Simulations of IEF in microchannel with variable cross‐sectional area

Abstract

This study develops a 1-D mass transport model to describe the electrophoresis transport behavior within a microchannel with a variable cross-sectional area. Utilizing three different numerical schemes, simulations are performed to investigate the IEF of proteins in ampholyte-based pH gradients within both a planar microchannel and a contraction-expansion microchannel, respectively. The simulation results obtained using the modified 1-D mass transport model and the finite-volume method (FVM) for the IEF separation of a single protein sample in a ten-ampholyte-based pH gradient within a planar microchannel are consistent with those presented by Shim et al. [Electrophoresis 2007, 28, 572-586] using a 2-D FVM scheme. In addition, the Courant-Friedrichs-Lewy number insensitive conservation element and solution element (CNI-CESE) method is found to be both more robust and more computationally efficient than the conventional CESE scheme when modeling IEF phenomena within a contraction-expansion microchannel. In modeling the IEF separation of four sample ampholytes in a 20-ampholtye-based pH gradient within a contraction-expansion microchannel, the results obtained using the CNI-CESE scheme are in good agreement with those published in literature. Moreover, the simulations can be performed significantly faster with the new 1-D model and the CNI-CESE scheme. Finally, the results obtained using the modified 1-D mass transport model and the CNI-CESE scheme demonstrate that the concentration of the focused test sample and the resolution of the pH gradient within the microchannel increase as the number of ampholytes used to accomplish the IEF separation process is increased.

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

“…Execution time, which can vary between a few seconds and a full month, depends on the numerical scheme [57,63,65,66,68,69,138], on the PC's chip (Fig. 1A), the PC's operational configuration (Fig.…”

“…behavior not expected to occur in an experiment, the simulation should be repeated without invoking smoothing, and the results compared with the suspect data. Instead of an increased mesh, as with the integration schemes employed in GENTRANS, SIMUL5 and the 2-D model, other algorithms have been tested in various laboratories [57,63,65,66,68,69,138]. Several of the proposed procedures, however, were found to provide data with undesired boundary distortions [57,63,65] and are therefore no longer in use.…”

“…Several of the proposed procedures, however, were found to provide data with undesired boundary distortions [57,63,65] and are therefore no longer in use. Recently described approaches [68,69,138], however, might pave the way for high-resolution simulations at high current densities that can be performed without peak distortions and with lower computation times. The adaptive grid employed by Bercovici et al [69] is a promising way to reach the latter goal.…”

“…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]. Similarly, Chou and Yang reported a 1-D reduced model for the description of ampholyte-based IEF in straight and contractionÀexpansion microchannels [138]. This model uses a conservation element and solution element scheme, which is insensitive to vDt/Dx, the product of local velocity and time interval/grid size.…”

“…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.…”