Volume 183, Number 1, January 2012

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  Matthew G. Reuter, Judith C. Hill, Robert J. Harrison: Solving PDEs in irregular geometries with multiresolution methods I: Embedded Dirichlet boundary conditions. 1-7
• 
  Nobuya Maeshima, Ken-ichi Hino: Parallelization of the R-matrix propagation method for the study of intense-laser-driven semiconductor superlattices. 8-14
• 
  Zhijie Xu, Hai Huang, Xiaoyi Li, Paul Meakin: Phase field and level set methods for modeling solute precipitation and/or dissolution. 15-19
• 
  S. Kaprzyk: An algebraic formulation of the simplex linear method for multiple integrals over the d-dimensional domain. 20-25
• 
  Filip A. Sala: Mobile phone as a platform for numerical simulation. 26-29
• 
  Chuan-Hui Zhang, Qiong Ran, Jiang Shen: Structural stability of silicene-like nanotubes. 30-33
• 
  Y. Nakamura, K.-I. Ishikawa, Y. Kuramashi, Tetsuya Sakurai, Hiroto Tadano: Modified block BiCGSTAB for lattice QCD. 34-37
• 
  Nicolas Bigaouette, Edward Ackad, Lora Ramunno: Nonlinear grid mapping applied to an FDTD-based, multi-center 3D Schrödinger equation solver. 38-45
• 
  Jiantong Weng, Tomoyoshi Shimobaba, Minoru Oikawa, Nobuyuki Masuda, Tomoyoshi Ito: Fast recurrence relation for computer-generated-hologram. 46-49
• 
  Tao Jiang, Jie Ouyang, Jin-Lian Ren, Bin-Xin Yang, Xiao-Yang Xu: A mixed corrected symmetric SPH (MC-SSPH) method for computational dynamic problems. 50-62
• 
  L. Gr. Ixaru: Runge-Kutta method with equation dependent coefficients. 63-69
• 
  J. Waltz, T. A. Gianakon: A comparison of mix models for the Rayleigh-Taylor instability. 70-79
• 
  Roberto Barrio, Marcos Rodríguez, Fernando Blesa: Computer-assisted proof of skeletons of periodic orbits. 80-85
• 
  Zhaoxia Chen, Xiong You, Wei Shi, Zhongli Liu: Symmetric and symplectic ERKN methods for oscillatory Hamiltonian systems. 86-98
• 
  M. S. Reis: Models for one-dimensional molecular magnets. 99-105

• 
  Yezhi Lin, Yinping Liu, Zhibin Li: Symbolic computation of analytic approximate solutions for nonlinear differential equations with initial conditions. 106-117
• 
  Jaroslaw Adam Miszczak: Generating and using truly random quantum states in Mathematica. 118-124
• 
  Valerio Novaresio, María García-Camprubí, Salvador Izquierdo, Pietro Asinari, Norberto Fueyo: An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells. 125-146
• 
  Guillem Carles, Carme Ferran, Artur Carnicer, Salvador Bosch: Design and implementation of a scene-dependent dynamically selfadaptable wavefront coding imaging system. 147-154
• 
  Beat Röthlisberger, Jörg Lehmann, Daniel Loss: libCreme: An optimization library for evaluating convex-roof entanglement measures. 155-165
• 
  Nicolas Schunck, J. Dobaczewski, J. McDonnell, W. Satula, J. A. Sheikh, Andrzej Staszczak, M. V. Stoitsov, P. Toivanen: Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis.: (VII) hfodd (v2.49t): A new version of the program. 166-192
• 
  N. D. Gagunashvili: CHICOM: A code of tests for comparing unweighted and weighted histograms and two weighted histograms. 193-196
• 
  A. E. Botha: General R-matrix approach for integrating the multiband k.p equation in layered semiconductor structures. 197-202
• 
  Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio: METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. 203-211

Volume 183, Number 2, February 2012

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  Andrzej Daniluk: Visual modeling for scientific software architecture design. A practical approach. 213-230
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  Carlos Alberto Jara, Francisco Esquembre, Wolfgang Christian, Francisco A. Candelas Herías, Fernando Torres, Sebastián Dormido: A new 3D visualization Java framework based on physics principles. 231-244
• 
  Luciano M. de Andrade Filho, José Manoel de Seixas, Roberto Agostino Vitillo, Brian Thomas Martin: Three-dimensional event visualization for the ATLAS calorimeter. 245-250
• 
  K. Roeller, S. Herminghaus, A. Hager-Fingerle: Sinusoidal shaking in event-driven simulations. 251-260
• 
  Yubao Zhen, Chengbiao Chu: A deformation-fluctuation hybrid method for fast evaluation of elastic constants with many-body potentials. 261-265
• 
  S. A. Galindo-Torres, D. M. Pedroso, D. J. Williams, L. Li: Breaking processes in three-dimensional bonded granular materials with general shapes. 266-277
• 
  Yong Gan, J. K. Chen: A hybrid method for integrated atomistic-continuum simulation of ultrashort-pulsed laser interaction with semiconductors. 278-284
• 
  F. Mahmoudi, Sven Heinemeyer, A. Arbey, A. Bharucha, T. Goto, Thomas Hahn, U. Haisch, S. Kraml, M. Mühlleitner, J. Reuter, P. Skands, P. Slavich: Flavour Les Houches Accord: Interfacing flavour related codes. 285-298
• 
  Georg Bergner, Jaïr Wuilloud: Acceleration of the Arnoldi method and real eigenvalues of the non-Hermitian Wilson-Dirac operator. 299-304
• 
  R. Kleiber, Roman Hatzky: A partly matrix-free solver for the gyrokinetic field equation in three-dimensional geometry. 305-308
• 
  Xuesong Li, Lin Ma: Minimizing binary functions with simulated annealing algorithm with applications to binary tomography. 309-315
• 
  Mingzhe Liu, Xianguo Tuo, Zhe Li, Jianbo Yang, Yang Gao: Asymmetric exclusion process for modeling of information flow. 316-319
• 
  Aleksander A. Stanislavsky, Karina Weron: Numerical scheme for calculating of the fractional two-power relaxation laws in time-domain of measurements. 320-323
• 
  P. M. C. Rourke, S. R. Julian: Numerical extraction of de Haas-van Alphen frequencies from calculated band energies. 324-332

