Computer Physics Communications, Volume 182

Volume 182, Number 1, January 2011

Editorial

• 
  James J. Y. Hsu:
  Preface. 1

Plenary and Invited Papers

• 
  Kai Schneider, Salah Neffaa, Wouter J. T. Bos:
  A pseudo-spectral method with volume penalisation for magnetohydrodynamic turbulence in confined domains. 2-7
• 
  Vítor Duarte Teodoro, Rui Gomes Neves:
  Mathematical modelling in science and mathematics education. 8-10
• 
  Amanda S. Barnard:
  Useful equations for modeling the relative stability of common nanoparticle morphologies. 11-13
• 
  Tak-San Ho, Herschel A. Rabitz, Shih-I Chu:
  A general formulation of monotonically convergent algorithms in the control of quantum dynamics beyond the linear dipole interaction. 14-17
• 
  Dmitry A. Telnov, Shih-I Chu:
  Time-dependent generalized pseudospectral method for accurate treatment of multiphoton processes of diatomic molecules in intense laser fields. 18-20
• 
  Xiao-Min Tong, Nobuyuki Toshima:
  Time-dependent method in the laser-atom interactions. 21-23
• 
  Huey-Wen Lin, Saul D. Cohen, Liuming Liu, Nilmani Mathur, Kostas Orginos, André Walker-Loud:
  Heavy-baryon spectroscopy from lattice QCD. 24-26
• 
  A. P. Young, Sergey Knysh, Vadim N. Smelyanskiy:
  The complexity of the Quantum Adiabatic Algorithm. 27-28
• 
  Hendrick W. de Haan, Michel G. Gauthier, Mykyta V. Chubynsky, Gary W. Slater:
  The importance of introducing a waiting time for Lattice Monte Carlo simulations of a polymer translocation process. 29-32
• 
  Stefan Kesselheim, Marcello Sega, Christian Holm:
  Applying ICC^* to DNA translocation: Effect of dielectric boundaries. 33-35
• 
  Chi-Tin Shih, Yun-Yin Cheng, Stephen A. Wells, Ching-Ling Hsu, Rudolf A. Römer:
  Charge transport in cancer-related genes and early carcinogenesis. 36-38

