Eur. Phys. J. E 29, 431-448 (2009)
DOI: 10.1140/epje/i2009-10482-x

Spatially resolved simulations of membrane reactions and dynamics: Multipolar reaction DPD

R. M. Füchslin, T. Maeke and J. S. McCaskill

Biomolecular Information Processing (BioMIP), Ruhr-Universität Bochum, Universitätstrasse 150, D-44780, Bochum, Germany

john.mccaskill@rub.de

Received 5 July 2008 / Revised version 9 June 2009 / Published online 21 August 2009

Abstract

Biophysical chemistry of mesoscale systems and quantitative modeling in systems biology now require a simulation methodology unifying chemical reaction kinetics with essential collective physics. This will enable the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex variety of different system constituents. In order to allow a direct link-up with experimental data (e.g. high-throughput fluorescence images) the simulations must be constructed locally, i.e. mesoscale phenomena have to emerge from local composition and interactions that can be extracted from experimental data. Under suitable conditions, the simulation of such local interactions must lead to processes such as vesicle budding, transport of membrane-bounded compartments and protein sorting, all of which result from a sophisticated interplay between chemical and mechanical processes and require the link-up of different length scales. In this work, we show that introducing multipolar interactions between particles in dissipative particle dynamics (DPD) leads to extended membrane structures emerging in a self-organized manner and exhibiting the necessary mechanical stability for transport, correct scaling behavior, and membrane fluidity so as to provide a two-dimensional self-organizing dynamic reaction environment for kinetic studies in the context of cell biology.

Supplementary material in the form of video files available from the Journal web page at 10.1140/epje/i2009-10482-x and are accessible for authorised users.

PACS
02.70.-c - Computational techniques; simulations.
87.16.-b - Subcellular structure and processes.
87.16.A- - Theory, modeling, and simulations.

Correspondence: john.mccaskill@rub.de


© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2009