Reports

[2007]

Computing Molecular Dynamics Averages:

S.D. Bond and B.J. Leimkuhler, Molecular Dynamics and the Accuracy of Numerically Computed Averages, Acta Numerica 16 (2006) 1-65. [Abstract/Text]

Finite Element Simulation of Neuromuscular Junctions:

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. [Abstract/Text]

Weighted Residual Methods for Free Energy Calculations:

E. Cyr and S. Bond, Using the Method of Weighted Residuals to Compute Potentials of Mean Force, Journal of Computational Physics 225 (2007) 714-729. [Abstract/Text]

Time-Dependent Smoluchowski Equation:

Y. Cheng, J. Suen, D. Zhang, S. Bond, Y. Zhang, Y. Song, N. Baker, C. 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. [Abstract/Text]

Integrators for Hard Sphere Hamiltonian Systems

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. [Abstract/Text]

Continuum modeling of Electrodiffusion:

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). [Abstract/Text]

[2006]

Texture Synthesis and Mixing:

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

[2004]

BPX Preconditioners:

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). [Abstract/Text]

[2003]

Finite Element Simulation of a Synaptic Gap:

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. [Abstract/Text]

Hierarchical Basis Multigrid Methods:

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. [Abstract/Text]

Approximation of Path Integrals:

S.D. Bond, B.B. Laird and B.J. Leimkuhler, On the approximation of Feynman-Kac path integrals, Journal of Computational Physics 185 (2003) 473-485. [Abstract/Text]

Molecular Dynamics Simulation of 1VII:

This web report demonstrates how to simulate a small solvated protein using a standard molecular simulation software package. This particular study focuses on the protein designated as "Villin Head Subdomain (1VII)" and uses the GROMACS software package. Visualization is provided by PyMol (for pdb files) and Matlab (for data).

[1999]

Constant Temperature Molecular Dynamics:

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. [Abstract/Text]

Simulation of Newton's Cradle:

This web report on the use of geometric integrators (reversible and symplectic) for simulating the dynamics of constrained Hamiltonian systems (e.g., Newton's Cradle) was prepared as a final project for B. Leimkuhler's special topics course on geometric integration (MATH 996) at the University of Kansas. The programing component involved developing code in C/C++/OpenGL and implementation of the SHAKE algorithm.

[1998]

Time-Reversible Variable Stepsize Algorithms:

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

Visualization of BPTI:

This web report on the use of various software packages for visualization of proteins (using PDB input files) was prepared as one of several projects for K. Kuczera's course on Biomolecular simulation (BIOL 801) at the University of Kansas.

[1996]

Time-Reversible Variable Stepsize Algorithms:

Some results from a simulation of a box of "hard/soft" spheres.
Some results from a 200eV C60 - C60 collision, using a semi-emperical potential model.
Some results from a high-speed C2-C2 collision, using a semi-emperical potential model.

Dynamics of a Heisenberg Magnet Chain:

Brief description of the Heisenberg Magnet Chain.

[1995]

Dynamics of a Single Spinning Rigid Body:

A short description of the problem.
Results showing convergence of the iteration.
A short movie (130K) showing the behavior of the error.