IGEM:Imperial/2010/2010/08/17: Difference between revisions

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(Autocreate 2010/08/17 Entry for IGEM:Imperial/2010)
 
(added notes from meeting with matthieu)
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==Entry title==
==Meeting with Matthieu==
* Insert content here...
'''Modelling of enzymatic reaction'''
*Simulation step might be too big. We need a very small simulation step, given our simulation time.
*Negative concentrations are impossible. Once our concentration goes negative once, the model will just not work properly anymore. So, we have to implement a minimum concentration of c = 0 into our Matlab program.  
*Look into the ode45 solver in Matlab and its different options regarding accuracy.
*Tinkercell uses a different algorithm!!!
*It is possible to multiply all quantities (i.e. concentrations) by a constant to get above a certain threshold (don't forget to rescale equations and especially k-values). However, this increases the margin of error.
'''Modelling of ComD receptor'''
*Important questions: Is the receptor working like an enzyme? Does it only work once?
*We need to be very precise when modelling the receptor. (Look into the biochemistry of the receptor.)
*Look into the binding of the receptor, e.g. can CSP unbind under any circumstances.
*Always check and list the assumptions of the model, e.g. for enzymatic reactions: quasi-steady state
*Check if the assumptions are met for the ComE-ComD system (look at the paper!)
*Look into crosstalk and any other possible reactions




Revision as of 04:22, 17 August 2010

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Meeting with Matthieu

Modelling of enzymatic reaction

  • Simulation step might be too big. We need a very small simulation step, given our simulation time.
  • Negative concentrations are impossible. Once our concentration goes negative once, the model will just not work properly anymore. So, we have to implement a minimum concentration of c = 0 into our Matlab program.
  • Look into the ode45 solver in Matlab and its different options regarding accuracy.
  • Tinkercell uses a different algorithm!!!
  • It is possible to multiply all quantities (i.e. concentrations) by a constant to get above a certain threshold (don't forget to rescale equations and especially k-values). However, this increases the margin of error.

Modelling of ComD receptor

  • Important questions: Is the receptor working like an enzyme? Does it only work once?
  • We need to be very precise when modelling the receptor. (Look into the biochemistry of the receptor.)
  • Look into the binding of the receptor, e.g. can CSP unbind under any circumstances.
  • Always check and list the assumptions of the model, e.g. for enzymatic reactions: quasi-steady state
  • Check if the assumptions are met for the ComE-ComD system (look at the paper!)
  • Look into crosstalk and any other possible reactions


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