Related papers: Ising model description of long range correlations…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
Long sequences occur in abundance within real-world scenarios, hence properly modelling them opens numerous down-stream use-cases. Deep neural networks, however, have often struggled with these for a variety of reasons. Recent advances,…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
A generalization of the ABC model, a one-dimensional model of a driven system of three particle species with local dynamics, is introduced, in which the model evolves under either (i) density-conserving or (ii) nonconserving dynamics. For…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
The depinning of an elastic line interacting with a quenched disorder is studied for long range interactions, applicable to crack propagation or wetting. An ultrametric distance is introduced instead of the Euclidean distance, allowing for…
The explosion of data on animal behavior in more natural contexts highlights the fact that these behaviors exhibit correlations across many time scales. But there are major challenges in analyzing these data: records of behavior in single…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
We consider N initially disentangled spins, embedded in a ring or d-dimensional lattice of arbitrary geometry, which interact via some long--range Ising--type interaction. We investigate relations between entanglement properties of the…
We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…
Long-range synchrony from short-range interactions is a familiar pattern in biological and physical systems, many of which share a common set of ``universal'' properties at the point of synchronization. Common biological systems of coupled…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
We consider the long-range random field Ising model in dimension $d = 1, 2$, whereas the long-range interaction is of the form $J_{xy} = |x-y|^{-\alpha}$ with $1< \alpha < 3/2$ for $d=1$ and with $2 < \alpha \leq 3$ for $d = 2$. Our main…
Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
We consider long-range percolation in dimension $d\geq 1$, where distinct sites $x$ and $y$ are connected with probability $p_{x,y}\in[0,1]$. Assuming that $p_{x,y}$ is translation invariant and that $p_{x,y}=\|x-y\|^{-s+o(1)}$ with $s>2d$,…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…