Detrapping particles in gel electrophoresis: a numerical study of different pulsed field sequences.

Large particles tend to get trapped in dead-ends more often than small particles when electrophoresed in random cross-linked gels. It is known that pulsed electric fields can be used to free particles from these traps, leading to an increase in velocity and improved size separation. Although numerical and theoretical models have been proposed for the mobility of smaller particles in the so-called Ogston sieving limit, the effect of pulsed fields on trapping has not been previously modeled. We present a numerical study of detrapping and we compare our results with those of To and Boyde (To, K.-Y., Boyde, T. R., Electrophoresis 1993, 14, 597). We use an exact numerical method to examine detrapping in various two-dimensional systems of obstacles. We also propose and investigate new ways to optimize the pulse sequence in order to separate particles of different sizes.

Modeling the separation of macromolecules: a review of current computer simulation methods.

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.