Contact Information Home Department: Beckman Institute Office: BI 3061 Email: dhardy@illinois.edu Education Ph.D., Computer Science, University of Illinois at Urbana-Champaign, 2006 M.S., Computer Science, University of Missouri-Rolla, 1997 B.S., Mathematics and Computer Science, Truman State University, 1994 Research Interests Multilevel summation method for calculating electrostatics GPU acceleration of molecular modeling applications Polarizable force fields for biomolecular modeling Multiple time stepping for molecular dynamics Software development for molecular dynamics Lead developer of NAMD.

Representative Publications

• Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. David J. Hardy, Matthew A. Wolff, Jianlin Xia, Klaus Schulten, and Robert D. Skeel. Journal of Chemical Physics, 144:114112, 2016. (16 pages).


• Multilevel summation method for electrostatic force evaluation. David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten. Journal of Chemical Theory and Computation, 11:766-779, 2015.


• High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell Jr., Klaus Schulten, and Benoît Roux. Journal of Physical Chemistry Letters, 2:87-92, 2011.


• GPU-accelerated molecular modeling coming of age. John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten. Journal of Molecular Graphics and Modelling, 29:116-125, 2010.


• Multilevel summation of electrostatic potentials using graphics processing units. David J. Hardy, John E. Stone, and Klaus Schulten. Journal of Parallel Computing, 35:164-177, 2009.


• Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.


• Symplectic variable stepsize integration for N-body problems. David J. Hardy, Daniel I. Okunbor, and R. D. Skeel. Applied Numerical Mathematics, 29:19-30, 1999.

Full list of publications

Presentations

• Multilevel Summation Method for Efficient Computation of Nonbonded Forces in Molecular Dynamics Simulations. Lecture presented at the SIAM Conference on Computational Science and Engineering, February 27-March 3, 2017, Atlanta, GA.


• Improving Performance and Scaling of Molecular Dynamics Simulation with the Multilevel Summation Method. Lecture presented at The 7th AICS International Symposium, February 23-24, 2017, RIKEN Advanced Institute for Computational Science (AICS), Kobe, Japan.


• Multilevel summation method in NAMD. Lecture presented at Langholmen Conference Center, Stockholm, Sweden, May 15, 2013.


• Co-organized with Berk Hess, NAIS Tutorial: Advanced Molecular Dynamics Algorithms for HPC, April 30-May 2, 2012, University of Edinburgh, Edinburgh, Scotland. Presented lectures: NAMD algorithms and HPC functionality; Demonstration: Using NAMD; Short-range (non-bonded) interactions in NAMD (with James Phillips); Generalized Born implicit solvent algorithm in NAMD (with David Tanner); Multilevel summation method in NAMD and VMD; Analysis and visualization algorithms in VMD (with John Stone); Future direction with NAMD.


• Efficient calculation of pairwise interactions with multilevel summation. Lightning talk presented at ICERM Workshop, Synchronization-reducing and Communication-reducing Algorithms and Programming Models for Large-scale Simulations, January 9-13, 2012, Brown University, Providence, RI.


• Prepared with Christopher Harrison and James Phillips, Multilevel summation method for large scale simulations of biomolecules. Lecture presented at SIAM Conference on Computational Science and Engineering, February 28-March 4, 2011, Reno, NV.


• Molecular dynamics simulations of biomolecules on GPUs using the multilevel summation method. Lecture presented at SIAM Conference on Computational Science and Engineering, February 28-March 4, 2011, Reno, NV.


• Simulating biomolecules on GPUs with the multilevel summation method. Lecture presented at Bio-molecular Simulations on Future Computing Architectures, September 16-17, 2010, ORNL, Oak Ridge, TN.


• Co-organized with John Stone, James Phillips, and Kirby Vandivort, Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL. Presented lecture: GPU particle-particle algorithms: non-bonded force calculation.


• Using GPUs to compute the multilevel summation of electrostatic forces. Lecture presented at Multiscale Molecular Modelling: Molecular Dynamics, Computational Statistical Mechanics, and Simulation Algorithms, June 30-July 3, 2010, University of Edinburgh, Edinburgh, Scotland.


• Using GPU computing to accelerate molecular modeling applications. Lecture presented at Algorithmic Re-Engineering for Modern Non-Conventional Processing Units, September 30-October 2 2009, CECAM-USI, Lugano, Switzerland.


• Multilevel summation of electrostatic potentials using GPUs. Lecture presented at CS&E Seminar, September 9, 2009, Purdue University, West Lafayette, IN.


• Prepared with Robert D. Skeel, Multilevel summation method for Coulomb interactions. Poster presented at IMA Summer Program, Classical and Quantum Approaches in Molecular Modeling, July 23-August 3, 2007, University of Minnesota, Minneapolis, MN.


• Multiple grid method for solving the N-body problem. Poster presented at CIMMS-IPAM Workshop, Molecular Modeling and Computation: Perspectives and Challenges, November 15-16, 2002, California Institute of Technology (Caltech), Pasadena, CA.


• Choosing stepsizes for molecular dynamics. Poster presented at International Workshop on Methods for Macromolecular Modeling (M3), October 12-14, 2000, New York University, New York, NY.


• Choosing stepsizes for molecular dynamics. Lecture presented at First SIAM Conference on Computational Science and Engineering, September 21-24, 2000, Washington, D.C.