Team:SydneyUni Australia/Modelling Results

From 2013.igem.org

Running the Model

The model was run using MATLAB’s ODE45. All enzyme concentrations were given a value of 0.1 mM. The temperature was set as T=298K. A plasma membrane distance of d=2nm was given. The cell concentration was given as 1E8 cells/mL. No cellular growth rate was implemented. Glycolate, ε, was left ‘unprocessed’, i.e. it is left to simply accumulate. Using the constants above the flux took the value: ???

Assumptions

• All enzymes follow MM kinetics as described in the literature.
• The enzymes and metabolites are homogeneously distributed within the cell.
• The metabolites in the pathway are processed only by the proposed enzymes.
• The enzyme concentrations remain constant.
• The partition coefficient for DCA in octanol and water is approximately the same as the partition coefficient for the cell membrane.
• The cells only grow/divide through DCA-derived-glycolate.
• Diffusion can accurately follow
• All cells are of the same size (ie equal membrane surface area)

Raw MATLAB code:

function dy = DCA(t,y)
 
dy=zeros(6,1);
 
dy(1)= -6*(10^4)*0.0463067*(y(1)-y(2));
dy(2)= 6*(10^4)*0.0463067*(y(1)-y(2))-3.3*0.1*(y(2)/(0.53+y(2)));
dy(3)= 3.3*0.1*(y(2)/(0.53+y(2)))-0.0871*0.1*(y(3)/(0.94+y(3)));
dy(4)= .0871*0.1*(y(3)/(0.94+y(3)))- 0.6*0.1*(y(4)/(0.16+y(4)));
dy(5)= 0.6*0.1*(y(4)/(0.16+y(4))) - 25.4*0.1*(y(5)/(20+y(5)));
dy(6)= 25.4*0.1*(y(5)/(20+y(5)));
 
end

Output:

Here is a link!