The techniques of electrophoresis have undergone rapid development in recent years. The problem of predicting and explaining results of electrophoretic experiments requires a well designed dynamical model that reproduces the proper dynamics under well-understood conditions. The challenge is to design a model which can predict complex dynamics in a variety of situations of interest and yet, be efficient enough to run on common workstations. We believe that we have been successful in achieving these goals. Our Brownian Dynamics model is sufficiently general for the investigation of a wide variety of problems (as we will demonstrate), moreover, it implements a simulation innovation, a dynamically self-regulating time increment which varies in accordance with the stresses in the system. This permits for reasonably long simulation times with good averaging statistics. After benchmarking the model with the well understood Rouse regime in isotropic and confined media, the model was applied to two case studies of particular interest: (i) electrophoretic collisions and stacking (chain pinning), and (ii), the onset of the entropic trapping regimes for low fields. We have found that, as far as simple isolated collisions are concerned, our model predicts a widening of electrophoretic molecular bands with an accompanying loss in spatial resolution. The onset of entropic regimes for low fields is demonstratedly counter-productive due to the wide variance of trapping times. Both these results are in accord with recent experimental observations. A more complete study is planned for a supercomputer to elaborate on these findings as well as to investigate kink-formations in pulsed-field gel electrophoresis (PFGE).
| Identifer | oai:union.ndltd.org:uottawa.ca/oai:ruor.uottawa.ca:10393/9525 |
| Date | January 1994 |
| Creators | Nixon, Grant Ian. |
| Contributors | Slater, Gary, |
| Publisher | University of Ottawa (Canada) |
| Source Sets | Université d’Ottawa |
| Detected Language | English |
| Type | Thesis |
| Format | 164 p. |
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