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David J. Hardy

University of Illinois System

24H-index
50Paper Count
6.3KCitation Count
Published Papers 17
Publication Date
Structure of the MlaC-MlaD complex reveals molecular basis of periplasmic phospholipid transport
err2024-07-30
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errWotherspoon, Peter; Johnston, Hannah; Hardy, David J.; Holyfield, Rachel; Bui, Soi; Ratkeviciute, Giedre; Sridhar, Pooja; Colburn, Jonathan; Wilson, Charlotte B.; Colyer, Adam; Cooper, Benjamin F.; Bryant, Jack A.; Hughes, Gareth W.; Stansfeld, Phillip J.; Bergeron, Julien R. C.; Knowles, Timothy J.
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An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system
err2024-01-16
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errCooper, Benjamin F.; Ratkeviciute, Giedre; Clifton, Luke A.; Johnston, Hannah; Holyfield, Rachel; Hardy, David J.; Caulton, Simon G.; Chatterton, William; Sridhar, Pooja; Wotherspoon, Peter; Hughes, Gareth W.; Hall, Stephen C. L.; Lovering, Andrew L.; Knowles, Timothy J.
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#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
err2022-10-02
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errDommer, Abigail; Casalino, Lorenzo; Kearns, Fiona; Rosenfeld, Mia; Wauer, Nicholas; Ahn, Surl-Hee; Russo, John; Oliveira, Sofia; Morris, Clare; Bogetti, Anthony; Trifan, Anda; Brace, Alexander; Sztain, Terra; Clyde, Austin; Ma, Heng; Chennubhotla, Chakra; Lee, Hyungro; Turilli, Matteo; Khalid, Syma; Tamayo-Mendoza, Teresa; Welborn, Matthew; Christensen, Anders; Smith, Daniel Ga; Qiao, Zhuoran; Sirumalla, Sai K.; O'Connor, Michael; Manby, Frederick; Anandkumar, Anima; Hardy, David; Phillips, James; Stern, Abraham; Romero, Josh; Clark, David; Dorrell, Mitchell; Maiden, Tom; Huang, Lei; McCalpin, John; Woods, Christopher; Gray, Alan; Williams, Matt; Barker, Bryan; Rajapaksha, Harinda; Pitts, Richard; Gibbs, Tom; Stone, John; Zuckerman, Daniel M.; Mulholland, Adrian J.; Miller, Thomas, III; Jha, Shantenu; Ramanathan, Arvind; Chong, Lillian; Amaro, Rommie E.
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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
err2022-08-05
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errTrifan, Anda; Gorgun, Defne; Salim, Michael; Li, Zongyi; Brace, Alexander; Zvyagin, Maxim; Ma, Heng; Clyde, Austin; Clark, David; Hardy, David J.; Burnley, Tom; Huang, Lei; McCalpin, John; Emani, Murali; Yoo, Hyenseung; Yin, Junqi; Tsaris, Aristeidis; Subbiah, Vishal; Raza, Tanveer; Liu, Jessica; Trebesch, Noah; Wells, Geoffrey; Mysore, Venkatesh; Gibbs, Thomas; Phillips, James; Chennubhotla, S. Chakra; Foster, Ian; Stevens, Rick; Anandkumar, Anima; Vishwanath, Venkatram; Stone, John E.; Tajkhorshid, Emad; Harris, Sarah A.; Ramanathan, Arvind
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py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD
err2022-05-27
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errBarhaghi, Mohammad Soroush; Crawford, Brad; Schwing, Gregory; Hardy, David J.; Stone, John E.; Schwiebert, Loren; Potoff, Jeffrey; Tajkhorshid, Emad
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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
err2021-04-20
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errCasalino, Lorenzo; Dommer, Abigail; Gaieb, Zied; Barros, Emilia P.; Sztain, Terra; Ahn, Surl-Hee; Trifan, Anda; Brace, Alexander; Bogetti, Anthony; Ma, Heng; Lee, Hyungro; Turilli, Matteo; Khalid, Syma; Chong, Lillian; Simmerling, Carlos; Hardy, David J.; Maia, Julio D. C.; Phillips, James C.; Kurth, Thorsten; Stern, Abraham; Huang, Lei; McCalpin, John; Tatineni, Mahidhar; Gibbs, Tom; Stone, John E.; Jha, Shantenu; Ramanathan, Arvind; Amaro, Rommie E.
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Multilevel summation for periodic electrostatics using B-splines
err2021-04-09
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errKaya, Huseyin; Hardy, David J.; Skeel, Robert D.
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Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD
err2020-08-17
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errChen, Haochuan; Maia, Julio D. C.; Radak, Brian K.; Hardy, David J.; Cai, Wensheng; Chipot, Christophe; Tajkhorshid, Emad
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
err2020-07-30
err1.9K
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errPhillips, James C.; Hardy, David J.; Maia, Julio D. C.; Stone, John E.; Ribeiro, Joao, V; Bernardi, Rafael C.; Buch, Ronak; Fiorin, Giacomo; Henin, Jerome; Jiang, Wei; McGreevy, Ryan; Melo, Marcelo C. R.; Radak, Brian K.; Skeel, Robert D.; Singharoy, Abhishek; Wang, Yi; Roux, Benoit; Aksimentiev, Aleksei; Luthey-Schulten, Zaida; Kale, Laxmikant, V; Schulten, Klaus; Chipot, Christophe; Tajkhorshid, Emad
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TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD
err2016-06-01
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errVermaas, Josh V.; Hardy, David J.; Stone, John E.; Tajkhorshid, Emad; Kohlmeyer, Axel
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Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations
err2016-03-21
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errHardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.
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Multilevel Summation Method for Electrostatic Force Evaluation
err2015-01-08
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errHardy, David J.; Wu, Zhe; Phillips, James C.; Stone, John E.; Skeel, Robert D.; Schulten, Klaus
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Multilevel Summation Method for Electrostatic Force Evaluation
err2015-01-01
err1
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errWu, Zhe; Hardy, David J.; Phillips, James C.; Stone, John E.; Skeel, Robert D.; Schulten, Klaus
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Accelerating molecular modeling applications with graphics processors
err2007-09-25
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errStone, John E.; Phillips, James C.; Freddolino, Peter L.; Hardy, David J.; Trabuco, Leonardo G.; Schulten, Klaus
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