Team:SJTU-BioX-Shanghai/Modeling

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Revision as of 14:27, 13 October 2014

Part I Single Cell

Our project is about the system involving various enzymes, mostly the series enzymes, combining into certain area. This area can be more efficient when it comes to synthesizing or degrading chemicals. So the first question is, whether this system can be so useful when distributing multiple similar areas in a single cell.

Four Types of Distribution

  • Type 1:
    The position of enzyme is distributed randomly in the cell membrane.
  • Type 2:
    The polymerization of certain enzymes, based on MembRing, is distributed randomly inside the cell.
  • Type 3:
    The position of enzyme is distributed randomly inside the cell.
  • Type 4:
    The polymerization of certain enzymes, based on MembRing, is distributed randomly inside the cell.

Hypothesis of Simulation

  1. Metabolism
    [图片一]
    Enzymes: E0, E1,E2
    Substrates:S0,S1,S2,S3
  2. Initial Distribution of Substrates
    All substrates are randomly distributed OUTSIDE the cell in all four simulations.
  3. Movement of Substrates
    The motion of molecules is random, including the rate and orientation.
  4. Catalytic reaction
    The time period of reaction is neglected. When the type of chemical match the type of enzyme, distance is less than threshold, then the enzyme reaction is recognized and recorded.
  5. Other Hypothesis
    Other physical and chemical parameters are under the scaling rule. The whole modeling combined with periodic boundary condition(PBC) to show the real performance of substrates and enzyme system.

Results:

  • Type 1
  • Type 2
  • Type 3
  • Type 4