• 
  Ben-Hao Sa, Dai-Mei Zhou, Yu-Liang Yan, Xiao-Mei Li, Sheng-Qin Feng, Bao-Guo Dong, Xu Cai: PACIAE 2.0: An updated parton and hadron cascade model (program) for the relativistic nuclear collisions. 333-346
• 
  S. Kaprzyk: An algebraic formulation and implementation of the tetrahedron linear method for the Brillouin zone integration of spectral functions. 347-362
• 
  T. Hynninen, C. L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A. S. Foster, T. Ala-Nissila: A molecular dynamics implementation of the 3D Mercedes-Benz water model. 363-369
• 
  Ulrich Hohenester, Andreas Trügler: MNPBEM - A Matlab toolbox for the simulation of plasmonic nanoparticles. 370-381
• 
  Joseph E. Curtis, Sindhu Raghunandan, Hirsh Nanda, Susan Krueger: SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints. 382-389
• 
  Dennis M. Elking, Lalith E. Perera, Lee G. Pedersen: HPAM: Hirshfeld partitioned atomic multipoles. 390-397
• 
  Matej Batic, Maria Grazia Pia, Sam J. Cipolla: ISICSoo: A class for the calculation of ionization cross sections from ECPSSR and PWBA theory. 398-404
• 
  Christian Clason, Gregory von Winckel: A general spectral method for the numerical simulation of one-dimensional interacting fermions. 405-417
• 
  N. D. Gagunashvili: CHIWEI: A code of goodness of fit tests for weighted and unweighted histograms. 418-421
• 
  Dominik Stöckinger, Philipp Varso: FeynArts model file for MSSM transition counterterms from DREG to DRED. 422-430
• 
  Sami Heinäsmäki: IONIS: Approximate atomic photoionization intensities. 431-437

• 
  Paolo Barletta: COOL: A code for Dynamic Monte Carlo Simulation of molecular dynamics. 438-439
• 
  Kwang Jin Oh, Ji Hoon Kang, Hun Joo Myung: mm_par2.0: An object-oriented molecular dynamics simulation program parallelized using a hierarchical scheme with MPI and OPENMP. 440-441
• 
  Xian-You Wang, Xing-Gang Wu: A trick to improve the efficiency of generating unweighted Bc events from BCVEGPY. 442-445
• 
  Min Hyung Cho, Wei Cai: Revision of wFMM - A Wideband Fast Multipole Method for the two-dimensional complex Helmholtz equation. 446-447

Volume 183, Number 3, March 2012

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  W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington: Implementing molecular dynamics on hybrid high performance computers - Particle-particle particle-mesh. 449-459
• 
  T. Hahn: The high-energy physicistʼs guide to MathLink. 460-469
• 
  A. A. Kosti, Zacharias A. Anastassi, Tom E. Simos: An optimized explicit Runge-Kutta-Nyström method for the numerical solution of orbital and related periodical initial value problems. 470-479
• 
  C. Espejo, T. Rangel, Yann Pouillon, A. H. Romero, Xavier Gonze: Wannier functions approach to van der Waals interactions in ABINIT. 480-485
• 
  Manamohan Prusty, Jia Ning Leaw, Shan Shang Chong, Siew Ann Cheong: Stochastic boundary conditions for grand-canonical-like molecular dynamics simulations of open systems. 486-496
• 
  Grady Schofield, James R. Chelikowsky, Yousef Saad: A spectrum slicing method for the Kohn-Sham problem. 497-505
• 
  U. D. Jentschura, E. Lötstedt: Numerical calculation of Bessel, Hankel and Airy functions. 506-519
• 
  A. Gray, I. Bethune, R. Kenway, L. Smith, Martyn F. Guest, Christine A. Kitchen, P. Calleja, A. Korzynski, S. Rankin, Mike Ashworth, A. Porter, Ilian T. Todorov, M. Plummer, E. Jones, L. Steenman-Clark, B. Ralston, C. Laughton: Mapping application performance to HPC architecture. 520-529
• 
  A. Kopp, I. Büsching, R. D. Strauss, M. S. Potgieter: A stochastic differential equation code for multidimensional Fokker-Planck type problems. 530-542
• 
  S. Ihnatsenka: Computation of electron quantum transport in graphene nanoribbons using GPU. 543-546
• 
  Qiao-Hong Sui, Zhong-Jun Ding, Rui Jiang, Wei Huang, Duo Sun, Bing-Hong Wang: Slow-to-start effect in two-dimensional traffic flow. 547-551
• 
  Shu-Sen Xie, Su-Cheol Yi, Tae In Kwon: Fourth-order compact difference and alternating direction implicit schemes for telegraph equations. 552-569
• 
  Andrei Bourchtein, Ludmila Bourchtein: A semi-implicit time-splitting scheme for a regional nonhydrostatic atmospheric model. 570-587
• 
  Chunye Gong, Jie Liu, Haowei Huang, Zhenghu Gong: Particle transport with unstructured grid on GPU. 588-593
• 
  B. Roostaei, Walter C. Ermler: Electric dipole transition moments and permanent dipole moments for spin-orbit configuration interaction wave functions. 594-599
• 
  Ram Jiwari, Sapna Pandit, R. C. Mittal: Numerical simulation of two-dimensional sine-Gordon solitons by differential quadrature method. 600-616
• 
  Jan L. Cieslinski, Boguslaw Ratkiewicz: Discrete gradient algorithms of high order for one-dimensional systems. 617-627
• 
  Lorenzo Pardini, Valerio Bellini, Franca Manghi, Claudia Ambrosch-Draxl: First-principles calculation of X-ray dichroic spectra within the full-potential linearized augmented planewave method: An implementation into the Wien2k code. 628-636

