Computer simulation of liquids

Parallel approaches to short range molecular dynamics simulations

Proceedings of the 1991 ACM/IEEE conference on Supercomputing

Achieving super computer performance with a DSP array processor

Proceedings of the 1992 ACM/IEEE conference on Supercomputing

Massively parallel methods for engineering and science problems

Communications of the ACM

Dynamic load balancing for the simulation of granular materials

ICS '95 Proceedings of the 9th international conference on Supercomputing

Analysis of an efficient algorithm for the hard-sphere problem

ACM Transactions on Modeling and Computer Simulation (TOMACS)

Performance improvement through overhead analysis: a case study in molecular dynamics

ICS '97 Proceedings of the 11th international conference on Supercomputing

Hyper-Systolic Parallel Computing

IEEE Transactions on Parallel and Distributed Systems

A comparative analysis of four parallelisation schemes

ICS '99 Proceedings of the 13th international conference on Supercomputing

Knowledge Mining With VxInsight: Discovery ThroughInteraction

Journal of Intelligent Information Systems - Special issue on information visualization: the next frontier

Lightweight computational steering of very large scale molecular dynamics simulations

Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing

Molecular simulation of rheological properties using massively parallel supercomputers

Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing

A wrapper generator for wrapping high performance legacy codes as Java/CORBA components

Proceedings of the 2000 ACM/IEEE conference on Supercomputing

Demonstrating the scalability of a molecular dynamics application on a Petaflop computer

ICS '01 Proceedings of the 15th international conference on Supercomputing

Bag-of-particles as a deformable model

VISSYM '02 Proceedings of the symposium on Data Visualisation 2002

Quick and easy interactive molecular dynamics using Java3D

Computing in Science and Engineering

A Rigorous Global Optimization Algorithm for Problems with Ordinary Differential Equations

Journal of Global Optimization

Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer

International Journal of Parallel Programming

Modeling Biomolecules: Larger Scales, Longer Durations

IEEE Computational Science & Engineering

Simulating Solvent Effects in Organic Chemistry: Combining Quantum and Molecular Mechanics

IEEE Computational Science & Engineering

Portrait of a Crack: Rapid Fracture Mechanics Using Parallel Molecular Dynamics

IEEE Computational Science & Engineering

How Computation Affects Science and Engineering: 5 Essays

Computing in Science and Engineering

Scalable Molecular-Dynamics, Visualization, and Data-Management Algorithms for Materials Simulations

Computing in Science and Engineering

Computational Nanotechnology with Carbon Nanotubes and Fullerenes

Computing in Science and Engineering

Computer Simulations of Protein Dynamics and Thermodynamics

Computer

An XML Based Component Model for Generating Scientific Applications and Performing Large Scale Simulations in a Meta-computing Environment

GCSE '99 Proceedings of the First International Symposium on Generative and Component-Based Software Engineering

Dynamic and Stochastic Properties of Molecular Systems: From Simple Liquids to Enzymes

ICCS '02 Proceedings of the International Conference on Computational Science-Part III

Determinism and Chaos in Decay of Metastable States

ICCS '02 Proceedings of the International Conference on Computational Science-Part III

Simulations of Surfactant-Enhanced Spreading

ICCS '01 Proceedings of the International Conference on Computational Sciences-Part I

Monte Carlo Simulations of a Biaxial Liquid Crystal Model Using the Condor Processing System

HPCN Europe 2001 Proceedings of the 9th International Conference on High-Performance Computing and Networking

Real Time Interactive Visualization System for Flexible Molecular Docking

IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium

Real Time Interactive Visualization System for Flexible Molecular Docking

IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium

Evaluation of MPI's One-Sided Communication Mechanism for Short-Range Molecular Dynamics on the Origin2000

PARA '00 Proceedings of the 5th International Workshop on Applied Parallel Computing, New Paradigms for HPC in Industry and Academia

The Performance of Different Communication Mechanisms and Algorithms Used for Parallelization of Molecular Dynamics Code

PPAM '01 Proceedings of the th International Conference on Parallel Processing and Applied Mathematics-Revised Papers

Development of large scale high performance applications with a parallelizing compiler

Practical parallel computing

Hyper-systolic algorithms with applications in linear algebra and molecular dynamics

Highly parallel computaions

Computation within the auxiliary field approach

Journal of Computational Physics

An influence matrix particle-particle particle-mesh algorithm with exact particle-particle correction

