Related papers: A Barrier Penetration Model for DNA Double Strand …
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
Absorbing boundary condition approach to nuclear breakup reactions is investigated. A key ingredient of the method is an absorbing potential outside the physical area, which simulates the outgoing boundary condition for scattered waves.…
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
We consider molecules made of two one-dimensional short-range-interacting bosonic atoms. We show that in the process of scattering of these molecules off a narrow barrier, odd incident waves produce \emph{no unbound atoms, even when the…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Phase segregation, the process by which the components of a binary mixture spontaneously separate, is a key process in the evolution and design of many chemical, mechanical, and biological systems. In this work, we present a data-driven…
A simple two-species asymmetric exclusion model in one dimension with bulk and boundary exchanges of particles is investigated for the existence of spontaneous symmetry breaking. The model is a generalization of the bridge model for which…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Using a microscopic phase-space model of the membrane system, the boundary condition at a membrane is derived. According to the condition, the substance flow across the membrane is proportional to the difference of the substance…
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
In this paper, we report dynamic Monte Carlo simulations of melting and crystallization in a single-chain system. Their free energy barriers are calculated by the umbrella sampling method and can be described well by a simple expression…
Diffusion through semipermeable structures arises in a wide range of processes in the physical and life sciences. Examples at the microscopic level range from artificial membranes for reverse osmosis to lipid bilayers regulating molecular…
Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel…