List of Publications

• TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel Kohlmeyer. Journal of Chemical Information and Modeling, 56(5):1112-1116, 2016.


• 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.


• Fast molecular electrostatics algorithms on GPUs. David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp. 43-58. Morgan Kaufmann Publishers, 2011.


• GPU-accelerated computation and interactive display of molecular orbitals. John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011.


• GPU algorithms for molecular modeling. John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten. In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors, Scientific Computing with Multicore and Accelerators, chapter 16, pp. 351-371. Chapman & Hall/CRC Press, 2011.


• 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, and Klaus Schulten. PLoS Computational Biology, 6:e1000939, 2010. (13 pages).


• 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.


• 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, New York, NY, USA, 2009. ACM.


• 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.

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