Team:USTC/Model
Protein expression, semi-conductor formation, and electron transfer are 3 important parts of our system and play an important role in both photo-catalysis and energy harvest processes in our system.
In our modeling part, we build several models to demonstrate and simulate protein expression, semi-conductor crystallization and electron transfer process of our system. Furthermore, we can use it to guide our experiments' design and predict our experiments' results.
DLA Cyrstal
In our project, CdS (Cadmium Sulfide) clusters are the source of electrons except for electrode. We were very curious about the structure of the CdS attached to the cell membrane of bacteria, for it could tell us the effective area of reaction which is related to the possibility of the electron transfer. We build a DLA model by fundamental physics laws to demonstrate the crystallization process of the semi-conductor on the membrane of E.coli.
Electron transfer
Semi-conductor
In this part, we focus on the distribution of electrons with their energy difference and the change of electron energy after absorbing the energy of a photon, which is the basis of energy transformation. By using some quantum mechanics rules, we recognize the feasibility of our design and calculated the efficiency of our photo-electron transform happened in our system. This model could help us understand more about the essence of photo-catalyst CdS clusters. Furthermore, guide our system design and pointed out the next step to improve our system.
Markov
As for electron transfer, Markov model is an approximate simulation for us to know the possibility of electrons' transition. We resultant the proteins' motion as Brownian motion. The direct contact of proteins is necessary for electron transfer. The contact of proteins can be described as a function of possibilities according to Markov pathway. By this method, we successfully simulate and predict the electron flux between cathode and cytoplasm.
MeCiM
For another way of thinking, we also build a current circle to simulate the whole process from the cathode to the cytoplasm of E.coli. By previous data from article and some reasonable assumptions, both of these two models successfully predict our experiment results.
UPEP
In the end, we build a platform called UPEP (Universal Protein Expression Platform) to predict the concentration of target proteins after induction of some compounds regulated by quorum sensing (QS) system, which is widely used in synthetic biology. By using basic biochemical reaction rate laws, we simulate the expression process of any protein. To describe the biochemical involved in the induction of protein expression, we employ law of mass action for steady state. This method can use in most of the protein expressions. For this reason, everyone can use this simulation to predict their protein expression according to the specific parameters relating to the properties of protein and induction condition.
