Shusuke Yamanaka, Yasushige Yonezawa, Kazuto Nakata, Satomichi Nishihara, Mitsutaka
Okumura, Toshikazu Takada, Kizashi Yamaguchi, and Haruki Nakamura 916

SESSION 8

Computational aspects of the modelling of vibrational properties of gases, liquids and solids
Philippe Carbonniere and Claude Pouchan 920

Quantum dynamics study of resonance states of vinylidene using normal mode Hamiltonian
Yinghui Ren, Bin Li, and Wensheng Bian 921

Using pruned basis sets to compute vibrational spectra

Gustavo Avila, Jason Cooper, and Tucker Carrington 925

Simulating and interpreting vibrational spectra of molecules: The resonant Raman spectra of
rhodamine 6G
Benoît Champagne and Julien Guthmuller 928

Density functional perturbation theory within the projector augmented-waves method: A few
benchmarks for molecules and solids
Andrea Dal Corso and Lorenzo Paulatto 932

Recent algorithmic development of parallel force decomposition and Hamiltonian splitting

methods for macromolecular simulation
Dusanka Janezic, Urban Borstnik, Matej Praprotnik, Matej Penca, Matej Janezic, and Ksenija
Poljanec 936

Computational experiment in non-crystalline materials from first-principles: A case study of

vibrations in hydrogenated amorphous silicon
Franco Gaspari, Anatoli I. Shkrebtii, Ihor M. Kupchak, Tim Teatro, and Laura Henderson 939

Implementation of density-functional perturbation theory within ABINIT: Projector augmented-

waves and spin-orbit
X. Gonze, M. Verstraete, C. Audouze, M. Torrent, and F. Jollet 944

Quantum dynamics of floppy molecular systems with ELVIBROT and TNUM

André Nauts and David Lauvergnat 948

Medium range structure of tetrahedrally-bonded glasses through the first principles

investigation of Raman spectra
Luigi Giacomazzi and Alfredo Pasquarello 953

Determination of conformational preferences in biomolecule mimics with localized orbital

coupled cluster methods
Daniel P. Schofield and Kenneth D. Jordan 957

xvi
Time-domain calculations of the 1D and 2D spectra of resonantly-coupled vibrations in liquids
and proteins
Hajime Torii 961

SESSION 9

Symposium on computing in experimental high energy physics

Tulika Bose 965

Web application for detailed real-time database transaction monitoring for CMS condition data
Michele de Gruttola, Salvatore Di Guida, Vincenzo Innocente, and Antonio Pierro 966

CMS alignment and calibration framework

Matthias Edelhoff and CMS Collaboration 971

The ATLAS computing model & distributed computing evolution

Roger W. L. Jones and ATLAS Collaboration 975

CMS dashboard for monitoring of the user analysis activities

Edward Karavakis, Julia Andreeva, Gerhild Maier, and Akram Khan 983

The physics analysis tools project for the ATLAS experiment

Bruno Lenzi and ATLAS collaboration 987

Distributed data analysis in ATLAS

Paul Nilsson and ATLAS Collaboration 991

ATLAS trigger: Design and commissioning

F. Pastore and ATLAS Collaboration 995

Probing methods for automatic error resolution in a heterogeneous software environment

Antonio Pierro, Salvatore Di Guida, Vincenzo Innocente, and Ilja Kuzborskij 999

Data quality monitoring of the CMS tracker

Karolos Potamianos and CMS Collaboration 1003

The CMS ECAL non-event data handling

Thomas Punz and CMS Collaboration 1005

CRAB: Distributed analysis tool for CMS

Leonardo Sala and CMS Collaboration 1009

TMVA - Toolkit for multivariate data analysis

Jan Therhaag and TMVA Core Developer Team 1013

The CMS muon reconstruction software

Daniele Trocino and CMS Collaboration 1017

xvii
A tour through the CMS data model
Roger Wolf and CMS Collaboration 1021

SESSION 10

Preface: 6th symposium on industrial and environmental case studies

Fragiskos Batzias 1025

Technology transfer by means of fault tree synthesis

Dimitris F. Batzias 1027

Technology transfer through a network of standard methods and recommended practices - The
case of petrochemicals
Dimitris F. Batzias and Sotirios Karvounis 1031

