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
Senior Member of Technical Staff. Sandia National Laboratories, Albuquerque, New Mexico, USA. Fall 2010 – present.
Assistant Professor. Department of Computer Science, University of Illinois, Urbana-Champaign, Illinois, USA. Fall 2003 – 2010.
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
N.V. Roberts, S.T. Miller, S.D. Bond, E.C. Cyr, An implicit-in-time DPG formulation of the 1D1V Vlasov-Poisson equations, Computers & Mathematics with Applications 154 (2023) 103–119. [DOI: 10.1016/j.camwa.2023.11.014]
B.N. Granzow, D.T. Seidl, S.D. Bond, Linearization errors in discrete goal-oriented error estimation, Computer Methods in Applied Mechanics and Engineering 416 (2023) 116364. [DOI: 10.1016/j.cma.2023.116364]
J.A. Mitchell, S.A. Silling, E. Chiu, S.D. Bond, T. Ruggles, Modeling additively manufactured metallic microstructures for dynamic response, Journal of Peridynamics and Nonlocal Modeling 5 (2023) 497–520. [DOI: 10.1007/s42102-022-00093-2]
S.T. Miller, N.V. Roberts, S.D. Bond, E.C. Cyr, Neural-Network Based Collision Operators for the Boltzmann Equation, Journal of Computational Physics 470 (2022) 111541. [DOI: 10.1016/j.jcp.2022.111541]
S.W. Chung, S.D. Bond, E.C. Cyr and J.B. Freund, Regular sensitivity computation avoiding chaotic effects in particle-in-cell plasma methods, Journal of Computational Physics 400 (2020) 1–32. [DOI: 10.1016/j.jcp.2019.108969]
S.D. Bond, B.C. Franke, R.B. Lehoucq and J.D. Smith, Developing and evaluating Malliavin estimators for intrusive sensitivity analysis of Monte Carlo radiation transport, Sandia National Laboratories Technical Report (2019) 1–8. [DOI: 10.2172/1568989]
J.B. Lechman, S.D. Bond, D.S. Bolintineanu, G.S. Grest, C.D. Yarrington and L.E. Silbert, Random walks on jammed networks: Spectral properties, Physical Review E 100 (2019) 1–6. [DOI: 10.1103/PhysRevE.100.012905]
T.B. Costa, S.D. Bond and D.J. Littlewood, Nonlocal and Mixed-Locality Multiscale Finite Element Method, SIAM Multiscale Modeling and Simulation 16 (2018) 503–527. [DOI: 10.1137/16M1090351]
Y. Chen, A. Mazumdar, C.F. Brooks, Bart G. van Bloemen Waanders, S.D. Bond and M.B. Nemer, Remote Distributed Vibration Sensing through Opaque Media using Permanent Magnets, IEEE Transactions on Magnetics 54 (2018) 1–13. [DOI: 10.1109/TMAG.2018.2816578]
M.B. Nemer, Bart G. van Bloemen Waanders, Ellen Yi Chen Mazumdar, O. Guba, A. Mazumdar, S.D. Bond, C.F. Brooks, C.C. Roberts, A.B. Dodd and S.S. Miller, Magnetic Methods for Tracking Particle Motions and Temperatures within Opaque Vessels, Sandia National Laboratories Technical Report (2017) 1–108. [DOI: 10.2172/1527320]
T.B. Costa, S.D. Bond, D.J. Littlewood and S.G. Moore, Peridynamic Multiscale Finite Element Methods, Sandia National Laboratories Technical Report (2015) 1-46. [DOI: 10.2172/1227915]
D.J. Littlewood, S.A. Silling, J.A. Mitchell, P.D. Seleson, S.D. Bond, M.L. Parks, D.Z. Turner, D.J. Burnett, J. Ostien and M. Gunzburger, Strong Local-Nonlocal Coupling for Integrated Fracture Modeling, Sandia National Laboratories Technical Report (2015) 1–100. [DOI: 10.2172/1221526]
Q. Wu, L. Shi, S. Bond and Y. Yu, Surface Texture Synthesis and Mixing Using Differential Colors, International Journal of Advanced Computer Science and Applications 5 (2014) 236–243. [DOI: 10.14569/IJACSA.2014.050433]
S.D. Bond, R.B. Lehoucq and S.T. Rowe, A Galerkin radial basis function method for nonlocal diffusion, In “Meshfree Methods for Partial Differential Equations VII”, Lecture Notes in Computational Science and Engineering 100 (2014) 1–21. [DOI: 10.1007/978-3-319-06898-5_1]
A.D. Baczewski and S.D. Bond, Numerical Integration of the Extended Variable Generalized Langevin Equation with a Positive Prony Representable Memory Kernel, Journal of Chemical Physics 139 (2013) 044107 (11 pages). [DOI: 10.1063/1.4815917]
B. Aksoylu, S.D. Bond, E.C. Cyr and M.J. Holst, Goal-Oriented Adaptivity and Multilevel Preconditioning for the Poisson-Boltzmann Equation, Journal of Scientific Computing 52 (2012) 202–225. [DOI: 10.1007/s10915-011-9539-6]
N. Arizumi and S.D. Bond, On the estimation and correction of discretization error in molecular dynamics averages, Applied Numerical Mathematics 62 (2012) 1938–1953. [DOI: 10.1016/j.apnum.2012.08.005]
