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Biomolecular swarms – an agent-based model of the lactose operon

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Abstract

We present our latest version of a swarm-based, 3-dimensional model of the lactose (lac) operon gene regulatory system. The lac operon is a well-understood genetic switch capable of self-regulation dependent on the energy source of lactose. Our model includes a 3D visualisation which simulates proteins as agents with physical properties that interact with DNA, molecules, and other proteins, incorporating many of the important aspects of a genetic regulatory system. Our model utilizes a decentralized swarm approach with multiple agents acting independently – according to local interaction rules – to exhibit complex emergent behaviours, which constitute the externally observable and measurable switching behaviour.

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References

  • B Alberts D Bray A Johnson J Lewis M Raff K Roberts P Walter (1998) Essential cell biology : An Introduction to the Molecular Biology of the Cell Garland New York

    Google Scholar 

  • LJS Allen (2003) An Introduction to Stochastic Processes with Applications to Biology Pearson Education Upper Saddle River, NJ

    Google Scholar 

  • JR Beckwith D Zipser (Eds) (1970) The Lactose Operon Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY

    Google Scholar 

  • E Bonabeau M Dorigo G Theraulaz (1999) Swarm Intelligence: From Natural to Artificial Systems Oxford University Press New York

    Google Scholar 

  • JM Bower H Bolouri (Eds) (2001) Computational Modeling of Genetic and Biochemical Networks MIT Press Cambridge, MA

    Google Scholar 

  • I Burleigh G Suen C Jacob (2003) DNA in action! a 3D swarm-based model of a gene regulatory system In: First Australian Conference on Artificial Life Canberra, Australia

    Google Scholar 

  • J Collado-Vides (1992) Towards a grammatical paradigm for the study of the regulation of gene expression B Goodwin P Saunders (Eds) Theoretical Biology. Epigenetic and Evolutionary Order from Complex Systems Johns Hopkins University Press Baltimore, ML 211–224

    Google Scholar 

  • MB Elowitz SA Leibler (2000) ArticleTitleSynthetic gene oscillatory network of transcriptional regulators Nature 403 335–338

    Google Scholar 

  • C Jacob (2001) Illustrating Evolutionary Computation with Mathematica Morgan Kaufmann Publishers San Francisco, CA

    Google Scholar 

  • F Jacob J Monod (1961) ArticleTitleGenetic regulatory mechanisms in the synthesis of proteins Molecular Biology 3 318–356

    Google Scholar 

  • Matsuno H, Doi A, Tanaka A, Aoshima H, Hirata Y and Miyano S (2001) Genomic object net: basic architecture for representing and simulating biopathways. In: Ninth International Conference on Intelligent Systems for Molecular Biology, Copenhagen, Denmark

  • B Müller-Hill (1996) The lac Operon – A Short History of a Genetic Paradigm Walter de Gryter Berlin

    Google Scholar 

  • M Ptashne A Gann (2002) Genes & Signals Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY

    Google Scholar 

  • S Salzberg D Searls S Kasif (Eds) (1998) Computational Methods in Molecular Biology. New Comprehensive Biochemistry Vol. 32 Elsevier Amsterdam

    Google Scholar 

  • G Suen C Jacob (2003) A Symbolic and Graphical Gene Regulation Model of the lac Operon. In: Fifth International Mathematica Symposium Imperial College Press London, England 77–80

    Google Scholar 

  • M Tomita K Hashimoto K Takahashi Y Matsuzaki R Matsushima K Saito K Yugi F Miyoshi H Nakano S Tanida Y Saito A Kawase N Watanabe T Shimizu Y Nakayama (2000) ArticleTitleThe E-CELL Project: towards integrative simulation of cellular processes New Generation Computing 18 IssueID1 1–12

    Google Scholar 

  • JD Watson FHC Crick (1953) ArticleTitleA structure for deoxyribose nucleic acid Nature 171 737–738

    Google Scholar 

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Correspondence to Christian jacob.

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jacob, C., Burleigh, I. Biomolecular swarms – an agent-based model of the lactose operon. Nat Comput 3, 361–376 (2004). https://doi.org/10.1007/s11047-004-2638-7

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  • DOI: https://doi.org/10.1007/s11047-004-2638-7

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