Loading...

Study Elongation of a Single Strend DNA on the Surface Under Potential Using Monte Carlo Simulation

Kiani, Sedighe | 2014

576 Viewed
  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 46762 (03)
  4. University: Sharif University of Technology
  5. Department: Chemistry
  6. Advisor(s): Parsafar, Gholamabbas; Tafazzoli, Mohsen; Ejtehadi, Mohammad Reza
  7. Abstract:
  8. In this project, the behavior of single strand DNA (ssDNA) that is end-tethred to surface (surface is covered with an layer of mercaptohexane ) through the Monte Carlo simulation has been investigated. To understand this behavior, a ssDNA has been studied through freely jointed chain (FJC) model with electrostatic, base paring, and base-pair stacking interaction. The concentration of sodium chloride salt in solution is 1 mM and the applied surface potential is -1.5 - +0.25 V. Computational results show that the ssDNA chain can have the following configurations: 1) “very closed”, 2) “closed”, and 3) “open” that considering the amount of energy, the mentioned configurations can be compared like this: open > closed > very closed. Distance of the last grain of chain from the surface were studied at different potential. It was found that the potential range of +0.25 - -1.0 V the distance from the surface increases with a slight slope while in the potential range of -1.25 - -1.0 V the distance from the surface suddenly increases. Curve of the distance of the last grain of chain from the surface over the potential fit to the experimental data where α = 0.04 (α is the coverage factor for mercaptohexane). Also, it was found that withinthe lower range of phase transition potential (-1.0 - -1.25 V), the molecule fluctuated in each of three mentioned phase. Based on the fluctuations, the histograms of the dwell steps has been plotted, and it was observed that the histograms can fit to simple exponentials
  9. Keywords:
  10. Biosensor ; Monte Carlo Simulation ; Single Strand DNA

 Digital Object List

 Bookmark

No TOC