Related papers: A Barrier Penetration Model for DNA Double Strand …
A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on a thermodynamic ground, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration…
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small…
We develop a theory of nucleation on top of two-dimensional islands bordered by steps with an additional energy barrier $\Delta E_S$ for descending atoms. The theory is based on the concept of the residence time of an adatom on the…
We present a class of 2D systems which shows a counterintuitive property that contradicts a semi classical intuition: A 2D quantum particle "prefers" tunneling through a barrier rather than traveling above it. Viewing the one particle 2D…
This paper describes the model for DNA in MATLAB taking into account all of component atoms. In this model, it is possible to generate sequences with length 10000 basis pairs available for introducing all types of sequences. Once the…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
A coarsened model for a binary system with limited miscibility of components is proposed; the system is described in terms of structural states in small parts of the material. The material is assumed to have two alternative types of…
There are many processes in cell biology that can be modeled in terms of particles diffusing in a two-dimensional (2D) or three-dimensional (3D) bounded domain $\Omega \subset \R^d$ containing a set of small subdomains or interior…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
A known limitation of time-dependent mean-field approaches is a lack of quantum tunneling for collective motions such as in sub-barrier fusion reactions. As a first step toward a solution, a time-dependent model is considered using a…
In many systems, nucleation of a stable solid may occur in the presence of other (often more than one) metastable phases. These may be polymorphic solids or even liquid phases. In such cases, nucleation of the solid phase from the melt may…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
A simple phenomenological model of a binary granular mixture is developed and investigated numerically. We attempt to model the experimental system of [1,2] where a horizontally vibrated binary monolayer was found to exhibit a transition…
For efficient application of protons and light ions in radiotherapy, detailed knowledge and realistic models of the corresponding radiobiological mechanism are necessary. Basic characteristics of this mechanism have been represented within…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…
Using the random matrix model, we discuss the effect of couplings to non-collective states on the penetrability of a one dimensional potential barrier. We show that these non-collective excitations hinder the penetrability and thus smear…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an…
In this paper we detail the mechanisms that drive substitutional binary diffusion and derive appropriate governing equations. We focus on the one-dimensional case with insulated boundary conditions. Asymptotic expansions are used in order…