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
• 
  Igor 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
• 
  Kozo Hoshino, Takuya Yoshikawa, Shuji 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
• 
  Cheng-Chien Chen, Brian Moritz, Chunjing Jia, Steve 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, Meir Lewkowicz, Y. Korniyenko, B. Rosenstein:
  Dynamical approach to ballistic transport in graphene. 112-114
• 
  Nils 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
• 
  Yasutaro 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, Thomas 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
• 
  Gianluca 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, Brendan 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, Stéphane 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