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Biomolecules and Polymers Translocation Through Biological Single Nanopores and Current Characteristics Analysis

Haji Abdolvahab, Rouhollah | 2012

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 42766 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza; Mobasheri, Hamid
  7. Abstract:
  8. Translocation processes are ubiquitous in biology and biotechnology. Translocation of small molecules, e. g. sugar from maltoporin, metabolites through bacteria and macromolecules like proteins, from channels of cellular organelles and or RNA translocation though
    nuclear pores are of vital importance for cellular metabolism. One of the important applications of translocation processes in biotechnology is to sense translocating macromolecules or small molecules by analyzing the current passing through natural or synthesis channels. Improving our knowledge about this process can also help us to develop new methods for designing the appropriate drugs. In this thesis by studying and analyzing the characteristics of electric current passing through OmpF channel, in presence of different nucleotides, we introduce some parameters which help recognize different nucleotides regarding to the different trends of these parameters versus voltages. Moreover we investigate the translocation of macromolecules inside a cell. With regard to the characteristics inside the living creatures, the mechanism of theses processes are different from the mechanism used in vitro, which is usually large electrical fields. In one of these processes some molecules called chaperone bind on the macromolecule and rectify its translocation through the organelle or cytoplasm. Here by considering stiff macromolecules, we study effects of macromolecule length and sequence, chaperone length and concentration and also its effective binding energy with macromolecule on probability density function of macromolecule translocation time through Nanopore. Monte Carlo simulations are employed to compare the theoretical results derived based on discrete master equation and related Fokker Plank equation. We show that the sequence effects on translocation time is definitely considerable and in some conditions it can even change its order of magnitude. We also show that using translocation time probability density function one can obtain suitable information about the sequence and length of the polymer. Regarding the difference between chaperone binding energies with polymer, polymer’s velocity versus adjacency probability can be decreased or increased. We also show that by selecting suitable parameters of concentration, length and binding energy one can change the regimes continuously from a completely diffusive to a completely bias one.
  9. Keywords:
  10. Sequence ; Macromolecule ; Time Series ; Translocation Phenomena ; Biological Nanopores

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