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Random sampling of the Green’s functions for reversible reactions with an intermediate state. (English) Zbl 1301.82030

Summary: Exact random variate generators were developed to sample Green’s functions used in Brownian Dynamics (BD) algorithms for the simulations of chemical systems. These algorithms, which use less than a kilobyte of memory, provide a useful alternative to the table look-up method that has been used in similar work. The cases that are studied with this approach are (1) diffusion-influenced reactions; (2) reversible diffusion-influenced reactions and (3) reactions with an intermediate state such as enzymatic catalysis. The results are validated by comparison with those obtained by the Independent Reaction Times (IRT) method. This work is part of our effort in developing models to understand the role of radiation chemistry in the radiation effects on human body and may eventually be included in event-based models of space radiation risk.

MSC:

82B80 Numerical methods in equilibrium statistical mechanics (MSC2010)
65C05 Monte Carlo methods
82-08 Computational methods (statistical mechanics) (MSC2010)
60J65 Brownian motion
81V55 Molecular physics
92C05 Biophysics

Software:

Algorithm 680
PDFBibTeX XMLCite
Full Text: DOI

References:

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