• 
  R. Ramis, K. Eidmann, J. Meyer-ter-Vehn, S. Hüller: MULTI-fs - A computer code for laser-plasma interaction in the femtosecond regime. 637-655
• 
  Aldée Charbonnier, Céline Combet, David Maurin: clumpy: A code for γ-ray signals from dark matter structures. 656-668
• 
  I. O. Bespamyatnov, W. L. Rowan, K. T. Liao: ALCBEAM - Neutral beam formation and propagation code for beam-based plasma diagnostics. 669-676
• 
  Gundra Kondayya, Alok Shukla: A Fortran 90 Hartree-Fock program for one-dimensional periodic π-conjugated systems using Pariser-Parr-Pople model. 677-689
• 
  David C. Lonie, Eva Zurek: Identifying duplicate crystal structures: XtalComp, an open-source solution. 690-697
• 
  T. C. Petersen, S. P. Ringer: Local electron tomography using angular variations of surface tangents: Stomo version 2. 698-704
• 
  A. Babaev, Yu. L. Pivovarov: Resonant coherent excitation of hydrogen-like ions planar channeled in a crystal; Transition into the first excited state. 705-710
• 
  Dean Lambert, Alasdair C. Hamilton, George Constable, Harsh Snehanshu, Sharvil Talati, Johannes Courtial: TIM, a ray-tracing program for METATOY research and its dissemination. 711-732
• 
  A. V. Nikitin: An efficient code for calculation of the 6C, 9C and 12C symbols for C3v, Td, and Oh point groups. 733-736
• 
  Bruno Juliá-Díaz, Tobias Graß: Strongdeco: Expansion of analytical, strongly correlated quantum states into a many-body basis. 737-745
• 
  Mikolaj Chojnacki, Adam Kisiel, Wojciech Florkowski, Wojciech Broniowski: THERMINATOR 2: THERMal heavy IoN generATOR 2. 746-773
• 
  Debottam Das, Ulrich Ellwanger, Ana M. Teixeira: NMSDECAY: A Fortran code for supersymmetric particle decays in the Next-to-Minimal Supersymmetric Standard Model. 774-779
• 
  Thomas Fischbacher: Numerical tools to validate stationary points of SO(8)-gauged N=8D=4 supergravity. 780-784
• 
  Benjamin C. Allanach, C. H. Kom, M. Hanussek: Computation of neutrino masses in R-parity violating supersymmetry: SOFTSUSY3.2. 785-793
• 
  Amparo Gil, Javier Segura, Nico M. Temme: An improved algorithm and a Fortran 90 module for computing the conical function f^m_-1/2+iτ(x). 794-799
• 
  Tomasz Dziubak, Jacek Matulewski: An object-oriented implementation of a solver of the time-dependent Schrödinger equation using the CUDA technology. 800-812
• 
  Stefan Weinzierl: The SISCone jet algorithm optimised for low particle multiplicities. 813-820
• 
  N. Davidson, G. Nanava, T. Przedzinski, Elzbieta Richter-Was, Z. Was: Universal interface of TAUOLA: Technical and physics documentation. 821-843

• 
  Evgeny Z. Liverts, Nir Barnea: S-states of helium-like ions. 844-845
• 
  Daniel Maître: Extension of HPL to complex arguments. 846

Volume 183, Number 4, April 2012

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  Juraci P. Reis, Artur F. Menezes, Edmilson M. Souza, Alessandro Facure, Jose A. C. C. Medeiros, Ademir X. Silva: Dose optimization in ¹²⁵I permanent prostate seed implants using the Monte Carlo method. 847-852
• 
  C. Bonati, G. Cossu, M. D'Elia, P. Incardona: QCD simulations with staggered fermions on GPUs. 853-863
• 
  Francisco de la Hoz, Fernando Vadillo: Numerical simulation of the N-dimensional sine-Gordon equation via operational matrices. 864-879
• 
  Mathias Winkel, Robert Speck, Helge Hübner, Lukas Arnold, Rolf Krause, Paul Gibbon: A massively parallel, multi-disciplinary Barnes-Hut tree code for extreme-scale N-body simulations. 880-889
• 
  Nathan Schmid, Clara D. Christ, Markus Christen, Andreas P. Eichenberger, Wilfred F. van Gunsteren: Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. 890-903
• 
  Cristóbal Bertoglio, Boris N. Khoromskij: Low-rank quadrature-based tensor approximation of the Galerkin projected Newton/Yukawa kernels. 904-912
• 
  Feng-Gong Lang, Xiao-Ping Xu: Quintic B-spline collocation method for second order mixed boundary value problem. 913-921
• 
  F. Merz, C. Kowitz, E. Romero, Jose E. Roman, Frank Jenko: Multi-dimensional gyrokinetic parameter studies based on eigenvalue computations. 922-930
• 
  V. Ogarko, S. Luding: A fast multilevel algorithm for contact detection of arbitrarily polydisperse objects. 931-936
• 
  Sergei Kucherenko, Stefano Tarantola, Paola Annoni: Estimation of global sensitivity indices for models with dependent variables. 937-946
• 
  J. Seebacher, A. Kendl: Towards a unified linear kinetic transport model with the trace ion module for EIRENE. 947-959
• 
  A. Buckley, A. Shilton, M. J. White: Fast supersymmetry phenomenology at the Large Hadron Collider using machine learning techniques. 960-970
• 
  M. Fitzgerald, J. Khachan: A 2-D PIC/MC/Vlasov method for electrostatic fusion discharges. 971-979
• 
  Eiji Tsuchida, Yoong-Kee Choe: Iterative diagonalization of symmetric matrices in mixed precision and its application to electronic structure calculations. 980-985
• 
  Christian Ringl, Herbert M. Urbassek: A LAMMPS implementation of granular mechanics: Inclusion of adhesive and microscopic friction forces. 986-992
• 
  C. A. Duarte: Compact expressions for the magnetoresistance and the electron/hole density of states under the application of magnetic fields. 993-997
• 
  Yueh-Cheng Kuo, Shih-Feng Shieh, Weichung Wang: Rotational quotient procedure: A tracking control continuation method for PDEs on radially symmetric domains. 998-1001

