Computer simulation of liquids

Efficient free-energy calculations by the simulation of nonequilibrium processes

Computing in Science and Engineering

Simulating complex systems without adjustable parameters

Computing in Science and Engineering

A performance comparison of tree data structures for N-body simulation

Journal of Computational Physics

An empirical performance evaluation of scalable scientific applications

Proceedings of the 2002 ACM/IEEE conference on Supercomputing

CAD challenges in BioMEMS design

Proceedings of the 41st annual Design Automation Conference

Blue Gene: a vision for protein science using a petaflop supercomputer

IBM Systems Journal - Deep computing for the life sciences

ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics

ACM Transactions on Mathematical Software (TOMS)

Developing design tools for biological and biomedical applications of micro- and nano-technology

CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis

Blue matter on blue gene/L: massively parallel computation for biomolecular simulation

CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis

The Monte Carlo Method in Science and Engineering

Computing in Science and Engineering

First Experiences with Group Projects in CSE Education

Computing in Science and Engineering

A family of time-staggered schemes for integrating hybrid DPD models for polymers: algorithms and applications

Journal of Computational Physics

Computing statistics for Hamiltonian systems: A case study

Journal of Computational and Applied Mathematics

A hybrid approach for simulating turbulent collisions of hydrodynamically-interacting particles

Journal of Computational Physics

Efficient constraint dynamics using MILC SHAKE

Journal of Computational Physics

Grid-Supported Simulation of Vapour-Liquid Equilibria with GridSFEA

ICCS '08 Proceedings of the 8th international conference on Computational Science, Part I

Parallel discrete element simulation of poly-dispersed granular material

Advances in Engineering Software

Beyond homogeneous decomposition: scaling long-range forces on Massively Parallel Systems

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis

Simulating hard rigid bodies

Journal of Computational Physics

A new method for locating the global optimum: application of the cutting angle method to molecular structure prediction

ICCS'03 Proceedings of the 2003 international conference on Computational science

Computer simulations of multiparticle-contacts dynamics

ICCS'03 Proceedings of the 1st international conference on Computational science: PartI

Spectrally accurate fast summation for periodic Stokes potentials

Journal of Computational Physics

Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization

Computational Optimization and Applications

GPGPU-based parallel computation: application to molecular dynamics problems

COMPUTE '11 Proceedings of the Fourth Annual ACM Bangalore Conference

Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

Journal of Computational Physics

Spectral accuracy in fast Ewald-based methods for particle simulations

Journal of Computational Physics

On the Existence and the Applications of Modified Equations for Stochastic Differential Equations

SIAM Journal on Scientific Computing

Efficient and validated simulation of crowds for an evacuation assistant

Computer Animation and Virtual Worlds

Nonequilibrium molecular dynamics simulation of shear viscosity by a uniform momentum source-and-sink scheme

Journal of Computational Physics

Optimization of intermolecular interaction potential energy parameters for monte-carlo and molecular dynamics simulations

LSSC'11 Proceedings of the 8th international conference on Large-Scale Scientific Computing

Runtime optimisation approaches for a real-time evacuation assistant

PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part I

Parallel verlet neighbor list algorithm for GPU-optimized MD simulations

Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Water (H2O)m or Benzene (C6H6)n aggregates to solvate the K+?

ICCSA'13 Proceedings of the 13th international conference on Computational Science and Its Applications - Volume 1

The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units

Journal of Computational Physics

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

Journal of Parallel and Distributed Computing

Modeling of laser annealing

Journal of Computational Electronics

Multiscale modelling of irradiation in nanostructures

Journal of Computational Electronics

Efficient techniques for bridging from atomic to mesoscopic scale in phase-field simulations

Journal of Computational Methods in Sciences and Engineering