Related papers: Mutation model for oligonucleotides fitting a Yule…
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…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
Theoretical predictions for the behavior of the slope of the nucleon-nucleon scattering and another parameters of the differential cross sections in the framework of the dynamic model are compared with the recent UA4 data at small transfer…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
The hyperfine interactions of the constituent quark model provide a natural explanation for many nucleon properties, including the Delta-N splitting, the charge radius of the neutron, and the observation that the proton's quark distribution…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
Spin waves are propagating disturbances of spin order in lattices with nearest-neighbor interactions. They are traditionally observed in magnetically ordered solids using inelastic neutron, light, or electron scattering, and ferromagnetic…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
We introduce and analyse ensembles of 2-regular random graphs with a tuneable distribution of short cycles. The phenomenology of these graphs depends critically on the scaling of the ensembles' control parameters relative to the number of…
We study the population genetics of two neutral alleles under reversible mutation in the \Lambda-processes, a population model that features a skewed offspring distribution. We describe the shape of the equilibrium allele frequency…
In this short communication, we shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a…
We investigate the statistical evolution of magnetic neutron stars, recycled in binary systems, simulating synthetic populations. To bracket uncertainties, we consider a soft (FP) and a stiff (PS) equation of state (EoS) for nuclear matter…
The spin dynamics of bilayer cuprate compounds are studied in a basic model. The magnetic spectral properties are calculated in linear spin-wave theory for several stripe configurations which differ by the relative location of the stripes…
The connection between the scaling function, directly extracted from the analysis of electron scattering data, and the nuclear spectral function or nuclear momentum density is investigated at depth. The dependence of the scaling function on…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
Evolving networks with a constant number of edges may be modelled using a rewiring process. These models are used to describe many real-world processes including the evolution of cultural artifacts such as family names, the evolution of…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions…