Related papers: Ising model description of long range correlations…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
We extend previous results due to Ding and Zhuang in order to prove that a phase transition occurs for the long range Ising model in lower dimensions. By making use of a recent argument due to Affonso, Bissacot and Maia from 2022 which…
We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
We present an exact solution of a one-dimensional Ising chain with both nearest neighbor and random long-range interactions. Not surprisingly, the solution confirms the mean field character of the transition. This solution also predicts the…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer…
We provide a non-trivial test of supersymmetry in the random-field Ising model at five spatial dimensions, by means of extensive zero-temperature numerical simulations. Indeed, supersymmetry relates correlation functions in a D-dimensional…
We study the 1d Ising model with long-range interactions decaying as $1/r^{1+s}$. The critical model corresponds to a family of 1d conformal field theories (CFTs) whose data depends nontrivially on $s$ in the range $1/2\leq s\leq 1$. The…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
We study random heteropolymer chain with gaussian distribution of kinds of monomers. The long-range correlations between kinds of monomers were introduce. The mean-field analysis of such heteropolymer indicates the existence of infinite…
In three-dimensional systems of the Ising universality class the ratio of correlation length amplitudes for the high- and low-temperature phases is a universal quantity. Its field theoretic determination apart from the $\epsilon$-expansion…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
We introduce a continuum percolation model defined on the points of a d-dimensional homogeneous Poisson process. Each Poisson point is connected to all points within its connection range, which depends on the distances to the other Poisson…