American Institute of Mathematical Sciences

Advanced
October  2011, 4(5): 995-1006. doi: 10.3934/dcdss.2011.4.995

Nonsymmetric moving breather collisions in the Peyrard-Bishop DNA model

Azucena Álvarez 1, , Francisco R. Romero 1, , José M. Romero 2, and  Juan F. R. Archilla 2,

1. 

Grupo de Física No Lineal. Facultad de Física. Universidad de Sevilla, Avda. Reina Mercedes, s/n. 41012-Sevilla, Spain, Spain
2. 

Grupo de Física No Lineal. ETSII. Universidad de Sevilla, Avda. Reina Mercedes, s/n. 41012-Sevilla, Spain, Spain

Received  October 2009 Revised  February 2010 Published  December 2010

We study nonsymmetric collisions of moving breathers (MBs) in the Peyrard-Bishop DNA model. In this paper we have considered the following types of nonsymmetric collisions: head-on collisions of two breathers traveling with different velocities; collisions of moving breathers with a stationary trapped breather; and collisions of moving breathers traveling with the same direction. The various main observed phenomena are: one moving breather gets trapped at the collision region, and the other one is reflected; breather fusion without trapping, with the appearance of a new moving breather; and breather generation without trapping, with the appearance of new moving breathers traveling either with the same or different directions. For comparison we have included some results of a previous paper concerning to symmetric collisions, where two identical moving breathers traveling with opposite velocities collide. For symmetric collisions, the main observed phenomena are: breather generation with trapping, with the appearance of two new moving breathers with opposite velocities and a stationary breather trapped at the collision region; and breather generation without trapping, with the appearance of new moving breathers with opposite velocities. A common feature for all types of collisions is that the collision outcome depends on the internal structure of the moving breathers and the exact number of pair-bases that initially separates the stationary breathers when they are perturbed. As some nonsymmetric collisions result in the generation of a new stationary trapped breather of larger energy, the trapping phenomenon could play an important part of the complex mechanisms involved in the initiation of the DNA transcription processes.
Keywords: Peyrard-Bishop DNA moedel, Moving breathers., Klein-Gordon chains, DNA.
Mathematics Subject Classification: Primary: 70Kxx, 82C22; Secondary: 92D2.
Citation: Azucena Álvarez, Francisco R. Romero, José M. Romero, Juan F. R. Archilla. Nonsymmetric moving breather collisions in the Peyrard-Bishop DNA model. Discrete & Continuous Dynamical Systems - S, 2011, 4 (5) : 995-1006. doi: 10.3934/dcdss.2011.4.995
References:
[1]

Focus issue edited by S. Flach and R. S. Mackay, Localization in nonlinear lattices,, Physica D, 119 (1999).   Google Scholar

[2]

Focus issue edited by Yu S. Kivshar and S. Flach, Nonlinear localized modes: Physics and applications,, Chaos, 13 (2003).   Google Scholar

[3]

Focus issue edited by T. Dauxois, R. S. Mackay and G. P. Tsironis, Condensed matter, dynamical systems and biophysics,, Physica D, 216 (2006).   Google Scholar

[4]

A. Alvarez, F. R. Romero, J. F. R. Archilla, J. Cuevas and P. V. Larsen, Breather trapping and breather tansmission in a DNA model with an interface,, Eur. Phys. J. B, 51 (2006).  doi: doi:10.1140/epjb/e2006-00191-0.  Google Scholar

[5]

A. Alvarez, F. R. Romero, J. Cuevas and J. F. R. Archilla, Discrete moving breather collisions in a Klein-Gordon chain of oscillators,, Phys. Lett. A, 372 (2008).  doi: doi:10.1016/j.physleta.2007.09.035.  Google Scholar

[6]

A. Alvarez, F. R. Romero, J. Cuevas and J. F. R. Archilla, Moving breather collisions in Klein-Gordon chains of oscillators,, Eur. Phys. J. B, 70 (2009).  doi: doi:10.1140/epjb/e2009-00256-6.  Google Scholar

[7]

S. Aubry, Breathers in nonlinear lattices: Existence, linear stability and quantization,, Physica D, 103 (1997).  doi: doi:10.1016/S0167-2789(96)00261-8.  Google Scholar

[8]

S. Aubry and T. Cretegny, Mobility and reactivity of discrete breathers,, Physica D, 119 (1998).  doi: doi:10.1016/S0167-2789(98)00062-1.  Google Scholar

[9]

D. Campbell, J. Schonfeld and C. Wingate, Resonance structure in kink-antikink interactions in $\phi^4$ theory,, Physica D, 9 (1983).  doi: doi:10.1016/0167-2789(83)90289-0.  Google Scholar

