Related papers: Dynamics of DNA Melting
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
Two-dimensional $CP^{N-1}$ models are investigated by Monte Carlo methods on the lattice, for values of $N$ ranging from 2 to 21. Scaling and rotation invariance are studied by comparing different definitions of correlation length $\xi$.…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
We study several one dimensional step flow models. Numerical simulations show that the slope of the profile exhibits scaling in all cases. We apply a scaling ansatz to the various step flow models and investigate their long time evolution.…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
We propose a model-independent scaling method to study the physical properties of high-temperature superconductors in the normal state. We have analyze the experimental data of the c-axis resistivity, the in-plane resistivity, the Hall…
The long-time dynamics of the 1D contact process suddenly brought out of an uncorrelated initial state is studied through a light-cone transfer-matrix renormalisation group approach. At criticality, the system undergoes ageing which is…
We use large-scale Monte Carlo simulations to obtain comprehensive results for domain growth and aging in the random field XY model in dimensions $d=2,3$. After a deep quench from the paramagnetic phase, the system orders locally via…
We study coarsening dynamics in the ferromagnetic random bond Ising model in d = 1; 2. We focus on the validity of super-universality and the scaling properties of the response functions. In the d = 1 case, we obtain a complete…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding…
Two significant consequences of quantum fluctuations are entanglement and criticality. Entangled states may not be critical but a critical state shows signatures of universality in entanglement. A surprising result found here is that the…
The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…