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William Holmes
Last active: 2/26/2016

Local perturbation analysis: a computational tool for biophysical reaction-diffusion models.

Holmes WR, Mata MA, Edelstein-Keshet L
Biophys J. 2015 108 (2): 230-6

PMID: 25606671 · PMCID: PMC4302203 · DOI:10.1016/j.bpj.2014.11.3457

Diffusion and interaction of molecular regulators in cells is often modeled using reaction-diffusion partial differential equations. Analysis of such models and exploration of their parameter space is challenging, particularly for systems of high dimensionality. Here, we present a relatively simple and straightforward analysis, the local perturbation analysis, that reveals how parameter variations affect model behavior. This computational tool, which greatly aids exploration of the behavior of a model, exploits a structural feature common to many cellular regulatory systems: regulators are typically either bound to a membrane or freely diffusing in the interior of the cell. Using well-documented, readily available bifurcation software, the local perturbation analysis tracks the approximate early evolution of an arbitrarily large perturbation of a homogeneous steady state. In doing so, it provides a bifurcation diagram that concisely describes various regimes of the model's behavior, reducing the need for exhaustive simulations to explore parameter space. We explain the method and provide detailed step-by-step guides to its use and application.

Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MeSH Terms (4)

Diffusion Models, Biological rho GTP-Binding Proteins Software

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