[10]

D. Chen, S. Aubry and G. P. Tsironis, Breather mobility in discrete $\varphi^4$ nonlinear lattices,, Phys. Rev. Lett., 77 (1996).  doi: doi:10.1103/PhysRevLett.77.4776.  Google Scholar

[11]

J. Cuevas, J. F. R. Archilla, Yu. B. Gaididei and F. R. Romero, Moving breathers in a DNA model with competing short and long range dispersive interactions,, Physica D, 163 (2002).  doi: doi:10.1016/S0167-2789(02)00351-2.  Google Scholar

[12]

J. Cuevas and J. C. Eilbeck, Soliton collisions in a waveguide array with saturable nonlinearity,, Phys. Lett. A, 358 (2006).  doi: doi:10.1016/j.physleta.2006.04.095.  Google Scholar

[13]

J. Cuevas, F. Palmero, J. F. R. Archilla and F. R. Romero, Moving breathers in a bent DNA-related model,, Phys. Lett. A, 299 (2002).  doi: doi:10.1016/S0375-9601(02)00731-4.  Google Scholar

[14]

J. Cuevas, F. Palmero, J. F. R. Archilla and F. R. Romero, Moving discrete breathers in a Klein-Gordon chain with an impurity,, J. Phys. A: Math. and Gen., 35 (2002).  doi: doi:10.1088/0305-4470/35/49/302.  Google Scholar

[15]

T. Dauxois and M. Peyrard, Energy localization in nonlinear lattices,, Phys. Rev. Lett., 70 (1993).  doi: doi:10.1103/PhysRevLett.70.3935.  Google Scholar

[16]

T. Dauxois, M. Peyrard and C. R. Willis, Localized breather-like solutions in a discrete Klein-Gordon model and application to DNA,, Physica D, 57 (1992).  doi: doi:10.1016/0167-2789(92)90003-6.  Google Scholar

[17]

S. Dmitriev, P. Kevrekidis and Y. Kivshar, Radiationless energy exchange in three-soliton collisions,, Phys. Rev. E, 78 (2008).  doi: doi:10.1103/PhysRevE.78.046604.  Google Scholar

[18]

Y. Doi, Energy exchange in collisions of intrinsic localized modes,, Phys. Rev. E, 68 (2003).  doi: doi:10.1103/PhysRevE.68.066608.  Google Scholar

[19]

S. Flach and C. R. Willis, Discrete breathers,, Phys. Rep., 295 (1998).  doi: doi:10.1016/S0370-1573(97)00068-9.  Google Scholar

[20]

K. Forinash, T. Cretegny and M. Peyrard, Local modes and localization in amulticomponent nonlinear lattice,, Phys. Rev. E, 55 (1997).  doi: doi:10.1103/PhysRevE.55.4740.  Google Scholar

[21]

K. Forinash, M. Peyrard and B. A. Malomed, Interaction of discrete breathers with impurity modes,, Phys. Rev. E, 49 (1994).  doi: doi:10.1103/PhysRevE.49.3400.  Google Scholar

[22]

P. G. Kevrekidis, K. Ø. Rasmussen and A. R. Bishop, The discrete nonlinear Schrödinger equation: A survey of recent results,, Int. J. Mod. Phys. B, 15 (2001).  doi: doi:10.1142/S0217979201007105.  Google Scholar

[23]

R. S. MacKay and S. Aubry, Proof of existence of breathers for time-reversible or Hamiltonian networks of weakly coupled oscillators,, Nonlinearity, 7 (1994).  doi: doi:10.1088/0951-7715/7/6/006.  Google Scholar

[24]

J. L. Marín and S. Aubry, Breathers in nonlinear lattices: Numerical calculation from the anticontinuous limit,, Nonlinearity, 9 (1996).  doi: doi:10.1088/0951-7715/9/6/007.  Google Scholar

[25]

M. Meister and L. M. Floría, Bound states of breathers in the Frenkel-Kontorova model,, Eur. Phys. J. B, 37 (2004).  doi: doi:10.1140/epjb/e2004-00049-5.  Google Scholar

[26]

I. E. Papacharalampous, P. G. Kevrekidis, B. A. Malomed and D. J. Frantzeskakis, Soliton collisions in discrete nonlinear Schrödinger equation,, Phys. Rev. E, 68 (2003).  doi: doi:10.1103/PhysRevE.68.046604.  Google Scholar

[27]

M. Peyrard and A. R. Bishop, Statistical mechanics of a nonlinear model for DNA denaturation,, Phys. Rev. Lett., 62 (1989).  doi: doi:10.1103/PhysRevLett.62.2755.  Google Scholar

