Physical simulation with complex states

Computer simulation is now an established tool in all the Sciences. Synthetic biology is no exception and heavily draws on a broad portfolio of biophysical simulation frameworks, ranging from deterministic and stochastic ordinary differential equations to spatially resolved particle dynamics simulations. Yet, most of these biophysical frameworks operate on a relatively small, and disappointingly static state space -- a situation not typically found in living organisms.

Computer science has devised formal language theory as a tool to formalize complex objects and transitions thereof. Formal calculi have been successfully developed to study dynamics of composed objects such as protein complexes, compartmentalized systems, and DNA assemblies. In my talk, I will showcase bottom-up synthetic biology projects primarily based on assemblies of biophysical compartments and DNA, and I will demonstrate how physical simulation and formal calcluli can help increase our understanding of these complex systems. Examples range from the bottom-up assembly of protocells and molecular replicators to programmable chemical synthesis and molecular computing in an artificial cytoplasm.