title: Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.
abstract: Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.
authors.affiliation: Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94143-2542, USA. Michael.Chevalier@ucsf.edu
authors.forename: Michael W
authors.initials: MW
authors.lastname: Chevalier
authors.forename: Hana
authors.initials: H
authors.lastname: El-Samad
mesh_terms: D000465:Algorithms; D002462:Cell Membrane / Q000737:chemistry*; D004058:Diffusion; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D013269:Stochastic Processes; D013997:Time Factors