Modeling and simulation of IEF in 2‐D microgeometries

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

doi:10.1002/elps.200600402

Cited by 45 publications

(83 citation statements)

References 21 publications

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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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Section: Introductionmentioning

confidence: 99%

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

2014

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“…Several reports deal with the dynamics of focusing in immobilized pH gradients [2,43,70,166]. One paper describes the focusing of proteins in absence of carrier ampholytes [167] whereas the majority of the work deals with the complex discontinuous IEF configuration composed of carrier ampholytes and has been investigated using GENTRANS.…”

Section: Fundamentals Of Iefmentioning

confidence: 99%

“…Finally, Shim et al recently developed a 2-D simulator and applied it to IEF simulations in straight and contractionÀexpansion microchannels of 1 cm length [70,71,179,180]. Most simulations were performed with 25 carrier ampholytes producing a pH 6-9 gradient and two model proteins, which were described by nine hypothetical pK values [71,179] or hen egg-white lysozyme whose pK a value input was determined from a titration curve [180].…”

Section: Fundamentals Of Iefmentioning

confidence: 99%

“…A historical overview together with information on the availability of dynamic simulators is given elsewhere [29]. Most of the dynamic simulators are 1-D. Roberts developed a model with two spatial dimensions [41,42] and Shim et al [70,71] reported the use of a 2-D simulator to provide insight into the behavior of electrophoretic zones migrating through tapered and curved channels. The advantages of a dynamic simulation are (i) the possibility of determining appropriate separation conditions well before any laboratory experiments are undertaken, making method development a simpler task, (ii) the gaining of insight into the result of a particular combination of experimental conditions, information, which provides the understanding of monitored zone patterns and peaks and permits the design of new and superior systems, and (iii) its use for educational purposes.…”

Section: Introductionmentioning

confidence: 99%

“…Models that are currently in use in various laboratories are the 1-D simulators GENTRANS of Mosher et al [44,49,[51][52][53][54][129][130][131][132] and SIMUL5 of Hruška et al [48] (available at http://www.natur.cuni.cz/ Gas), which succeeded SIMUL 4.0 [47]. Interesting new models are those of Bercovici et al [69] (available as the Stanford's Public Release Electrophoretic Separation Solver (SPRESSO), http://microfluidics.stanford.edu/spresso), the 2-D model of Shim et al [70,71,135,136] and the models of Yang and his collaborators [68,138]. The purposes of this review are (i) to provide a brief overview of the specifications of these simulators and how a dynamic simulation is performed, (ii) to demonstrate the versatility and benefits of dynamic computer simulation by discussing high-resolution simulation examples for ZE, ITP, IEF and EKC and (iii) to comprehensively list the applications in which dynamic simulations were reported and used for the description of electrophoretic behavior of sample and buffer components.…”

Section: Introductionmentioning

confidence: 99%

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Dynamic computer simulations of electrophoresis: A versatile research and teaching tool

et al. 2010

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Software is available, which simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. These dynamic models are based upon equations derived from the transport concepts such as electromigration, diffusion, electroosmosis and imposed hydrodynamic buffer flow that are applied to user-specified initial distributions of analytes and electrolytes. They are able to predict the evolution of electrolyte systems together with associated properties such as pH and conductivity profiles and are as such the most versatile tool to explore the fundamentals of electrokinetic separations and analyses. In addition to revealing the detailed mechanisms of fundamental phenomena that occur in electrophoretic separations, dynamic simulations are useful for educational purposes. This review includes a list of current high-resolution simulators, information on how a simulation is performed, simulation examples for zone electrophoresis, ITP, IEF and EKC and a comprehensive discussion of the applications and achievements.

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A pK determination method for proteins from titration curves using principle component analysis

2008

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in Wiley InterScience (www.interscience.wiley.com).Principal component analysis (PCA) technique is used for the precise determination of pK values from titration curves of amphoteric molecules, such as proteins and amino acids. A regression model is developed based on the effective charge of amphoteric molecules. Partial domain method, a new algorithm, is introduced to minimize or remove errors in extracted pK values from experimental (titration curve) data with hidden errors, such as sampling errors or experimental uncertainties. For the validation of our algorithm, 3 pK values are determined from the titration curves of glutamic acid and lysine. The extracted pKs are in exact agreement with the original pKs if partial domain method is used to obtain pKs from an exact (uncertainty free) titration curve. In addition, the effects of various uncertainty levels (1%, 2% and 3% noise) in the experimental titration curves are tested using both partial and full domain methods. Analytic results show that partial domain method is very effective in reducing the errors in extracted pKs especially at larger value of redundant number. Next, partial domain based PCA method is applied to extract 5 pKs from the experimental titration curve of hen egg-white lysozyme protein. These pK values are then used to simulate the isoelectric focusing of lysozyme protein in the presence of 25 biprotic ampholytes in a 2-D (two-dimensional) straight microchannel. The transient, as well as focused state behaviors of lysozyme protein are compared between original titration curve (20 pKs) and approximated titration curve (5 pKs) cases. Although there are minor differences at the early stages of focusing, the focusing time, position, and shapes of protein and ampholytes are identical at focused state.

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Modeling and simulation of IEF in 2‐D microgeometries

Cited by 45 publications

References 21 publications

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

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

Dynamic computer simulations of electrophoresis: A versatile research and teaching tool

A pK determination method for proteins from titration curves using principle component analysis

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