The Multigrid N-Body Solver. - David J. Hardy (International Conference on Computational Science (2), 2001)

Practical Construction of Modified Hamiltonians. - Robert D. Skeel; David J. Hardy (SIAM J. Sci. Comput., 2001)

Multiple grid methods for classical molecular dynamics. - Robert D. Skeel; Ismail Tezcan; David J. Hardy (J. Comput. Chem., 2002)

Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules - David J. Hardy (2006)

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)

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)

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 (Conf. Computing Frontiers, 2008)

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 (GPGPU, 2009)

Multilevel summation of electrostatic potentials using graphics processing units. - David J. Hardy; John E. Stone; Klaus Schulten (Parallel Comput., 2009)

GPU Algorithms for Molecular Modeling. - John E. Stone; David J. Hardy; Barry Isralewitz; Klaus Schulten (Scientific Computing with Multicore and Accelerators, 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)

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)

Scalable molecular dynamics with NAMD on the Summit system. - Bilge Acun; David J. Hardy; Laxmikant V. Kalé; Keqin Li 001; James C. Phillips; John E. Stone (IBM J. Res. Dev., 2018)

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)

Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. - David J. Hardy; John E. Stone; Barry Isralewitz; Emad Tajkhorshid (UrgentHPC@SC, 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; et al. (Int. J. High Perform. Comput. Appl., 2021)

Experiences Porting NAMD to the Data Parallel C++ Programming Model. - David J. Hardy; Jaemin Choi; Wei Jiang; Emad Tajkhorshid (IWOCL, 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; et al. (CoRR, 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 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

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; et al. (HPC Asia Workshops, 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 A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)