Contributed Papers

• 
  Chih-Kai Yang:
  Exploring the interaction between the boron nitride nanotube and biological molecules. 39-42
• 
  I. V. Solovyev:
  Realistic modeling of complex oxide materials. 43-45
• 
  Vidar Gudmundsson, Chi-Shung Tang, Cosmin Mihai Gainar, Valeriu Moldoveanu, Andrei Manolescu:
  Time-dependent magnetotransport in semiconductor nanostructures via the generalized master equation. 46-48
• 
  K. Hoshino, T. Yoshikawa, S. Munejiri:
  Pressure-induced structural change from low-density to high-density amorphous ice by molecular-dynamics simulations. 49-51
• 
  Tianxing Ma, Feiming Hu, Zhongbing Huang, Hai-Qing Lin:
  Magnetic correlation in the Hubbard model on a honeycomb lattice. 52-54
• 
  Dingping Li, B. Rosenstein, Shou Chen, H. H. Lin, Dan Berco:
  Glass transition and the replica symmetry breaking in vortex matter: MC study. 55-57
• 
  Shuji Munejiri, Fuyuki Shimojo, Kozo Hoshino:
  Real-space investigation of a transverse wave in a liquid system generated by a molecular-dynamics simulation. 58-61
• 
  K. H. Tsai, Ten-Ming Wu:
  Entropy of a model for liquid Ga: Contribution due to Friedel oscillations. 62-64
• 
  Chi-Shung Tang, Kristinn Torfason, Vidar Gudmundsson:
  Magnetotransport in a time-modulated double quantum point contact system. 65-67
• 
  C. H. Lee, S. C. Chen, C. K. Yang, Wan-Sheng Su, M. F. Lin:
  Low-energy electronic structures of nanotube-nanoribbon hybrid systems. 68-70
• 
  Chia-Hei Yang, Ching-Ling Hsu, Nan-Yow Chen, Chi-Tin Shih:
  Temporal dynamics of site percolation in nanoparticle assemblies. 71-73
• 
  Feiming Hu, Tianxing Ma, Hai-Qing Lin:
  Numerical study of geometrical frustration: From square to triangular lattices. 74-76
• 
  Jen-Hsien Wong, Bi-Ru Wu, Ming-Fa Lin:
  Electronic properties of rhombohedral graphite. 77-80
• 
  R. F. Hung, Dan Berco, I. Ya. Shapiro, B. Shapiro, B. Rosenstein:
  Electrodynamics of type-II superconductor with periodic pinning array. 81-83
• 
  J. C. Tung, G. Y. Guo:
  An ab initio study of the magnetic and electronic properties of Fe, Co, and Ni nanowires on Cu(001) surface. 84-86
• 
  Shoichi Sakamoto, Hiroyoshi Tsuyuki, Mitsuyoshi Tomiya:
  Stochastic mechanics of electron transfer in graphene. 87-89
• 
  Naomi Hirayama, Akira Endo, Kazuhiro Fujita, Yasuhiro Hasegawa, Naomichi Hatano, Hiroaki Nakamura, Ryoen Shirasaki:
  Temperature distribution in nano-devices under a strong magnetic field. 90-92
• 
  Tay-Rong Chang, Horng-Tay Jeng, Chen-Shiung Hsue:
  Electronic structures of quasi-one-dimensional ferrimagnetic insulator Ca₃Co₂O₆. 93-95
• 
  Yiming Li, Hui-Wen Cheng, Ming-Hung Han:
  Quantum hydrodynamic simulation of discrete-dopant fluctuated physical quantities in nanoscale FinFET. 96-98
• 
  Wan-Sheng Su, Bi-Ru Wu, T. C. Leung:
  A first-principles study on the electromechanical effect of graphene nanoribbon. 99-102
• 
  Yoshiyuki Egami, Keita Yamada:
  First-principles study on quantum-transport properties of single molecule depending on adsorption conditions. 103-105
• 
  C.-C. Chen, Brian Moritz, C. J. Jia, S. Johnston, A. P. Sorini, L.-Q. Lee, K. Ko, T. P. Devereaux:
  Numerical studies of photon-based spectroscopies on high-T_c superconductors. 106-108
• 
  Brian Moritz, T. P. Devereaux, James K. Freericks:
  Temporal response of nonequilibrium correlated electrons. 109-111
• 
  H. C. Kao, M. Lewkowicz, Y. Korniyenko, B. Rosenstein:
  Dynamical approach to ballistic transport in graphene. 112-114
• 
  N. Blümer, E. V. Gorelik:
  Quantum Monte Carlo simulations of antiferromagnetism in ultracold fermions on optical lattices within real-space dynamical mean-field theory. 115-118

Atom, Molecules and Optics (AMO)

• 
  Sabyasachi Kar, Y. K. Ho:
  Resonance states of Ps^- using correlated wave functions. 119-121
• 
  Arijit Ghoshal, Y. K. Ho:
  Doubly excited resonance states of two-electron systems in exponential cosine-screened Coulomb potentials. 122-124
• 
  C. Y. Lin, Y. K. Ho:
  The photoionization of excited hydrogen atom in plasmas. 125-129
• 
  S. Paul, Y. K. Ho:
  Solution of the generalized exponential cosine screened Coulomb potential. 130-133
• 
  M. Chane-Yook, J. Dubau:
  Update of UCL computer codes for the calculation of fine-structure electron-atom collision cross-section. 134-135
• 
  Ju-Tang Hsiao, Keh-Ning Huang:
  Applications of the relativistic equation of motion to photoionization of Mg-like ions. 136-139
• 
  Yun-Min Lee, T.-F. Jiang, Z.-Y. Su, Jong-Shinn Wu:
  Three-dimensional simulation of the femto-second pulsed laser interacting with a nitrogen molecule. 140-142
• 
  M.-C. Wu, W.-C. Liu:
  Non-perturbative time-dependent numerical simulation for electromagnetically induced transparency and slow light in three-level Lambda-type atoms. 143-145
• 
  Ying-Jun Jin, Xiao-Min Tong, Nobuyuki Toshima:
  Ionization of hydrogen molecular ions in an intense laser field via a resonant state. 146-148
• 
  Alexei Deinega, Ilya Valuev:
  Long-time behavior of PML absorbing boundaries for layered periodic structures. 149-151

