A parallel plasma membrane simulation

Burrage, P. M., Burrage, K., Kurowski, K., Lorenc, M., Nicolau Jr., D. V., Swain, M. and Ragan, M. A. (2009). A parallel plasma membrane simulation. In: 2009 International Workshop on High Performance Computational Systems Biology (HiBi 2009). Proceedings. HiBi 09: 1st International Workshop on High Performance Computational Systems Biology, Trento, Italy, (105-112). 14-16 October, 2009. doi:10.1109/HiBi.2009.18


Author Burrage, P. M.
Burrage, K.
Kurowski, K.
Lorenc, M.
Nicolau Jr., D. V.
Swain, M.
Ragan, M. A.
Title of paper A parallel plasma membrane simulation
Conference name HiBi 09: 1st International Workshop on High Performance Computational Systems Biology
Conference location Trento, Italy
Conference dates 14-16 October, 2009
Proceedings title 2009 International Workshop on High Performance Computational Systems Biology (HiBi 2009). Proceedings
Place of Publication Piscataway, NJ, U.S.A.
Publisher I E E E
Publication Year 2009
Sub-type Fully published paper
DOI 10.1109/HiBi.2009.18
ISBN 9781424449743
9780769538099
Start page 105
End page 112
Total pages 7
Language eng
Formatted Abstract/Summary
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.
Keyword Plasma membrane
Simulation
Parallel programming
Mathematical modelling
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Conference Paper
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Sun, 14 Mar 2010, 10:06:31 EST