Transforming incomplete fault tree to Ishikawa diagram as an alternative method for technology
transfer
Dimitris F. Batzias 1035

Analytic estimation of recycled products added value as a means for effective environmental
management
Dimitris F. Batzias 1039

Numerical simulation of the neutrally stratified ABL flow over complex geometry
L. Beneš, T. Bodnár, and K. Kozel 1043

A generalized model for simulating adsorption on porous media and checking for reversibility by
desorption
Fragiskos Batzias, Athanasia Bountri, and Dimitris Sidiras 1047

Searching for correspondence between mechanismic/deductive and empirical/inductive models at

industrial level by means of dimensional analysis
Fragiskos Batzias, Athanasia Bountri, and Dimitris Sidiras 1051

Introducing economic parameters in industrial flotation dimensionless models used for intra-
factory technology transfer
Dimitris Batzias and Konstantina Ifanti 1055

Industrial wastewater treatment in fixed-bed systems

Dimitris Tsatiris and Dimitris Sidiras 1059

Parameter identification of process simulation models as a means for knowledge acquisition and
technology transfer
Dimitris F. Batzias and Konstantina Ifanti 1063

Endogenous estimation of safety coefficient for optimal design of biochemical reactors at

industrial level
Christina G. Siontorou and Angeliki Karydi 1067

xviii
Introducing a conditional 'Willingness to Pay' index as a quantifier for environmental impact
assessment
Fragiskos Batzias and Odysseas Kopsidas 1071

Evaluating environmental impact caused by industrial activities - Implementation of the WTP-

WTA approach
Odysseas Kopsidas and Fragiskos Batzias 1075

Chromium (VI) purification using pine sawdust in batch systems

Dorothea Politi and Dimitris Sidiras 1079

Determination of optimal environmental policy for reclamation of land unearthed in lignite

mines - Strategy and tactics
Dimitris F. Batzias and Yannis A. Pollalis 1083

Tracing the transition path between optimal strategies combinations within a competitive market
of innovative industrial products
Dimitris F. Batzias and Yannis A. Pollalis 1087

Simulation of acid hydrolysis of lignocellulosic residues to fermentable sugars for bioethanol

production
Dimitris Sidiras 1091

Computer aided design of medicinal products based on interactive chemical/herbal ingredients –

An R&D approach
Christina G. Siontorou 1095

On the optimal design of molecular sensing interfaces with lipid bilayer assemblies – A
knowledge based approach
Christina G. Siontorou 1099

Industrial production index forecast: Methods comparison

M. Filomena Teodoro 1103

SESSION 11

Preface: Numerical methods for eigenvalue problems

Paolo Bientinesi 1108

Level-3 BLAS on a GPU: Picking the low hanging fruit

Francisco D. Igual, Gregorio Quintana-Ortí, and Robert A. van de Geijn 1109

FLECS, a flexible coupling shell - Parallel application to fluid-structure interaction

Margreet Nool, Erik Jan Lingen, Sander van Zuijlen, Martijn Stroeven, and Hester Bijl 1113

Robust computation of determinant

Takeshi Ogita 1119

Pseudoinverse preconditioner for saddle point problem

Felicja Okulicka-Dłużewska 1124

xix
Matrix multiplication with guaranteed accuracy by level 3 BLAS
Katsuhisa Ozaki, Takeshi Ogita, and Shin'ichi Oishi 1128

