Related papers: Ising model description of long range correlations…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a…
We considered a long-range Ising model under Glauber dynamics and calculated the difference from the mean-field approximation in a finite-size system using perturbation theory. To deal with the BBGKY hierarchy, we assumed that certain types…
We present simulation results for the contact process on regular, cubic networks that are composed of a one-dimensional lattice and a set of long edges with unbounded length. Networks with different sets of long edges are considered, that…
The study of random graphs has become very popular for real-life network modeling such as social networks or financial networks. Inhomogeneous long-range percolation (or scale-free percolation) on the lattice $\mathbb Z^d$, $d\ge1$, is a…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
We study the random-field Ising model on a Dyson hierarchical lattice, where the interactions decay in a power-law-like form, $J(r)\sim r^{-\alpha}$, with respect to the distance. Without a random field, the Ising model on the Dyson…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
The fact that mean field theory is appropriate to describe an Ising model with long-range interactions has been already shown by Cannas and Tamarit. Although not explicited in our Letter, we have used periodic boundary conditions in all our…
We present a simple and general way to accurately describe long-range interactions between atoms and molecules through combining neural networks with physical models. Demonstrations on the H$_3$, Li$_3$ and 2KRb systems illustrate the…
A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…