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

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, SIMU...

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Bibliographic Details
Published in:Electrophoresis 2011-02, Vol.32 (5), p.532-541
Main Authors: Mosher, Richard A, Breadmore, Michael C, Thormann, Wolfgang
Format: Article
Language:English
Subjects:
Borders
Boundaries
Chemical Phenomena
Computer Simulation
Data smoothing
Dynamics
Electrophoresis - instrumentation
Electrophoresis - methods
Electrophoretic boundary
Flight simulators
Mathematical analysis
Modules
Multivalent components
Organic Chemicals - chemistry
Oscillations
Software
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Summary: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.
ISSN:0173-0835
1522-2683
1522-2683
DOI:10.1002/elps.201000517