IGEM:Imperial/2010/2010/08/26

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Meeting with Dr. Matthieu Bultelle

Output Amplification Model (Catechol)

  • Costrain the system: Force our system to be positive by imposing constraints (use max-function in Matlab).
  • Change time scale, remember to rescale constraints (we have tried this but it didn't seem to work).
  • Look up spline-function in Matlab.
  • Look up Rouge-Kutta, which is a better way of solving ODEs than Euler. Rouch-Kutta is what the Matlab ode-solvers is based on.
  • Create an interpolated array to allow running the program until a certain point in time. (This is because Matlab does not deal very well with memory allocation?)
  • ode45: All we need as inputs is initial condition, initial time and final time. ode-solvers do not adapt themselves, which can be a problem!
  • Simulate the system with very high precision for a very short period of time. (Very important for time periods where our system varies very fast.)
  • For the reaction A + B <--> C: Solve this equation by conservation of mass. i.e. X = k(A0 - X)(Bo - X). Solve this equation for Xlimit to obtain an analytical solution. This is to get an idea of how fast A, B or C increase (or decrease) to their final value. This is the crucial timestep that we need to simulate with high precision!

Protein Display Model

  • Check this model for false positives.
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