Electrophoresis of spheres with uniform zeta potential in a gel modeled as an effective medium

Allison, Stuart A.; Yao, Xin; Pei, Hongxia

doi:10.1016/j.jcis.2007.04.030

Cited by 46 publications

(68 citation statements)

References 43 publications

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“…A persistence length of this magnitude is consistent with independent studies [44]. Also, a gel fiber radius of 2.5 nm is consistent with earlier modeling studies of DNA diffusion [16] as well as the electrophoresis of Au nanoparticles [15] in agarose gels. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA.…”

Section: Discussionsupporting

confidence: 90%

“…This motivated the choice of 1.52 nm. The choice of the higher values comes from fitting the electrophoretic mobility of Au nanoparticles in agarose gels [15]. From Figure 4, a gel fiber radius of about 2.5 nm appears to be most consistent with experiment.…”

Section: Experimental Section: Rotational Relaxation Of Dna In a Dilusupporting

confidence: 52%

“…The diffusion of a host particle through a rigid gel matrix is reduced, relative to diffusion in "free solution", by long range hydrodynamic interaction and short range steric effects. For translational diffusion, these two effects can be considered separately [3,[15][16][17]. A simple way of dealing with the contribution of long range hydrodynamic interaction makes use of the Effective Medium (EM) model originally developed by Brinkman [18], and Debye and Bueche [19].…”

Section: Introductionmentioning

confidence: 99%

“…Starting from a microscopic model, Felderhof and Deutch were able to derive the Brinkman equation as a mean field approximation [20]. The EM model has been applied to translational diffusion [3,4,16,21], rotational diffusion [20], electrophoresis [15,22], and the electrophoretic stretch of duplex DNA in gels [23,24].…”

Section: Introductionmentioning

confidence: 99%

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Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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Abstract:In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM) model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M  0.010 gm/mL), good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing. OPEN ACCESSPolymers 2011, 3 847

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Section: Discussionsupporting

confidence: 90%

Section: Experimental Section: Rotational Relaxation Of Dna In a Dilusupporting

confidence: 52%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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“…A test of the terms arising from the ion-concentration perturbations was undertaken by comparison with independently calculated mobilities for charged gels (without regulation), provided by Professor S. A. Allison (private communication), using a hybrid methodology based on the works of Allison et al [25] and Allison et al [16].…”

Section: Perturbationsmentioning

confidence: 99%

Hydrogel charge regulation and electrolyte ion-concentration perturbations in nanoparticle gel electrophoresis

Hill¹

2015

Proc. R. Soc. A.

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Gel electrophoresis of spherical nanoparticles (NPs) is studied using an electrokinetic model that couples the ion conservation equations to the Poisson and fluid momentum equations, thus including the so-called polarization and relaxation processes. This model is therefore the chargedgel electrophoresis analogue of the well-known O'Brien and White solution of the standard electrokinetic model for free-solution electrophoresis. Results are provided for the small NPs (size ∼ 10 nm) to which gelelectrophoresis is relevant, since particles must be small enough to permeate the gel: these include the particle drag coefficient (or Brownian diffusivity), which is subject to hydrodynamic screening and electroviscous effects, and the electrophoretic mobility, which is subject to non-linear electrostatic and charge polarization influences. Also addressed are the influences of charge-regulating gels and the accompanying particle-induced immobile charge-density perturbations. Ion-concentration perturbations attenuate the electrophoretic mobility and enhance the drag coefficient according to the particle charge and the mobility of the most abundant counterion. However, dynamic regulation of the hydrogel charge-termed the secondary immobile charge-density perturbation-has a negligible influence on the particle mobility, and may therefore be neglected for most practical purposes.

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Review modeling the free solution and gel electrophoresis of biopolymers: The bead array‐effective medium model

2007

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Free solution and gel electrophoresis is an extremely useful tool in the separation of biopolymers. The complex nature of biopolymers, coupled with the usefulness of electrophoretic methods, has stimulated the development of theoretical modeling over the last 30 years. In this work, these developments are first reviewed with emphasis on Boundary Element and bead methodologies that enable the investigator to design realistic models of biopolymers. In the present work, the bead methodology is generalized to include the presence of a gel through the Effective Medium model. The biopolymer is represented as a bead array. A peptide, for example, made up of N amino acids is modeled as 2N beads. Duplex DNA is modeled as a discrete wormlike chain consisting of touching beads. The technical details of the method are placed in three Appendices. To illustrate the accuracy and effectiveness of the approach, two applications are considered. Model studies on both the free solution mobility of 73 peptides ranging in size from 2 to 42 amino acids, and the mobility of short duplex DNA in dilute agarose gels are discussed.

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Electrophoresis of spheres with uniform zeta potential in a gel modeled as an effective medium

Cited by 46 publications

References 43 publications

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Hydrogel charge regulation and electrolyte ion-concentration perturbations in nanoparticle gel electrophoresis

Review modeling the free solution and gel electrophoresis of biopolymers: The bead array‐effective medium model

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