Computer Physics Communications, Volume 169

Volume 169, Numbers 1-3, July 2005

Proceedings of the Europhysics Conference on Computational Physics 2004
1. Nanostructure and materials science

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  Jeffrey B. Neaton, Khoong Hong Khoo, C. D. Spataru, Steven G. Louie:
  Electron transport and optical properties of carbon nanostructures from first principles. 1-8
• 
  Rosa Di Felice, Stefano Corni:
  Computational approach to study electron-transfer proteins: Azurin for bio-molecular devices. 9-13
• 
  Jean-Yves Raty, Giulia Galli:
  First principle study of nanodiamond optical and electronic properties. 14-19
• 
  Xiaobao Yang, Jun Ni:
  Ground states of potassium adsorbate on single-walled carbon nanotubes. 20-23
• 
  Caetano R. Miranda, Sandro Scandolo:
  Computational materials science meets geophysics: dislocations and slip planes of MgO. 24-27
• 
  Abdallah Qteish, Abdullah Al-Sharif, M. Fuchs, Matthias Scheffler, Sixten Boeck, Jörg Neugebauer:
  Exact-exchange calculations of the electronic structure of AlN, GaN and InN. 28-31
• 
  C. Sbraccia, C. A. Pignedoli, Alessandra Catellani, R. Di Felice, P. L. Silvestrelli, F. Toigo, F. Ancilotto, Carlo Maria Bertoni:
  Acetylene on Si(111) from computer simulations. 32-35
• 
  Christoph Dellago, Mor M. Naor:
  Dipole moment of water molecules in narrow pores. 36-39
• 
  Alessandro Mattoni, Luciano Colombo, Fabrizio Cleri:
  Crack-tip stress shielding by a hard fiber in beta-SiC: an atomistic study. 40-43
• 
  Fabrizio Cleri:
  Evolution of dislocation cell structures in plastically deformed metals. 44-49
• 
  Maria Clelia Righi, C. A. Pignedoli, R. Di Felice, Carlo Maria Bertoni, Alessandra Catellani:
  Kinetic Monte Carlo simulations of C diffusion on sqrt(3)×sqrt(3) beta-SiC(111) based on ab initio calculations. 50-53
• 
  Erik Johansson, Kim Bolton, Peter Ahlström:
  Simulation of water vapor clusters in equilibrium with liquid water. 54-56
• 
  Michael Schreiber, Sibylle Gemming:
  Density-functional investigation of alloyed metallic nanowires. 57-59
• 
  Ilya Valuev:
  Reactive potentials for molecular dynamics with cluster multi-range interpolation. 60-63

2. Biostructures and soft matter (polymers, membranes, proteins, etc)

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  Ronald Blaak, Hartmut Löwen:
  Umbrella sampling in non-equilibrium computer simulations. 64-68
• 
  Nicolas Levy, Daniel Borgis, Massimo Marchi:
  A dielectric continuum model of solvation for complex solutes. 69-74
• 
  Kurt Kremer, Sathish K. Sukumaran, Ralf Everaers, Gary S. Grest:
  Entangled polymer systems. 75-81
• 
  Doros N. Theodorou:
  Hierarchical modeling of amorphous polymers. 82-88
• 
  Jean-Paul Ryckaert:
  From local jumps to entangled chain dynamics in polyethylene melts. 89-94
• 
  Irene Burghardt, Lorenz S. Cederbaum, James T. Hynes:
  Ultrafast excited-state charge transfer at a conical intersection: effects of an environment. 95-98
• 
  Claire Loison, Michel Mareschal, Friederike Schmid:
  Fluctuations and defects in lamellar stacks of amphiphilic bilayers. 99-103
• 
  Kang Kim, Yasuya Nakayama, Ryoichi Yamamoto:
  A smoothed profile method for simulating charged colloidal dispersions. 104-106
• 
  Andrey Milchev, Kurt Binder:
  Adsorption-induced polymer translocation through a nanopore: a Monte Carlo investigation. 107-110
• 
  Michael Bachmann, Wolfhard Janke:
  Conformational transitions of heteropolymers. 111-113
• 
  Hsiao-Ping Hsu, Walder Nadler, Peter Grassberger:
  Statistics of lattice animals. 114-116
• 
  Tanja Schilling, Daan Frenkel:
  Nucleation in suspensions of anisotropic colloids. 117-121
• 
  Enzo Orlandini, Davide Marenduzzo, Julia M. Yeomans:
  Shear dynamics in cholesterics. 122-125
• 
  Ana Damjanovic, Bertrand García-Moreno E., Eaton E. Lattman, Angel E. García:
  Molecular dynamics study of hydration of the protein interior. 126-129
• 
  Manuela Cavallari, Alessandro Desideri, Mattia Falconi, Mauro Ferrario:
  Molecular dynamics simulations of the Trp repressor-DNA complex and the AV77 mutant. 130-134
• 
  Carlo Cavazzoni, Renato Colle, Riccardo Farchioni, Giuseppe Grosso:
  Base and salt 3D forms of Emeraldine II polymers by Car-Parrinello molecular dynamics. 135-138
• 
  Hiroaki Nakamura, Yuichi Tamura:
  Phase diagram for self-assembly of amphiphilic molecule C₁₂E₆ by dissipative particle dynamics simulation. 139-143

