Scientific Computing Group Department of Computer Science University of Illinois at Urbana-Champaign

Publications

Selected Recent Papers

• B. Aksoylu, S. Bond, and M. Holst, An odyssey into local refinement and multilevel preconditioning III: implementation and numerical experiments, SIAM J. Sci. Comput 25:478-498, 2003.
• S. Ashby, M. Holst, T. Manteuffel and P. Saylor, The role of the inner product in stopping criteria for conjugate gradient iterations, BIT, 41:26-53, 2001.
• S. Bond, B. Laird, and B. Leimkuhler, The Nose-Poincare method for constant temperature molecular dynamics, J. Comput. Physics, 151:114-134, 1999.
• S. Bond, B. Laird, and B. Leimkuhler, On the approximation of Feynman-Kac path integrals, J. Comput. Physics, 185:472-483, 2003.
• S. Bond and B. Leimkuhler, Time-transformations for reversible variable stepsize integration, Numerical Algorithms 19:55-71, 1998.
• M. Desbrun, A. N. Hirani, and J. E. Marsden, Discrete Exterior Calculus for Variational Problems in Computer Vision and Graphics, Proc. 42nd IEEE Conf. Decision and Control, Honolulu, 2003.
• H. De Sterck, T. J. Manteuffel, S. F. McCormick, and L. N. Olson, Numerical conservation properties of H(div)-conforming least-squares finite element methods for the Burgers equation, SIAM J. Sci. Comput., to appear.
• H. De Sterck, T. J. Manteuffel, S. F. McCormick, and L. N. Olson, Least-squares finite element methods and algebraic multigrid solvers for linear hyperbolic PDEs, SIAM J. Sci. Comput., to appear.
• E. de Sturler, Truncation strategies for optimal Krylov subspace methods, SIAM J. Numer. Anal., 36:864-889, 1999.
• E. de Sturler and J. Liesen, Block-diagonal and constraint preconditioners for nonsymmetric indefinite linear systems. Part I: Theory, SIAM J. Sci. Comput., 26:1598-1619, 2005.
• W. A. Dick and M. T. Heath, Whole system simulation of solid propellant rockets, AIAA 2002-4345, 38th AIAA/ASME/SAE/ASEE Joint Propulsion Conf., July 2002. R. D. Engle, R. D. Skeel, and M. Drees, Monitoring energy drift with shadow Hamiltonians, J. Comput. Phys., 206:432-452, 2005.
• E. Grinspun, A. N. Hirani, M. Desbrun, and P. Schroder, Discrete Shells, Proc. Eurographics/SIGGRAPH Symposium on Computer Animation, July 2003.
• D. J. Hardy and D. I. Okunbor and R. D. Skeel, Symplectic variable stepsize integration for N-body problems, Appl. Numer. Math., 29:19-30, 1999.
• M. T. Heath and W. A. Dick, Virtual rocketry: rocket science meets computer science, IEEE Comput. Sci. Engr., 5(1):16-26, January-March 1998.
• M. T. Heath and W. A. Dick, Virtual prototyping of solid propellant rockets, Comput. Sci. Engr., 2(2):21-32, March-April 2000.
• J. J. Heys, T. A. Manteuffel, S. F. McCormick, and L. N. Olson, Algebraic multigrid (AMG) for higher-order finite elements, J. Comp. Phys., to appear.
• A. N. Hirani and R. P. Russell, Approximations of Distant Retrograde Orbits for Mission Design, Paper AAS 06-116, 16th AAS/AIAA Space Flight Mechanics Meeting, Tampa, Florida, Jan. 22-26, 2006.
• A. N. Hirani and M. W. Lo, Surface Structure of an Invariant Manifold of a Halo Orbit, AAS/AIAA Astrodynamics Specialists Conference, Paper AAS 05-379, August 2005.
• A. N. Hirani, J. E. Marsden, and J. Arvo, Averaged Template Matching Equations, Proc. Energy Minimization Methods in Computer Vision and Pattern Recognition Springer LNCS 2134, 2001
• A. N. Hirani and T. Totsuka, Combining Frequency and Spatial Domain Information for Fast Interactive Image Noise Removal, Proc. ACM SIGGRAPH, pp. 269-276, 1996.
• A. N. Hirani and T. Totsuka, Dual Domain Image Noise Removal, IEEE Conf. Image Processing, 1996.
• J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, and R. D. Skeel, Langevin stabilization of molecular dynamics, J. Chem. Phys., 114:2090-2098, 2000.
• J. Izaguirre, S. Reich and R. D. Skeel, Longer time steps for molecular dynamics, J. Chemical Physics, 110, pp. 9853-9864, 1999.
• X. Jiao, and M. T. Heath, Overlaying surface meshes, part I: algorithms, Internat. J. Comput. Geom. Appl., 14:379-402, 2004.
• X. Jiao, and M. T. Heath, Overlaying surface meshes, part II: topology preservation and feature matching, Internat. J. Comput. Geom. Appl., 14:403-419, 2004.
