A Framework for Modeling DNA Based Molecular Systems

Recent successes in building large scale DNA nanostructures and in constructing DNA nanomechanical devices have inspired scientists to design more complex nanoscale systems. The design process can be made considerably more efficient and robust with the help of simulators that can model such systems accurately prior to their experimental implementation. In this paper, we propose a framework for a discrete event simulator for simulating the DNA based nanorobotical systems. It has two major components: a physical model and a kinetic model. The physical model captures the conformational changes of molecules, molecular motions and molecular collisions. The kinetic model governs the modeling of various chemical reactions in a DNA nanorobotical systems including the hybridization, dehybridization and strand displacement. The feasibility of such a framework is demonstrated by some preliminary implementations.

• Type: Conference
• Year: 2006
• Where: DNA
• Authors: Sudheer Sahu, Bei Wang, John H. Reif
• Keywords: Bioinformatics, DNA 2006, DNA Nanomechanical Devices, Kinetic Model, Physical Model