An example of symmetry exploitation for energy-related eigencomputations

M. Petschow, E. Di Napoli, and P. Bientinesi 1134

SESSION 12

Heterogeneous domain decomposition of surface and porous media flow

Heiko Berninger, Ralf Kornhuber, and Oliver Sander 1138

Molecular dynamics simulation of polymerization of p-xylylene

Cezary Czaplewski, Artur Giełdon, Krzystof Smalara, and Maciej Bobrowski 1142

Modeling of delamination propagation in composite laminated beam structures

C. Harvey and S. Wang 1146

Vibrational spectra and anharmonic effects in crystals studied by molecular dynamics simulation
E. B. Dolgusheva and V. Yu. Trubitsin 1150

A multi-threaded and distributed framework for pedestrian simulation analysis

Edward Karavakis and Akram Khan 1154

Sheaf construction
Elena Şendroiu 1158

Relative production yields in homologous metallofullerene series: Computations for X@C 74 and
Z@C82 endohedrals
Filip Uhlík, Zdeněk Slanina, Takeshi Akasaka, and Shigeru Nagase 1162

Quantum mechanical study on the fragmentation of the POPOP molecule

Jelena Tamuliene 1166

Slate characterization using 3D laser scanning

M. López, J. Taboada, J. Martínez, J. M. Matías, and J. A. Vilán 1170

Stratified atmospheric flow modeling

Aleš Jirk and Josef Brechler 1174

Non-linear thermal analysis of the efficiency of light concrete big-holed bricks by FEM
J. J. del Coz Díaz, P. J. García Nieto, A. Lozano Martínez-Luengas, and J. Domínguez Hernández 1178

Construction of an optimized explicit Runge-Kutta method with increased phase-lag order for
the numerical solution of the Schrödinger equation
A. A. Kosti, Z. A. Anastassi, and T. E. Simos 1182

xx
Construction of an explicit Runge-Kutta-Nyström method with constant coefficients and of a
phase-fitted and amplification-fitted explicit Runge-Kutta-Nyström method for the numerical
solution of the Schrödinger equation
A. A. Kosti, Z. A. Anastassi, and T. E. Simos 1185

The analytic solution of the firm's cost-minimization problem with box constraints and the Cobb-
Douglas model
L. Bayón, J. M. Grau, M. M. Ruiz, and P. M. Suárez 1188

Detection of broken rotor bars in induction machines: An approach using wavelet packets in
MCSA
León Escobar-Moreira, José Antonino-Daviu, and Martin Riera-Guasp 1192

Application in DSP/FPGA design of Matlab/Simulink

Yong-mei Liu, Yong Guan, Jie Zhang, Min-hua Wu, and Lin-wei Wu 1196

A neural network approach for detection of damage in a vibrating beam

L. Dihoru, N. Alexander, C. A. Taylor, H. Grumbar, and E. Newton 1200

Analysis of three dimensional textures through use of photometric stereo, co-occurrence matrices
and neural networks
Lyndon N. Smith and Melvyn L. Smith 1205

Numerical modeling of transport barrier formation

M. Z. Tokar 1210

High performance implementations for computing the maximal Lyapunov exponent on

distributed memory architectures
I. Marín Carrión, E. Arias Antúnez, M. M. Artigao Castillo, and J. J. Miralles Canals 1214

Characterization of forest fires in the Mediterranean area

M. Marí-Benlloch, M. Martínez-Gómez, C. Maroto, J. Suárez, and F. Crespo 1218

Aromaticity variation in BN substituted triphenylene: A theoretical study

A. G. Papadopoulos, N. D. Charistos, and M. P. Sigalas 1223

Computational aspects of crack growth in sandwich plates from reinforced concrete and foam
G. Papakaliatakis, V. P. Panoskaltsis, and A. Liontas 1227

Non-linear analysis and calculation of the performance of a shelving protection system by FEM
P. J. García Nieto, J. J. del Coz Díaz, J. A. Vilán Vilán, and J. L. Suárez Sierra 1231

