Theory and numerical simulations play a major role in the development of improved and novel separation methods. In some cases, computer simulations predict counterintuitive effects that must be taken into account in order to properly optimize a device. In other cases, simulations allow the scientist to focus on a subset of important system parameters. Occasionally, simulations even generate entirely new separation ideas! In this article, we review the main simulation methods that are currently being used to model separation techniques of interest to the readers of Electrophoresis. In the first part of the article, we provide a brief description of the numerical models themselves, starting with molecular methods and then moving towards more efficient coarse-grained approaches. In the second part, we briefly examine nine separation problems and some of the methods used to model them. We conclude with a short discussion of some notoriously hard-to-model separation problems and a description of some of the available simulation software packages.
The dynamic behavior of polyelectrolyte chains in the oligomer range is investigated with coarse-grained molecular dynamics simulation and compared to data obtained by two different experimental methods, namely, capillary electrophoresis and electrophoresis NMR. We find excellent agreement of experiments and simulations when hydrodynamic interactions are accounted for in the simulations. We show that the electrophoretic mobility exhibits a maximum in the oligomer range and for the first time illustrate that this maximum is due to the hydrodynamical shielding between the chain monomers. Our findings demonstrate convincingly that it is possible to model dynamic behavior of polyelectrolytes using coarse-grained models for both the polyelectrolyte chains and the solvent induced hydrodynamic interactions.
We use a coarse-grained molecular dynamics model to study the electrophoretic behaviour of flexible polyelectrolyte chains. We first characterize the static properties of the model with respect to the chain length, the polyelectrolyte concentration, additional salt and the influence of an applied external field. Next we investigate the dynamic behaviour in the oligomer range and compare to data obtained by two different experimental methods, namely capillary electrophoresis and PFG-NMR. We find excellent agreement of experiments and simulations when hydrodynamic interactions are accounted for in the simulations. We then present novel estimators for the dynamical effective charge during free solution electrophoresis and compare them to static estimators. We find complete agreement between the static and the dynamic estimators. We further evaluate the scaling behaviour of the effective friction of the polyelectrolyte-counterion complex with the surrounding fluid. We identify a hydrodynamic screening length beyond which the friction during electrophoresis is linear depending on the chain length resulting in a constant mobility for long polyelectrolyte chains. Our results show a convincing agreement with experimental data and demonstrate that it is possible to model dynamic behaviour of polyelectrolytes using coarse
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