Understanding Molecular Simulation

Efficient free-energy calculations by the simulation of nonequilibrium processes

Computing in Science and Engineering

Computation within the auxiliary field approach

Journal of Computational Physics

Statistical error in particle simulations of hydrodynamic phenomena

Journal of Computational Physics

Improved algorithm for geometry optimisation using damped molecular dynamics

Journal of Computational Physics

A new technique to calculate dipolar energy and its implementation onto an application specific processor

Proceedings of the 1st conference on Computing frontiers

Measurement bias of fluid velocity in molecular simulations

Journal of Computational Physics

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

ACM Transactions on Mathematical Software (TOMS)

Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules

Journal of Computational Physics

Packing a trunk: now with a twist!

Proceedings of the 2005 ACM symposium on Solid and physical modeling

Heterogeneous multiscale method for the modeling of complex fluids and micro-fluidics

Journal of Computational Physics

Elaborating transition interface sampling methods

Journal of Computational Physics

Fluid Simulation with the Geometric Cluster Monte Carlo Algorithm

Computing in Science and Engineering

An Eclipse-based environment for molecular simulation

eclipse '05 Proceedings of the 2005 OOPSLA workshop on Eclipse technology eXchange

Far-field approximation for hydrodynamic interactions in parallel-wall geometry

Journal of Computational Physics

Modelling multi-viscosity systems with dissipative particle dynamics

Journal of Computational Physics

Blue matter: approaching the limits of concurrency for classical molecular dynamics

Proceedings of the 2006 ACM/IEEE conference on Supercomputing

Density distribution for a dense hard-sphere gas in micro/nano-channels: Analytical and simulation results

Journal of Computational Physics

Analytical first derivatives of the RE-squared interaction potential

Journal of Computational Physics

A Complexity O(1) priority queue for event driven molecular dynamics simulations

Journal of Computational Physics

Using the method of weighted residuals to compute potentials of mean force

Journal of Computational Physics

Analytical and numerical study of coupled atomistic-continuum methods for fluids

Journal of Computational Physics

A seamless approach towards stochastic modeling: Sparse grid collocation and data driven input models

Finite Elements in Analysis and Design

General purpose molecular dynamics simulations fully implemented on graphics processing units

Journal of Computational Physics

Biomolecular committor probability calculation enabled by processing in network storage

Parallel Computing

A comparison of generalized hybrid Monte Carlo methods with and without momentum flip

Journal of Computational Physics

A combined Event-Driven/Time-Driven molecular dynamics algorithm for the simulation of shock waves in rarefied gases

Journal of Computational Physics

Cell-level canonical sampling by velocity scaling for multiparticle collision dynamics simulations

Journal of Computational Physics

Spatially adaptive stochastic numerical methods for intrinsic fluctuations in reaction-diffusion systems

Journal of Computational Physics

Simulating hard rigid bodies

Journal of Computational Physics

A workflow management and grid computing approach to molecular simulation-based bio/nano experiments

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

Progress in scaling biomolecular simulations to petaflop scale platforms

Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing

A new Monte Carlo method for the titration of molecules and minerals

PARA'06 Proceedings of the 8th international conference on Applied parallel computing: state of the art in scientific computing

Coarse graining biomolecular systems

PARA'06 Proceedings of the 8th international conference on Applied parallel computing: state of the art in scientific computing

Exploiting molecular dynamics for multi-objective optimization

Expert Systems with Applications: An International Journal

Exploiting locality for query processing and compression in scientific databases

Proceedings of the Fourth SIGMOD PhD Workshop on Innovative Database Research

Free energy reconstruction from steered dynamics without post-processing

Journal of Computational Physics

Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

Journal of Computational Physics

GPGPU-based parallel computation: application to molecular dynamics problems

COMPUTE '11 Proceedings of the Fourth Annual ACM Bangalore Conference

Finite Element Approximation to a Finite-Size Modified Poisson-Boltzmann Equation

Journal of Scientific Computing

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

Journal of Computational Physics

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

The VLDB Journal — The International Journal on Very Large Data Bases

Spectral accuracy in fast Ewald-based methods for particle simulations

Journal of Computational Physics

Copernicus: a new paradigm for parallel adaptive molecular dynamics

Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis

Improved Scaling for Quantum Monte Carlo on Insulators

SIAM Journal on Scientific Computing

A patch that imparts unconditional stability to explicit integrators for Langevin-like equations

Journal of Computational Physics

Effects of confinement on chemical reaction equilibrium in nanoporous materials

ICCSA'06 Proceedings of the 2006 international conference on Computational Science and Its Applications - Volume Part V

Scalable parallel debugging with statistical assertions

Proceedings of the 17th ACM SIGPLAN symposium on Principles and Practice of Parallel Programming

Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system

Journal of Computational Physics

Learning by doing: software projects in CSE education

ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II

Optimized local basis set for Kohn-Sham density functional theory

Journal of Computational Physics

Distance histogram computation based on spatiotemporal uniformity in scientific data

Proceedings of the 15th International Conference on Extending Database Technology

Simulation of magnetophoretic separation processes in dispersions of superparamagnetic nanoparticles in the noncooperative regime

Journal of Nanomaterials - Special issue on Magnetic Interfaces at the Nanoscale: From Fundamentals to Technological Applications

Metadynamics study of mutant human interferon-gamma forms

Computers & Mathematics with Applications

Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques

SIAM Journal on Scientific Computing

On the estimation and correction of discretization error in molecular dynamics averages

Applied Numerical Mathematics

Efficient SDH computation in molecular simulations data

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

Two-level parallelization of Ehrenfest force calculations in ab initio molecular dynamics simulation

Cluster Computing

No-slip boundary condition in finite-size dissipative particle dynamics

Journal of Computational Physics

Implementation of non-uniform FFT based Ewald summation in dissipative particle dynamics method

Journal of Computational Physics

Adjoint design sensitivity analysis of reduced atomic systems using generalized Langevin equation for lattice structures

Journal of Computational Physics

Static analysis for probabilistic programs: inferring whole program properties from finitely many paths

Proceedings of the 34th ACM SIGPLAN conference on Programming language design and implementation

Atomistic modeling of gas adsorption in nanocarbons

Journal of Nanomaterials

Performance-reliability tradeoff analysis for multithreaded applications

DATE '12 Proceedings of the Conference on Design, Automation and Test in Europe

Phase-coexistence simulations of fluid mixtures by the Markov Chain Monte Carlo method using single-particle models

Journal of Computational Physics

GPU-based Monte Carlo simulation for the Gibbs ensemble

Proceedings of the High Performance Computing Symposium

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

Advances in Data Analysis and Classification

Hybrid continuum-particle method for fluctuating lipid bilayer membranes with diffusing protein inclusions

Journal of Computational Physics

The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units

Journal of Computational Physics

Multiscale modeling and uncertainty quantification in nanoparticle-mediated drug/gene delivery

Computational Mechanics

The archetype-genome exemplar in molecular dynamics and continuum mechanics

Computational Mechanics

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

Journal of Computational Methods in Sciences and Engineering