Related papers: DNA denaturation bubbles: free-energy landscape an…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
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…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
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 denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
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…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…