Speaker
Description
I will introduce a graph grammar-based formalism to handle (bio)chemical reaction networks. The formalism provides a set of powerful techniques to specify, construct and analyze chemical reaction spaces. A chemical space is defined by a set of compounds and a "reaction chemistry" defined as a collection of graph transformation rules. This algebraic model of chemical transformation in combination with mathematical optimization techniques makes it possible to explore the bio-synthetic design space in a systematic manner. Questions such as "Does a specified chemical space harbor multiple, possibly competing, routes to a target molecule or harbors reaction motifs of interest?" is rephrased in the mathematical language of integer hyperflows on hyper-graphs offering an efficient way to identify functional networks in the chemical space, such as auto-catalysis, that conform to a formal flow specification. I will briefly touch the question of randomization of chemical reaction networks, and what needs to be preserved to remain during randomization in the realm of chemical reaction networks. If appropriate thermodynamic and kinetic parameterization is available, questions concerning the cost of maintaining pathways that run at a constant throughput can be asked. Finally, rule-base stochastic simulations of closed and open reactive system can be performed, allowing to discover mechanistic ideas how an event of interest, e.g. the construction of a particular molecule is achieved by the concurrent dynamic system.
