David J. Hardy

21 papers Misc 1Journal 13Unranked 5

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia A. 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
2023	—	`conf`	Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. HPC Asia Workshops 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 Seckin Simsek, Kate Clark, Filippo Spiga, Jeff R. Hammond, John E. Stone, David J. Hardy, Sebastian Keller, Jean-Guillaume Piccinali, Christian Trott
2022	J	`jnl`	Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform. CoRR 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 Seckin Simsek, Filippo Spiga, Klaus Steiniger, Jan Stephan, John E. Stone, Christian Trott, René Widera, Jeffrey Young
2022	—	`conf`	Experiences Porting NAMD to the Data Parallel C++ Programming Model. IWOCL David J. Hardy, Jaemin Choi, Wei Jiang, Emad Tajkhorshid
2022	J	`jnl`	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. Int. J. High Perform. Comput. Appl. 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
2021	J	`jnl`	AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 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
2021	—	`conf`	Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. UrgentHPC@SC David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid
2020	J	`jnl`	Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. J. Chem. Inf. Model. Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai, Christophe Chipot, Emad Tajkhorshid
2018	J	`jnl`	Scalable molecular dynamics with NAMD on the Summit system. IBM J. Res. Dev. Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone
2016	J	`jnl`	TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. J. Chem. Inf. Model. Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer
2010	—	`ch.`	GPU Algorithms for Molecular Modeling. Scientific Computing with Multicore and Accelerators John E. Stone, David J. Hardy, Barry Isralewitz, Klaus Schulten
2010	J	`jnl`	Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases. PLoS Comput. Biol. Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, Klaus Schulten
2009	—	`conf`	High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. GPGPU John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten
2009	J	`jnl`	Multilevel summation of electrostatic potentials using graphics processing units. Parallel Comput. David J. Hardy, John E. Stone, Klaus Schulten
2008	—	`conf`	GPU acceleration of cutoff pair potentials for molecular modeling applications. Conf. Computing Frontiers Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-mei W. Hwu
2007	J	`jnl`	Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. John E. Stone, James C. Phillips, P. L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
2007	J	`jnl`	Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. J. Comput. Phys. Robert D. Skeel, David J. Hardy, James C. Phillips
2006	—	`—`	Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules David J. Hardy
2002	J	`jnl`	Multiple grid methods for classical molecular dynamics. J. Comput. Chem. Robert D. Skeel, Ismail Tezcan, David J. Hardy
2001	J	`jnl`	Practical Construction of Modified Hamiltonians. SIAM J. Sci. Comput. Robert D. Skeel, David J. Hardy
2001	Misc	`conf`	The Multigrid N-Body Solver. International Conference on Computational Science (2) David J. Hardy