Monte Carlo simulation studies of neurofilament brushes

Yongkyu Kwak, Rakwoo Chang, and Yeshitila Gebremichael 1235

Grand-canonical Monte Carlo simulation study of polyelectrolyte diode

Eonji Lee, Ji-hyung Han, Rakwoo Chang, and Taek Dong Chung 1239

Analysis of errors in MLPG methods

Roman Trobec 1243

xxi
Mobile agent location in distributed environments
S. G. Fountoukis and I. P. Argyropoulos 1247

Pattern oriented design of cluster running object medical information systems

S. G. Fountoukis and D. T. Chatzistavrou 1248

Reactions of parylenes with double bonds: An ab initio study

Sylwia Smuczyńska, Piotr Skurski, and Maciej Bobrowski 1249

Calculations of μ− wave functions in muonic atoms using a genetic algorithm

I. S. Kardaras, V. N. Stavrou, I. G. Tsoulos, and T. S. Kosmas 1253

Density functional theory orbital energies for predicting ionization energies

Ulrike Salzner and Roi Baer 1257

A neural network model for olfactory glomerular activity prediction

Zu Soh, Toshio Tsuji, Noboru Takiguchi, and Hisao Ohtake 1261

Parabolic problems with parameters arising in evolution model for phytromediation

Aida Sahmurova and Veli Shakhmurov 1265

Optimal regular differential operators with VMO coefficients

Veli Shakhmurov 1269

Simultaneous phase, amplitude, and polarization control of femtosecond laser pulses

A. Lindinger, S. M. Weber, M. Plewicki, and F. Weise 1275

A new approach of watermarking technique by means multichannel wavelet functions

Santa Agreste and Luigia Puccio 1279

Finite element solutions of nanophotonics devices

B. M. A. Rahman, D. M. H. Leung, N. Kejalakshmy, A. Agrawal, and K. T. V. Grattan 1283

Alignment, segmentation and 3-D reconstruction of serial sections based on automated algorithm
Weiguo Bian, Shaojie Tang, Qiong Xu, Qin Lian, Jin Wang, and Dichen Li 1287

The application of RESCUER software to PDAEs translation into VHDL-AMS models

Mariusz Zubert and Andrzej Napieralski 1293

Optimization of the place of the plastic hinges by steel braces at RC buildings

Farzad Hatami, Mohammad Ragheb, and Meysam Namazi 1297

Presenting numerical mathematical formulas to design composite steel shear walls

Farzad Hatami, Mahdi Ragheb, and Ali Ghamari 1301

Revealing effects of dynamic characteristics in process monitoring and their influences on quality
prediction
Melanie Senn and Norbert Link 1306

xxii
Central schemes on unstructured grids
R. Touma and G. Jannoun 1310

A new method for DtN maps of a differential equation with constant coefficients
Sasamoto Akira 1314

On spectral approximation of laguerre type

S. Shindin and N. Parumasur 1318

Mixture density estimation in aggregated random fields

Nikolai Leonenko and Emanuele Taufer 1322

Fractional calculus and morphogen gradient formation

Santos Bravo Yuste, Enrique Abad, and Katja Lindenberg 1323

MAST solution of irrotational flow problems in 2D domains with strongly unstructured

triangular meshes
T. Tucciarelli 1327

Modelling the permeability of textiles using mesh adaptatino

A. Giavaras, A. C. Long, and M. J. Clifford 1333

Hyperbolic diffusion equation

Leopold Herrmann 1337

A note on local superderivations and 2-local superderivations on M n(ԧ

ԧ)
Ajda Foĺner and Maja Foĺner 1341

Optimized explicit symmetric linear multistep methods for the numerical solution of the
Schrödinger equation and related orbital problems
G. A. Panopoulos, Z. A. Anastassi, and T. E. Simos 1344

Symmetries of the CR sublaplacian

Zuzana Vlasáková 1348

Existence results for nonlinear variational inequalities via topological methods

Irene Benedetti, Francesco Mugelli, and Pietro Zecca 1352

Author Index

xxiii