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David J. Hardy

Contact Information Home Department: Beckman Institute Office: BI 3047 Phone: 217-244-5493 Fax: 217-244-6078 Email: dhardy@ks.uiuc.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 Numerical methods for molecular dynamics GPU acceleration of molecular modeling applications Software development for molecular dynamics

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Publications

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, and Klaus Schulten. In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, 2009.

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.

GPU acceleration of cutoff pair potentials for molecular modeling applications. Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-mei W. Hwu. In CF'08: Proceedings of the 2008 conference on Computing Frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.

Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.

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.

Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. Robert D. Skeel, David J. Hardy, and James C. Phillips. Journal of Computational Physics, 225(1):1-5, 2007.

Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules. David J. Hardy. Ph.D. thesis, University of Illinois at Urbana-Champaign, 2006.

Multiple grid methods for classical molecular dynamics. Robert D. Skeel, Ismail Tezcan, and David J. Hardy. Journal of Computational Chemistry, 23:673-684, 2002.

Practical construction of modified Hamiltonians. Robert D. Skeel and David J. Hardy. SIAM Journal on Scientific Computing, 23(4):1172-1188, 2001.

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.

Deza graphs: A generalization of strongly regular graph. M. Erickson, S. Fernando, W. H. Haemers, D. Hardy, and J. Hemmeter. Journal of Combinatorial Designs, 7:395-405, 1999.

Qualitative study of the symplectic Störmer-Verlet integrator. David J. Hardy and Daniel I. Okunbor. Journal of Chemical Physics, 102(22):8978-8982, 1995.

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
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