J.H. Chaudhry, S.D. Bond and L.N. Olson, A Weighted Adaptive Least-Squares Finite Element Method for the Poisson-Boltzmann Equation, Applied Mathematics and Computation 218 (2012) 4892–4902. [DOI: 10.1016/j.amc.2011.10.054]
J.H. Chaudhry, S.D. Bond and L.N. Olson, Finite element approximation to a finite-size modified Poisson-Boltzmann equation, Journal of Scientific Computing 47 (2011) 347–364. [DOI: 10.1007/s10915-010-9441-7]
S.D. Bond, J.H. Chaudhry, E.C. Cyr and L.N. Olson, A First-Order Systems Least-Squares Finite Element Method for the Poisson-Boltzmann Equation, Journal of Computational Chemistry 31 (2010) 1625–1635. [DOI: 10.1002/jcc.21446]
R.J. Lavarello, S.D. Bond and M.L. Oelze, Regularized Tomographic Density Imaging Using Multiple Frequency Information, 2010 IEEE International Ultrasonics Symposium Proceedings (2010) 2336–2339. [DOI: 10.1109/ULTSYM.2010.5935476]
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]
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]
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], [PMID: 17307283]
Y. Cheng, J.K. Suen, D. Zhang, S.D. Bond, Y. Zhang, Y. Song, N.A. Baker, C.L. Bajaj, M.J. 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], [PMID: 17307827]
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]
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). [DOI: 10.1063/1.2775933], [PMID: 17919055]
Q. Wu, L. Shi, S. Bond and Y. Yu, Laplacian Texture Synthesis and Mixing on Surfaces, Pacific Graphics (2006).
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, October (2004).
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]
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. [DOI: 10.1016/S0006-3495(03)75029-2], [PMID: 12668432]
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]
Funding
LDRD Early Career Award: 157688, 06/2011 – 05/2013
NSF CCF 08-30578: “Collaborative Research: Laplacian-Centered Poisson Solvers and Multilevel Summation Algorithms”, 09/2008 – 08/2011.
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, & Spring 2008
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
June 16 – 20, 2014, MCM3: Multiscale Computational Methods in Materials Modelling Meeting and Tutorial, ICMS, Edinburgh, Scotland (tutorial co-leader).
December 2 – 6, 2013, Stochastic Modeling of Multiscale Systems, Eindhoven Multicale Institute, Eindhoven, Netherlands (talk)
August 7 – 8, 2013, LAMMPS Users’ Workshop and Symposium, Albuquerque, NM (talk)
July 22 – 25, 2013, 12th U.S. National Congress on Computation Mechanics, Raleigh, NC (talk)
June 25 – 29, 2012 Nonlocal Continuum Models for Diffusion, Mechanics, and Other Applications, SAMSI, Research Triangle Park, NC (poster).
July 18 – 22, 2011, International Congress on Industrial and Applied Mathematics, Vancouver, Canada (session chair; talk).
November 11 – 15, 2009, Algorithms for Macromolecular Modeling V, University of Texas, Austin (talk).
September 1, 2009, Computer Science Research Institute, Sandia National Laboratories, Albuquerque (talk).
July 27 – 29, 2009, CECAM Workshop on Fundamental Aspects of Deterministic Thermostats, CECAM-HQ-EPFL, Lausanne, Switzerland (talk).June 1 – 5, 2009, EPSRC Symposium Workshop on Molecular Dynamics, Warwick Mathematics Institute, Coventry, England (talk).
March 2 – 6, 2009, SIAM Conference on Computational Science and Engineering, Hilton Hotel, Miami (talk).
January 5 – 8, 2009, AMS/MAA Joint Mathematics Meeting, Marriott Hotel, Washington, DC (talk).
December 8 – 12, 2008, IMA Workshop on Solvation, University of Minnesota, Minneapolis (session chair).
August 11 – 15, 2008, Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods, University of California at San Diego (talk; tutorial).
June 15 – 20, 2008, Mathematical and Numerical Methods for Free Energy Calculations in Molecular Systems, Banff International Research Station, Canada (session chair; talk).
May 6 – 9, 2008, Numerical Modelling of Complex Dynamical Systems, Lorentz Center, Leiden, Netherlands (talk).
February 29 – March 1, 2008, Gene Golub Symposium, University of Illinois, Urbana, Illinois (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.