Related papers: Moving breathers in bent DNA with realistic parame…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation…
In this work, the quantum confinement effect is proposed as the cause of the displacement of the vibrational spectrum of molecular groups that involve hydrogen bonds. In this approach the hydrogen bond imposes a space barrier to hydrogen…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Most of the investigations to date on tight-binding, quantum percolation models focused on the quantum percolation threshold, i.e., the analogue to the Anderson transition. It appears to occur if roughly 30% of the hopping terms are…
The interaction of discrete breathers with the primary lattice defects in transition metals such as vacancy, dislocation, and surface is analyzed on the example of bcc iron employing atomistic simulations. Scattering of discrete breathers…
We study metastable behavior in a discrete nonlinear Schr\"odinger equation from the viewpoint of Hamiltonian systems theory. When there are $n < \infty$ sites in this equation, we consider initial conditions in which almost all the energy…
We give definitions for different types of moving spatially localized objects in discrete nonlinear lattices. We derive general analytical relations connecting frequency, velocity and localization length of moving discrete breathers and…
The transport of a dimer, consisting of two Brownian particles bounded by a harmonic potential, moving on a periodic substrate is investigated both numerically and analytically. The mobility and diffusion of the dimer center of mass present…
Magnetic metamaterials composed of split-ring resonators or $U-$type elements may exhibit discreteness effects in THz and optical frequencies due to weak coupling. We consider a model one-dimensional metamaterial formed by a discrete array…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
We review research on the role of nonlinear coherent phenomena (e.g breathers and kinks) in the formation linear decorations in mica crystal. The work is based on a new model for the motion of the mica hexagonal K layer, which allows…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
We consider momentum transfer using frequency-chirped standing wave fields. Novel atom-beam splitter and mirror schemes based on Bragg scattering are presented. It is shown that a predetermined number of photon momenta can be transferred to…
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework…
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…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
The stochastic trajectories of molecules in living cells, as well as the dynamics in many other complex systems, often exhibit memory in their path over long periods of time. In addition, these systems can show dynamic heterogeneities due…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…