[28]

B. Sánchez-Rey, G. James, J. Cuevas and J. F. R. Archilla, Bright and dark breathers in Fermi-Pasta-Ulam lattices,, Phys. Rev. B, 70 (2004).  doi: doi:10.1103/PhysRevB.70.014301.  Google Scholar

[29]

M. Sanz-Serna and M. P. Calvo, "Numerical Hamiltonian Problems,", Chapman and Hall, (1994).   Google Scholar

[30]

A. J. Sievers and S. Takeno, Intrinsic localized modes in anharmonic crystals,, Phys. Rev. Lett., 61 (1988).  doi: doi:10.1103/PhysRevLett.61.970.  Google Scholar

show all references

References:
[1]

Focus issue edited by S. Flach and R. S. Mackay, Localization in nonlinear lattices,, Physica D, 119 (1999).   Google Scholar

[2]

Focus issue edited by Yu S. Kivshar and S. Flach, Nonlinear localized modes: Physics and applications,, Chaos, 13 (2003).   Google Scholar

[3]

Focus issue edited by T. Dauxois, R. S. Mackay and G. P. Tsironis, Condensed matter, dynamical systems and biophysics,, Physica D, 216 (2006).   Google Scholar

[4]

A. Alvarez, F. R. Romero, J. F. R. Archilla, J. Cuevas and P. V. Larsen, Breather trapping and breather tansmission in a DNA model with an interface,, Eur. Phys. J. B, 51 (2006).  doi: doi:10.1140/epjb/e2006-00191-0.  Google Scholar

[5]

A. Alvarez, F. R. Romero, J. Cuevas and J. F. R. Archilla, Discrete moving breather collisions in a Klein-Gordon chain of oscillators,, Phys. Lett. A, 372 (2008).  doi: doi:10.1016/j.physleta.2007.09.035.  Google Scholar

[6]

A. Alvarez, F. R. Romero, J. Cuevas and J. F. R. Archilla, Moving breather collisions in Klein-Gordon chains of oscillators,, Eur. Phys. J. B, 70 (2009).  doi: doi:10.1140/epjb/e2009-00256-6.  Google Scholar

[7]

S. Aubry, Breathers in nonlinear lattices: Existence, linear stability and quantization,, Physica D, 103 (1997).  doi: doi:10.1016/S0167-2789(96)00261-8.  Google Scholar

[8]

S. Aubry and T. Cretegny, Mobility and reactivity of discrete breathers,, Physica D, 119 (1998).  doi: doi:10.1016/S0167-2789(98)00062-1.  Google Scholar

[9]

D. Campbell, J. Schonfeld and C. Wingate, Resonance structure in kink-antikink interactions in $\phi^4$ theory,, Physica D, 9 (1983).  doi: doi:10.1016/0167-2789(83)90289-0.  Google Scholar

[10]

D. Chen, S. Aubry and G. P. Tsironis, Breather mobility in discrete $\varphi^4$ nonlinear lattices,, Phys. Rev. Lett., 77 (1996).  doi: doi:10.1103/PhysRevLett.77.4776.  Google Scholar

[11]

J. Cuevas, J. F. R. Archilla, Yu. B. Gaididei and F. R. Romero, Moving breathers in a DNA model with competing short and long range dispersive interactions,, Physica D, 163 (2002).  doi: doi:10.1016/S0167-2789(02)00351-2.  Google Scholar

[12]

J. Cuevas and J. C. Eilbeck, Soliton collisions in a waveguide array with saturable nonlinearity,, Phys. Lett. A, 358 (2006).  doi: doi:10.1016/j.physleta.2006.04.095.  Google Scholar

[13]

J. Cuevas, F. Palmero, J. F. R. Archilla and F. R. Romero, Moving breathers in a bent DNA-related model,, Phys. Lett. A, 299 (2002).  doi: doi:10.1016/S0375-9601(02)00731-4.  Google Scholar

[14]

J. Cuevas, F. Palmero, J. F. R. Archilla and F. R. Romero, Moving discrete breathers in a Klein-Gordon chain with an impurity,, J. Phys. A: Math. and Gen., 35 (2002).  doi: doi:10.1088/0305-4470/35/49/302.  Google Scholar

[15]

T. Dauxois and M. Peyrard, Energy localization in nonlinear lattices,, Phys. Rev. Lett., 70 (1993).  doi: doi:10.1103/PhysRevLett.70.3935.  Google Scholar

[16]

T. Dauxois, M. Peyrard and C. R. Willis, Localized breather-like solutions in a discrete Klein-Gordon model and application to DNA,, Physica D, 57 (1992).  doi: doi:10.1016/0167-2789(92)90003-6.  Google Scholar

