David J. Hardy

According to our database, David J. Hardy authored at least 21 papers between 2001 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.

Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'Connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas F. Miller III, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro

Int. J. High Perform. Comput. Appl., 2023

Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.

Wael R. Elwasif, William F. Godoy, Nick Hagerty, James Austin Harris, Oscar R. Hernandez, Bálint Joó, Paul R. C. Kent, Damien Lebrun-Grandié, Elijah A. MacCarthy, Verónica G. Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei I. Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan, René Widera, Spencer H. Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey Young, Sunita Chandrasekaran, Florina M. Ciorba, Osman Simsek, Kate Clark, Filippo Spiga, Jeff R. Hammond, John E. Stone, David J. Hardy, Sebastian Keller, Jean-Guillaume Piccinali, Christian Trott

Proceedings of the HPC Asia 2023 Workshops, 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.

Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei Huang, John D. McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Tom Gibbs, James C. Phillips, S. Chakra Chennubhotla, Ian T. Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, Arvind Ramanathan

Int. J. High Perform. Comput. Appl., 2022

Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform.

Wael R. Elwasif, Sergei I. Bastrakov, Spencer H. Bryngelson, Michael Bussmann, Sunita Chandrasekaran, Florina M. Ciorba, Michael A. Clark, Alexander Debus, William F. Godoy, Nick Hagerty, Jeff R. Hammond, David J. Hardy, James Austin Harris, Oscar R. Hernandez, Bálint Joó, Sebastian Keller, Paul R. C. Kent, Henry Le Berre, Damien Lebrun-Grandié, Elijah A. MacCarthy, Verónica G. Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Jean-Guillaume Piccinali, Anand Radhakrishnan, Osman Simsek, Filippo Spiga, Klaus Steiniger, Jan Stephan, John E. Stone, Christian Trott, René Widera, Jeffrey Young

CoRR, 2022

Experiences Porting NAMD to the Data Parallel C++ Programming Model.

David J. Hardy, Jaemin Choi, Wei Jiang, Emad Tajkhorshid

Proceedings of the IWOCL'22: International Workshop on OpenCL, Bristol, United Kingdom, May 10, 2022

2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.

Lorenzo Casalino, Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony T. Bogetti, Austin Clyde, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian T. Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham C. Stern, Lei Huang, John D. McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro

Int. J. High Perform. Comput. Appl., 2021

Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus.

David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid

Proceedings of the IEEE/ACM HPC for Urgent Decision Making, 2021

2020

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.

Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai, Christophe Chipot, Emad Tajkhorshid

J. Chem. Inf. Model., 2020

2018

Scalable molecular dynamics with NAMD on the Summit system.

Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone

IBM J. Res. Dev., 2018

2016

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer

J. Chem. Inf. Model., 2016

2010

Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases.

Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, Klaus Schulten

PLoS Comput. Biol., 2010

GPU Algorithms for Molecular Modeling.

John E. Stone, David J. Hardy, Barry Isralewitz, Klaus Schulten

Proceedings of the Scientific Computing with Multicore and Accelerators., 2010

2009

Multilevel summation of electrostatic potentials using graphics processing units.

David J. Hardy, John E. Stone, Klaus Schulten

Parallel Comput., 2009

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs.

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten

Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, 2009

2008

GPU acceleration of cutoff pair potentials for molecular modeling applications.

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-mei W. Hwu

Proceedings of the 5th Conference on Computing Frontiers, 2008

2007

Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations.

Robert D. Skeel, David J. Hardy, James C. Phillips

J. Comput. Phys., 2007

Accelerating molecular modeling applications with graphics processors.

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten

J. Comput. Chem., 2007

2006

Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules

David J. Hardy

PhD thesis, 2006

2002

Multiple grid methods for classical molecular dynamics.

Robert D. Skeel, Ismail Tezcan, David J. Hardy

J. Comput. Chem., 2002

2001

Practical Construction of Modified Hamiltonians.

Robert D. Skeel, David J. Hardy

SIAM J. Sci. Comput., 2001

The Multigrid N-Body Solver.

David J. Hardy

Proceedings of the Computational Science - ICCS 2001, 2001