Design of a Biomolecular Device That Executes Process Algebra

摘要

Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic π-calculus, at the molecular scale by providing a design for a DNA-based biomolecular device that simulates a process algebraic machine. Our design of the molecular stochastic π-calculus system makes use of a modified form of Whiplash-PCR (WPCR) machines. In this design, we connect (via a tethering DNA nanostructure) a number of DNA strands, each of which corresponds to a WPCR machine. This collection of WPCR machines are used to execute distinct concurrent processes, each with its own distinct program. Furthermore, their close proximity enables computation to proceed via communication.