[17]

S. Dmitriev, P. Kevrekidis and Y. Kivshar, Radiationless energy exchange in three-soliton collisions,, Phys. Rev. E, 78 (2008).  doi: doi:10.1103/PhysRevE.78.046604.  Google Scholar

[18]

Y. Doi, Energy exchange in collisions of intrinsic localized modes,, Phys. Rev. E, 68 (2003).  doi: doi:10.1103/PhysRevE.68.066608.  Google Scholar

[19]

S. Flach and C. R. Willis, Discrete breathers,, Phys. Rep., 295 (1998).  doi: doi:10.1016/S0370-1573(97)00068-9.  Google Scholar

[20]

K. Forinash, T. Cretegny and M. Peyrard, Local modes and localization in amulticomponent nonlinear lattice,, Phys. Rev. E, 55 (1997).  doi: doi:10.1103/PhysRevE.55.4740.  Google Scholar

[21]

K. Forinash, M. Peyrard and B. A. Malomed, Interaction of discrete breathers with impurity modes,, Phys. Rev. E, 49 (1994).  doi: doi:10.1103/PhysRevE.49.3400.  Google Scholar

[22]

P. G. Kevrekidis, K. Ø. Rasmussen and A. R. Bishop, The discrete nonlinear Schrödinger equation: A survey of recent results,, Int. J. Mod. Phys. B, 15 (2001).  doi: doi:10.1142/S0217979201007105.  Google Scholar

[23]

R. S. MacKay and S. Aubry, Proof of existence of breathers for time-reversible or Hamiltonian networks of weakly coupled oscillators,, Nonlinearity, 7 (1994).  doi: doi:10.1088/0951-7715/7/6/006.  Google Scholar

[24]

J. L. Marín and S. Aubry, Breathers in nonlinear lattices: Numerical calculation from the anticontinuous limit,, Nonlinearity, 9 (1996).  doi: doi:10.1088/0951-7715/9/6/007.  Google Scholar

[25]

M. Meister and L. M. Floría, Bound states of breathers in the Frenkel-Kontorova model,, Eur. Phys. J. B, 37 (2004).  doi: doi:10.1140/epjb/e2004-00049-5.  Google Scholar

[26]

I. E. Papacharalampous, P. G. Kevrekidis, B. A. Malomed and D. J. Frantzeskakis, Soliton collisions in discrete nonlinear Schrödinger equation,, Phys. Rev. E, 68 (2003).  doi: doi:10.1103/PhysRevE.68.046604.  Google Scholar

[27]

M. Peyrard and A. R. Bishop, Statistical mechanics of a nonlinear model for DNA denaturation,, Phys. Rev. Lett., 62 (1989).  doi: doi:10.1103/PhysRevLett.62.2755.  Google Scholar

[28]

B. Sánchez-Rey, G. James, J. Cuevas and J. F. R. Archilla, Bright and dark breathers in Fermi-Pasta-Ulam lattices,, Phys. Rev. B, 70 (2004).  doi: doi:10.1103/PhysRevB.70.014301.  Google Scholar

[29]

M. Sanz-Serna and M. P. Calvo, "Numerical Hamiltonian Problems,", Chapman and Hall, (1994).   Google Scholar

[30]

A. J. Sievers and S. Takeno, Intrinsic localized modes in anharmonic crystals,, Phys. Rev. Lett., 61 (1988).  doi: doi:10.1103/PhysRevLett.61.970.  Google Scholar

[1]

Hironobu Sasaki. Remark on the scattering problem for the Klein-Gordon equation with power nonlinearity. Conference Publications, 2007, 2007 (Special) : 903-911. doi: 10.3934/proc.2007.2007.903
[2]

Karen Yagdjian. The semilinear Klein-Gordon equation in de Sitter spacetime. Discrete & Continuous Dynamical Systems - S, 2009, 2 (3) : 679-696. doi: 10.3934/dcdss.2009.2.679
[3]

Satoshi Masaki, Jun-ichi Segata. Modified scattering for the Klein-Gordon equation with the critical nonlinearity in three dimensions. Communications on Pure & Applied Analysis, 2018, 17 (4) : 1595-1611. doi: 10.3934/cpaa.2018076
[4]

Aslihan Demirkaya, Panayotis G. Kevrekidis, Milena Stanislavova, Atanas Stefanov. Spectral stability analysis for standing waves of a perturbed Klein-Gordon equation. Conference Publications, 2015, 2015 (special) : 359-368. doi: 10.3934/proc.2015.0359
[5]

