Related papers: A Gibbs approach to Chargaff's second parity rule
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
There are numerous examples of approximately degenerate states of opposite parity in molecular physics. Theory indicates that these doubles can occur in molecules that are reflection-asymmetric. Such parity doubles occur in nuclear physics…
Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
Connections of a spectral nature are formed between Gibbs samplers and their blocked and collapsed variants. The solidarity principle of the spectral gap for full Gibbs samplers is generalized to different cycles and mixtures of Gibbs…
Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…
DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
Due to its light mass of order Lambda_QCD, the strange quark can play a special role in Chiral Symmetry Breaking (ChSB): differences in the pattern of ChSB in the limits N_f=2 (m_u,m_d->0, m_s physical) and N_f=3 (m_u,m_d,m_s->0) may arise…
The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…
We establish a one-to-one correspondence between one-sided and two-sided regular systems of conditional probabilities on the half-line that preserves the associated chains and Gibbs measures. As an application, we determine uniqueness and…
It has recently been suggested that the observed structure of parity doublets, seen in the spectrum of highly excited baryons, may be due to the effective restoration of chiral symmetry for these states. This chiral symmetry restoration…
Low-density parity-check codes with irregular constructions have been recently shown to outperform the most advanced error-correcting codes to date. In this paper we apply methods of statistical physics to study the typical properties of…
For random matrix ensembles with non-gaussian matrix elements that may exhibit some correlations, it is shown that centered traces of polynomials in the matrix converge in distribution to a Gaussian process whose covariance matrix is…
Charge symmetry breaking (CSB) in the strong interaction occurs because of the difference between the masses of the up and down quarks. The use of effective field theories allows us to follow this influence of confined quarks in hadronic…
The Gibbs ensemble of the truncated KdV (TKdV) equation has been shown to accurately describe the anomalous wave statistics observed in laboratory experiments, in particular the emergence of extreme events. Here, we introduce a novel…
Random-scan Gibbs samplers possess a natural hierarchical structure. The structure connects Gibbs samplers targeting higher dimensional distributions to those targeting lower dimensional ones. This leads to a quasi-telescoping property of…