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.