3. Computational statistical physics, turbulence plasmas and reactive flows

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  Peter Young:
  Recent numerical results on spin glasses. 144-148
• 
  D. P. Landau, F. Tavazza, Joan Adler:
  Monte Carlo simulations of a compressible Ising ferromagnet at constant volume. 149-152
• 
  Stefano Atzeni, Angelo A. Schiavi, Francesco Califano, F. Cattani, F. Cornolti, D. Del Sarto, T. V. Liseykina, A. Macchi, Francesco Pegoraro:
  Fluid and kinetic simulation of inertial confinement fusion plasmas. 153-159
• 
  Anthony C. Maggs, Jörg Rottler:
  Auxiliary field simulation and Coulomb's law. 160-165
• 
  Francesco Sciortino, Sergey V. Buldyrev, Cristiano De Michele, Giuseppe Foffi, Neda Ghofraniha, Emilia La Nave, Angel J. Moreno, Stefano Mossa, Ivan Saika-Voivod, Piero Tartaglia, Emanuela Zaccarelli:
  Routes to colloidal gel formation. 166-171
• 
  Cedric Thieulot, Pep Español:
  Non-isothermal diffusion in a binary mixture with smoothed particle hydrodynamics. 172-176
• 
  Jörg Rottler, Mark O. Robbins:
  Macroscopic friction laws and shear yielding of glassy solids. 177-182
• 
  Eytan Domany:
  Analysis of DNA-chip and antigen-chip data: studies of cancer, stem cells and autoimmune diseases. 183-187
• 
  Alberto Rosso, Werner Krauth:
  Variant Monte Carlo algorithm for driven elastic strings in random media. 188-191
• 
  Ignacio Pagonabarraga, Fabrizio Capuani, Daan Frenkel:
  Mesoscopic lattice modeling of electrokinetic phenomena. 192-196
• 
  Kerstin Franzrahe, Peter Henseler, A. Ricci, Wolfram Strepp, S. Sengupta, Markus Dreher, Chr. Kircher, M. Lohrer, Wolfram Quester, Kurt Binder, Peter Nielaba:
  Two-dimensional model colloids and nano wires: phase transitions, effects of external potentials and quantum effects. 197-202
• 
  Simone Melchionna, Sauro Succi:
  Lattice Boltzmann-Poisson method for electrorheological nanoflows in ion channels. 203-206
• 
  Chiara Marchetto, Francesco Califano, Maurizio Lontano:
  Turbulence healing via plasma-wave interaction: the results of a study via kinetic codes. 207-209
• 
  Giuliano De Stefano, Oleg V. Vasilyev, Daniel E. Goldstein:
  A-priori dynamic test for deterministic/stochastic modeling in large-eddy simulation of turbulent flow. 210-213
• 
  Paola Gallo, Andrea Attili, Mauro Rovere:
  Glass transition in confinement: a Lennard-Jones binary mixture study. 214-217
• 
  Ta-Yuan Chen, Li-Ching Hsieh, Hoong-Chien Lee:
  Shannon information and self-similarity in whole genomes. 218-221
• 
  Wolfhard Janke, Adriaan M. J. Schakel:
  Geometrical phase transitions. 222-225
• 
  Kurt Binder, Marcus Müller, Andrey Milchev, D. P. Landau:
  Monte Carlo simulations of Ising models and polymer blends in double wedge geometry: Evidence for novel types of critical phenomena. 226-229
• 
  Rudolf Hilfer, Bibudhananda Biswal, Hans-Georg Mattutis, Wolfhard Janke:
  Multicanonical simulations of the tails of the order-parameter distribution of the two-dimensional Ising model. 230-233
• 
  Alexander K. Hartmann, Wolfgang Barthel, Martin Weigt:
  Phase transition and finite-size scaling in the vertex-cover problem. 234-237
• 
  Dan Skandera:
  Different strategies of the central approach to the numerical hydrodynamics. 238-242
• 
  Sylvain Reynal, Hung T. Diep:
  Hybrid multicanonical cluster algorithm for efficient simulations of long-range spin models. 243-246
• 
  Vladimir V. Stegailov:
  Homogeneous and heterogeneous mechanisms of superheated solid melting and decay. 247-250
• 
  John Loverich, Uri Shumlak:
  A discontinuous Galerkin method for the full two-fluid plasma model. 251-255

