Literature DB >> 25514045

Deriving appropriate boundary conditions, and accelerating position-jump simulations, of diffusion using non-local jumping.

P R Taylor1, R E Baker, C A Yates.   

Abstract

In this paper we explore lattice-based position-jump models of diffusion, and the implications of introducing non-local jumping; particles can jump to a range of nearby boxes rather than only to their nearest neighbours. We begin by deriving conditions for equivalence with traditional local jumping models in the continuum limit. We then generalize a previously postulated implementation of the Robin boundary condition for a non-local process of arbitrary maximum jump length, and present a novel implementation of flux boundary conditions, again generalized for a non-local process of arbitrary maximum jump length. In both these cases we validate our results using stochastic simulation. We then proceed to consider two variations on the basic diffusion model: a hybrid local/non-local scheme suitable for models involving sharp concentration gradients, and the implementation of biased jumping. In all cases we show that non-local jumping can deliver substantial time savings for stochastic simulations.

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Year:  2014        PMID: 25514045     DOI: 10.1088/1478-3975/12/1/016006

Source DB:  PubMed          Journal:  Phys Biol        ISSN: 1478-3967            Impact factor:   2.583


  5 in total

1.  Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches.

Authors:  P R Taylor; R E Baker; M J Simpson; C A Yates
Journal:  J R Soc Interface       Date:  2016-07       Impact factor: 4.118

2.  Incorporating domain growth into hybrid methods for reaction-diffusion systems.

Authors:  Cameron A Smith; Christian A Yates
Journal:  J R Soc Interface       Date:  2021-04-14       Impact factor: 4.118

3.  A hybrid algorithm for coupling partial differential equation and compartment-based dynamics.

Authors:  Jonathan U Harrison; Christian A Yates
Journal:  J R Soc Interface       Date:  2016-09       Impact factor: 4.118

Review 4.  Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.

Authors:  Stephen Smith; Ramon Grima
Journal:  Bull Math Biol       Date:  2018-05-21       Impact factor: 1.758

5.  The blending region hybrid framework for the simulation of stochastic reaction-diffusion processes.

Authors:  Christian A Yates; Adam George; Armand Jordana; Cameron A Smith; Andrew B Duncan; Konstantinos C Zygalakis
Journal:  J R Soc Interface       Date:  2020-10-21       Impact factor: 4.118

  5 in total

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