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A Parallel Plasma Membrane Simulation

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7 Author(s)
Burrage, P.M. ; Inst. for Mol. Biosci. Australia, Univ. of Queensland, Brisbane, QLD, Australia ; Burrage, K. ; Kurowski, K. ; Lorenc, M.
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The plasma membrane protects a cell and even though it is only about 10nm thick it is an incredibly complex and crowded environment, with ensembles of channels, membrane and trans-membrane proteins and microdomains. Hence modelling transport and dynamical processes on the plasma membrane is computationally demanding and in order for a simulation to model an entire cell membrane for several real-time seconds, a high-performance computing implementation is essential. Here we describe the domain decomposition of a plasma membrane simulation in a grid-computing environment. We discuss the issues that arise in balancing the communication requirements with the computational complexity, in both a master-slave and a slave-slave communication model. We also discuss performance and fidelity limitations arising through the necessity of frequent inter-process communication. This parallel implementation will allow systems biology researchers to analyse computationally the complex dynamical processes taking place on an entire cell membrane over a non-trivial time scale.

Published in:

High Performance Computational Systems Biology, 2009. HIBI '09. International Workshop on

Date of Conference:

14-16 Oct. 2009

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