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.