Team:HZAU-China/Modeling/Coupling

Mixed-Reality CellBidirectional coupling between real and virtual bio-oscillators

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Coupling

Virtual-virtual coupling

Based on the experimental result, we select the dual-feedback oscillator to finish the modulating and coupling process. First, we will finish the virtual-virtual coupling. So different initial values of parameters are set to the simulation to form two e-oscillators which are of the same properties.

Then how could they adjust to each other and be strongly coupled or synchronized? We think about the dynamic equilibrium of wolf and rabbit. If the number of wolves increases rapidly, lots of rabbits would be eaten and the number would reduce. Faced with the decrease of prey, the quantity of wolves would also cut down. On the contrary, rabbits would multiply with fewer natural predators. Cycling like these, wolf and rabbit would finally reach the dynamic balance.

According to the above mechanism, we make the two e-oscillators pass the parameters and affect each other. In terms of the transfer function, with the enhancement of the light intensity, the expression of lacI will reduce, which is proportional to the other e-oscillator’s light intensity. It means that the illumination intensity of e-oscillator 2 will decrease and the corresponding lacI will increase. Then lacI will also be inversely linked to the e-oscillator 1. With the circulation and regulation, the two e-oscillator will be coupled or synchronized gradually.

To achieve the process of coupling or synchronization, we write programs in MATLAB and get the simulation result shown in video 1.

video 1. Simulation result of virtual-virtual coupling.

Mixed-reality of physics

In the second stage, LED lamp controlled by single-chip replace the fluorescence released by E.coli. Based on the virtual-virtual coupling, LED will glow following one of the e-oscillators simulated above as the physical real part, while the other e-oscillator will be the virtual part.

Through a camera, intensity of LED will be transfer to computer and affect the e-oscillator. The returned value of e-oscillator will also be passed to the physical real part by single-chip. With the interaction, the two parts will get coupled in the end. The details of connecting device are specified in our Interface Hardware part.

Figure 1. The complete design of physical device.

We program scripts in Python with an embedded code in MATLAB(You can click here to download the codes). And then we put the LED lamp and camera in dark place and run the program. We get the simulation result in Video 2.

video 2. Simulation result of mixed-reality of physics.

Oscillator 1 is the dynamic trajectory of e-oscillator in computer, while Oscillator 2 represents the state of LED. The blue square in the upper right corner is the light intensity image of LED observed by camera(we only read the B values of RGB). As you can see, the brightness of blue changes following the interaction. Besides, the small box in the upper left corner shows the facade of LED lamp, which is manually shot by us in dark environment. From the oscillation images, we can find that the virtual part and the physical real part get synchronized gradually.

So far we have finished the second stage of our project. The next step, we will achieve the third stage, mixed-reality state.

Reference

1.Arthur P, Jangir S, Howard L, et al. Rapid and tunable post-translational coupling of genetic circuits.[J]. Nature, 2014, 508(7496):387-391.

2.Stricker J, Cookson S, Bennett M R, et al. A fast, robust and tunable synthetic gene oscillator[J]. Nature, 2008, 456(7221):516-519.

3.O’Brien E L, Itallie E V, Bennett M R. Modeling synthetic gene oscillators[J]. Mathematical Biosciences, 2012, 236(1):1–15.

4.Tabor J J, Salis H M, Simpson Z B, et al. A synthetic genetic edge detection program.[J]. Cell, 2009, 137(7):1272-1281.

5.Hubler A, Gintautas V. Experimental evidence for mixed reality states[J]. Complexity, 2011, 13(6):7–10.

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