Related papers: Bending and Base-Stacking Interactions in Double-S…
The experimental data on elastic and inelastic scattering of 270 MeV 3He particles to several low lying states in 90Zr, 116Sn and 208Pb are analyzed within the double folding model (DFM). Fermi density distribution (FDD) of target nuclei is…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a…
Recently, altermagnetism (AM) has emerged as a new category of magnetism, alongside conventional antiferromagnetism (AFM) and ferromagnetism (FM). In an AM, superconductivity (SC) is faced with a dilemma that the spin-polarized bands,…
We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
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…
We discuss theoretically the force F between two colloidal particles, each of them carrying one single strand DNA. The two strands are complementary only on a finite sequence of consecutive base pairs. We define an adjustment length (a few…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
Directed polymers (strings) and semiflexible polymers (filaments) are one-dimensional objects governed by tension and bending energy, respectively. They undergo unbinding transitions in the presence of a short-range attractive potential.…
Using a coarse-grained bead-spring model for semi-flexible macromolecules forming a polymer brush, structure and dynamics of the polymers is investigated, varying chain stiffness and grafting density. The anchoring condition for the grafted…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
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…
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square…