Large scale molecular dynamics simulations with fast multipole implementations
SC '99 Proceedings of the 1999 ACM/IEEE conference on Supercomputing
Virtual prototyping of solid propellant rockets
Computing in Science and Engineering
A system for interactive molecular dynamics simulation
I3D '01 Proceedings of the 2001 symposium on Interactive 3D graphics
Scalable molecular dynamics for large biomolecular systems
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
AfriGraph '01 1st International Conference on Virtual Reality, Computer Graphics and Visualization in Southern Africa ( formerly known as SAGA 2001 )
Exploiting flexibly assignable work to improve load balance
Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures
A dimensionality reduction approach to modeling protein flexibility
Proceedings of the sixth annual international conference on Computational biology
Scalable atomistic simulation algorithms for materials research
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
A Parallel Framework for Explicit FEM
HiPC '00 Proceedings of the 7th International Conference on High Performance Computing
Adaptive Load Balancing for MPI Programs
ICCS '01 Proceedings of the International Conference on Computational Science-Part II
NAMD: biomolecular simulation on thousands of processors
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Parallelizing a DNA Simulation Code for the Cray MTA-2
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
EUROGRID: European computational grid testbed
Journal of Parallel and Distributed Computing - Special issue on computational grids
Nonlinear instability in multiple time stepping molecular dynamics
Proceedings of the 2003 ACM symposium on Applied computing
Programming Environment Based on Distributed Shared Arrays for High-Performance Scientific Computing
SAINT-W '04 Proceedings of the 2004 Symposium on Applications and the Internet-Workshops (SAINT 2004 Workshops)
Investigation of bend and shear waves in a geometrically exact elastic rod model
Journal of Computational Physics
Life sciences grid in EUROGRID and GRIP projects
New Generation Computing - Grid systems for life sciences
Performance and modularity benefits of message-driven execution
Journal of Parallel and Distributed Computing
Load balancing of molecular dynamics simulation with NWChem
IBM Systems Journal - Deep computing for the life sciences
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
ACM Transactions on Mathematical Software (TOMS)
A prototype of distributed molecular visualization on computational grids
Future Generation Computer Systems - Special issue: Computational chemistry and molecular dynamics
Assessing Fault Sensitivity in MPI Applications
Proceedings of the 2004 ACM/IEEE conference on Supercomputing
Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope
Journal of Computational Physics
Power and performance optimization at the system level
Proceedings of the 2nd conference on Computing frontiers
Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials
International Journal of High Performance Computing Applications
Monitoring energy drift with shadow Hamiltonians
Journal of Computational Physics
Revisiting and parallelizing SHAKE
Journal of Computational Physics
Parallel multigrid summation for the N-body problem
Journal of Parallel and Distributed Computing
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
Modal reduction of mathematical models of biological molecules
Journal of Computational Physics
Scaling applications to massively parallel machines using Projections performance analysis tool
Future Generation Computer Systems
Simulation-based performance prediction for large parallel machines
International Journal of Parallel Programming - Special issue: The next generation software program
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Parallelization of a level set method for simulating dendritic growth
Journal of Parallel and Distributed Computing
Scalable molecular dynamics for large biomolecular systems
Scientific Programming
Scalable atomistic simulation algorithms for materials research
Scientific Programming - Best papers from SC 2001
De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers
International Journal of High Performance Computing Applications
Anton, a special-purpose machine for molecular dynamics simulation
Communications of the ACM - Web science
A study of the effects of machine geometry and mapping on distributed transpose performance
Proceedings of the 5th conference on Computing frontiers
GPU acceleration of cutoff pair potentials for molecular modeling applications
Proceedings of the 5th conference on Computing frontiers
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM Journal of Research and Development
Adapting a message-driven parallel application to GPU-accelerated clusters
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Proceedings of the 23rd international conference on Supercomputing
A Parallel Simulator for Mercury (Hg) Porosimetry
Proceedings of the 16th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Using piecewise polynomials for faster potential function evaluation
Journal of Computational Physics
Proceedings of the 5th Grid Computing Environments Workshop
Future Generation Computer Systems
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Scaling applications to massively parallel machines using Projections performance analysis tool
Future Generation Computer Systems
Scaling molecular dynamics to 3000 processors with projections: a performance analysis case study
ICCS'03 Proceedings of the 2003 international conference on Computational science
Uniform access to the distributed resources for the computational chemistry using UNICORE
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartII
ProtoMol: a molecular dynamics research framework for algorithmic development
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Jade: a parallel message-driven java
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
An interface model for parallel components
LCPC'01 Proceedings of the 14th international conference on Languages and compilers for parallel computing
Interactive molecular dynamics simulations on the grid
EUROCAST'07 Proceedings of the 11th international conference on Computer aided systems theory
Asynchronous parallel molecular dynamics simulations
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Supporting NAMD application on the grid using GPE
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Optimizing molecular dynamics simulations with product lines
Proceedings of the 5th Workshop on Variability Modeling of Software-Intensive Systems
Review: Large scale distributed visualization on computational Grids: A review
Computers and Electrical Engineering
Characterization of a solid state DNA nanopore sequencer using multi-scale (nano-to-device) modeling
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part III
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
A new scalable parallel method for molecular dynamics based on cell-block data structure
ISPA'04 Proceedings of the Second international conference on Parallel and Distributed Processing and Applications
A runtime adaptive load balancing algorithm for particle simulations
PARA'04 Proceedings of the 7th international conference on Applied Parallel Computing: state of the Art in Scientific Computing
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
Education and research challenges in parallel computing
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Blue matter: strong scaling of molecular dynamics on blue gene/l
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
A haptic rendering algorithm for molecular interaction
EG VCBM'08 Proceedings of the First Eurographics conference on Visual Computing for Biomedicine
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
On-Board Multi-GPU molecular dynamics
Euro-Par'13 Proceedings of the 19th international conference on Parallel Processing
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