Abstract.
The internal mobility of the DNA molecule, in a weakly damped medium, is studied. Inspired by the microscopic Peyrard-Bishop-Dauxois model, a zigzag model, which considers longitudinal and transverse vibrations of base pairs is used. The damped limit is considered and the whole system is shown to be governed by a dissipative nonlinear Schrödinger equation. The linear stability analysis of a plane wave solution is thereafter performed. The oscillations and open states of the DNA duplex are also addressed, where two hyperbolic functions are used to construct DNA bubbles in the form of bright- and kink-type soliton solutions. The confirmation of analytical predictions is verified through direct numerical experiments. There are good accuracy and good agreement between the quantitative and qualitative influence of damping forces on the width and amplitude of the moving soliton. Such relevant results could be used to predict the generation of moving bubbles along the DNA molecule, and to explain energy transfer and localization processes during the fundamental processes of DNA replication and transcription.
Similar content being viewed by others
References
L. Styer, Biochemistry, 4th ed. (W. H. Freeman and Company, New York, 1995)
L.V. Yakushevich, A.V. Savin, L.I. Manevitch, Phys. Rev. E 66, 016614 (2002)
S.W. Englander, N.R. Kallenbach, A.J. Heeger, J.A. Krumhansl, S. Litwin, Proc. Natl. Acad. Sci. U.S.A. 77, 7222 (1980)
S. Yomosa, Phys. Rev. A 27, 2120 (1983)
S. Homma, S. Takeno, Prog. Theor. Phys. 70, 308 (1983)
S. Takeno, S. Homma, Prog. Theor. Phys. 72, 679 (1984)
M. Peyrard, A.R. Bishop, Phys. Rev. Lett. 62, 2755 (1989)
T. Dauxois, Phys. Lett. A l59, 390 (1991)
L.V. Yakushevich, Phys. Lett. A 136, 413 (1989)
T.A. Knotts IV, N. Rathore, D.C. Schwartz, J.J. de Pablo, J. Chem. Phys. 126, 084901 (2007)
L.V. Yakushevich, Phys. Lett. A 253, 358 (1999)
M. Salerno, Phys. Rev. A 44, 5292 (1991)
V. Muto, P.S. Lomdahl, P.L. Christiansen, Phys. Rev. A 42, 7452 (1990)
K. De-Xing, L. Sen-Yue, Z. Jin, Commun. Theor. Phys. 36, 737 (2001)
A. Campa, A. Giansanti, Phys. Rev. E 58, 3585 (1998)
A.J. Sievers, S. Takeno, Phys. Rev. Lett. 61, 970 (1988)
R.S. MacKay, S. Aubry, Nonlinearity 7, 1623 (1994)
T.B. Benjamin, J.E. Feir, J. Fluid Mech. 27, 417 (1967)
C.B. Tabi, A. Mohamadou, T.C. Kofane, Math. Biosci. Eng. 5, 205 (2008)
C.B. Tabi, A. Mohamadou, T.C. Kofane, J. Comput. Theor. Nanosci. 5, 647 (2008)
C.B. Tabi, A. Mohamadou, T.C. Kofane, Chin. Phys. Lett. 26, 068703 (2009)
S. Zdravković, M.V. Satarić, Phys. Scr. 64, 612 (2001)
S. Zdravković, M.V. Satarić, A.Yu. Parkhomenko, A.N. Bugay, Chaos 28, 113103 (2018)
S. Zdravković, M.V. Satarić, Chin. Phys. Lett. 24, 1210 (2007)
S. Zdravković, M.V. Satarić, L. Hadžievski, Chaos 20, 043141 (2010)
S. Zdravković, M.V. Satarić, J. Comput. Theor. Nanosci. 2, 1 (2005)
A. Sulaimana, F.P. Zenb, H. Alatasc, L.T. Handoko, Physica D 241, 1640 (2012)
V. Vasumathi, M. Daniel, Phys. Rev. E 80, 061904 (2009)
T. Lipniacki, Phys. Rev. E 58, 7253 (1999)
G. Careri, M. Geraci, A. Ginansanti, J.A. Ruply, Proc. Natl. Acad. Sci. U.S.A. 82, 5342 (1985)
H. Khesbak, O. Savchuk, S. Tsushima, K. Fahmy, J. Am. Chem. Soc 82, 5834 (2011)
W. Alka, A. Goyal, C.N. Kumar, Phys. Lett. A 375, 480 (2011)
J.B. Okaly, A. Mvogo, R.L. Woulaché, T.C. Kofané, Wave Motion 82, 1 (2018)
M.A. Knyazev, D.M. Knyazev, J. Phys. Stud. 16, 1001 (2012)
H.M. Baskonus, C. Cattani, P. Agarwal, S.S. Dragomir, M. Jleli, B. Samet, in Advances in Mathematical Inequalities and Applications, (Birkhäuser, Singapore, Springer, Nature, Singapore, Pte Ltd., 2018)
F. II Ndzana, A. Mohamadou, Chaos 29, 013116 (2019)
E. Kengne, A. Lakhssassi, W.M. Liu, Phys. Rev. E 91, 062915 (2015)
S.B. Smith, Y. Cui, C. Bustamante, Science, New Series 271, 795 (1996)
J.B. Okaly, A. Mvogo, R.L. Woulache, T.C. Kofane, Commun. Nonlinear Sci. Numer. Simul. 55, 183 (2018)
M. Peyrard, I. Daumont, Europhys. Lett. 59, 834 (2002)
I. Daumont, M. Peyrard, Chaos 13, 624 (2003)
C. Brunhuber, F.G. Mertens, Phys. Rev. E 73, 016614 (2006)
E. Arévalo, Y. Gaididei, F.G. Mertens, Eur. Phys. J. B 27, 63 (2002)
M. Peyrard, Nonlinearity 17, R1 (2004)
M. Remoissenet, Phys. Rev. B 33, 2386 (1986)
F.M. Moukam Kakmeni, E.M. Inack, E.M. Yamakou, Phys. Rev. E 89, 052919 (2014)
J.B. Okaly, A. Mvogo, R.L. Woulaché, T.C. Kofané, Chin. J. Phys. 56, 2613 (2018)
C.B. Tabi, A. Mohamadou, T.C. Kofane, Eur. Phys. J. D 50, 307 (2008)
F. II Ndzana, A. Mohamadou, T.C. Kofane, Phys. Rev. E 78, 016606 (2008)
S. Abdoulkary, A.D. Aboubakar, M. Aboubakar, A. Mohamadou, L. Kavitha, Commun. Nonlinear Sci. Numer. Simul. 22, 1288 (2015)
M.J. Lighthill, J. Inst. Math. Appl. 1, 269 (1965)
T.B. Benjamin, J.E. Feir, J. Fluid Mech. 27, 417 (1967)
V.E. Zakharov, Zh. Eksp. Teor. Fiz. 51, 688 (1966) (Sov. Phys. JETP 24
J.E. Feir, Proc. R. Soc. London, Ser. A 299, 54 (1967)
S. Nikitenkova, N. Singh, Y. Stepanyants, Chaos 25, 123113 (2015)
M.I. Fakhretdinov, F.K. Zakir'yanov, Russ. Phys. J. 54, 1304 (2012)
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
The EPJ Publishers remain neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Okaly, J.B., Ndzana, F.I., Woulaché, R.L. et al. Solitary wavelike solutions in nonlinear dynamics of damped DNA systems. Eur. Phys. J. Plus 134, 598 (2019). https://doi.org/10.1140/epjp/i2019-12992-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1140/epjp/i2019-12992-3