Design of a Biomolecular Device That Executes Process Algebra

Authors:
Urmi Majumder;John H. Reif
Affiliations:
Department of Computer Science, Duke University, Durham, USA;Department of Computer Science, Duke University, Durham, USA
Venue:
DNA Computing and Molecular Programming
Year:
2009

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Abstract

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 驴-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 驴-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.