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Modelling Molecular Processes by Individual-Based
Simulations Applied to Actin Polymerisation
Stefan Pauleweit 1 , J. Barbara Nebe 2 , and Olaf Wolkenhauer 1
1 Institute of Computer Science, Dept. of Systems Biology & Bioinformatics,
University of Rostock, 18051 Rostock, Germany
2 Center for Biomedical Research, Dept. of Cell Biology,
University of Rostock 18051 Rostock, Germany
sp173@informatik.uni-rostock.de,
barbara.nebe@med.uni-rostock.de
http://www.sbi.uni-rostock.de
Abstract. Used in ecology, economics and social science, agent-based mod-
elling is also increasingly used in the life science. We use this technique to model
and simulate the processing of actin filaments. These filaments form a major part
of the cell-shape determining cytoskeleton and contribute to a number of cell
functions. In our paper, we develop and investigate three models with different
levels of detail. Our work demonstrates the potential of individual-based mod-
elling in systems biology.
1
Introduction
Agent-based simulations are a promising application emerging in life sciences [15].
Applications of agent-based technologies in systems biology include studies in which
each cell is modelled as an agent [28]. Examples include bacterial chemotaxis [6], the
phenomenon where cells direct their movements in response to external signals, models
of epidermal tissue [10], the formation of a 3D skin epithelium [26] or a hybrid model,
and combination of agent-based simulations and differential equations to analyse the
cell response to epidermal growth factors [30]. Moreover, agent-based models for in-
tracellular interactions representing the carbohydrate oxidation cell metabolism [4], the
cell cycle [27], the NF- κ B signalling pathway [21] and molecular self-organisation,
with the focus on packing rigid molecules [29], have been proposed.
Actin polymerisation is a molecular process that generates long filaments with a
barbed and a pointed end from single actin molecules that become part of the cytoskele-
ton. The cytoskeleton provides the physical structure and shape of cells, as well as plays
an important role in a number of cell functions, including cell motility [3,19], endocyto-
sis [8], or cell division [20]. Understanding of actin organisation has important implica-
tions for practical medical applications, including the development of new topographies
for implant surfaces [14,17].
Here we focus on the spatial and time dependent simulation of actin polymerisa-
tion. The literature describes a number of models analysing the cell motility driven by
actin filaments, using partial differential equations [16]. Another study used Brownian
 
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