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Okaly JB, Mvogo A, Tabi CB, Ekobena Fouda HP, Kofané TC. Base pair opening in a damped helicoidal Joyeux-Buyukdagli model of DNA in an external force field. Phys Rev E 2020; 102:062402. [PMID: 33465949 DOI: 10.1103/physreve.102.062402] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/21/2020] [Indexed: 11/07/2022]
Abstract
Upon the Joyeux-Buyukdagli model of DNA, the helicoidal interactions are introduced, and their effects on the dynamical behaviors of the molecule investigated. A theoretical framework for the analysis is presented in an external force field, taking into account Stokes and hydrodynamics viscous forces. In the semi-discrete approximation, the dynamics of the molecule is found governed by the cubic complex Ginzburg-Landau (CGL) equation. By choosing an appropriate decoupling ansatz, the cubic CGL equation is transformed into a nonlinear differential equation whose analytical solitary wave-like solutions can be explored by means of the direct method, which is more tractable in case where the form of soliton solutions is known. Based on this, a dissipative bright-like soliton solution is obtained. Numerical experiments have been done, and relevant results were brought out, such as the quantitative and qualitative influences of the helical interactions on the parameters of the traveling bubble. The important role-played by these interactions in the DNA biological processes is brought out, showing that depending on the wave number, their effects can increase, decrease, or keep constant the bubble angular frequency, velocity, amplitude, and width, as well as the energy involved by enzymes in the initiation of DNA biological processes. This can prevent some coding or reading errors and resulting genetic damages. Analytical predictions and numerical experiments were in good agreement.
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Affiliation(s)
- J B Okaly
- Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde, Cameroon
- African Centre of Excellence in Information and Communication Technologies, University of Yaounde I, P.O. Box 8390, Yaounde, Cameroon
| | - A Mvogo
- Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde, Cameroon
- African Centre of Excellence in Information and Communication Technologies, University of Yaounde I, P.O. Box 8390, Yaounde, Cameroon
| | - C B Tabi
- Botswana International University of Science and Technology, Private Bag 16 Palapye, Botswana
| | - H P Ekobena Fouda
- Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde, Cameroon
| | - T C Kofané
- Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde, Cameroon
- African Centre of Excellence in Information and Communication Technologies, University of Yaounde I, P.O. Box 8390, Yaounde, Cameroon
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Xie S, Jiao Y. That’s A Scientist Should Do—A Dialog with Tomas Lindahl. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:223-225. [PMID: 31323385 PMCID: PMC6818360 DOI: 10.1016/j.gpb.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 11/18/2022]
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Wang J, Lindahl T. Maintenance of Genome Stability. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:119-121. [PMID: 27329679 PMCID: PMC4936602 DOI: 10.1016/j.gpb.2016.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Tomas Lindahl
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms EN6 3LD, United Kingdom.
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