Related papers: Kink solitons in DNA
The ac driven sine-Gordon equation is studied analytically and numerically, with the aim of providing a full description of how soliton solutions behave. To date, there is much controversy about when ac driven dc motion is possible. Our…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
The sine-Gordon model with space- and time-dependent parameters is considered. A highly accurate effective model with two degrees of freedom is constructed, allowing the description of the kink movement in this model even for extremely long…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
The cross section for scattering of x-rays by solitons is calculated. The authors consider solitons corresponding to the formation of a kink in a system of adatoms on the surface of a substrate, or of a crowdion in a chain of atoms in a…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
Directed motion of topological solitons (kinks or antikinks) in the damped and AC-driven discrete sine-Gordon system is investigated. We show that if the driving field breaks certain time-space symmetries, the soliton can perform…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
To show that steadily propagating nonlinear waves in active matter can be driven internally, we develop a prototypical model of a topological kink moving with a constant supersonic speed. We use a model of a bi-stable mass-spring (FPU)…
The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
In the present paper we investigate the influence of inhomogeneities in the dynamics and stability of DNA open states, modeled as propagating solitons in the spirit of a Generalized Yakushevish Model. It is a direct consecuence of our model…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…