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An application of graphical numerical accelerators in simulations of ion-transport through biological membranes

A. Gorecki
Warsaw University of Life Sciences WULS-SGGW, Nowoursynowska St. 159, 02-787 Warsaw, Poland
Computational Methods in Science and Technology, 19(1), 2013

@article{gorecki2013application,

   title={An application of graphical numerical accelerators in simulations of ion-transport through biological membranes},

   author={G{‘o}recki, A},

   journal={COMPUTATIONAL METHODS IN SCIENCE AND TECHNOLOGY},

   volume={19},

   pages={1},

   year={2013}

}

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The modeling of ion-transport through biological membranes is important for understanding many life processes. The transmembrane potential and ion concentrations in the stationary state can be measured in in-vivo experiments. They can also be 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 I have developed an application for simulation of the ion-flows through a membrane starting from an ensemble of initial conditions, optimized for a Graphical Processing Unit (GPU). The application has been designed for the CUDA (Compute Unified Device Architecture) technology. It is written in CUDA C programming language and runs on NVIDIA TESLA family of numerical accelerators. The calculation speed can be increased almost 1000 times compared with a sequential program running on the Central Processing Unit (CPU) of a typical PC.
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