This toggle works as a switch that is on with light of 390 nm wavelength. The activation could be implemented in the model by the same expression as in AsLOVpep:

In addition, a reaction of tetramerization occurs with 390nm light irradiation. This means a loss in the amount of D* activator, and our model must contemplate that reaction in order to predict if the efficiency of this alternative circuit could be harmed.

We included in our Matlab model the possibility that VP16 tetramerizes with the light pulse like this:

Being t4 the percentage ϵ (0 - 1) of Dronpa145N-VP16 that tetramerizes with the light pulse.

We have done several simulations with t4={0, 0.3, 0.5, 0.8} with the combination Red-Blue in order to obtain beta:

We can observe that the quantity of D* decreases with the percentage of t4, this makes sense because they are directly related. The quantity of D divides itself into D* and the tetramer. Apparently, in those graphs we cannot identify a big change in the production of the final products that should be affected by the formation of the tetramer: beta and Omega.

In order to be able to appreciate the influence of the tetramerization in products, we got data from our model of the production of beta and Omega: (We also made the numbers relative, dividing by the first one t4=0, in order to see better the influence)

Values for in t=800 (end of blue pulse)

In this graph it’s clear to see that the leakage values of Omega decrease more rapidly than the values of the product we want (beta). The leakage is more affected by tetramerization than the priority production.

This way we can see that tetramerization could even be a good way of decreasing the leakage for values of t4 around 0,4-0,5. The values are looked in t=800, because it’s the end of the second pulse, the maximum value of beta production.

Biological infrastructures which provide this toggle, are actually those that we use in our circuit: PIF6 and PhyB. Here, the novelty would be implemented in the device, which should include a far red light, in order to switch off the toggle after red light irradiation.

If we also considered the blue toggle, then we will have an activation with 390nm light, and switch off with 490 nm

In our model, this would make unnecessary the tagging of B and D. Their disappearance would be achieved by a third input that represents the far red light activation. When this input is activated, the red toggle would be switched off, increasing the grade of AladDNA’s optogenetic control.

function [dxdt] = model_switch_v1(t,x,input_t,input_u1,input_u2,input_u3,input_u4,param)

Far_Red variable would be implemented as a product with Red, as well as Cyan with Blue:

dxdt(m+5,1) = param.kBlue.*x(m+3).*Blue.*Cyan.*(1-param.t4) - param.dDstar.*x(m+5); if ((x(m+5)<=0.0)&& dxdt(m+5,1)<0), dxdt(m+5,1)=0.0; end

Its input would be represented similarly to input_red and input_blue, with the difference that if Far Red is ON, then Far_Red=0. Whereas if it is OFF, Far_Red=1. It is comparable to Cyan and Blue light.

input_red =[zeros(length(input_t),1)];

input_blue =[zeros(length(input_t),1)];

input_far_red =[zeros(length(input_t),1)];

input_cyan =[zeros(length(input_t),1)];

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