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A Framework for Modeling DNA Based Molecular Systems

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DNA Computing (DNA 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4287))

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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.

The work is supported by NSF EMT Grants CCF-0523555 and CCF-0432038.

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Authors and Affiliations

  1. Department of Computer Science, Duke University, Box 90129, Durham, NC, 27708-0129, USA

    Sudheer Sahu, Bei Wang & John H. Reif

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  1. Sudheer Sahu
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  2. Bei Wang
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  3. John H. Reif
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  1. Department of Chemistry, Purdue University, 560 Oval Drive, 47907-2084, West Lafayette, IN, USA

    Chengde Mao

  2. Faculty of Education and Integrated Arts and Sciences, Department of Mathematics, Waseda University, 1-6-1 Nishiwaseda, Shinjuku-ku, 169-8050, Tokyo, Japan

    Takashi Yokomori

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Sahu, S., Wang, B., Reif, J.H. (2006). A Framework for Modeling DNA Based Molecular Systems. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_19

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