IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v362y2006i2p403-422.html
   My bibliography  Save this article

An Ising model of transcription polarity in bacterial chromosomes

Author

Listed:
  • Baran, Robert H.
  • Ko, Hanseok

Abstract

Bacterial genes form clusters of the same transcription polarity and typically exhibit a preference to be coded on the leading strand of replication. An Ising model is proposed to quantify these two phenomena by analogy to the behavior of magnetic dipoles (spins) in a one-dimensional lattice. Corresponding to magnetic forces that co-orient adjacent spins and align them with an externally applied field, we imagine pseudo-forces that influence transcription polarity. Bonds of uniform strength 12J between adjacent sites will model the adhesive (or repulsive) interactions while a polarity entraining force of strength H has the direction of replication. Ten bacterial chromosomes are reduced to spin configurations from which the model parameters are estimated by the method of maximum likelihood under the assumption of thermal equilibrium, following the application of established methods to locate replication origins and termini. χ2-tests show that the model fits the data well in about half the cases but cluster size exhibits excess variance in general. These findings lead to a speculative interpretation of the pseudo-forces as the net effects of numerous insertions and deletions that succeed or fail according to their impact on the motions of enzymatic complexes involved in replication and transcription.

Suggested Citation

  • Baran, Robert H. & Ko, Hanseok, 2006. "An Ising model of transcription polarity in bacterial chromosomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 362(2), pages 403-422.
  • Handle: RePEc:eee:phsmap:v:362:y:2006:i:2:p:403-422
    DOI: 10.1016/j.physa.2005.08.034
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437105008071
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

    File URL: https://libkey.io/10.1016/j.physa.2005.08.034?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Stauffer, Dietrich, 1997. "Relaxation of Ising models near and away from criticality," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 244(1), pages 344-357.
    2. Stanley, H.Eugene, 2000. "Exotic statistical physics: Applications to biology, medicine, and economics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 285(1), pages 1-17.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Eftaxias, Konstantinos & Minadakis, George & Potirakis, Stelios. M. & Balasis, Georgios, 2013. "Dynamical analogy between epileptic seizures and seismogenic electromagnetic emissions by means of nonextensive statistical mechanics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(3), pages 497-509.
    2. Tanya Araújo & Francisco Louçã, 2008. "Bargaining Clouds, or Mathematics as a Metaphoric Exploration of the Unexpected," Working Papers Department of Economics 2008/27, ISEG - Lisbon School of Economics and Management, Department of Economics, Universidade de Lisboa.
    3. Potirakis, Stelios M. & Zitis, Pavlos I. & Eftaxias, Konstantinos, 2013. "Dynamical analogy between economical crisis and earthquake dynamics within the nonextensive statistical mechanics framework," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(13), pages 2940-2954.
    4. Eftaxias, K., 2010. "Footprints of nonextensive Tsallis statistics, selfaffinity and universality in the preparation of the L’Aquila earthquake hidden in a pre-seismic EM emission," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(1), pages 133-140.
    5. Shedrack Tamunoiyowuna & Nduudee, Joy Nenalebari, 2021. "Effect of Video-Taped Instruction and Gender on Senior Secondary Students’ Performance in Physics Practical in Port- Harcourt, Rivers State, Nigeria," International Journal of Research and Scientific Innovation, International Journal of Research and Scientific Innovation (IJRSI), vol. 8(4), pages 210-215, April.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:362:y:2006:i:2:p:403-422. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.