Simul 6: A fast dynamic simulator of electromigration

Gaš, Bohuslav; Bravenec, Petr

doi:10.1002/elps.202100048

Cited by 21 publications

(31 citation statements)

References 35 publications

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“…• Model with multithreaded computation for monovalent and multivalent components, incl. ampholytes, data base of components, in situ detector profiles; options: variable cross-section, electrolyte swapping, input of set of ampholytes for IEF, specific mobilities and pKa values for specified column segments [72] SPYCE 2) Fourier pseudo-spectral method…”

Section: One-dimensional Modelsmentioning

confidence: 99%

“…It includes faster procedures for the numerical integration of partial differential equations and uses multithreaded computation. This made the simulator up to 15 times faster compared to SIMUL5 [ 72 ]. SIMUL6 runs on Windows‐based 64‐bit computers, Linux 64‐bit, and macOS 64‐bit, and it has a user‐friendly interface to input all parameters.…”

Section: Dynamic Simulators For Electrokinetic Separationsmentioning

confidence: 99%

“…3 . The input data of all components used are those provided as example in SIMUL6 [ 72 ] and stemmed from ref. [ 74 ].…”

Section: Dynamic Simulators For Electrokinetic Separationsmentioning

confidence: 99%

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Dynamic computer simulations of electrophoresis: 2010–2020

Thormann

Mosher²

2021

Electrophoresis

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The transport of components in liquid media under the influence of an applied electric field can be described with the continuity equation. It represents a nonlinear conservation law that is based upon the balance laws of continuous transport processes and can be solved in time and space numerically. This procedure is referred to as dynamic computer simulation. Since its inception four decades ago, the state of dynamic computer simulation software and its use has progressed significantly. Dynamic models are the most versatile tools to explore the fundamentals of electrokinetic separations and provide insights into the behavior of buffer systems and sample components of all electrophoretic separation methods, including moving boundary electrophoresis, CZE, CGE, ITP, IEF, EKC, ACE, and CEC. This article is a continuation of previous reviews (Electrophoresis 2009, 30, S16-S26 and Electrophoresis 2010, 31, 726-754) and summarizes the progress and achievements made during the 2010 to 2020 time period in which some of the existing dynamic simulators were extended and new simulation packages were developed. This review presents the basics and extensions of the three most used one-dimensional simulators, provides a survey of new one-dimensional simulators, outlines an overview of multi-dimensional models, and mentions models that were briefly reported in the literature. A comprehensive discussion of simulation applications and achievements of the 2010 to 2020 time period is also included.

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Section: One-dimensional Modelsmentioning

confidence: 99%

Section: Dynamic Simulators For Electrokinetic Separationsmentioning

confidence: 99%

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Dynamic computer simulations of electrophoresis: 2010–2020

Thormann

Mosher²

2021

Electrophoresis

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“…A majority of electrophoresis simulations are based on spatial‐discretization schemes having second‐order accuracy. In particular, electrophoresis simulators such as SIMUL [8] and GENTRANS [17] are based on the second‐order central differencing scheme. The SPRESSO simulator [9,16] offers a choice between the sixth‐order compact finite difference scheme and other first‐ and second‐order accurate spatial‐discretization schemes.…”

Section: Introductionmentioning

confidence: 99%

“…With the advances in mathematical modeling of electrophoretic phenomena, numerical methods, and computing power over the past four decades [1,2], realistic simulations of electrophoresis techniques such as capillary zone electrophoresis (CZE) [3], isotachophoresis (ITP) [4], transient-ITP (t-ITP) [5], isoelectric focusing (IEF) [6], and field amplified sample stacking (FASS) [7] can now be performed on personal computers. Moreover, the availability of open-source electrophoresis simulators such as SIMUL [8], SPRESSO [9], and SPYCE [10] and commercial multiphysics simulation packages such as COMSOL [11] have popularized the use of simulations for research and teaching activities.…”

Section: Introductionmentioning

confidence: 99%

Electrophoresis simulations using Chebyshev pseudo‐spectral method on a moving mesh

Bahga

Gupta

2021

Electrophoresis

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We present the implementation and demonstration of the Chebyshev pseudo‐spectral method coupled with an adaptive mesh method for performing fast and highly accurate electrophoresis simulations. The Chebyshev pseudo‐spectral method offers higher numerical accuracy than all other finite difference methods and is applicable for simulating all electrophoresis techniques in channels with open or closed boundaries. To improve the computational efficiency, we use a novel moving mesh scheme that clusters the grid points in the regions with poor numerical resolution. We demonstrate the application of the Chebyshev pseudo‐spectral method on a moving mesh for simulating nonlinear electrophoretic processes through examples of isotachophoresis (ITP), isoelectric focusing (IEF), and electromigration‐dispersion in capillary zone electrophoresis (CZE) at current densities as high as 1000 A/m2$^{2}$. We also show the efficacy of our moving mesh method over existing methods that cluster the grid points in the regions with large concentration gradients. We have integrated the adaptive Chebyshev pseudo‐spectral method in the open‐source SPYCE simulator and verified its implementation with other electrophoresis simulators.

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On‐capillary fluorescent labeling of saccharides for capillary electrophoresis

2022

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The feasibility of on-capillary derivatization of saccharides by aromatic aminebased fluorescent labeling agents was tested. To avoid the problematic evolution of gaseous hydrogen cyanide, the Schiff base reduction by sodium cyanoborohydride, as the second step of the standard reductive amination protocol, was omitted. Glucose was used as a model analyte and 7-amino-1,3-naphthalenedisulfonic acid as the labeling agent. Our experiments showed that the direct reaction of the saccharide with the labeling agent in 2.5-M acetic acid yields a labeled product that is sufficiently stable to be separated from the labeling agent in 20-mM phosphate buffer, pH 3.5, and detected using UV detection. The glucose and label zones were introduced separately into the capillary and mixed using a negative voltage. Mixing voltage, its duration, the concentration of acetic acid in the reaction zone, and the waiting time between mixing and separation were optimized. To show the applicability of the procedure to a broader range of analytes, a mixture of different types of saccharides, that is, xylose (pentose), fucose (hexose), glucose (hexose), N-acetylglucosamine (N-acetylaminosaccharide), and lactose (disaccharide), was subjected to derivatization and analysis under the optimal conditions. The linearity and repeatability of the process were evaluated as critical parameters for its analytical applications. Six-point calibration dependences in the 1-50 mM range showed excellent determination coefficients of 0.9992 or higher for all five saccharides tested. The repeatability of the labeled saccharide peak areas was between 2.2% and 4.3%.

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Simul 6: A fast dynamic simulator of electromigration

Cited by 21 publications

References 35 publications

Dynamic computer simulations of electrophoresis: 2010–2020

Dynamic computer simulations of electrophoresis: 2010–2020

Electrophoresis simulations using Chebyshev pseudo‐spectral method on a moving mesh

On‐capillary fluorescent labeling of saccharides for capillary electrophoresis

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