Journal of Computational Physics

Statistical error in particle simulations of hydrodynamic phenomena

Journal of Computational Physics

Comparing high-level and low-level implementations of a molecular dynamics algorithm

HIPS '97 Proceedings of the 1997 Workshop on High-Level Programming Models and Supportive Environments (HIPS '97)

PHYSALIS: a new method for particle simulation part II: two-dimensional Navier--Stokes flow around cylinders

Journal of Computational Physics

Incorporation of lubrication effects into the force-coupling method for particulate two-phase flow

Journal of Computational Physics

A treecode algorithm for computing Ewald summation of dipolar systems

Proceedings of the 2003 ACM symposium on Applied computing

Parallel molecular dynamics simulation of Lennard-Jones liquids on a small Beowulf cluster

ICCMSE '03 Proceedings of the international conference on Computational methods in sciences and engineering

Engineering high-performance legacy codes as CORBA components for problem-solving environments

Journal of Parallel and Distributed Computing

Event-driven molecular dynamics in parallel

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

A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins

Journal of VLSI Signal Processing Systems - Special issue on signal processing and neural networks for bioinformatics

Computational challenges in structural and functional genomics

IBM Systems Journal - Deep computing for the life sciences

Constant temperature molecular dynamics simulations of energetic particle-solid collisions: comparison of temperature control methods

Journal of Computational Physics

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

Journal of Computational Physics

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations

Proceedings of the 2003 ACM/IEEE conference on Supercomputing

Parallel Particle Simulations of Thin-Film Deposition

International Journal of High Performance Computing Applications

A Rigid-Body-Based Multiple Time Scale Molecular Dynamics Simulation of Nanophase Materials

International Journal of High Performance Computing Applications

Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials

International Journal of High Performance Computing Applications

The Monte Carlo Method in Science and Engineering

Computing in Science and Engineering

Reactions in complex biologically relevant systems: challenges for computational approaches

Future Generation Computer Systems

Molecular dynamics study of velocity slip in microchannels

MS'06 Proceedings of the 17th IASTED international conference on Modelling and simulation

Electrophoretic properties of charged colloidal suspensions: application of a hybrid MD/LB method

Mathematics and Computers in Simulation - Special issue: Discrete simulation of fluid dynamics in complex systems

Preliminary investigation of advanced electrostatics in molecular dynamics on reconfigurable computers

Proceedings of the 2006 ACM/IEEE conference on Supercomputing

Analytical first derivatives of the RE-squared interaction potential

Journal of Computational Physics

Parallelization of an Euler-Lagrange model using mixed domain decomposition and a mirror domain technique: Application to dispersed gas-liquid two-phase flow

Journal of Computational Physics

GPU accelerated molecular dynamics simulation of thermal conductivities

Journal of Computational Physics

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

Journal of Computational Physics

Wavelet-based multi-scale coarse graining approach for DNA molecules

Finite Elements in Analysis and Design

Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

Journal of Computational Physics

Electrostatic force computation for bio-molecules on supercomputers with torus networks

Parallel Computing

A boundary element formulation of protein electrostatics with explicit ions

Journal of Computational Physics

Application of Pfortran and Co-Array Fortran in the parallelization of the GROMOS96 molecular dynamics module

Scientific Programming

Individual-based simulation of the clustering behaviour of epidermal growth factor receptors

Scientific Programming

A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment

Proceedings of the 21st annual international conference on Supercomputing

A stochastic boundary forcing for dissipative particle dynamics

Journal of Computational Physics

Numerical implementation of the exact dynamics of free rigid bodies

Journal of Computational Physics

Path sampling with stochastic dynamics: Some new algorithms

Journal of Computational Physics

A continuum-atomistic simulation of heat transfer in micro- and nano-flows

Journal of Computational Physics

Visual Verification and Analysis of Cluster Detection for Molecular Dynamics

IEEE Transactions on Visualization and Computer Graphics

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

Journal of Computational Physics

Parallel simulation of particle suspensions with the lattice Boltzmann method

Computers & Mathematics with Applications

Computational mechanical modeling of the behavior of carbon nanotubes

ISTASC'07 Proceedings of the 7th Conference on 7th WSEAS International Conference on Systems Theory and Scientific Computation - Volume 7

Molecular dynamics modelling and simulation of nanoscale ductile cutting of silicon

International Journal of Computer Applications in Technology

GSHMC: An efficient method for molecular simulation

Journal of Computational Physics

General purpose molecular dynamics simulations fully implemented on graphics processing units

