Stephen D. Bond

Education:

Ph.D., Honors, Fall 2000. University of Kansas, Lawrence, KS, USA. Department of Mathematics. Dissertation Title: Numerical Methods for Extended Hamiltonian Systems with Applications in Statistical Mechanics. Advisors: B. Leimkuhler (Mathematics, Committee Chair), B. Laird (Chemistry), W. Huang (Mathematics), D. Lerner (Mathematics), G. Szabo (Mathematics).

B.Sci., Spring 1994. University of Kansas, Lawrence, KS, USA. Department of Mechanical Engineering. Final Project: The Design and Construction of a Formula SAE Racing Car.

Exchange Student, 1996-97. Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland. Departments of Mathematics and Chemistry. Supported by the Graduate Direct Exchange Program. Visitor of the W. van Gunsteren research group.

Experience:

Assistant Professor. Department of Computer Science, University of Illinois, Urbana/Champaign, Illinois, USA. Fall 2003 - Present.

Postdoc. McCammon (Chemistry and Biochemistry) and Holst (Mathematics) Research Groups, University California, San Diego, La Jolla, CA, USA. Fall 2000 - 2003. Project: Mathematical Techniques for Problems in Computational Chemistry and Biochemistry.

Visiting Researcher. Department of Mathematics and Computer Science, University of Leicester, Leicester, England. Spring 2000. Project: Approximation of Feynman Path-Integrals.

Graduate Research Assistant. Department of Mathematics, University of Kansas, Lawrence, Kansas, USA. Fall 1995 - 1999. Project: Geometric Integration, Computational Statistical Mechanics, and Hamiltonian Dynamics.

Graduate Teaching Assistant. Department of Mathematics, University of Kansas, Lawrence, Kansas, USA. Fall 1994 - 1997. Courses: Ordinary Differential Equations Lab, Calculus, and Algebra .

Publications:

S.D. Bond and B.J. Leimkuhler, Molecular Dynamics and the Accuracy of Numerically Computed Averages, Acta Numerica 16 (2007) 1-65. [DOI: 10.1017/S0962492906280012]

Y. Cheng, J.K. Suen, Z. Radić, S.D. Bond, M.J. Holst and J.A. McCammon, Continuum Simulations of Acetylcholine Diffusion with Reaction-determined Boundaries in Neuromuscular Junction Models, Biophysical Chemistry 127 (2007) 129-139. [DOI: 10.1016/j.bpc.2007.01.003, PubMed: 17307283]

S.D. Bond and B.J. Leimkuhler, Stabilized Integration of Hamiltonian Systems with Hard-Sphere Inequality Constraints, SIAM Journal on Scientific Computing 30 (2007) 134-147. [DOI: 10.1137/06066552X]

E.C. Cyr and S.D. Bond, Using the Method of Weighted Residuals to Compute Potentials of Mean Force, Journal of Computational Physics 225 (2007) 714-729. [DOI: 10.1016/j.jcp.2006.12.015]

Y. Cheng, J.K. Suen, D. Zhang, S.D. Bond, Y. Zhang, Y. Song, N. Baker, C.L. Bajaj, M. Holst, and J.A. McCammon, Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations, Biophysical Journal 92 (2007) 3397-3406. [DOI: 10.1529/biophysj.106.102533, PubMed: 17307827]

B. Lu, Y.C. Zhou, G.A. Huber, S.D. Bond, M.J. Holst and J.A. McCammon, Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution, Journal of Chemical Physics 127 (2007) 135102 (17 pages). [Virtual Journal of Biological Physics Research, Volume 14, Issue 8] [DOI: 10.1063/1.2775933, PubMed: 17919055]

Q. Wu, L. Shi, S. Bond and Y. Yu, Laplacian Texture Synthesis and Mixing on Surfaces, Pacific Graphics 2006. [Abstract]

B. Aksoylu, M. Holst, and S. Bond, Implementation and Theoretical Aspects of the BPX Preconditioner in the Three Dimensional Local Mesh Refinement Setting, Institute for Computational Engineering and Sciences, The University of Texas at Austin, ICES Technical Report 04-50, October 2004. [ICES Report: 04-50]

K. Tai, S.D. Bond, H.R. MacMillan, N.A. Baker, M.J. Holst, and J.A. McCammon, Finite element simulations of acetylcholine diffusion in neuromuscular junctions, Biophysical Journal 84 (2003) 2234-2241. [BiophysJ: 84/4/2234, PubMed: 12668432]