Plasma/ Space Physics

• 
  S. W. Chau, S. Y. Lu, P. J. Wang:
  Modeling of axis-symmetric steam plasma flow in a non-transferred torch. 152-154
• 
  Jang-Yu Hsu:
  Relativistic theory of mode conversion at plasma frequency - the finite difference time domain simulation. 155-157
• 
  Y. Nishimura:
  A perturbation method for guiding center orbit following calculations in the presence of Coulomb collisions. 158-160
• 
  Chieh-Tsan Hung, Yuan-Ming Chiu, Feng-Nan Hwang, Jong-Shinn Wu:
  Development of a parallel implicit solver of fluid modeling equations for gas discharges. 161-163
• 
  K.-W. Cheng, Chieh-Tsan Hung, M.-H. Chiang, F.-N. Hwang, Jong-Shinn Wu:
  One-dimensional simulation of nitrogen dielectric barrier discharge driven by a quasi-pulsed power source and its comparison with experiments. 164-166
• 
  Y.-M. Chiu, Chieh-Tsan Hung, F.-N. Hwang, M.-H. Chiang, Jong-Shinn Wu, S.-H. Chen:
  Effect of plasma chemistry on the simulation of helium atmospheric-pressure plasmas. 167-169
• 
  Matthew R. Smith, Chieh-Tsan Hung, Kun-Mo Lin, Jong-Shinn Wu, Jen-Perng Yu:
  Development of a semi-implicit fluid modeling code using finite-volume method based on Cartesian grids. 170-172
• 
  Xuefei Yuan, Stephen C. Jardin, David E. Keyes:
  Moving grids for magnetic reconnection via Newton-Krylov methods. 173-176
• 
  Ying-Yi Lo, Chung-Ming Ko, Chih-Yueh Wang:
  3D Magneto-hydrodynamic simulations of Parker instability with cosmic rays. 177-179
• 
  Alexei Pankin, Alexander Pletzer, Srinath Vadlamani, John R. Cary, Ammar Hakim, Scott Kruger, Mahmood Miah, Thomas D. Rognlien, Svetlana G. Shasharina, Glenn Bateman, Arnold Kritz, Tariq Rafiq:
  Simulation of anomalous transport in tokamaks using the FACETS code. 180-184

Complex Systems - Statistical Physics, Nonlinear Physics, Biological Physics, Biomaterials

