A framework for modeling DNA based molecular systems

Authors:
Sudheer Sahu;Bei Wang;John H. Reif
Affiliations:
Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC
Venue:
DNA'06 Proceedings of the 12th international conference on DNA Computing
Year:
2006

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Abstract

In this paper, we propose a framework for a discrete event simulator for simulating the DNA based nano-robotical systems. We describe a physical model that captures the conformational changes of the solute molecules. We also present methods to simulate various chemical reactions due to the molecular collisions, including hybridization, dehybridization and strand displacement. The feasibility of such a framework is demonstrated by some preliminary results.