B. Aksoylu, S. Bond, and M. Holst, An Odyssey into Local Refinement and Multilevel Preconditioning III: Implementation and Numerical Experiments, SIAM Journal on Scientific Computing, 25 (2003) 478-498. [DOI: 10.1137/S1064827502407676]

S.D. Bond, B.B. Laird and B.J. Leimkuhler, On the approximation of Feynman-Kac path integrals, Journal of Computational Physics 185 (2003) 472-483. [DOI: 10.1016/S0021-9991(02)00066-9]

S.D. Bond, B.J. Leimkuhler and B.B. Laird, The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics, Journal of Computational Physics 151 (1999) 114-134. [DOI: 10.1006/jcph.1998.6171]

S.D. Bond and B.J. Leimkuhler, Time-Transformations for Reversible Variable Stepsize Integration, Numerical Algorithms 19 (1998) 55-71. [DOI: 10.1023/A:1019127111709]

Selected Awards:

Selected for the "Rose Award for Teaching Excellence" by the School of Engineering at UIUC (2006).

Rated as Excellent on the "List of Instructors" compiled by the Center for Teaching Excellence Fall 2004, Spring 2005, Fall 2006, Spring 2007, & Fall 2007

Received an "Accenture Engineering Council Award" for "Excellence in Advising" from the School of Engineering at UIUC (2005).

Selected for the La Jolla Interfaces in Science Postdoctoral Fellowship for interfacing research in Mathematics and Computational Biochemistry (2000).

Selected Conferences:
August 11 - 15, 2008, Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods, University of California at San Diego (talk).
June 15 - 20, 2008, Mathematical and Numerical Methods for Free Energy Calculations in Molecular Systems, Banff International Research Station, Canada (talk).
May 6 - 9, 2008, Numerical Modelling of Complex Dynamical Systems, Lorentz Center, Leiden, Netherlands (talk).
July 23 - August 3, 2007, IMA Workshop on Classical and Quantum Approaches in Molecular Modeling, University of Minnesota, Minneapolis (talk; tutorial).
February 19 - 23, 2007, SIAM Conference on Computational Science and Engineering, Hilton Orange County, Costa Mesa, California (session chair; talk).
November 22 - 24, 2006, Maxwell Institute Meeting on Understanding Molecular Simulation, University of Edinburgh, Scotland (talk).
June 4 - 9, 2005, Workshop on Mathematical Issues in Molecular Dynamics, Banff International Research Station, Canada (talk)
May 23 - 27, 2005, International Conference on Scientific Computation and Differential Equations, Nagoya Congress Center, Japan (talk).
August 18 - 21, 2004, Algorithms for Macromolecular Modelling IV, University of Leicester, England (talk).
June 30 - July 4, 2003, International Conference on Scientific Computation and Differential Equations, NTNU, Trondheim, Norway (talk).
May 27 - 31, 2003, SIAM Conference on Applications of Dynamical Systems, Snowbird Resort, Snowbird, Utah (talk).
July 29 - August 3, 2001, Conference on Scientific Computation and Differential Equations, Coast Plaza Hotel, Vancouver, Canada (talk).
May 28 - 30, 2001, International Conference on Computational Science, Hilton, San Francisco, California (talk).
July 13 - 23, 2000, LMS Durham Symposium on Geometric Integration, University of Durham, England.
May 15 - 17, 2000, CECAM meeting on Advanced Integration Methods for Molecular-Dynamics Centre Européen de Calcul Atomique et Moléculaire, Lyon, France (talk).
August 1 - 7, 1999, EquaDiff 99 Conference on Differential Equations, Free University, Berlin, Germany (poster).
July 18 - 28, 1999, Foundations of Computational Mathematics, Oxford University, Oxford, England.
June 28 - July 3, 1998, Gordon Research Conference on Computational Chemistry Tilton School, New Hampshire (poster).
May 26 - 28, 1997, Symposium on Differential-Algebraic Equations: Algebraic and Numerical Aspects, Institut d'Informatique et de Mathématiques Appliquées, Grenoble, France (paper).
May 21 - 24, 1997, Second International Symposium on Algorithms for Macromolecular Modelling, Konrad-Zuse-Zentrum für Informationstechnik, Berlin, Germany (paper).
July 22 - 26, 1996, SIAM Annual Meeting, Hyatt, Kansas City, Missouri (talk).
March 28 - April 1, 1995, Conference on Scientific Computation and Differential Equations, Stanford University, California.