2024
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.
J. Chem. Inf. Model., 2024
2023
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.
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Int. J. High Perform. Comput. Appl., 2023
2022
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.
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Int. J. High Perform. Comput. Appl., 2022
2021
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
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Int. J. High Perform. Comput. Appl., 2021
2020
The challenges of theory-software translation.
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F1000Research, 2020
2019
Theory-Software Translation: Research Challenges and Future Directions.
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CoRR, 2019
2018
Scalable molecular dynamics with NAMD on the Summit system.
IBM J. Res. Dev., 2018
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore.
Proceedings of the Practice and Experience on Advanced Research Computing, 2018
2016
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing.
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Parallel Comput., 2016
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.
Proceedings of the High Performance Computing, 2016
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016
2014
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Comput. Phys. Commun., 2014
Petascale Tcl with NAMD, VMD, and Swift/T.
Proceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages, 2014
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
Proceedings of the International Conference for High Performance Computing, 2014
2013
Scalable Molecular Dynamics with NAMD.
Proceedings of the Parallel Science and Engineering Applications - The Charm++ Approach., 2013
2012
Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6.
Proceedings of the SC Conference on High Performance Computing Networking, 2012
2011
NAMD (NAnoscale Molecular Dynamics).
Proceedings of the Encyclopedia of Parallel Computing, 2011
Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime.
Proceedings of the Conference on High Performance Computing Networking, 2011
2010
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters.
Proceedings of the International Green Computing Conference 2010, 2010
2009
Implementation of scientific computing applications on the Cell Broadband Engine.
Sci. Program., 2009
Probing Biomolecular Machines with Graphics Processors.
ACM Queue, 2009
Beta-sandwich - beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates.
Int. J. Medical Eng. Informatics, 2009
GPU clusters for high-performance computing.
Proceedings of the 2009 IEEE International Conference on Cluster Computing, August 31, 2009
2008
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system.
IBM J. Res. Dev., 2008
Adapting a message-driven parallel application to GPU-accelerated clusters.
Proceedings of the ACM/IEEE Conference on High Performance Computing, 2008
Overcoming scaling challenges in biomolecular simulations across multiple platforms.
Proceedings of the 22nd IEEE International Symposium on Parallel and Distributed Processing, 2008
2007
Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations.
J. Comput. Phys., 2007
Accelerating molecular modeling applications with graphics processors.
J. Comput. Chem., 2007
2006
Poster reception - Charm++ simplifies coding for the cell processor.
Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006
2005
Bond strain and defects at interfaces in high-k gate stacks.
Microelectron. Reliab., 2005
Scalable molecular dynamics with NAMD.
J. Comput. Chem., 2005
2002
NAMD: biomolecular simulation on thousands of processors.
Proceedings of the 2002 ACM/IEEE conference on Supercomputing, 2002
2000
Speech/Gesture Interface to a Visual-Computing Environment.
IEEE Computer Graphics and Applications, 2000
Scalable Molecular Dynamics for Large Biomolecular Systems.
Proceedings of the Proceedings Supercomputing 2000, 2000
1999
Application Performance of a Linux Cluster Using Converse.
Proceedings of the Parallel and Distributed Processing, 1999
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code.
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999
1998
Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations.
Comput. Chem., 1998
1997
NAMD: A Case Study in Multilingual Parallel Programming.
Proceedings of the Languages and Compilers for Parallel Computing, 1997
A Visual Computing Environment for Very Large Scale Biomolecular Modeling.
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Proceedings of the 1997 International Conference on Application-Specific Systems, 1997