Related papers: DNA unzipping via stopped birth and death processe…

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein.…

We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an…

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 use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…

We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…

The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…

Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…

We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…

A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…

Using the criterion that the mechanical unzipping transition in a bound homopolymer is triggered when the average force exerted by the single unbound strands on the first base pair in the bound section exceeds the force binding the pair…

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…

As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…

The opening of the Y-fork - the first step of DNA replication - is shown to be a critical phenomenon under an external force at one of its ends. From the results of an equivalent delocalization in a non-hermitian quantum-mechanics problem…

The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…

We propose a new simple model for DNA denaturation bases on the pendulum model of Englander\cite{A1} and the microscopic model of Peyrard {\it et al.},\cite{A3} so called "combined model". The main parameters of our model are: the coupling…