Modeling the separation of macromolecules: A review of current computer simulation methods
Abstract Theory and numerical simulations play a major role in the development of improved
and novel separation methods. In some cases, computer simulations predict counterintuitive …
and novel separation methods. In some cases, computer simulations predict counterintuitive …
Theory of DNA electrophoresis (∼ 1999–2002 ½)
GW Slater, S Guillouzic, MG Gauthier… - …, 2002 - Wiley Online Library
Over the last two decades, the introduction of new methods such as pulsed‐field gel
electrophoresis and capillary array electrophoresis has made it possible to map and …
electrophoresis and capillary array electrophoresis has made it possible to map and …
Influence of confinement on the spreading of bacterial populations
DB Amchin, JA Ott, T Bhattacharjee… - PLoS computational …, 2022 - journals.plos.org
The spreading of bacterial populations is central to processes in agriculture, the
environment, and medicine. However, existing models of spreading typically focus on cells …
environment, and medicine. However, existing models of spreading typically focus on cells …
Gel electrophoretic mobility of single‐stranded DNA: The two reptation field‐dependent factors
The reptation model is the dominant theory in understanding the electrophoretic separation
of single‐stranded DNA molecules in gels or entangled polymer solutions. Recently, we …
of single‐stranded DNA molecules in gels or entangled polymer solutions. Recently, we …
An exactly solvable Ogston model of gel electrophoresis. 7. Diffusion and mobility of hard spherical particles in three-dimensional gels
JF Mercier, GW Slater - Macromolecules, 2001 - ACS Publications
We extend our lattice model of gel electrophoresis (and diffusion) to the study of the
continuum limit (no lattice effect) for hard spherical particles migrating in periodic and …
continuum limit (no lattice effect) for hard spherical particles migrating in periodic and …
Numerically exact diffusion coefficients for lattice systems with periodic boundary conditions. II. Numerical approach and applications
JF Mercier, GW Slater - The Journal of chemical physics, 1999 - pubs.aip.org
In the first part of this short series Mercier Slater and Guo, J. Chem. Phys. 110, 6050 1999,
preceding paper, we derived two algebraically exact methods to calculate the scaled …
preceding paper, we derived two algebraically exact methods to calculate the scaled …
Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles
MW Stefferson, SL Norris, FJ Vernerey… - Physical …, 2017 - iopscience.iop.org
Crowded environments modify the diffusion of macromolecules, generally slowing their
movement and inducing transient anomalous subdiffusion. The presence of obstacles also …
movement and inducing transient anomalous subdiffusion. The presence of obstacles also …
Optimizing the accuracy of lattice Monte Carlo algorithms for simulating diffusion
MV Chubynsky, GW Slater - Physical Review E—Statistical, Nonlinear, and …, 2012 - APS
The behavior of a lattice Monte Carlo (LMC) algorithm (if it is designed correctly) must
approach that of the continuum system that it is designed to simulate as the time step and …
approach that of the continuum system that it is designed to simulate as the time step and …
[HTML][HTML] Communication: Distinguishing between short-time non-Fickian diffusion and long-time Fickian diffusion for a random walk on a crowded lattice
AJ Ellery, RE Baker, MJ Simpson - The Journal of Chemical Physics, 2016 - pubs.aip.org
The motion of cells and molecules through biological environments is often hindered by the
presence of other cells and molecules. A common approach to modeling this kind of …
presence of other cells and molecules. A common approach to modeling this kind of …
An exactly solvable Ogston model of gel electrophoresis VI. Towards a theory for macromolecules
J Boileau, GW Slater - Electrophoresis, 2001 - Wiley Online Library
In this article, we present a generalized version of our lattice model of low‐field gel
electrophoresis that allows us to treat the case of macromolecules such as short linear or …
electrophoresis that allows us to treat the case of macromolecules such as short linear or …