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Brownian dynamics simulation of systems with transitions, particularly conformational transitions in chain molecules

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  • Helfand, Eugene

Abstract

Computer simulations are an effective means of probing complex nonlinear phenomena, and in particular transitions. Most real systems can not be simulated in their entirety because of limitations on computer time and storage. One useful simplification is to replace some degrees of freedom by mean field, frictional, and stochastic terms acting on the remaining degrees of freedom. Numerical techniques for solving the resulting stochastic differential equations of motion have been advanced recently. A problem with simulations is to analyze the wealth of data generated. For the study of transitions, hazard analysis has proved to be effective. An example of the above program, which led to new insights, is the study of conformational transition mechanisms in chain molecules. A crank-like counterrotation of parallel, second-neighbor bonds has been shown to be an important feature of such transition processes.

Suggested Citation

  • Helfand, Eugene, 1983. "Brownian dynamics simulation of systems with transitions, particularly conformational transitions in chain molecules," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 118(1), pages 123-135.
    • Handle: RePEc:eee:phsmap:v:118:y:1983:i:1:p:123-135
    DOI: 10.1016/0378-4371(83)90181-4
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