Benoît Grébert, Tiphaine Jézéquel, Laurent Thomann. Dynamics of Klein-Gordon on a compact surface near a homoclinic orbit. Discrete & Continuous Dynamical Systems - A, 2014, 34 (9) : 3485-3510. doi: 10.3934/dcds.2014.34.3485
[6]

Chi-Kun Lin, Kung-Chien Wu. On the fluid dynamical approximation to the nonlinear Klein-Gordon equation. Discrete & Continuous Dynamical Systems - A, 2012, 32 (6) : 2233-2251. doi: 10.3934/dcds.2012.32.2233
[7]

Hironobu Sasaki. Small data scattering for the Klein-Gordon equation with cubic convolution nonlinearity. Discrete & Continuous Dynamical Systems - A, 2006, 15 (3) : 973-981. doi: 10.3934/dcds.2006.15.973
[8]

Masahito Ohta, Grozdena Todorova. Strong instability of standing waves for nonlinear Klein-Gordon equations. Discrete & Continuous Dynamical Systems - A, 2005, 12 (2) : 315-322. doi: 10.3934/dcds.2005.12.315
[9]

Jun Yang. Vortex structures for Klein-Gordon equation with Ginzburg-Landau nonlinearity. Discrete & Continuous Dynamical Systems - A, 2014, 34 (5) : 2359-2388. doi: 10.3934/dcds.2014.34.2359
[10]

Marco Ghimenti, Stefan Le Coz, Marco Squassina. On the stability of standing waves of Klein-Gordon equations in a semiclassical regime. Discrete & Continuous Dynamical Systems - A, 2013, 33 (6) : 2389-2401. doi: 10.3934/dcds.2013.33.2389
[11]

Changxing Miao, Jiqiang Zheng. Scattering theory for energy-supercritical Klein-Gordon equation. Discrete & Continuous Dynamical Systems - S, 2016, 9 (6) : 2073-2094. doi: 10.3934/dcdss.2016085
[12]

Michinori Ishiwata, Makoto Nakamura, Hidemitsu Wadade. Remarks on the Cauchy problem of Klein-Gordon equations with weighted nonlinear terms. Discrete & Continuous Dynamical Systems - A, 2015, 35 (10) : 4889-4903. doi: 10.3934/dcds.2015.35.4889
[13]

Elena Kopylova. On dispersion decay for 3D Klein-Gordon equation. Discrete & Continuous Dynamical Systems - A, 2018, 38 (11) : 5765-5780. doi: 10.3934/dcds.2018251
[14]

Stefano Pasquali. A Nekhoroshev type theorem for the nonlinear Klein-Gordon equation with potential. Discrete & Continuous Dynamical Systems - B, 2018, 23 (9) : 3573-3594. doi: 10.3934/dcdsb.2017215
[15]

Nabil Bennenni, Kenza Guenda, Sihem Mesnager. DNA cyclic codes over rings. Advances in Mathematics of Communications, 2017, 11 (1) : 83-98. doi: 10.3934/amc.2017004
[16]

Soichiro Katayama. Global existence for systems of nonlinear wave and klein-gordon equations with compactly supported initial data. Communications on Pure & Applied Analysis, 2018, 17 (4) : 1479-1497. doi: 10.3934/cpaa.2018071
[17]

Andrew Comech. Weak attractor of the Klein-Gordon field in discrete space-time interacting with a nonlinear oscillator. Discrete & Continuous Dynamical Systems - A, 2013, 33 (7) : 2711-2755. doi: 10.3934/dcds.2013.33.2711
[18]

Baoxiang Wang. Scattering of solutions for critical and subcritical nonlinear Klein-Gordon equations in $H^s$. Discrete & Continuous Dynamical Systems - A, 1999, 5 (4) : 753-763. doi: 10.3934/dcds.1999.5.753
[19]

Panayotis G. Kevrekidis, Vakhtang Putkaradze, Zoi Rapti. Non-holonomic constraints and their impact on discretizations of Klein-Gordon lattice dynamical models. Conference Publications, 2015, 2015 (special) : 696-704. doi: 10.3934/proc.2015.0696
[20]

Zaihui Gan. Cross-constrained variational methods for the nonlinear Klein-Gordon equations with an inverse square potential. Communications on Pure & Applied Analysis, 2009, 8 (5) : 1541-1554. doi: 10.3934/cpaa.2009.8.1541

2018 Impact Factor: 0.545

Tools

Metrics

  • PDF downloads (11)
  • HTML views (0)
  • Cited by (0)

Other articles
by authors

[Back to Top]

Copyright © 2019 American Institute of Mathematical Sciences