Studies of Electrophoresis of Model ssDNA between Two Parallel Plates with Barriers by Monte Carlo Simulations
Date Issued
2005
Date
2005
Author(s)
Tsai, Ho-Gung
DOI
zh-TW
Abstract
There are two topics studied in this work on the basis of Monte Carlo simulation and scaling analysis. Firstly, the diffusion-limited loop formation is investigated for the ssDNA owing to the reversible intrachain reaction. The ssDNA modeled as worm-like chain has reactive sites at both ends with binding energy . The open-to-closed crossover is characterized by the probability curve which depicts the variation of the open-state probability with temperature. According to our study, we find the open-state probability increases as temperature increases. The two-state model is found to be valid. The chain needs to overcome only the binding energy for closed-to-open transition. However, the energy barrier for the open-to-closed transition is found to include both the entropy effect and bending energy.
In the second part of the work, we study the electrophoresis of model ssDNA between two parallel plates with barriers. The barriers can hinder the movements of the chains to achieve the purpose of separation. If the distance between plates (dp) is large compared to the barrier height, the result is similar to the free solution electrophoresis. For small dp, the mobility of the chains decreases at first and then increases as chain length increases. This phenomenon may be attributed to the different degree of compression to the chains of different lengths. An uncharged drag-tag attached to the charged chain is also applied in the work. We find that the end-labeled effect is more significant than the barriers effect. However, the mobility of the end-labeled chain becomes slower and thus it needs more time to separate chains of different sizes.
Subjects
蒙地卡羅
電泳
障礙
模擬
Monte Carlo
electrophoresis
barrier
simulation
Type
thesis
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