Team:SCU-China/Model
MODELING
OVERVIEW
Modeling in synthetic biology is a bridge liaising the past and the future of the experiments. Bringing the elements from physics and chemistry and using the language of math to depict the picture of the design, modeling is indeed a process starting before the begining of the experiments and finishing after the end of them. Here in the project of 2019 SCU-China, we conducted computational structural biological simulation before experiments, delay system simulation during the experiments and enzyme kinetic simulation after the experiments. More details about our project.
Integrated modeling
- Structural prediction which gives a fairly reliable structure of the poorly studied enzyme Cns1, Cns2 and Cns3 and examines the effect of His tag.
- Molecular dynamic simulation which calibrates the improperty of the predicted structure, gives a structural guildline of the linker determination with the help of molecular docking and illustrates the binding processes between the enzymes and the substrates.
- Enzyme kinetic simulation which states the necessity of fusion expression and the concentration relationship between pentostatin and cordycepin.
- Genetic analysis about the delay system using ordinary differential equations which reveals the delay time of the system with the different addition of the methionine concentration.
Computational Structural Biology
We constructed various kinds of simulations using the methods in computational structural biology to enrich the characterisation of the structural properties of the enzymes.
Enzyme Kinetic Simulation
We use enzyme kinetic simulation to illustrate how fusion expression is beneficial in the theory of diffusion and to show the concentration relationship between pentostatin and cordycepin.
Delay System Simulation
We developed a model to simulate the expression level of our genetic circuit in our project which connects the delay time with the concentration of added methionine.