Team:Wageningen UR/Notebook/OptogeneticKillSwitchModel
This modeling work was done by Mario Beck.
June
Week 1-3
Literature research on pDusk and pDawn system as well as mazEF toxin antitoxin system.
Week 4
Getting familiar with Matlab and setting backbone model structure
July
Week 5-6
First dynamic model structure of pDusk and pDawn was built. Light unit conversion was is given here:
h = 6.63*10-34 ([Js] Planck's constant)
c = 2.988*108 ([m/s] speed of light)
lambdanm = 470 (% [nm] wavelength)
NA = 6.022*1023 ([mol-1] Avogadro's constant)
Ninterm = Ninitial*10-2 ([µW*cm^-2] → [W*m-2])
Ep = h*c/lambdanm (distinct energy quanta of a photon)
Np = Ninterm*lambdanm*106/(1.988*10-16) (number of photons; lambda in [nm])
Eq = Np/NA (photonflux N = Eq in [µmol*m-2*s-1])
N = Eq*60*60 ([µmol*m-2*s-1] → [µmol*m^-2*h^-1])
Week 7-8
Vacation
August
Week 9-11
Improved the equations for pDusk and pDawn. And added the equations for mazE and mazF.
Week 12
Got first useful model results for pDusk and pDawn individually. At this point, there was no weighted means approach.
September
Week 13-14
Realised, that we should combine both the pDusk and pDawn scoring function with a weighted means approach. Started to rewrite the whole script.
Week 15
Vacation
Week 16
Noticed problem with the complex formation. Read up on the complex formation of mazEF. There are actually several stages of the complex. After some iterations, we concluded to model the complex as done in the current equations.
October
Week 17-18
Worked on updating last adjustments. Rewrote all Matlab files to a readable format - noticed quite some small bugs on the way. Ran the analysis and the evaluation. Got some preliminary results from the lab! Implemented that in my analysis last minute.
Week 19
The Wiki Week. Matlab Code.