Journal of Computational Physics

Extending stability beyond CPU millennium: a micron-scale atomistic simulation of Kelvin-Helmholtz instability

Proceedings of the 2007 ACM/IEEE conference on Supercomputing

Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

Parallel Computing

Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

Computational Biology and Chemistry

Programming Environment for a High-Performance Parallel Supercomputer with Intelligent Communication

Scientific Programming - Parallel Computing Projects of the Swiss Priority Programme

Speeding up N-body Calculations on Machines without Hardware Square Root

Scientific Programming

Linear polymers transport through nanometer pores under constant force

MCBC'08 Proceedings of the 9th WSEAS International Conference on Mathematics & Computers In Biology & Chemistry

A sequential Monte Carlo/Quantum Mechanics study of the dipole polarizability of liquid benzene

Journal of Computational Methods in Sciences and Engineering - Computational aspects of electric polarizability calculations: Atoms, Molecules and clusters Part II

A mean-field approach for the determination of the polarizabilities for the water molecule in liquid state

Journal of Computational Methods in Sciences and Engineering - Computational aspects of electric polarizability calculations: Atoms, Molecules and clusters Part II

Modelling spectroscopic properties of large molecular systems. The combined Density Functional Theory/Molecular Mechanics approach

Journal of Computational Methods in Sciences and Engineering

369 Tflop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

Proceedings of the 2008 ACM/IEEE conference on Supercomputing

Parallel DEM Software for Simulation of Granular Media

Informatica

Characterisation of the Surfactant Shell Stabilising Calcium Carbonate Dispersions in Overbased Detergent Additives: Molecular Modelling and Spin-Probe-ESR Studies

ICCS '07 Proceedings of the 7th international conference on Computational Science, Part II

Modeling the magnetic interactions between paramagnetic beads in magnetorheological fluids

Journal of Computational Physics

RAT: RC Amenability Test for Rapid Performance Prediction

ACM Transactions on Reconfigurable Technology and Systems (TRETS)

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

Journal of Computational Physics

Force-coupling method for flows with ellipsoidal particles

Journal of Computational Physics

Particle filtering with path sampling and an application to a bimodal ocean current model

Journal of Computational Physics

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology

A scalable parallel algorithm for the direct numerical simulation of three-dimensional incompressible particulate flow

International Journal of Computational Fluid Dynamics

Use of computer simulation and molecular modeling techniques for the design of molecularly organized urea-urethane prototypes for thermal insulation

COMPUCHEM'08 Proceedings of the 2nd WSEAS international conference on Computational chemistry

Erratum: Erratum to "A comparison of generalized hybrid Monte Carlo methods with and without momentum flip" [J. Comput. Phys. 228 (2009) 2256-2265]

Journal of Computational Physics

Enhanced bounding techniques to reduce the protein conformational search space

Optimization Methods & Software - GLOBAL OPTIMIZATION

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

Using piecewise polynomials for faster potential function evaluation

Journal of Computational Physics

Simulations of large-scale WiFi-based wireless networks: Interdisciplinary challenges and applications

Future Generation Computer Systems

Reactions in complex biologically relevant systems: challenges for computational approaches

Future Generation Computer Systems

Simulation of the quasi-static mechanics and scalar transport properties of ideal granular assemblages

Journal of Computational Physics

Hybrid atomistic-continuum method for the simulation of dense fluid flows

Journal of Computational Physics

An improved hybrid global optimization method for protein tertiary structure prediction

Computational Optimization and Applications

Physically based node distributions for mesh generation

International Journal of Modelling and Simulation

Alcohol sensors based on SWNT as chemical sensors: Monte Carlo and Langevin dynamics simulation

Microelectronics Journal

OpenMP in the field: anecdotes from practice

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

Parallelisation of nonequilibrium molecular dynamics code for polymer melts using OpenMP

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

Parallelization of the discrete gradient method of non-smooth optimization and its applications

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

FPGA-accelerated molecular dynamics simulations: an overview

ARC'07 Proceedings of the 3rd international conference on Reconfigurable computing: architectures, tools and applications

A Component-Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media

International Journal of High Performance Computing Applications

A novel force matrix transformation with optimal load-balance for 3-body potential based parallel molecular dynamics using atom-decomposition in a heterogeneous cluster environment

HiPC'07 Proceedings of the 14th international conference on High performance computing

Asynchronous parallel molecular dynamics simulations

PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics

Exploiting molecular dynamics for multi-objective optimization

Expert Systems with Applications: An International Journal

Molecular simulations of electroosmotic flows in rough nanochannels

Journal of Computational Physics

Application of discrete element method to the analysis of free-flow outlet of coal from high coals at underground coal mining