• 
  Jiann-wien Hsu, Ding-wei Huang:
  Dynamics of citation distribution. 185-187
• 
  Gabriel Villalobos, Dorian L. Linero, José D. Muñoz:
  A statistical model of fracture for a 2D hexagonal mesh: The Cell Network Model of Fracture for the bamboo Guadua angustifolia. 188-191
• 
  Susumu Fujiwara, Daiki Funaoka, Takashi Itoh, Masato Hashimoto:
  Molecular dynamics simulation for phase behavior of amphiphilic solution. 192-194
• 
  Chi-Tin Shih, Hsuan-Wen Lin, Ann-Shyn Chiang:
  Statistical analysis and modeling of the temperature-dependent sleep behavior of drosophila. 195-197
• 
  J. L. Huang, H. J. Chen, H. C. Tseng:
  The flow of a reversible ratchet. 198-200
• 
  Hao-Yun Wu, Chung-I Chou, Jie-Jun Tseng:
  A simple marriage model for the power-law behaviour in the frequency distributions of family names. 201-204
• 
  Yu-Cih Peng, Chung-I Chou:
  Simulation of pedestrian flow through a "T" intersection: A multi-floor field cellular automata approach. 205-208
• 
  Chung-I Chou:
  A Knowledge-based Evolution Algorithm approach to political districting problem. 209-212
• 
  B. J. Huang, Ten-Ming Wu:
  Numerical studies for localization-delocalization transition in vibrational spectra. 213-215
• 
  Moon Yong Cha, Jae Woo Lee, Deok-Sun Lee, Doo Hwan Kim:
  Wealth dynamics in world trade. 216-218
• 
  Jaewon Choi, Gyuchang Lim, Soo Yong Kim, Kyungsik Kim:
  Information of group-correlations in Korean financial market. 219-222
• 
  Nen Saito, Yukito Iba:
  Probability of graphs with large spectral gap by multicanonical Monte Carlo. 223-225
• 
  Chien-Fu Chen, An-Chung Cheng, Yi-Duen Wang, Chai-Yu Lin:
  Universal scaling functions of a dissipative Manna model. 226-228
• 
  M. Hasegawa:
  Positive role of glassy dynamics in finite-time optimization by threshold algorithms. 229-231
• 
  Chih-Hsien Huang, Jing-Nuo Wu, Szu-Cheng Cheng, Wen-Feng Hsieh:
  The evolution of solitons in coupled resonator optical waveguides and photonic-crystal waveguides. 232-236
• 
  Shin-ichi Tadaki:
  Effects of fast noises on long-range correlations. 237-239
• 
  Naohito Urakami, Junko Imada, Takashi Yamamoto:
  Simulation of chain length recognition observed in formation of inclusion complex. 240-242
• 
  Doo Hwan Kim, Moon Yong Cha, Jae Woo Lee:
  The persistence probability and the price-price correlation functions in the Korean stock market. 243-244
• 
  Mitsuyoshi Tomiya, Hiroyoshi Tsuyuki, Shoichi Sakamoto:
  Quantum fidelity and dynamical scar states on chaotic billiard system. 245-248
• 
  Yao-Chen Hung, Chin-Kun Hu:
  Constructive role of noise in p53 regulatory network. 249-250
• 
  Akimasa Kitajima, Yukito Iba:
  Multicanonical sampling of rare trajectories in chaotic dynamical systems. 251-253

High Energy Physics, Quantum Information, Physics Education, and New Method

• 
  Ke-Jung Chen, Alexander Heger, Ann S. Almgren:
  Multidimensional simulations of pair-instability supernovae. 254-256
• 
  Masayuki Ohzeki, Hidetoshi Nishimori:
  Quantum annealing with Jarzynski equality. 257-259
• 
  Hui-Wen Cheng, Yiming Li, Jung-Yen Yang:
  Investigation of Raman enhancement in hydrothermally roughened SERS-active substrates. 260-262
• 
  Hongsuk Yi:
  Performance evaluation of GAIA supercomputer using NPB multi-zone benchmarks. 263-265
• 
  Chao-Tung Yang, Chih-Lin Huang, Cheng-Fang Lin:
  Hybrid CUDA, OpenMP, and MPI parallel programming on multicore GPU clusters. 266-269
• 
  J. H. Kim, S. Ahn, K. Cho, M. Bracko, Z. Drasal, T. Fifield, R. Frühwirth, R. Grzymkowski, T. Hara, M. Heck, S. Hwang, Y. Iida, Ryosuke Itoh, Go Iwai, H. Jang, Nobu Katayama, Yutaka Kawai, Christian Kiesling, B. K. Kim, T. Kuhr:
  The advanced data searching system with AMGA at the Belle II experiment. 270-273
• 
  Shinichi Miura:
  A variational path integral molecular dynamics study of a solid helium-4. 274-276
• 
  Soonwook Hwang, Hangi Kim, Seyong Kim:
  Large-scale deployment of two-color QCD simulations on the grid using Ganga. 277-279

