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Register a new userNonlinear molecular excitations in a completely inhomogeneous DNA chain
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We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state configuration with small fluctuation. The perturbation due to inhomogeneities changes the velocity of the soliton. However, the width of the soliton remains constant.
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We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Domi nguez-Adame {em et al.}, Phys. Rev. E {bf 52}, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on the specific sequence. The results of our model are consistent with the stick-slip dynamics of the unzipping process observed in experiments. We also show that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A {bf 193}, 263 (1994)] is a useful tool to identify key regions in DNA that control the dynamical behavior of large segments. Additionally, our results lead to further insights in the phenomenology observed in aperiodic systems.
In the present work we explore a pre-stretched oscillator chain where the nodes interact via a pairwise Lennard-Jones potential. In addition to a homogeneous solution, we identify solutions with one or more (so-called) `breaks, i.e., jumps. As a function of the canonical parameter of the system, namely the precompression strain $d$, we find that the most fundamental one break solution changes stability when the monotonicity of the Hamiltonian changes with $d$. We provide a proof for this (motivated by numerical computations) observation. This critical point separates stable and unstable segments of the one break branch of solutions. We find similar branches for 2 through 5 break branches of solutions. Each of these higher `excited state solutions possesses an additional unstable pair of eigenvalues. We thus conjecture that $k$ break solutions will possess at least $k-1$ (and at most $k$) pairs of unstable eigenvalues. Our stability analysis is corroborated by direct numerical computations of the evolutionary dynamics.
We study - experimentally, theoretically, and numerically - nonlinear excitations in lattices of magnets with long-range interactions. We examine breather solutions, which are spatially localized and periodic in time, in a chain with algebraically-decaying interactions. It was established two decades ago [S. Flach, Phys. Rev. E 58, R4116 (1998)] that lattices with long-range interactions can have breather solutions in which the spatial decay of the tails has a crossover from exponential to algebraic decay. In this Letter, we revisit this problem in the setting of a chain of repelling magnets with a mass defect and verify, both numerically and experimentally, the existence of breathers with such a crossover.
We study the escape of a chain of coupled units over the barrier of a metastable potential. It is demonstrated that a very weak external driving field with suitably chosen frequency suffices to accomplish speedy escape. The latter requires the passage through a transition state the formation of which is triggered by permanent feeding of energy from a phonon background into humps of localised energy and elastic interaction of the arising breather solutions. In fact, cooperativity between the units of the chain entailing coordinated energy transfer is shown to be crucial for enhancing the rate of escape in an extremely effective and low-energy cost way where the effect of entropic localisation and breather coalescence conspire.
A nonlinear chain with six-order polynomial on-site potential is used to analyze the evolution of the total to kinetic energy ratio during development of modulational instability of extended nonlinear vibrational modes. For the on-site potential of hard-type (soft-type) anharmonicity, the instability of $q=pi$ mode ($q=0$ mode) results in the appearance of long-living discrete breathers (DBs) that gradually radiate their energy and eventually the system approaches thermal equilibrium with spatially uniform and temporally constant temperature. In the hard-type (soft-type) anharmonicity case, the total to kinetic energy ratio is minimal (maximal) in the regime of maximal energy localization by DBs. It is concluded that DBs affect specific heat of the nonlinear chain and for the case of hard-type (soft-type) anharmonicity they reduce (increase) the specific heat.
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