A Parallel Plasma Membrane Simulation

Abstract

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.