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Effects of Graphene Nanopores and Temperature on DNA Sequencing Using Molecular Dynamics

Majdi, Amin | 2016

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 49147 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Meghdari, Ali; Khoshnood, Atefeh
  7. Abstract:
  8. Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value, identifying the bases separately is possible. The effect of cell shape, the temperature and voltage size on kinetics and the dynamics of passing Double-Stranded DNA through two geraphene sheet and the ion flow obstruction has been studied in this research by using molecular dynamics simulation. The applied joint-pair's diameter of 2-3 nm, the applied Bias voltage of 0.8 to 2.5 volts range, CHARMM27 field force for Double-Stranded DNA and grapheme, and the TIP3P model for water were used in the present research.Simulation results have shown that by reducing the diameter of the pore pair, reducing the temperature and Bias Voltage, the pore resistance increases; in addition, increasing temperature and voltage and also reducing the distance between two Layer will increase the speed of DoubleStranded DNA transfer and the blocking of the flow
  9. Keywords:
  10. Bias Voltage ; DNA ; Molecular Dynamic Simulation ; Graphene Nanopores ; Complete Current Suppression (CCS)

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