#To do

## Update overleaf with texstudio from desktop!

### Compare complex V results to Nath 2000

* Read over Nath 2000 and compare parameter values (compare order)
* Correct p1, p2, p3 to Vmax, K1, Km
* Discuss how rho is multiplied by ATP Synthase
* If you plug in values for proton ratio and p3 ratio then the only real term
in the denominator that matters is p2, since it is much larger, thus the
magnitude difference between p3 and the paper's p3 is negligible
* This will be a big section in the results
* Add table to compare all the parameter values

### Compare parameter results to literature
* Compare each value and see if these values can be found elsewhere
*

### Discussion
* Talk about the good fit, but the methods have some uncertainty with regard
to whether or not these fits are always the best (parameter space limitation)
* Need more work to test the robustness of the model

#To do

## Update overleaf with texstudio from desktop!

## Read robustness paper from Steph
* Need this for testing robustness and for applicability of the model
* Need this for publishing

### Compare complex V results to Nath 2000

* Read over Nath 2000 and compare parameter values (compare order)
* Correct p1, p2, p3 to Vmax, K1, Km
* Discuss how rho is multiplied by ATP Synthase
* If you plug in values for proton ratio and p3 ratio then the only real term
in the denominator that matters is p2, since it is much larger, thus the
magnitude difference between p3 and the paper's p3 is negligible
* This will be a big section in the results
* Add table to compare all the parameter values

### Compare parameter results to literature
* Compare each value and see if these values can be found elsewhere
* Add table for full comparison as well

## Test Results
* In what case will the mitochondria NOT utilize oxygen
* Try to 'Simulate' to see if the system responds realistically
* We need to compare different situations in the model with experimental
conditions
* See how everything behaves when for instance:
** r = 0 --> run simulation
** We can play with pH (Read over textbook for pH)
** Very small oxygen/and lots and lots of oxygen
* So try all possible behavior combinations
** Say r -> 0, r -> inf
** or O2 -> 0, r -> inf, etc.
** See how these compare to biological expectations
* Fit for just the baseline model, discuss the results of fitting just this
model

### Discussion
* Talk about the good fit, but the methods have some uncertainty with regard
to whether or not these fits are always the best (parameter space limitation)
* Need more work to test the robustness of the model

## For Friday
* Run the simulation with r --> 0 (say r = 10^-10)
* Finish poster
* Have a thesis proposal ready
* Start simulating different conditions
* Fit for JUST the baseline condition

Add final updates from meeting
Add final updates from meeting