• 
  M. Hirai, S. Kumano: Numerical solution of Q² evolution equations for fragmentation functions. 1002-1013
• 
  Shigeru Odaka, Yoshimasa Kurihara: GR@PPA 2.8: Initial-state jet matching for weak-boson production processes at hadron collisions. 1014-1028
• 
  R. J. Casperson: IBAR: Interacting boson model calculations for large system sizes. 1029-1035
• 
  M. Kachelrieß, S. Ostapchenko, R. Tomàs: ELMAG: A Monte Carlo simulation of electromagnetic cascades on the extragalactic background light and in magnetic fields. 1036-1043
• 
  K. T. Vu, G. F. Jefferson, J. Carminati: Finding higher symmetries of differential equations using the MAPLE package DESOLVII. 1044-1054
• 
  I. V. Grossu, C. Besliu, Al. Jipa, E. Stan, T. Esanu, D. Felea, C. C. Bordeianu: Code C# for chaos analysis of relativistic many-body systems with reactions. 1055-1059

• 
  Tobias Huber, Daniel Maître: HypExp 2, expanding hypergeometric functions about half-integer parameters. 1060

Volume 183, Number 5, May 2012

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  Stefano Tarantola, William Becker, Dirk Zeitz: A comparison of two sampling methods for global sensitivity analysis. 1061-1072
• 
  Omar Awile, Ferit Büyükkeçeci, Sylvain Reboux, Ivo F. Sbalzarini: Fast neighbor lists for adaptive-resolution particle simulations. 1073-1081
• 
  Yiqiang Xu, Luming Zhang: Alternating direction implicit method for solving two-dimensional cubic nonlinear Schrödinger equation. 1082-1093
• 
  Takayuki Umeda, Yasuhiro Nariyuki, Daichi Kariya: A non-oscillatory and conservative semi-Lagrangian scheme with fourth-degree polynomial interpolation for solving the Vlasov equation. 1094-1100
• 
  Omar Ramadan: Unified matrix-exponential FDTD formulations for modeling electrically and magnetically dispersive materials. 1101-1106
• 
  A. Bierwage, C. Di Troia, Sergio Briguglio, Gregorio Vlad: Orbit-based representation of equilibrium distribution functions for low-noise initialization of kinetic simulations of toroidal plasmas. 1107-1123

• 
  Tomoyoshi Shimobaba, Jiantong Weng, Takahiro Sakurai, Naohisa Okada, Takashi Nishitsuji, Naoki Takada, Atsushi Shiraki, Nobuyuki Masuda, Tomoyoshi Ito: Computational wave optics library for C++: CWO++ library. 1124-1138
• 
  Constantinos Voglis, Konstantinos E. Parsopoulos, Dimitris G. Papageorgiou, Isaac E. Lagaris, Michael N. Vrahatis: MEMPSODE: A global optimization software based on hybridization of population-based algorithms and local searches. 1139-1154

Volume 183, Number 6, June 2012

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  Yukihiro Komura, Yutaka Okabe: GPU-based Swendsen-Wang multi-cluster algorithm for the simulation of two-dimensional classical spin systems. 1155-1161
• 
  Wanjie Xiong, Fan Zhong, Shuangli Fan: Positive specific-heat critical exponent of a three-dimensional three-state random-bond Potts model. 1162-1171
• 
  Fengshun Lu, Junqiang Song, Fukang Yin, Xiaoqian Zhu: Performance evaluation of hybrid programming patterns for large CPU/GPU heterogeneous clusters. 1172-1181
• 
  D. Melazzi, D. Curreli, M. Manente, J. Carlsson, D. Pavarin: SPIREs: A Finite-Difference Frequency-Domain electromagnetic solver for inhomogeneous magnetized plasma cylinders. 1182-1191
• 
  Xingang Ren, Zhixiang Huang, Xianliang Wu, Silong Lu, Hui Wang, Lei Wu, Shen Li: High-order unified symplectic FDTD scheme for the metamaterials. 1192-1200
• 
  Céline Degrande, Claude Duhr, Benjamin Fuks, David Grellscheid, Olivier Mattelaer, Thomas Reiter: UFO - The Universal FeynRules Output. 1201-1214
• 
  C. Alexandrou, K. Hadjiyiannakou, G. Koutsou, A. O'Cais, A. Strelchenko: Evaluation of fermion loops applied to the calculation of the η mass and the nucleon scalar and electromagnetic form factors. 1215-1224
• 
  Kun-Mo Lin, Chieh-Tsan Hung, Feng-Nan Hwang, Matthew R. Smith, Y.-W. Yang, Jong-Shinn Wu: Development of a parallel semi-implicit two-dimensional plasma fluid modeling code using finite-volume method. 1225-1236
• 
  Janis Timoshenko, Alexei Kuzmin, Juris Purans: Reverse Monte Carlo modeling of thermal disorder in crystalline materials from EXAFS spectra. 1237-1245
• 
  Michaël Magoga, Fabien Archambault, Jorge I. Cerdá: Nt_STM: A step forward in Scanning Tunneling Microscopy (STM) simulations. 1246-1249
• 
  Wei Shi, Xinyuan Wu: On symplectic and symmetric ARKN methods. 1250-1258
• 
  Reza Mokhtari, Majid Mohseni: A meshless method for solving mKdV equation. 1259-1268

• 
  Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, Steven G. Louie: BerkeleyGW: A massively parallel computer package for the calculation of the quasiparticle and optical properties of materials and nanostructures. 1269-1289
• 
  Markus Q. Huber, Jens Braun: Algorithmic derivation of functional renormalization group equations and Dyson-Schwinger equations. 1290-1320
• 
  Albert Deuzeman, Siebren Reker, Carsten Urbach: Lemon: An MPI parallel I/O library for data encapsulation using LIME. 1321-1335
• 
  Simon Catterall, Anosh Joseph: An object oriented code for simulating supersymmetric Yang-Mills theories. 1336-1353
• 
  Pawel Jakubczyk, Andrzej Wal, D. Jakubczyk, Tadeusz Lulek: Computer implementation of the Kerov-Kirillov-Reshetikhin algorithm. 1354-1362
• 
  H. P. Nilles, S. Ramos-Sánchez, P. K. S. Vaudrevange, A. Wingerter: The orbifolder: A tool to study the low-energy effective theory of heterotic orbifolds. 1363-1380
• 
  András Vukics: C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems. 1381-1396
• 
  A. Deveikis: A computer program for two-particle intrinsic coefficients of fractional parentage. 1397-1401

