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ORCIDJohn E. Stone
- > Home > Persons > John E. Stone
Publications
- 2023
[j25]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:
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37(1): 28-44 (2023)- [c22]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:
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. HPC Asia Workshops 2023: 35-49 - 2022
- [j21]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:
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. 36(5-6): 603-623 (2022) - [i1]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:
Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform. CoRR abs/2209.09731 (2022) - 2021
- [j20]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:
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35(5) (2021) - [c20]David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid:
Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. UrgentHPC@SC 2021: 1-10 - 2018
- [j14]Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone:
Scalable molecular dynamics with NAMD on the Summit system. IBM J. Res. Dev. 62(6): 4:1-4:9 (2018) - 2016
- [j13]Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer:
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. J. Chem. Inf. Model. 56(6): 1112-1116 (2016) - 2010
- [p1]John E. Stone, David J. Hardy, Barry Isralewitz, Klaus Schulten:
GPU Algorithms for Molecular Modeling. Scientific Computing with Multicore and Accelerators 2010: 351-371 - 2009
- [j4]David J. Hardy, John E. Stone, Klaus Schulten:
Multilevel summation of electrostatic potentials using graphics processing units. Parallel Comput. 35(3): 164-177 (2009) - [c6]John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten:
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. GPGPU 2009: 9-18 - 2008
- [c3]Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-mei W. Hwu:
GPU acceleration of cutoff pair potentials for molecular modeling applications. Conf. Computing Frontiers 2008: 273-282 - 2007
- [j1]John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten:
Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28(16): 2618-2640 (2007)
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