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A Framework for Modeling DNA Based Molecular Systems

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Abstract:

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.

Keywords: KINETIC MODEL; NANOROBOTICS; PHYSICAL MODEL; SIMULATOR

Document Type: Research Article

DOI: https://doi.org/10.1166/jctn.2008.1108

Publication date: 2008-11-01

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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