Numerical simulations are nowadays an indispensable (essential) part of modern engineering. The idea behind iGEM to design a biological machine implies, that biology becomes step by step an engineering science the synthetic biology. With the insistence of theoretical models and computational methods we can analyze the evolution of single enzyme molecules by simulation of their dynamics and substrate specificity's. We than use this information to build a whole new metabolic network of our synthetic biological machine.
Within single-molecule simulations we focus on analyzing the enzymes of the degradation group. Therefore, we use reduced models (elastic network models ENM's) of these enzymes to quantify the mechanical dynamics. According to this we increase the complexity with force field based molecular dynamics simulations.
For the sequence analysis we quantify evolutionary relations of the amino acid sequence of the proteins used in our project. Therefore we utilize a spectrum of methods obtained from information science.
We use force-field based docking simulations for detailed analysis of the interaction with substrate (Polyethylenterphtalat; short: PET) and enzyme. Moreover we analyze possible influence of the degradation process caused by additives of PET such as plasticizer.
To get a better understanding of all implemented Biobrick functions of our synthetic biological machine our group will illustrate these processes with graphical simulations by Autodesk Molecular Maya.