• X. Jiao and M. T. Heath, Common-refinement-based data transfer between non-matching meshes in multiphysics simulations, Internat. J. Numer. Meth. Engrg., 61:2402-2427, 2004.
• T. Kerkhoven, F. Bodine, W. F. Chow, 3D pseudospectral self-consistent field approximation, Proc. Sixth Internat. Workshop Comput. Electronics, October 1998.
• M. Kilmer and E. de Sturler, Recycling subspace information for diffuse optical tomography, SIAM J. Sci. Comput., to appear.
• T. Lam, A. N. Hirani, and J. A. Kangas, Characteristics of Transfers to and Captures at Europa, Paper AAS 06-188, 16th AAS/AIAA Space Flight Mechanics Meeting, Tampa, Florida, Jan. 22-26, 2006.
• J. Liesen, E. de Sturler, A. Sheffer, Y. Aydin, C. Siefert, Preconditioners for indefinite linear systems arising in surface parameterization, Proc. 10th Internat. Meshing Round Table, October 7-10, 2001.
• V. Lopez, P. Boyland, M. T. Heath, and R. D. Moser, Relative periodic solutions of the complex Ginzburg-Landau equation, SIAM J. Appl. Dynamical Systems, 4:1042-1075, 2005.
• Q. Ma, J. Izaguirre, and R. D. Skeel, Verlet-I/r-RESPA is limited by nonlinear instability, SIAM J. Sci. Comput., 24:1951-1973, 2003.
• P. Saylor and D. Smolarski, Why Gaussian quadrature in the complex plane? Numerical Algorithms, 26:251-280, 2001.
• A. Sheffer and E. de Sturler, Parameterization of faceted surfaces for meshing using angle based flattening, Engineering with Computers 17:326-337, 2001.
• A. Sheffer and E. de Sturler, Smoothing an overlay grid to minimize linear distortion in texture mapping, ACM Trans. Graphics 21:874-890, 2002.
• R. D. Skeel, Symplectic integration with floating-point arithmetic and other approximations, Appl. Numer. Math. 29:3-18, 1999.
• R. D. Skeel and D. J. Hardy, Practical construction of modified Hamiltonians, SIAM J. Sci. Comput., 23:1172-1188, 2001.
• R. D. Skeel and J. Izaguirre, An impulse integrator for Langevin dynamics, Mol. Phys., 100:3885-3891, 2002.
• R. D. Skeel and K. Srinivas, Nonlinear stability analysis of area-preserving integrators, SIAM J. Numer. Anal., 38:129-148, 2000.
• R. D. Skeel, I. Tezcan, and D. J. Hardy, Multiple grid methods for classical molecular dynamics, J. Comput. Chemistry, 23:673-684, 2002.
• K. Tai, S. Bond, H. MacMillan, N. Baker, M. Holst, and J. A. McCammon, Finite element simulations of acetylcholine diffusion in neuromuscular junctions, Biophysical J., 84:2234-2241, 2003.
• Y. Tong, S. Lombeyda, A. N. Hirani, and M. Desbrun, Discrete Multiscale Vector Field Decomposition, ACM Trans. Graphics, 22:445-452, 2003.
• A. Trellakis, M. Qian, T. Kerkhoven, and U. Ravaioli, Efficient 3-D computation of resonant modes in dielectric optical cavities. Internat. Conf. Comput. Physics, October 1997.
• W. Wang and R. D. Skeel, Analysis of a few numerical integration methods for the Langevin equation, Mol. Phys., 101:2149-2156, 2003.
• G. Zou and R. D. Skeel, Robust biased Brownian dynamics for rate constant calculation, Biophysical J., 85:2147-2157, 2003.
• G. Zou and R. D. Skeel, Robust variance reduction for random walk methods, SIAM J. Sci. Comput., 25:1964-1981, 2004.
• G. Zou, R. D. Skeel and S. Subramaniam, Biased Brownian dynamics for rate constant calculation, Biophys. J. 79:638-645, 2000.

Books

• M. T. Heath, Scientific Computing: An Introductory Survey, Second Edition, McGraw-Hill, New York, 2002.
• M. T. Heath, A. Ranade, and R. S. Schreiber, editors, Algorithms for Parallel Processing, Springer-Verlag, New York, 1999.
• M. T. Heath, V. Torczon, et al., editors, Proc. Eighth SIAM Conf. on Parallel Processing for Scientific Computing, SIAM, Philadelphia, PA, 1997.
• R. D. Skeel and J. B. Keiper, Elementary Numerical Computing with Mathematica, McGraw-Hill, New York, 1993.

Software

• NAMD: Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems

• ParaGraph: Performance visualization tool for MPI parallel programs

Scientific Computing Group, Department of Computer Science, University of Illinois at Urbana-Champaign, 201 N. Goodwin Ave., Urbana, IL 61801, USA.