High-resolution electrophoretic simulations: performance characteristics of one-dimensional simulators

Mosher, Richard A; Breadmore, Michael C; Thormann, Wolfgang (2011). High-resolution electrophoretic simulations: performance characteristics of one-dimensional simulators. Electrophoresis, 32(5), pp. 532-41. Weinheim: Wiley-VCH 10.1002/elps.201000517

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Three comprehensive one-dimensional simulators were used on the same PC to simulate the dynamics of different electrophoretic configurations, including two migrating hybrid boundaries, an isotachophoretic boundary and the zone electrophoretic separation of ten monovalent anions. Two simulators, SIMUL5 and GENTRANS, use a uniform grid, while SPRESSO uses a dynamic adaptive grid. The simulators differ in the way components are handled. SIMUL5 and SPRESSO feature one equation for all components, whereas GENTRANS is based on the use of separate modules for the different types of monovalent components, a module for multivalent components and a module for proteins. The code for multivalent components is executed more slowly compared to those for monovalent components. Furthermore, with SIMUL5, the computational time interval becomes smaller when it is operated with a reduced calculation space that features moving borders, whereas GENTRANS offers the possibility of using data smoothing (removal of negative concentrations), which can avoid numerical oscillations and speed up a simulation. SPRESSO with its adaptive grid could be employed to simulate the same configurations with smaller numbers of grid points and thus is faster in certain but not all cases. The data reveal that simulations featuring a large number of monovalent components distributed such that a high mesh is required throughout a large proportion of the column are fastest executed with GENTRANS.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Laboratory for Clinical Pharmacology

UniBE Contributor:

Thormann, Wolfgang

ISSN:

0173-0835

Publisher:

Wiley-VCH

Language:

English

Submitter:

Factscience Import

Date Deposited:

04 Oct 2013 14:25

Last Modified:

06 Dec 2013 13:30

Publisher DOI:

10.1002/elps.201000517

PubMed ID:

21308696

Web of Science ID:

000288094500007

URI:

https://boris.unibe.ch/id/eprint/8914 (FactScience: 214566)

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