4. New methods in computer simulation

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  Jochen Blumberger, Yoshitaka Tateyama, Michiel Sprik:
  Ab initio molecular dynamics simulation of redox reactions in solution. 256-261
• 
  Gaurav Arya, Athanassios Z. Panagiotopoulos:
  Molecular modeling of shear-induced alignment of cylindrical micelles. 262-266
• 
  Sara Bonella, David F. Coker:
  Linearized, time-dependent, non-adiabatic quantum correlation functions. 267-273
• 
  Robert H. Swendsen, Marc Fasnacht, John M. Rosenberg:
  The adaptive integration method for calculating general free energy functions. 274-276
• 
  Ron Elber:
  Computer simulations of protein folding: Classical trajectories by optimization of action. 277-283
• 
  Thomas Bligaard, Hannes Jónsson:
  Optimization of hyperplanar transition states: Application to 2D test problems. 284-288
• 
  Matthew J. McGrath, J. Ilja Siepmann, I-Feng W. Kuo, Christopher J. Mundy, Joost VandeVondele, Michiel Sprik, Jürg Hutter, Fawzi Mohamed, Matthias Krack, Michele Parrinello:
  Toward a Monte Carlo program for simulating vapor-liquid phase equilibria from first principles. 289-294
• 
  Young C. Kim, Michael E. Fisher:
  Fluid coexistence close to criticality: scaling algorithms for precise simulation. 295-300
• 
  Ryoichi Yamamoto, Yasuya Nakayama, Kang Kim:
  A method to resolve hydrodynamic interactions in colloidal dispersions. 301-304
• 
  Daniele Passerone, Teodoro Laino:
  Exploring conical intersection spaces using pseudo-dynamics and band optimization: a novel strategy. 305-308
• 
  Yiming Li, Shao-Ming Yu:
  A numerical iterative method for solving Schrödinger and Poisson equations in nanoscale single, double and surrounding gate metal-oxide-semiconductor structures. 309-312
• 
  Mitsuyoshi Tomiya, Naotaka Yoshinaga, Shoichi Sakamoto, Aki Hirai:
  A large number of higher-energy eigenvalues of a huge dimensional matrix for a quantum chaotic study of a quartic potential. 313-316
• 
  Hisashi Okumura, Yuko Okamoto:
  Molecular simulations in the multibaric-multithermal ensembles. 317-321
• 
  David Quigley, Matt I. J. Probert:
  Constant pressure Langevin dynamics: theory and application. 322-325
• 
  Roland G. Winkler, Marisol Ripoll, Kiaresch Mussawisade, Gerhard Gompper:
  Simulation of complex fluids by multi-particle-collision dynamics. 326-330
• 
  Marco Masia, Michael Probst, Rossend Rey:
  On the performance of molecular polarization methods close to a point charge. 331-334
• 
  David Curcó, Jordi Casanovas, Marc Roca, Carlos Alemán:
  A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima. 335-338
• 
  Branislav Brutovsky, Gerald R. Kneller:
  Linear prediction of force time series to accelerate molecular dynamics simulations. 339-342
• 
  Godehard Sutmann, Bernhard Steffen:
  A particle-particle particle-multigrid method for long-range interactions in molecular simulations. 343-346

