Robert D. Skeel

Robert D. Skeel

Professor of Computer Science
Professor of Mathematics (courtesy)

Joined department: 2004

Education:
BSc, (Honours) Applied Mathematics
University of Alberta (1969)
MS, Mathematics
University of Toronto (1970)
PhD, Computing Science
University of Alberta (1974)

Professor Skeel's research interest is in computational methods for biomolecular simulation, which seeks to aid in the discovery of the structures and mechanisms that are basic to life. Such simulations are very demanding computationally, running for days, weeks, and even months on parallel computers. Current research of Professor Skeel embraces three challenges: (1) the N-body problem for calculating nonbonded interactions as well as dense matrix "inversion" for implicit solvent, (2) the problem of doing dynamics simulations on biological time scales, and (3) the problem of calculating free energy differences and transition paths in very high dimensional configuration space. Professor Skeel has previously taught full time at the University of Illinois where he initiated the development of the scalable parallel molecular dynamics program NAMD.

Professor Skeel has, with Jerry Keiper, co-authored a textbook Elementary Numerical Computing with Mathematica.

Selected Publications
R. Zhao, J. Shen, and R.D. Skeel, "Maximum flux transition paths of conformational change", J. Chem. Theory Comput., 6, pp. 2411-2423, 2010.
R. D. Skeel, "What Makes Molecular Dynamics Work?", SIAM J. Sci. Comput., 31, 1363-1378, 2009.
J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E.Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, andK. Schulten, "Scalable molecular dynamics with NAMD", J. Comput. Chem. 26, 1781-1802, 2005.