Related papers: Ising model description of long range correlations…
We study the kinetics after a low temperature quench of the one-dimensional Ising model with long range interactions between spins at distance $r$ decaying as $r^{-\alpha}$. For $\alpha =0$, i.e. mean field, all spins evolve coherently…
After a zero temperature quench, we study the kinetics of the one-dimensional Ising model with long-range interactions between spins at distance $r$ decaying as $r^{-\alpha}$, with $\alpha \le 1$. As shown in our recent study [SciPost Phys…
A one dimensional network on which there are long range bonds at lattice distances $l>1$ with the probability $P(l) \propto l^{-\delta}$ has been taken under consideration. We investigate the critical behavior of the Ising model on such a…
The correlation length plays a pivotal role in finite-size scaling and hyperscaling at continuous phase transitions. Below the upper critical dimension, where the correlation length is proportional to the system length, both finite-size…
We calculate the mutual information function for each of the 24 chromosomes in the human genome. The same correlation pattern is observed regardless the individual functional features of each chromosome. Moreover, correlations of different…
We study the ferromagnetic Ising model with long-range interactions in two dimensions. We first present results of a Monte Carlo study which shows that the long-range interactions dominate over the short-range ones in the intermediate…
Recently, it has been found that an effective long-range interaction is realized among local bistable variables (spins) in systems where the elastic interaction causes ordering of the spins. In such systems, generally we expect both…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
We define sequence patterns of length $n$ and level $\ell$ to be equivalence classes of sequences that have $n$ elements from the set of $\ell$ integer symbols $\{1,2,\ldots,\ell\}$ with no restriction on repetition, where the equivalence…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…
Distance correlation has become an increasingly popular tool for detecting the nonlinear dependence between a pair of potentially high-dimensional random vectors. Most existing works have explored its asymptotic distributions under the null…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
We report analytic results for the correlation functions of long-range quantum Ising models in arbitrary dimension. In particular, we focus on the long-time evolution and the relevant timescales on which correlations relax to their…
Many networks of physical and biological interest are characterized by a long-range coupling mediated by a chemical which diffuses through a medium in which oscillators are embedded. We considered a one-dimensional model for this effect for…
In this paper, we propose a map which connects nucleons bound in nuclei and Ising spins in Ising model. This proposal is based on the fact that the description of states of nucleons and Ising spins could share the same type of observables.…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We investigate heterogeneous and homogeneous nucleation in nearest-neighbor and long-range Ising models for various quench depths. We find that the system has a true crossover from heterogeneous to homogeneous nucleation for increasing…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…