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


Füchslin, R M; Maeke, T; McCaskill, J S (2009). Spatially resolved simulations of membrane reactions and dynamics: Multipolar reaction DPD. European Physical Journal E - Soft Matter and Biological Physics, 29(4):431-448.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:03 Faculty of Economics > Department of Informatics
Dewey Decimal Classification:000 Computer science, knowledge & systems
Language:English
Date:August 2009
Deposited On:07 Apr 2010 09:46
Last Modified:07 Dec 2017 02:03
Publisher:Springer
ISSN:1292-8941
Additional Information:The original publication is available at www.springerlink.com
Publisher DOI:https://doi.org/10.1140/epje/i2009-10482-x

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