Volume 183, Number 7, July 2012

• 
  François Fillion-Gourdeau, Emmanuel Lorin, André D. Bandrauk: Numerical solution of the time-dependent Dirac equation in coordinate space without fermion-doubling. 1403-1415
• 
  Massimo Bernaschi, Massimiliano Fatica, Giorgio Parisi, L. Parisi: Multi-GPU codes for spin systems simulations. 1416-1421
• 
  M. Hutchinson, M. Widom: VASP on a GPU: Application to exact-exchange calculations of the stability of elemental boron. 1422-1426
• 
  Haokai Lu, Peng Li: Stochastic projective methods for simulating stiff chemical reacting systems. 1427-1442
• 
  Andreas Mayer, Hanna Salopaasi, Katariina Pussi, Renee D. Diehl: A novel method for the extraction of intensity-energy spectra from low-energy electron diffraction patterns. 1443-1447

• 
  I. Akushevich, O. F. Filoti, A. Ilyichev, N. Shumeiko: Monte Carlo generator ELRADGEN 2.0 for simulation of radiative events in elastic ep-scattering of polarized particles. 1448-1467
• 
  J. M. Cherfils, G. Pinon, E. Rivoalen: JOSEPHINE: A parallel SPH code for free-surface flows. 1468-1480
• 
  Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp: MH²c: Characterization of major histocompatibility α-helices - an information criterion approach. 1481-1490
• 
  Benjamin Lindner, Jeremy C. Smith: Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers. 1491-1501
• 
  C. Schimeczek, D. Engel, G. Wunner: A highly optimized code for calculating atomic data at neutron star magnetic field strengths using a doubly self-consistent Hartree-Fock-Roothaan method. 1502-1510
• 
  Luiz C. Mostaço-Guidolin, Rafael B. Frigori, Leonid Ruchko, Ricardo M. O. Galvão: SCTE: An open-source Perl framework for testing equipment control and data acquisition. 1511-1518
• 
  Feng Feng: A recursive method to calculate UV-divergent parts at one-loop level in dimensional regularization. 1519-1524
• 
  S. Fritzsche: The Ratip program for relativistic calculations of atomic transition, ionization and recombination properties. 1525-1559

• 
  Daniel J. Sindhikara: Modular reweighting software for statistical mechanical analysis of biased equilibrium data. 1560-1561

Volume 183, Number 8, August 2012

• 
  Andrey Asadchev, Mark S. Gordon: Mixed-precision evaluation of two-electron integrals by Rys quadrature. 1563-1567
• 
  Junqi Yin, D. P. Landau: Massively parallel Wang-Landau sampling on multiple GPUs. 1568-1573
• 
  Su Do Yi, Beom Jun Kim: Force correlations in molecular and stochastic dynamics. 1574-1577
• 
  Ezequiel E. Ferrero, Juan Pablo De Francesco, Nicolás Wolovick, Sergio A. Cannas: q-state Potts model metastability study using optimized GPU-based Monte Carlo algorithms. 1578-1587
• 
  Yan Zhao, Xuesong Li, Lin Ma: Multidimensional Monte Carlo model for two-photon laser-induced fluorescence and amplified spontaneous emission. 1588-1595
• 
  K. C. Tseng, T. C. Kuo, S. C. Lin, C. C. Su, J. S. Wu: Simulations of subsonic vortex-shedding flow past a 2D vertical plate in the near-continuum regime by the parallelized DSMC code. 1596-1608
• 
  Liquan Mei, Yaping Chen: Numerical solutions of RLW equation using Galerkin method with extrapolation techniques. 1609-1616
• 
  R.-L. Jiang, C. Fang, P.-F. Chen: A new MHD code with adaptive mesh refinement and parallelization for astrophysics. 1617-1633
• 
  Adnane Hamiaz, Rudy Klein, Xavier Ferrieres, Olivier Pascal, Jean-Pierre Boeuf, Jean-Rene Poirier: Finite Volume Time Domain modelling of microwave breakdown and plasma formation in a metallic aperture. 1634-1640
• 
  Andrea Colagrossi, B. Bouscasse, M. Antuono, S. Marrone: Particle packing algorithm for SPH schemes. 1641-1653
• 
  Hanz Y. Ramírez, Alejandro Santana: Two interacting electrons confined in a 3D parabolic cylindrically symmetric potential, in presence of axial magnetic field: A finite element approach. 1654-1657
• 
  Xi Chen, Z. J. Ding: Solving extra-high-order Rubik's Cube problem by a dynamic simulated annealing. 1658-1663
• 
  Nobuko Ohba, Shuji Ogata, Takahisa Kouno, Tomoyuki Tamura, Ryo Kobayashi: Linear scaling algorithm of real-space density functional theory of electrons with correlated overlapping domains. 1664-1673
• 
  Edoardo Di Napoli, Stefan Blügel, Paolo Bientinesi: Correlations in sequences of generalized eigenproblems arising in Density Functional Theory. 1674-1682
• 
  Georgios Kalantzis, Dimitrios Emfietzoglou, Panagiotis E. Hadjidoukas: A unified spatio-temporal parallelization framework for accelerated Monte Carlo radiobiological modeling of electron tracks and subsequent radiation chemistry. 1683-1695
• 
  Asimina Maniopoulou, Erlend R. M. Davidson, Ricardo Grau-Crespo, Aron Walsh, Ian J. Bush, C. Richard A. Catlow, Scott M. Woodley: Introducing k-point parallelism into VASP. 1696-1701
• 
  B. Pekmen, M. Tezer-Sezgin: Differential quadrature solution of nonlinear Klein-Gordon and sine-Gordon equations. 1702-1713
• 
  Isaac Gabriel Salib, Shimon Haber: Is the cutoff radius in DPD simulations with a fluid of constant density arbitrary? 1714-1718
• 
  J. A. Heikkinen, T. Korpilo, S. J. Janhunen, T. P. Kiviniemi, S. Leerink, F. Ogando: Interpolation for momentum conservation in 3D toroidal gyrokinetic particle simulation of plasmas. 1719-1727
• 
  Pengfei Wei, Zhenzhou Lu, Wenrui Hao, Jun Feng, Bintuan Wang: Efficient sampling methods for global reliability sensitivity analysis. 1728-1743
• 
  Gary Yuan, François Gygi: A distributed approach to verification and validation of electronic structure simulation data using ESTEST. 1744-1748
• 
  Gui-Yang Huang, Chong-Yu Wang, Jian-Tao Wang: Detailed check of the LDA + U and GGA + U corrected method for defect calculations in wurtzite ZnO. 1749-1752
• 
  Elena Eremina, Yuri Eremin, Natalia Grishina, Thomas Wriedt: New scheme of the Discrete Sources Method for investigation of a near field enhancement by coupled particles. 1753-1759

