Dark breather using symmetric Morse, solvent and external potentials for DNA breathing
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Gutierrez, H. O. C., Gutierrez, M. M. C., Fuentes Rivera, G. I. C., Fuentes Rivera, L. J. C., & Vallejo, D. F. R. (2018). Dark breather using symmetric Morse, solvent and external potentials for DNA breathing. Eclética Química, 43(4), 44–49. https://doi.org/10.26850/1678-4618eqj.v43.4.2018.p44-49

Abstract

We analyze the dynamics and the quantum thermodynamics of DNA in Symmetric-Peyrard-Bishop-Dauxois model (S-PBD) with solvent and external potentials and describe the transient conformational fluctuations using dark breather and the ground state wave function of the associate Schrodinger differential equation.  We used the S-PBD, the Floquet theory, quantum thermodynamic and finite difference methods. We show that for lower coupling dark breather is present.  We estimate the fluctuations or breathing of DNA. For the S-PBD model we have the stability of dark breather for k<0.004 and mobile breathers with coupling k=0.004. The fluctuations of the dark breather in the S-PBD model is approximately zero with the quantum thermodynamics. The viscous and external potential effect is direct proportional to hydrogen bond stretching.
https://doi.org/10.26850/1678-4618eqj.v43.4.2018.p44-49
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References

von Hippel, P., Johnson, N., Marcus, A., 50 years of DNA ‘Breathing’: Reflections on Old and New Approaches, Biopolymers 99 (12) (2013) 923-954. https://doi.org/10.1002/bip.22347.

Hidayat, W., Sulaiman, A., Viridi, S, Zen, F. P., The viscous and external forces effect on the thermal denaturation of Peyrard-Bishop, Physical Chemistry & Biophysics 5 (5) (2015) 1-5 (186). https://doi.org/10.4172/2161-0398.1000186.

Flach, S., Gorbach, A., Discrete breathers-Advance in theory and applications, Physics Reports 467 (1-3) (2008) 1-116. https://doi.org/10.1016/j.physrep.2008.05.002.

Mackay, R. S., Aubry, S., Proof of existence of breathers for time-reversible for Hamiltonian networks of weakly coupled oscillators, Nonlinearity 7 (1994) 1623-1643. https://doi.org/10.1088/0951-7715/7/6/006.

Cuevas J., Localizacion y Transferencia de Energia en Redes Anarmónicas No Homogéneas, Ph. D. Thesis, Universidad de Sevilla, Sevilla, España (2003). http://grupo.us.es/gfnl/thesis.htm.

Aubry, S., Cretegny, T., Mobility and Reactivity of Discrete Breathers, Physica D 119 (1-2) (1998) 34-46. https://doi.org/10.1016/S0167-2789(98)00062-1.

Ambjomsson, T., Banik, S. K., Krichevsky, O., Metzler, R., Breathing dynamics in Heteropolymer DNA, Biophysics J. 92 (8) (2007) 2674-2684. https://doi.org/10.1529/biophysj.106.095935.

Cortez, H., Drigo Filho, E., Ruggiero, J. R., Breather stability in one dimensional Lattices with a symmetric Morse Potential, TEMA, Tend. Mat. Apl. Comput. 9 (2) (2008) 205-212. https://doi.org/10.5540/tema.2008.09.02.0205.

Cortez, H., Drigo Filho, E., Ruggiero., J. R., Cortez, M., Mobile breathers in a nonlinear model for DNA breathing, Eclética Química Journal 42 (2017) 71-75. https://doi.org/10.26850/1678-4618eqj.42.1.2017.p71-75.

Sulaiman, A., Zen, F. P., Alatas, H., Handoko, L. T., Dynamics of DNA breathing in the Peyrard-Bishop weth damping and external force, Physica D 241 (2012) 1640-1647. https://doi.org/10.1016/j.physd.2012.06.011.

Cortez, H., Tese de doutorado, Modelo Dinâmico e estatístico aplicado à transição de fase. UNESP.(2009) https://repositorio.unesp.br/bitstream/handle/11449/100461/cortezgutierrez_ho_dr_sjrp.pdf?sequence=1&isAllowed=y.

Cortez, H., Drigo Filho, E., Ruggiero, J. R., Gutierrez, M. C., Fuentes Rivera, L. C., Thermodynamics of DNA with “hump” Morse potential, Eclética Química Journal 41 (2016) 60-65. https://doi.org/10.26850/1678-4618eqj.v41.1.2016.p60-65.

Bustamante, C. Smith, S.B., Liphardt,J., Smith, D., Single-molecule studies of DNA mechanics, Current Opinion in Structural Biology 10 (3) (2000) 279-285. https://doi.org/10.1016/S0959-440X(00)00085-3.

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