Pursuing Laplace's Vision on Modern Computers
This contribution is an informal essay based on a talk delivered at the
Institute for Mathematics and its Applications (IMA) in Minneapolis, under
the summer program in molecular biology, July 18-22, 1994. I
exclude many technical details, which can be found elsewhere, and instead
focus on the basic ideas of molecular dynamics simulations, with the goal
of conveying to students and non-specialists the key concepts of the theory
and practice of large-scale simulations. Following a description of the
basic idea in molecular dynamics, I will discuss some of the practical
details involved in simulations of large biological molecules, the numerical
timestep problem, and approaches to this problem based on implicit-integration
techniques. I will end with a perspective of open challenges in the field
and directions for future research.
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