5. Computational aspects of lattice gauge theory, elementary particle physics and astrophysics

• 
  Zoltán Fodor:
  Lattice gauge theory and elementary particle physics. 347-352
• 
  Ewald Müller:
  Simulating astrophysical phenomena: challenges and achievements. 353-361
• 
  Karl Jansen:
  Going chiral: twisted mass versus overlap fermions. 362-364
• 
  Roberto Capuzzo-Dolcetta:
  High performance computing for self-gravitating systems. 365-369
• 
  Fabien Alet, Biagio Lucini, Michele Vettorazzo:
  A cluster algorithm for lattice gauge theories. 370-373
• 
  Ian Hawke, Luca Baiotti, Luciano Rezzolla, Erik Schnetter:
  Gravitational waves from the 3D collapse of a neutron star to a Kerr black hole. 374-377
• 
  Claudio Gheller, Gianfranco Brunetti:
  Merging clusters and the formation of radio haloes. 378-381
• 
  Norbert Attig, Gunnar S. Bali, Thomas Düssel, Thomas Lippert, Hartmut Neff, Z. Prkaçin, Klaus Schilling:
  Demonstration of string breaking in quantum chromodynamics by large-scale eigenvalue computations. 382-385

6. Quantum simulation (many-body, dynamics, lattice models, etc)

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  Michele Casula, Seiji Yunoki, Claudio Attaccalite, Sandro Sorella:
  Resonating valence bond wave function: from lattice models to realistic systems. 386-393
• 
  Shiwei Zhang, Henry Krakauer, Wissam A. Al-Saidi, Malliga Suewattana:
  Quantum simulations of realistic systems by auxiliary fields. 394-399
• 
  Alessandro Sergi, Raymond Kapral:
  Nonadiabatic chemical reactions. 400-403
• 
  Saverio Moroni, Stefano Baroni:
  Computational spectroscopy of doped He clusters. 404-407
• 
  Takahiro Mizusaki, Masatoshi Imada:
  Path-integral renormalization group method with quantum-number projection. 408-411
• 
  Peter D. Drummond, Joel F. Corney:
  Quantum phase-space simulations of fermions and bosons. 412-415
• 
  Marcos Rigol, Alejandro Muramatsu:
  Exact numerical approach to hard-core bosons on one-dimensional lattices. 416-420
• 
  Markus Holzmann, Carlo Pierleoni, David M. Ceperley:
  Coupled Electron-Ion Monte Carlo calculations of atomic hydrogen. 421-425
• 
  Florian R. Krajewski, Martin H. Müser:
  Many-body quantum dynamics by adiabatic path-integral molecular dynamics: Disordered Frenkel Kontorova models. 426-429
• 
  Massimo Rontani, Carlo Cavazzoni, Guido Goldoni:
  The crossover between liquid and solid electron phases in quantum dots: A large-scale configuration-interaction study. 430-432

7. Fronties in large scale computing

• 
  Michael P. Allen:
  Computer simulation of multiscale phenomena in colloidal liquid crystals. 433-437
• 
  Achi Brandt:
  Multiscale solvers and systematic upscaling in computational physics. 438-441
• 
  Raffaele Tripiccione:
  Strategies for dedicated computing for lattice gauge theories. 442-448
• 
  Andrew Canning, David Raczkowski:
  Scaling first-principles plane-wave codes to thousands of processors. 449-453
• 
  Carlo Cavazzoni, Tomaso Esposti Ongaro, Giovanni Erbacci, Augusto Neri, Giovanni Macedonio:
  High performance computing simulations of pyroclastic flows. 454-456
• 
  Wolfhard Janke, Des Johnston, Ralph Kenna:
  Critical exponents from general distributions of zeroes. 457-461
• 
  Simone Meloni, Mario Rosati, Alessandro Federico, Luca Ferraro, Alessandro Mattoni, Luciano Colombo:
  Computational Materials Science application programming interface (CMSapi): a tool for developing applications for atomistic simulations. 462-466