An equation-free computational approach for extracting population-level behavior from individual-based models of biological dispersal

DOI10.1016/J.PHYSD.2006.01.008MaRDI QIDQ2489660zbMATH OpenOpenAlexFDO

Authors Radek Erban, I. G. Kevrekidis, Hans G. Othmer

Publication date 28 April 2006

Published in Physica D (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/physics/0505179

zbMATH Keywords

Monte Carlo simulationsProjective integrationRandom walkChemotaxisIndividual-based modelsCoarse integration

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Population dynamics (general) (92D25) Cell movement (chemotaxis, etc.) (92C17)

Abstract: The movement of many organisms can be described as a random walk at either or both the individual and population level. The rules for this random walk are based on complex biological processes and it may be difficult to develop a tractable, quantitatively-accurate, individual-level model. However, important problems in areas ranging from ecology to medicine involve large collections of individuals, and a further intellectual challenge is to model population-level behavior based on a detailed individual-level model. Because of the large number of interacting individuals and because the individual-level model is complex, classical direct Monte Carlo simulations can be very slow, and often of little practical use. In this case, an equation-free approach may provide effective methods for the analysis and simulation of individual-based models. In this paper we analyze equation-free coarse projective integration. For analytical purposes, we start with known partial differential equations describing biological random walks and we study the projective integration of these equations. In particular, we illustrate how to accelerate explicit numerical methods for solving these equations. Then we present illustrative kinetic Monte Carlo simulations of these random walks and show a decrease in computational time by as much as a factor of a thousand can be obtained by exploiting the ideas developed by analysis of the closed form PDEs. The illustrative biological example here is chemotaxis, but it could be any random walker which biases its movement in response to environmental cues.

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Cited in

(13)

• A toolbox of equation-free functions in Matlab/Octave for efficient system level simulation
• Biased random walks, partial differential equations and update schemes
• Taxis equations for amoeboid cells
• Multiscale analysis of collective motion and decision-making in swarms: an advection-diffusion equation with memory approach
• Portraits of self-organization in fish schools interacting with robots
• Projective and coarse projective integration for problems with continuous symmetries
• From microscopic to macroscopic descriptions of cell migration on growing domains
• Error analysis of diffusion approximation methods for multiscale systems in reaction kinetics
• Learning black- and gray-box chemotactic PDEs/closures from agent based Monte Carlo simulation data
• Multiscale modeling and simulation of traveling waves in biology: a review
• Coarse-grained computational stability analysis and acceleration of the collective dynamics of a Monte Carlo simulation of bacterial locomotion
• Hybrid modelling of individual movement and collective behaviour
• ADM-CLE approach for detecting slow variables in continuous time Markov chains and dynamic data

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