Regensburg 2010 – scientific programme

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DY: Fachverband Dynamik und Statistische Physik

DY 5: Statistical Physics of Biological Systems II (joint session of BP + DY)

DY 5.2: Talk

Monday, March 22, 2010, 14:30–14:45, H45

Using GFRD to Study Pattern Formation due to the Interplay of Active and Passive Transport — •Thomas Sokolowski, Nils Becker, Laurens Bossen, Thomas Miedema, and Pieter Rein ten Wolde — FOM Institute AMOLF, Science Park 113, 1098 XG Amsterdam, The Netherlands

Cells exploit the interplay of active transport along cytoskeletal tracks and cytosolic passive diffusion to establish a wide range of spatial patterns of functional proteins, mRNA and specialized organelles. Such systems are not well-stirred, so standard simulation techniques can be very expensive while coarse-graining may be inappropriate.

Green's function reaction dynamics (GFRD) is an exact event-driven chemical simulation scheme based on analytical solutions of the Smoluchowski equation with appropriately chosen boundary conditions. For sufficiently low particle concentrations up to 1uM it allows for spatially resolved stochastic simulations of many-particle-systems with an efficiency orders of magnitude higher as compared to common Brownian dynamics schemes.

Based on GFRD we develop a framework which allows for a spatio-temporal stochastic simulation of both active and diffusive movement in different geometries to study pattern formation arising from the interplay the two transport types.