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Simulation of Biomanipulation Using Molecular Dynamics

Mahjour Firouzi, Mohammad Ali | 2011

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  1. Type of Document: M.Sc. Thesis
  2. Language: English
  3. Document No: 41979 (58)
  4. University: Sharif University of Technology, International Campus, Kish Island
  5. Department: Science and Engineering
  6. Advisor(s): Meghdari, Ali; Nejat Pishkenari, Hossein
  7. Abstract:
  8. This thesis is devoted to the simulation of biomolecules manipulation using Molecular dynamics (MD). In order to investigate the manipulation behavior, we have used the Ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a graphene sample as substrate. Along this line, a lot of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between tip and substrate, initial orientation of protein, and the simulation environment (dry or wet). The results demonstrate that tips with bigger diameters and smaller distances with respect to the substrate increase the chance for successful manipulation. Also when the tip touches the middles of the β-strands, the manipulation process is successful while pushing the α-helix direction of the protein leads to an unacceptable manipulation. In addition, the simulation results elucidate that a dry environment improves the quality of biomanipulation. Another feature needing attention is that since the simulation system includes a lot of atoms, and therefore large number of computations, we have used packages employing parallel processing techniques
  9. Keywords:
  10. Molecular Dynamics ; Carbon Nanotubes ; Biomanipulation

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