Volume 182, Number 2, February 2011

Computational physics

• 
  Laura E. Walizer, John F. Peters:
  A bounding box search algorithm for DEM simulation. 281-288
• 
  B. M. Stupovski, J. V. Crnjanski, D. M. Gvozdic:
  Application of coordinate transformation and finite differences method in numerical modeling of quantum dash band structure. 289-298
• 
  Remi Baron, Philippe Boucaud, Jaume Carbonell, Vincent Drach, Federico Farchioni, Gregorio Herdoiza, Karl Jansen, Chris Michael, Istvan Montvay, Elisabetta Pallante, Olivier Pène, Siebren Reker, Carsten Urbach, Marc Wagner, Urs Wenger:
  Computing K and D meson masses with N_f=2+1+1 twisted mass lattice QCD. 299-316
• 
  Frederic Wrobel, Frédéric Saigné:
  MC-ORACLE: A tool for predicting Soft Error Rate. 317-321
• 
  Raffaele D'Ambrosio, Liviu Gr. Ixaru, Beatrice Paternoster:
  Construction of the ef-based Runge-Kutta methods revisited. 322-329
• 
  Gian Luca Delzanno, John M. Finn:
  The fluid dynamic approach to equidistribution methods for grid adaptation. 330-346
• 
  G. Zuccaro, Giovanni Lapenta, F. Ferrero, G. Maizza:
  Multiphase and multiphysics particle in cell simulation of soot deposition inside a diesel particulate filter single channel. 347-359
• 
  Min Hyung Cho, Haiyu Zheng, Yuehui Lu, YoungPak Lee, Wei Cai:
  Improved rigorous coupled-wave analysis for polar magnetic gratings. 360-365
• 
  Moussa Smadi, Derradji Bahloul:
  A compact split step Padé scheme for higher-order nonlinear Schrödinger equation (HNLS) with power law nonlinearity and fourth order dispersion. 366-371

Computer programs in physics

• 
  David C. Lonie, Eva Zurek:
  XtalOpt: An open-source evolutionary algorithm for crystal structure prediction. 372-387
• 
  Paolo Barletta:
  COOL: A code for dynamic Monte Carlo simulation of molecular dynamics. 388-399
• 
  Mohammad A. Charsooghi, Ehsan A. Akhlaghi, Sharareh Tavaddod, H. R. Khalesifard:
  A MATLAB program to calculate translational and rotational diffusion coefficients of a single particle. 400-408
• 
  Joel Ekstrand:
  Lambda: A Mathematica package for operator product expansions in vertex algebras. 409-418
• 
  Alexander Kramida:
  The program LOPT for least-squares optimization of energy levels. 419-434
• 
  Ronald Kleiss, G. van den Oord:
  CAMORRA: A C++ library for recursive computation of particle scattering amplitudes. 435-447
• 
  Dmitri Sokolovski, Elena V. Akhmatskaya, S. K. Sen:
  Extracting S-matrix poles for resonances from numerical scattering data: Type-II Padé reconstruction. 448-466
• 
  Tarcísio M. Rocha Filho, Annibal Figueiredo:
  [SADE] a Maple package for the symmetry analysis of differential equations. 467-476
• 
  Boaz Keren-Zur:
  HidSecSOFTSUSY: Incorporating effects from hidden sectors in the numerical computation of the MSSM spectrum. 477-484
• 
  Fabian Czerwinski, Lene B. Oddershede:
  TimeSeriesStreaming.vi: LabVIEW program for reliable data streaming of large analog time series. 485-489
• 
  M. Botje:
  QCDNUM: Fast QCD evolution and convolution. 490-532
• 
  José M. Badía, J. L. Movilla, J. I. Climente, Maribel Castillo, Mercedes Marqués, Rafael Mayo, Enrique S. Quintana-Ortí, J. Planelles:
  Large-scale linear system solver using secondary storage: Self-energy in hybrid nanostructures. 533-539