• 
  J. R. Johansson, P. D. Nation, Franco Nori: QuTiP: An open-source Python framework for the dynamics of open quantum systems. 1760-1772
• 
  A. Jablonski: An effective algorithm for calculating the Chandrasekhar function. 1773-1782
• 
  Moti Umansky, Daphne Weihs: Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-square displacement. 1783-1792
• 
  Carsten Svaneborg: LAMMPS framework for dynamic bonding and an application modeling DNA. 1793-1802
• 
  Jingjing Zheng, Steven L. Mielke, Kenneth L. Clarkson, Donald G. Truhlar: MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity. 1803-1812
• 
  T. Pálmai: Regularization of multi-soliton form factors in sine-Gordon model. 1813-1821
• 
  A. Arbey: AlterBBN: A program for calculating the BBN abundances of the elements in alternative cosmologies. 1822-1831
• 
  M. F. Ciappina, T. Kirchner: SymbMat: Symbolic computation of quantum transition matrix elements. 1832-1840

• 
  Russell M. Pitzer: Atomic self-consistent-field program by the basis set expansion method: Columbus version. 1841-1842
• 
  Christian Clason, Gregory von Winckel: A general spectral method for the numerical simulation of one-dimensional interacting fermions. 1843-1844

Volume 183, Number 9, September 2012

• 
  Barbara Schmidt, Matthias Steinhauser: CRunDec: A C++ package for running and decoupling of the strong coupling and quark masses. 1845-1848
• 
  Wanxiang Feng, Jun Wen, Jinjian Zhou, Di Xiao, Yugui Yao: First-principles calculation of Z₂ topological invariants within the FP-LAPW formalism. 1849-1859
• 
  Luigi Brugnano, Felice Iavernaro, Donato Trigiante: A two-step, fourth-order method with energy preserving properties. 1860-1868
• 
  Elizabeth Williams, James Tickner: Efficient Monte Carlo simulation of coincidence effects in radioisotope decays including y-y angular correlations. 1869-1876
• 
  Jose Luis Velasco, Andrés Bustos, Francisco Castejón, L. A. Fernandez, Victor Martin-Mayor, Alfonso Tarancón: ISDEP: Integrator of stochastic differential equations for plasmas. 1877-1883
• 
  Topi Siro, Ari Harju: Exact diagonalization of the Hubbard model on graphics processing units. 1884-1889
• 
  Saeed Ovaysi, Mohammad Piri: Multi-GPU acceleration of direct pore-scale modeling of fluid flow in natural porous media. 1890-1898
• 
  Tomasz M. Gwizdalla: The hybrid algorithm for the study of geometric configurations of 2D clusters of uniformly charged classical particles. 1899-1903
• 
  Alberto Talamo, Zhaopeng Zhong, Yousry Gohar: Monte Carlo and deterministic calculation of the Bell and Glasstone spatial correction factor. 1904-1910
• 
  Kevin Jorissen, Fernando D. Vila, John J. Rehr: A high performance scientific cloud computing environment for materials simulations. 1911-1919
• 
  Ydalia Delgado Mercado, Hans Gerd Evertz, Christof Gattringer: Worm algorithms for the 3-state Potts model with magnetic field and chemical potential. 1920-1927
• 
  André Barka, Nicolas Douchin: Asymptotic simplifications for hybrid BEM/GO/PO/PTD techniques based on a Generalized Scattering Matrix approach. 1928-1936
• 
  Siham Tabik, Luis F. Romero, Petar Mimica, Oscar G. Plata, Emilio L. Zapata: VLBI-resolution radio-map algorithms: Performance analysis of different levels of data-sharing on multi-socket, multi-core architectures. 1937-1946
• 
  Enying Li, Hu Wang, Guangyao Li: High dimensional model representation (HDMR) coupled intelligent sampling strategy for nonlinear problems. 1947-1955
• 
  Haochen Li, Jianqiang Sun: A new multi-symplectic scheme for the generalized Kadomtsev-Petviashvili equation. 1956-1965
• 
  M. Gherardi, T. Jourdan, S. Le Bourdiec, G. Bencteux: Hybrid deterministic/stochastic algorithm for large sets of rate equations. 1966-1973
• 
  S. Dalena, P. Chuychai, R. L. Mace, A. Greco, G. Qin, W. H. Matthaeus: Streamline generation code for particle dynamics description in numerical models of turbulence. 1974-1985
• 
  S. Maeyama, A. Ishizawa, Tomohiko Watanabe, N. Nakajima, S. Tsuji-Iio, H. Tsutsui: A hybrid method of semi-Lagrangian and additive semi-implicit Runge-Kutta schemes for gyrokinetic Vlasov simulations. 1986-1992
• 
  Waseem Kamleh, Mike Peardon: Polynomial filtered HMC-an algorithm for lattice QCD with dynamical quarks. 1993-2000
• 
  Evandro F. da Silva, Mário J. de Oliveira: Two versions of the threshold contact model in two dimensions. 2001-2005

