MAS 2012 Proceeding

GPU-accelerated modelling of biological membranes ION-transport

Authors:   Adam Gorecki, Krzysztof Dolowy


The ion-transport modeling through biological membranes is important for understanding of many life processes. The transmembrane potential and ion concentrations in the stationary state can be measured in in-vivo experiments. They can be also simulated within membrane models. Here we consider a basic model of ion transport that describes the time evolution of ion concentrations and potentials through a set of nonlinear ordinary differential equations. To reduce the computation time we have developed a GPU-optimized application for simulation of the ion-flows through a membrane starting from an ensemble of initial conditions. The application is written in CUDA programming language and runs on NVIDIA TESLA family of numerical accelerators. The calculation speed can be increased over 10000 times compared with a sequential program running on a PC.

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