An Object Oriented Simulation of Real Occurring Molecular Biological Processes for DNA Computing and Its Experimental Verification

  • Thomas Hinze
  • Uwe Hatnik
  • Monika Sturm
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2340)


We present a simulation tool for frequently used DNA operations on the molecular level including side effects based on a probabilistic approach. The specification of the considered operations is directly adapted from detailed observations of molecular biological processes in laboratory studies. Bridging the gap between formal models of DNA computing, we use process description methods from biochemistry and show the closeness of the simulation to the reality.


Simulation Tool Bonding Rate Molecular Reaction Polymerase Chain Reaction Cycle Star Activity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    K. Chen, E. Winfree. Error correction in DNA computing: Misclassification and strand loss. In E. Winfree, D.K. Gifford, editors. Proceedings 5th DIMACS Workshop on DNA Based Computers, Cambridge, MA, USA, DIMACS Vol. 54, pp. 49–64, 2000Google Scholar
  2. 2.
    M. Garzon, R.J. Deaton, J.A. Rose, D.R. Franceschetti. Soft molecular computing. In E. Winfree, D.K. Gifford, editors. Proceedings 5th DIMACS Workshop on DNA Based Computers, Cambridge, MA, USA, DIMACS Vol. 54, pp. 91–100, 2000Google Scholar
  3. 3.
    U. Hatnik, J. Haufe, P. Schwarz. Object Oriented System Simulation of Large Heterogeneous Communication Systems. Workshop on System Design Automation SDA2000, Rathen, pp. 178–184, March 13–14, 2000Google Scholar
  4. 4.
    T. Hinze, M. Sturm. A universal functional approach to DNA computing and its experimental practicability. PreProceedings 6th International Meeting on DNA Based Computers, University of Leiden, Leiden, The Netherlands, p. 257, 2000Google Scholar
  5. 5.
    J.A. Joines, S.D. Roberts. Fundamentals of object-oriented simulation. In D.J. Medeiros, E.F. Watson, J.S. Carson, M.S. Manivannan, ed., Proceedings of 1998 conference on Winter Simulation, Washington, USA, pp. 141–150, December 13–16, 1998Google Scholar
  6. 6.
    P.D. Kaplan, G. Cecchi, A. Libchaber. Molecular computation: Adleman’s experiment repeated. Technical report, NEC Research Institute, 1995Google Scholar
  7. 7.
    F. Lottspeich, H. Zorbas. Bioanalytik. Spektrum Akad. Verlag Heidelbg., Berlin, 1998Google Scholar
  8. 8.
    M. Sturm, T. Hinze. Distributed Splicing of \( \mathcal{R}\mathcal{E} \) with 6 Test Tubes. Romanian Journal of Information Science and Technology, Publishing House of the Romanian Academy 4(1–2):211–234, 2001Google Scholar
  9. 9.
    G. Zobrist, J.V. Leonard. Object-Oriented Simulation — Reusability, Adaptability, Maintainability. IEEE Press, 1997Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Thomas Hinze
    • 1
  • Uwe Hatnik
    • 2
  • Monika Sturm
    • 1
  1. 1.Institute of Theoretical Computer ScienceDresden University of Technologyi DresdenGermany
  2. 2.Institute of Computer EngineeringDresden University of Technologyi DresdenGermany

Personalised recommendations