New version announcements

• 
  Ling Ti Kong, Colin Denniston, Martin H. Müser:
  An improved version of the Green's function molecular dynamics method. 540-541
• 
  George Opletal, Timothy C. Petersen, B. O'Malley, I. K. Snook, D. G. McCulloch, Irene Yarovsky:
  HRMC_1.1: Hybrid Reverse Monte Carlo method with silicon and carbon potentials. 542

Volume 182, Number 3, March 2011

Computational physics

• 
  Sixten Boeck, Christoph Freysoldt, A. Dick, L. Ismer, Jörg Neugebauer:
  The object-oriented DFT program library S/PHI/nX. 543-554
• 
  Rodrigo Coura Torres, André Rabello dos Anjos, José Manoel de Seixas, Igor Soloviev:
  Automatizing the online filter test management for a general-purpose particle detector. 555-563
• 
  W. W. Lee, T. G. Jenkins, S. Ethier:
  A generalized weight-based particle-in-cell simulation scheme. 564-569
• 
  N. Mellet, W. A. Cooper, P. Popovich, Laurent Villard, Stephan Brunner:
  Convolution and iterative methods applied to low-frequency waves in 3D warm configurations. 570-589
• 
  David Romero-Laorden, Oscar Martinez-Graullera, Carlos Julian Martín-Arguedas, M. Pérez, Luis G. Ullate:
  Field modelling acceleration on ultrasonic systems using graphic hardware. 590-599
• 
  Miroslav Morhác, Vladislav Matousek:
  Event sorting methods of gamma-ray spectroscopic data. 600-610
• 
  Ulrich Welling, Guido Germano:
  Efficiency of linked cell algorithms. 611-615
• 
  Huajun Zhu, Songhe Song, Yifa Tang:
  Multi-symplectic wavelet collocation method for the nonlinear Schrödinger equation and the Camassa-Holm equation. 616-627
• 
  Néstor Ferrando, M. A. Gosálvez, Joaquín Cerdá, Rafael Gadea Gironés, Kazuo Sato:
  Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces. 628-640
• 
  Viktor K. Decyk, Tajendra V. Singh:
  Adaptable Particle-in-Cell algorithms for graphical processing units. 641-648
• 
  Zhen F. Tian:
  A rational high-order compact ADI method for unsteady convection-diffusion equations. 649-662
• 
  Liang-Wu Cai:
  On the computation of spherical Bessel functions of complex arguments. 663-668
• 
  Jacinto Javier Ibáñez, Vicente Hernández:
  Solving differential matrix Riccati equations by a piecewise-linearized method based on diagonal Padé approximants. 669-678
• 
  T. F. Silva, M. N. Martins:
  Statistical treatment of misalignments in particle accelerators. 679-682
• 
  M. S. Zakynthinaki, R. O. Barakat, C. A. Cordente Martínez, J. Sampedro Molinuevo:
  Stochastic optimization for the detection of changes in maternal heart rate kinetics during pregnancy. 683-691
• 
  Vadim Demchik:
  Pseudo-random number generators for Monte Carlo simulations on ATI Graphics Processing Units. 692-705
• 
  Hanquan Wang, Weibiao Xu:
  An efficient numerical method for simulating the dynamics of coupling Bose-Einstein condensates in optical resonators. 706-718
• 
  A. G. Cunha-Netto, Ronald Dickman:
  Critical behavior of hard-core lattice gases: Wang-Landau sampling with adaptive windows. 719-725
• 
  Binh Trieu, Kristel Michielsen, Hans De Raedt:
  Event-based simulation of light propagation in lossless dielectric media. 726-734

Computer programs in physics

•