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Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level
Published on: September 26, 2016
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
Radek Erban1, S Jonathan Chapman
1Mathematical Institute, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK. erban@maths.ox.ac.uk
Abstract:
Several stochastic simulation algorithms (SSAs) have recently been proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecules and their reactive collisions. In both cases, it is shown that the commonly used implementation of bimolecular reactions (i.e. the reactions of the form A + B --> C or A + A --> C) might lead to incorrect results. Improvements of both SSAs are suggested which overcome the difficulties highlighted. In particular, a formula is presented for the smallest possible compartment size (lattice spacing) which can be correctly implemented in the first model. This implementation uses a new formula for the rate of bimolecular reactions per compartment (lattice site).
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