Proceedings of the International Conference on Applications of Computer and Information Sciences to Nature Research

Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

Journal of Computational Physics

Parallel implementation of particle tracking and collision in a turbulent flow

PPAM'09 Proceedings of the 8th international conference on Parallel processing and applied mathematics: Part II

Performance and cost effectiveness of a cluster of workstations and MD-GRAPE 2 for MD simulations

ISPDC'03 Proceedings of the Second international conference on Parallel and distributed computing

Molecular structural transformation of 2:1 clay minerals by a constant-pressure molecular dynamics simulation method

Journal of Nanomaterials

Initial stage of consolidation of silicon-carbide nanocrystals under pressure: a tight-binding molecular-dynamics study

Journal of Nanomaterials - Special issue on nanocrystals-related synthesis, assembly, and energy applications

An analytical model for multilevel performance prediction of Multi-FPGA systems

ACM Transactions on Reconfigurable Technology and Systems (TRETS)

Dynamic bond-order force field

Journal of Computational Electronics

A multigrid solver for modeling complex interseismic stress fields

Computers & Geosciences

Performance analysis and optimization of molecular dynamics simulation on Godson-T many-core processor

Proceedings of the 8th ACM International Conference on Computing Frontiers

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

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

An adaptive hierarchical domain decomposition method for parallel contact dynamics simulations of granular materials

Journal of Computational Physics

Improved Scaling for Quantum Monte Carlo on Insulators

SIAM Journal on Scientific Computing

Model dependence of solvent separated sodium chloride ion pairs in Water-DMSO mixtures

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

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

Journal of Computational Physics

A hybrid molecular continuum method using point wise coupling

Advances in Engineering Software

The implementation of polarizable and flexible models in molecular dynamics simulations

HPCS'09 Proceedings of the 23rd international conference on High Performance Computing Systems and Applications

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

A grid computing-based monte carlo docking simulations approach for computational chiral discrimination

RSFDGrC'05 Proceedings of the 10th international conference on Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing - Volume Part II

Scheduling many-body short range MD simulations on a cluster of workstations and custom VLSI hardware

HiPC'04 Proceedings of the 11th international conference on High Performance Computing

Charge group partitioning in biomolecular simulation

RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology

A collective model for the formation of public opinion: An application to nuclear public acceptance

Mathematical and Computer Modelling: An International Journal

Parallel short range molecular dynamics simulations on computer clusters: Performance evaluation and modeling

Mathematical and Computer Modelling: An International Journal

Cubic-to-tetragonal phase transitions in Ag-Cu nanorods

Journal of Nanomaterials - Special issue on Nanomaterial Properties: Size and Shape Dependencies

The effects of radial compression on thermal conductivity of carbon and boron nitride nanotubes

Journal of Nanomaterials - Special issue on Low-Dimensional Carbon Nanomaterials 2012

A parallel Lowe-Andersen thermostat for soft matter simulations

Proceedings of the ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way?

Boundary treatment effects on molecular dynamics simulations of interface thermal resistance

Journal of Computational Physics

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

Applied Numerical Mathematics

Hardware-accelerated glyphs for mono- and dipoles in molecular dynamics visualization

EUROVIS'05 Proceedings of the Seventh Joint Eurographics / IEEE VGTC conference on Visualization

An FPGA design to achieve fast and accurate results for molecular dynamics simulations

ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications

A multiscale method for micro/nano flows of high aspect ratio

Journal of Computational Physics

Transitional failure of carbon nanotube systems under a combination of tension and torsion

Journal of Nanomaterials - Special issue on 1D Nanomaterials 2012

An efficient parallel simulation of interacting inertial particles in homogeneous isotropic turbulence

Journal of Computational Physics

Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

Journal of Computational Physics

Hard-sphere collision simulations with multiple GPUs, PCIe extension buses and GPU-GPU communications

AusPDC '12 Proceedings of the Tenth Australasian Symposium on Parallel and Distributed Computing - Volume 127

Scalability study of molecular dynamics simulation on Godson-T many-core architecture

Journal of Parallel and Distributed Computing

A smooth dissipative particle dynamics method for domains with arbitrary-geometry solid boundaries

Journal of Computational Physics

Accelerating solidification process simulation for large-sized system of liquid metal atoms using GPU with CUDA

Journal of Computational Physics

Particle-based simulation and visualization of fluid flows through porous media

Journal of Visualization