• 
  Carroll L. Wainwright: CosmoTransitions: Computing cosmological phase transition temperatures and bubble profiles with multiple fields. 2006-2013
• 
  Timothy J. McIntyre, Alexis I. Bishop: Fringe - A Java-based finite fringe analysis package. 2014-2018

• 
  J. Avellar, L. G. S. Duarte, L. A. C. P. da Mota, N. de Melo, J. E. F. Skea: The Ndynamics package - Numerical analysis of dynamical systems and the fractal dimension of boundaries. 2019-2020
• 
  Dusan Vudragovic, Ivana Vidanovic, Antun Balaz, Paulsamy Muruganandam, Sadhan K. Adhikari: C programs for solving the time-dependent Gross-Pitaevskii equation in a fully anisotropic trap. 2021-2025

Volume 183, Number 10, October 2012

• 
  Masaharu Matsumoto, Yoshihiro Kajimura, Hideyuki Usui, Ikkoh Funaki, Iku Shinohara: Application of a total variation diminishing scheme to electromagnetic hybrid particle-in-cell plasma simulation. 2027-2034
• 
  N. Dubray, D. Regnier: Numerical search of discontinuities in self-consistent potential energy surfaces. 2035-2041
• 
  D. Viganò, J. A. Pons, J. A. Miralles: A new code for the Hall-driven magnetic evolution of neutron stars. 2042-2053
• 
  Kevin B. Daly, Jay B. Benziger, Pablo G. Debenedetti, Athanassios Z. Panagiotopoulos: Massively parallel chemical potential calculation on graphics processing units. 2054-2062
• 
  Yanchao Wang, Jian Lv, Li Zhu, Yanming Ma: CALYPSO: A method for crystal structure prediction. 2063-2070
• 
  Cathal Ó Broin, L. A. A. Nikolopoulos: An OpenCL implementation for the solution of the time-dependent Schrödinger equation on GPUs and CPUs. 2071-2080
• 
  Bokui Chen, Chuanfei Dong, Yike Liu, Wei Tong, Wenyao Zhang, Jie Liu, Binghong Wang: Real-time information feedback based on a sharp decay weighted function. 2081-2088
• 
  Alejandro León: An efficient model for studying the dynamics of frustrated systems. 2089-2097
• 
  Ram K. Pandey, Om P. Singh, Vipul K. Baranwal, Manoj P. Tripathi: An analytic solution for the space-time fractional advection-dispersion equation using the optimal homotopy asymptotic method. 2098-2106
• 
  Hyun Geun Lee, Junseok Kim: An efficient and accurate numerical algorithm for the vector-valued Allen-Cahn equations. 2107-2115
• 
  H. Kohno, J. R. Myra, D. A. D'Ippolito: A finite element procedure for radio-frequency sheath-plasma interactions in the ion cyclotron range of frequencies. 2116-2127
• 
  Alexei Deinega, Sajeev John: Finite difference discretization of semiconductor drift-diffusion equations for nanowire solar cells. 2128-2135
• 
  Fukuko Yuasa, Elise de Doncker, Nobuyuki Hamaguchi, Tadashi Ishikawa, K. Kato, Yoshimasa Kurihara, Junpei Fujimoto, Yoshimitsu Shimizu: Numerical computation of two-loop box diagrams with masses. 2136-2144

• 
  Bernd A. Berg, Hao Wu: Fortran code for SU(3) lattice gauge theory with and without MPI checkerboard parallelization. 2145-2157
• 
  Feng Feng: $Apart: A generalized Mathematica Apart function. 2158-2164
• 
  Florian Staub, Thorsten Ohl, Werner Porod, Christian Speckner: A tool box for implementing supersymmetric models. 2165-2206
• 
  Lutz Foucar, Anton Barty, Nicola Coppola, Robert Hartmann, Peter Holl, Uwe Hoppe, Stephan Kassemeyer, Nils Kimmel, Jochen Küpper, Mirko Scholz, Simone Techert, Thomas A. White, Lothar Strüder, Joachim Ullrich: CASS - CFEL-ASG software suite. 2207-2213
• 
  Alfonso García-Parrado Gómez-Lobo, José M. Martín-García: Spinors: A Mathematica package for doing spinor calculus in General Relativity. 2214-2225
• 
  Gonzalo Alvarez: Implementation of the SU(2) Hamiltonian symmetry for the DMRG algorithm. 2226-2232
• 
  Victor Liu, Shanhui Fan: S⁴ : A free electromagnetic solver for layered periodic structures. 2233-2244
• 
  A. Buraczewski, M. Stobinska: Numerical model for macroscopic quantum superpositions based on phase-covariant quantum cloning. 2245-2253
• 
  Priscila de Aquino, William Link, Fabio Maltoni, Olivier Mattelaer, Tim Stelzer: ALOHA: Automatic libraries of helicity amplitudes for Feynman diagram computations. 2254-2263
• 
  Piotr Magierski, Gabriel Wlazlowski: LINPRO: Linear inverse problem library for data contaminated by statistical noise. 2264-2271
• 
  Miguel A. L. Marques, Micael J. T. Oliveira, Tobias Burnus: Libxc: A library of exchange and correlation functionals for density functional theory. 2272-2281
• 
  Daniel Kuchelmeister, Thomas Müller, Marco Ament, Günter Wunner, Daniel Weiskopf: GPU-based four-dimensional general-relativistic ray tracing. 2282-2290
• 
  Amna Noreen, Kåre Olaussen: High precision series solutions of differential equations: Ordinary and regular singular points of second order ODEs. 2291-2297
• 
  Renato M. Fonseca: Calculating the renormalisation group equations of a SUSY model with Susyno. 2298-2306
• 
  H. Hluchá, H. Eberl, W. Frisch: SFOLD - A program package for calculating two-body sfermion decays at full one-loop level in the MSSM. 2307-2312

• 
  J. Avellar, L. G. S. Duarte, L. A. C. P. da Mota: PSsolver: A Maple implementation to solve first order ordinary differential equations with Liouvillian solutions. 2313-2314

