Related papers: Kink solitons in DNA
We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…
To study the propagation of nonlinear waves across Y- and T-type junctions, we consider the 2D sine--Gordon equation as a model and study the dynamics of kinks and breathers in such geometries. The comparison of the energies reveals that…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Holographic superconductor model represents various inhomogeneous solutions with homogeneous sources. In this paper, we study inhomogeneous structures in the presence of the homogeneous current and the chemical potential. We find single…
We present a stability theory for kink propagation in chains of coupled oscillators and a new algorithm for the numerical study of kink dynamics. The numerical solutions are computed using an equivalent integral equation instead of a system…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
We study kink-antikink collisions in a particular case of the double sine-Gordon model depending on only one parameter $r$. The scattering process of large kink-antikink shows the changing of the topological sector. For some parameter…
Evolution of the nonequilibrium inhomogeneities and topological defects is studied in terms of complex kink solutions of the sine-Gordon equation. The weakly damped oscillation of the sine-Gordon kink, named as the kink quasimode, is…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
We study the collision of a kink and an antikink in the double sine-Gordon model with and without the excited vibrational mode. In the latter case, we find that there is a limited range of the parameters where the resonance windows exist,…
The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have…
The nonlinear dynamics of a one-dimensional molecular crystal in the form of a chain of planar coronene molecules is analyzed. Using molecular dynamics, it is shown that a chain of coronene molecules supports acoustic solitons,…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…