Journal article
Parallel implementation of finite volume based method for isoelectric focusing
Journal of mechanical science and technology, Vol.23(12), pp.3169-3178
12/2009
Handle:
https://hdl.handle.net/2376/106373
Abstract
A message passing interface (MPI) based parallel simulation algorithm is developed to simulate protein behavior in non-linear isoelectric focusing (IEF). The mathematical model of IEF is formulated based on mass conservation, charge conservation, ionic dissociation-association relations of amphoteric molecules and the electroneutrality condition. First, the concept of parallelism is described for isoelectric focusing, and the isoelectric focusing model is implemented for 96 components: 94 ampholytes and 2 proteins. The parallelisms were implemented for two equations (mass conservation equation and electroneutrality equation). The CPU times are presented according to the increase of the number of processors (1, 2, 4 and 8 nodes). The maximum reduction of CPU time was achieved when four CPUs were employed, regardless of the input components in isoelectric focusing. The speed enhancement was defined for comparison of parallel efficiency. Computational speed was enhanced by maximum of 2.46 times when four CPUs were used with 96 components in isoelectric focusing.
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Details
- Title
- Parallel implementation of finite volume based method for isoelectric focusing
- Creators
- Jaesool Shim - School of Mechanical Engineering Yeungnam University Kyeongsan, Kyongbuk Korea 712-749Prashanta Dutta - School of Mechanical and Materials Engineering Washington State University Pullman WA 99164-2920 USACornelius Ivory - School of Chemical Engineering and Bioengineering Washington State University Pullman WA 99164-2710 USA
- Publication Details
- Journal of mechanical science and technology, Vol.23(12), pp.3169-3178
- Academic Unit
- Chemical Engineering and Bioengineering, School of; Mechanical and Materials Engineering, School of
- Publisher
- Korean Society of Mechanical Engineers; Heidelberg
- Identifiers
- 99900546739301842
- Language
- English
- Resource Type
- Journal article