Parallel implementation of finite volume based method for isoelectric focusing

Shim, Jaesool; Dutta, Prashanta; Ivory, Cornelius F.

doi:10.1007/s12206-009-1001-4

Cited by 6 publications

(9 citation statements)

References 14 publications

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“…Simulation work on IEF was performed with GENTRANS [21–30,37,49–55], other one‐dimensional simulators [59–64], and several multi‐dimensional simulators [31,65–73]. Most data dealing with pH gradient drifts were generated with GENTRANS.…”

Section: Computer Modeling Of Isoelectric Focusing On Ampholyte‐basedmentioning

confidence: 99%

Instabilities of the pH gradient in carrier ampholyte‐based isoelectric focusing: Elucidation of the contributing electrokinetic processes by computer simulation

Thormann

Mosher

2020

Electrophoresis

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Electrokinetic processes that lead to pH gradient instabilities in carrier ampholyte‐based IEF are reviewed. In addition to electroosmosis, there are four of electrophoretic nature, namely (i) the stabilizing phase with the plateau phenomenon, (ii) the gradual isotachophoretic loss of carrier ampholytes at the two column ends in presence of electrode solutions, (iii) the inequality of the mobilities of positively and negatively charged species of ampholytes, and (iv) the continuous penetration of carbonate from the catholyte into the focusing column. The impact of these factors to cathodic and anodic drifts was analyzed by simulation of carrier ampholyte‐based focusing in closed and open columns. Focusing under realistic conditions within a 5 cm long capillary in which three amphoteric low molecular mass dyes were focused in a pH 3–10 gradient formed by 140 carrier ampholytes was investigated. In open columns, electroosmosis displaces the entire gradient toward the cathode or anode whereas the electrophoretic processes act bidirectionally with a transition around pH 4 (drifts for pI > 4 and pI < 4 typically toward the cathode and anode, respectively). The data illustrate that focused zones of carrier ampholytes have an electrophoretic flux and that dynamic simulation can be effectively used to assess the magnitude of each of the electrokinetic destabilizing factors and the resulting drift for a combination of these effects. Predicted drifts of focused marker dyes are compared to those observed experimentally in a setup with coated capillary and whole column optical imaging.

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Section: Computer Modeling Of Isoelectric Focusing On Ampholyte‐basedmentioning

confidence: 99%

Instabilities of the pH gradient in carrier ampholyte‐based isoelectric focusing: Elucidation of the contributing electrokinetic processes by computer simulation

Thormann

Mosher

2020

Electrophoresis

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“…Recently, due to the availability of high performance computers and the development of efficient parallel algorithms, it is possible to simulate several hundred ampholytes in order to form smooth profiles for both narrow-and broad-range IEF. 6,7 Although the aforementioned IEF simulations have been used to explain experimental behavior in 1-D 8,9 and twodimensional (2-D) [10][11][12] problems qualitatively, none of these models have accounted for the effect of temperature. All previous IEF models were based on the same reference temperature, with no consideration of Joule heating in the capillary tube or microchannels.…”

Section: Introductionmentioning

confidence: 99%

Effect of Joule heating on isoelectric focusing of proteins in a microchannel

2014

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Electric field-driven separation and purification techniques, such as isoelectric focusing (IEF) and isotachophoresis, generate heat in the system that can affect the performance of the separation process. In this study, a new mathematical model is presented for IEF that considers the temperature rise due to Joule heating. We used the model to study focusing phenomena and separation performance in a microchannel. A finite volume-based numerical technique is developed to study temperature-dependent IEF. Numerical simulation for narrow range IEF (6 < pH < 10) is performed in a straight microchannel for 100 ampholytes and two model proteins: staphylococcal nuclease and pancreatic ribonuclease. Separation results of the two proteins are obtained with and without considering the temperature rise due to Joule heating in the system for a nominal electric field of 100 V/cm. For the no Joule heating case, constant properties are used, while for the Joule heating case, temperature-dependent titration curves and thermo-physical properties are used. Our numerical results show that the temperature change due to Joule heating has a significant impact on the final focusing points of proteins, which can lower the separation performance considerably. In the absence of advection and any active cooling mechanism, the temperature increase is the highest at the midsection of a microchannel. We also found that the maximum temperature in the system is a strong function of the DpK value of the carrier ampholytes. Simulation results are also obtained for different values of applied electric fields in order to find the optimum working range considering the simulation time and buffer temperature. Moreover, the model is extended to study IEF in a straight microchip where pH is formed by supplying H þ and OH À , and the thermal analysis shows that the heat generation is negligible in ion supplied IEF. V C 2014 AIP Publishing LLC.

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“…This is why efforts of researchers have been devoted to increasing the speed of simulation of electromigration by the parallelization of computation. Two papers of the Dutta group by Shim et al [19] and Yoo et al [20] have shown how the partial differential equations for isoelectric focusing can be efficiently discretized to allow for open multi-processing (OpenMP) or message passing interface (MPI) parallelization, both of which have brought about an increase of the speed of computation. The group of Kler is also active in the simulation of electromigration techniques by using modern software means.…”

Section: Introductionmentioning

confidence: 99%

“…Two papers of the Dutta group by Shim et al. [19] and Yoo et al. [20] have shown how the partial differential equations for isoelectric focusing can be efficiently discretized to allow for open multi‐processing (OpenMP) or message passing interface (MPI) parallelization, both of which have brought about an increase of the speed of computation.…”

Section: Introductionmentioning

confidence: 99%

Simul 6: A fast dynamic simulator of electromigration

Gaš

Bravenec

2021

Electrophoresis

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Simul 6 is a 1D dynamic simulator of electromigration based on the mathematical model of electromigration in free solutions. The model consists of continuity equations for the movement of electrolytes in a separation channel, acid-base equilibria of weak electrolytes, and the electroneutrality condition. It accounts for any number of multivalent electrolytes or ampholytes and provides a complete picture about dynamics of electromigration and diffusion in the separation channel. The equations are solved numerically using software means which allow for parallelization and multithreaded computation. Simul 6 has a userfriendly graphical interface. It is typically used for inspection of system peaks (zones) in electrophoresis, stacking and preconcentrating analytes, optimization of separation conditions, method development in either capillary zone electrophoresis, isotachophoresis, and isoelectric focusing. Simul 6 is the successor of Simul 5, and has been launched as a free software available for download at https://simul6.app/.

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Parallel implementation of finite volume based method for isoelectric focusing

Cited by 6 publications

References 14 publications

Instabilities of the pH gradient in carrier ampholyte‐based isoelectric focusing: Elucidation of the contributing electrokinetic processes by computer simulation

Instabilities of the pH gradient in carrier ampholyte‐based isoelectric focusing: Elucidation of the contributing electrokinetic processes by computer simulation

Effect of Joule heating on isoelectric focusing of proteins in a microchannel

Simul 6: A fast dynamic simulator of electromigration

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