Volume 183, Number 11, November 2012

• 
  Tarik Hadzibeganovic, F. Welington S. Lima, Dietrich Stauffer: Evolution of tag-mediated altruistic behavior in one-shot encounters on large-scale complex networks. 2315-2321
• 
  Mario Arioli, Serge Gratton: Linear regression models, least-squares problems, normal equations, and stopping criteria for the conjugate gradient method. 2322-2336
• 
  T. V. S. Sekhar, B. Hema Sundar Raju: An efficient higher order compact scheme to capture heat transfer solutions in spherical geometry. 2337-2345
• 
  P. J. Knight, A. Thyagaraja, T. D. Edwards, J. Hein, M. Romanelli, K. G. McClements: CENTORI: A global toroidal electromagnetic two-fluid plasma turbulence code. 2346-2363
• 
  Ki-Hwan Kim, Q.-Han Park: Overlapping computation and communication of three-dimensional FDTD on a GPU cluster. 2364-2369
• 
  Alan R. Levin, Deyin Zhang, Eric Polizzi: FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem. 2370-2375
• 
  Shin-ichi Satake, Hajime Yoshimori, Takayuki Suzuki: Optimizations of a GPU accelerated heat conduction equation by a programming of CUDA Fortran from an analysis of a PTX file. 2376-2385
• 
  Fernando Casas, Ander Murua, Mladen Nadinic: Efficient computation of the Zassenhaus formula. 2386-2391
• 
  Venera Khoromskaia, D. Andrae, Boris N. Khoromskij: Fast and accurate 3D tensor calculation of the Fock operator in a general basis. 2392-2404
• 
  M. Joulaian, A. Pishevar, S. Khajepor, F. Schmid, Y. Afshar: A new algorithm for simulating flows of conducting fluids in the presence of electric fields. 2405-2412
• 
  Ram Jiwari: A Haar wavelet quasilinearization approach for numerical simulation of Burgers' equation. 2413-2423
• 
  Tiziano Leidi, Giulio Scocchi, Loris Grossi, Simone Pusterla, Claudio D'Angelo, Jean-Philippe Thiran, Alberto Ortona: Computing effective properties of random heterogeneous materials on heterogeneous parallel processors. 2424-2433
• 
  Frederick Ira Moxley III, Tim Byrnes, Fumitaka Fujiwara, Weizhong Dai: A generalized finite-difference time-domain quantum method for the N-body interacting Hamiltonian. 2434-2440

• 
  Markus Q. Huber, Mario Mitter: CrasyDSE: A framework for solving Dyson-Schwinger equations. 2441-2457
• 
  Werner Porod, Florian Staub: SPheno 3.1: extensions including flavour, CP-phases and models beyond the MSSM. 2458-2469
• 
  A. A. Azooz, S. H. Al-Nia'emi, M. A. Al-Jubbori: A parameterization of nuclear track profiles in CR-39 detector. 2470-2479
• 
  Anton Nazarov: Affine.m - Mathematica package for computations in representation theory of finite-dimensional and affine Lie algebras. 2480-2493

• 
  Ján Busa Jr., Shura Hayryan, Ming-Chya Wu, Ján Busa, Chin-Kun Hu: ARVO-CL: The OpenCL version of the ARVO package - An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations. 2494-2497

Volume 183, Number 12, December 2012

• 
  Beatrice Paternoster: Present state-of-the-art in exponential fitting. A contribution dedicated to Liviu Ixaru on his 70th birthday. 2499-2512

• 
  Liang Chen, Cheng Lv, Xunya Jiang: A re-formulation of the transfer matrix method for calculating wave-functions in higher dimensional disordered open systems. 2513-2518
• 
  Valentin V. Karasiev, Samuel B. Trickey: Issues and challenges in orbital-free density functional calculations. 2519-2527
• 
  Marcelo Fiori, J. E. Miraglia: New approach for approximating the continuum wave function by Gaussian basis set. 2528-2534
• 
  Suzanne Varet, Sidonie Lefebvre, Gérard Durand, Antoine Roblin, Serge Cohen: Effective discrepancy and numerical experiments. 2535-2541
• 
  C. S. Bresolin, A. A. M. Oliveira: An algorithm based on collision theory for the lattice Boltzmann simulation of isothermal mass diffusion with chemical reaction. 2542-2549
• 
  Kun-Mo Lin, M.-H. Hu, Chieh-Tsan Hung, Jong-Shinn Wu, F.-N. Hwang, Y.-S. Chen, G. Cheng: A parallel hybrid numerical algorithm for simulating gas flow and gas discharge of an atmospheric-pressure plasma jet. 2550-2560
• 
  Gabriel Voitcu, Marius Echim, Richard Marchand: Comparative study of forward and backward test-kinetic simulation approaches. 2561-2569
• 
  M. Antuono, Andrea Colagrossi, S. Marrone: Numerical diffusive terms in weakly-compressible SPH schemes. 2570-2580
• 
  Alejandro Soba, Edgar Alejandro Bea, Guillaume Houzeaux, Hadrien Calmet, José María Cela: Real-space density functional theory and time dependent density functional theory using finite/infinite element methods. 2581-2588
• 
  E. Hirvijoki, A. Snicker, T. Korpilo, P. Lauber, E. Poli, M. Schneller, T. Kurki-Suonio: Alfvén Eigenmodes and Neoclassical tearing modes for orbit-following implementations. 2589-2593
• 
  Santos B. Yuste, Joaquín Quintana-Murillo: A finite difference method with non-uniform timesteps for fractional diffusion equations. 2594-2600
• 
  R. Krivec: Numerical regularization of Klauder effect in QLM. 2601-2607
• 
  Jean-Luc Fattebert, David F. Richards, James N. Glosli: Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions. 2608-2615
• 
  Suman Sinha: Performance of Wang-Landau algorithm in lattice model of liquid crystals. 2616-2621

• 
  Darko Veberic: Lambert W function for applications in physics. 2622-2628
• 
  T. A. Heltemes, G. A. Moses: BADGER v1.0: A Fortran equation of state library. 2629-2646

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