Design of a Biomolecular Device That Executes Process Algebra

Process algebras are widely used for defining the formal semantics of concurrent communicating processes. In process algebra, concurrent processes can be specified to execute distinct programs. Processes can also communicate repeatedly with other processes via handshake communication protocols that requires acknowledgment of message reception. Furthermore, processes can branch into multiple processes. This paper considers stochastic π-calculus which is a particularly expressive kind of process algebra providing a specification of probabilities of process behavior such as stochastic delays, communication and branching, as well as rates of execution. Previously, stochastic π-calculus has been used to specify a wide variety of chemical and biological processes. In this paper, we implement stochastic π-calculus at the molecular scale, providing a design for a DNA-based biomolecular device that executes the stochastic πcalculus. Designing this device is challenging due to the requir...

• Type: Conference
• Year: 2009
• Where: DNA
• Authors: Urmi Majumder, John H. Reif
• Keywords: Computational Biology, Concurrent Communicating Processes, DNA 2009, Process Algebra, Stochastic