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Chin. Phys. B, 2013, Vol. 22(12): 129402    DOI: 10.1088/1674-1056/22/12/129402
GEOPHYSICS, ASTRONOMY, AND ASTROPHYSICS Prev   Next  

Transcription’s bubble under the influence of long-range interactions and helicoidal coupling

Mirabeau Sahaa, Timoléon C. Kofanéa b
a Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaoundé, P. O. Box 812, Yaoundé, Cameroon;
b The Abdus Salam International Center for Theoretical Physics, P. O. Box 586, Strada Costiera 11, I-34014 Trieste, Italy
Abstract  The influence of power-low long-range interactions (LRI) and helicoidal coupling (HC) on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase (RNAP) binds to it at the physiological temperature is analytically and numerically investigated in this paper. We have made an analogy with the Heisenberg model Hamiltonian of an anisotropic spin ladder with ferromagnetic legs and anti-ferromagnetic rung coupling. When we limit ourselves to the second-order terms in the Taylor expansion, the DNA dynamics is found to be governed by a completely integrable nonlinear Schrödinger (NLS) equation. In this case, results show that increasing the value of HC force or LRI parameter enhances the bubble height and reduces the number of base pairs which form the bubble. For the fourth-order terms in a Taylor expansion, results are closely resembling those of second-order terms, and are confirmed by numerical investigation. These results match with some experimental data and thus provide a better representation of the base pairs opening in DNA which is essential for the transcription process.
Keywords:  DNA      helicoidal coupling      RNA-polymerase      spin model      Riemann zeta function      power-law long-range interaction      breather-like soliton     
Received:  24 March 2013      Published:  25 October 2013
PACS:  94.05.Fg (Solitons and solitary waves)  
  87.10.Tf (Molecular dynamics simulation)  
  87.14.gk (DNA)  
  87.53.Ay (Biophysical mechanisms of interaction)  
Corresponding Authors:  Mirabeau Saha, Timoléon C. Kofané     E-mail:  sahamirabeau@yahoo.fr;tckofane@yahoo.com

Cite this article: 

Mirabeau Saha, Timoléon C. Kofané Transcription’s bubble under the influence of long-range interactions and helicoidal coupling 2013 Chin. Phys. B 22 129402

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