Loading...

All-Atom Molecular Dynamics Simulation of DNA in Nanoscale

Rezaei, Meisam | 2012

649 Viewed
  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 43000 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. Molecule of DNA is one of the most important biomolecule in cell which contains genetic information to supply the required proteins for body. Evidence shows prefered binding sequence for proteins exist to interact with proteins which this preference is determined not only by specefic chemical interactions between DNA and protein, but also specific suitable geometrical arrangements of DNA have important role to inding DNA oligomer and protein, such as winding DNA around histon to creating nucleosome is related to curvature and deformability of DNA. Thus knowing elastic behaviour and properties of DNA helps us to approach the answer of such questions. Despite the recent dvancement in labratory in nanoscale, it is not completely clear way of exact function of DNA. One of the problems is flexibility of DNA, that this flexibility is affected by external forces due to crystal lattice in crystallography experiments. For such reasons, scientists step into simulation ways in order to study mechanical behaviour of DNA. To study DNA in different scales, different ways are applied .All-atom molecular dynamics simulation be applied for studing DNA in nanometer dimensions and yeild acceptable responses for description of complex behaviour of DNA.The main objective of thesis is all-atom molecular dynamics simulation of DNA. Then we study quantity of Da(L) which shows nonlocal property of DNA structure and compare our results with all-atom molecular dynamics simulaiton by others. Also we study difference in intrinsic curvature of two sequence A4T4 and T4A4 in DNA structure by all-atom molecular dynamics simulation
  9. Keywords:
  10. Molecular Dynamic Simulation ; Nonlocal Interaction ; DNA Molecule Elastic Properties ; DNA ; A-tract Model ; Coarse-grained Model at Base Pair Level

 Digital Object List

 Bookmark

No TOC