相关论文: The common origin of symmetry and structure in gen…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
This paper discusses the interplay of symmetries and stability in the analysis and control of nonlinear dynamical systems and networks. Specifically, it combines standard results on symmetries and equivariance with recent convergence…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Component systems - ensembles of realizations built from a shared repertoire of modular parts - are ubiquitous in biological, ecological, technological, and socio-cultural domains. From genomes to texts, cities, and software, these systems…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
Symmetry arguments are frequently used -- often implicitly -- in mathematical modeling of natural selection. Symmetry simplifies the analysis of models and reduces the number of distinct population states to be considered. Here, I introduce…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
I give a highly selective overview of the way statistical mechanics explains the microscopic origins of the time asymmetric evolution of macroscopic systems towards equilibrium and of first order phase transitions in equilibrium. These…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
Surnames and nonrecombining alleles are inherited from a single parent in a highly similar way. A simple birth-death model with mutations can accurately describe this process. Exponentially growing and constant populations are investigated,…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Spontaneous symmetry breaking plays a fundamental role in many areas of condensed matter and particle physics. A fundamental problem in ecology is the elucidation of the mechanisms responsible for biodiversity and stability. Neutral theory,…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
Discrete (family) symmetries might play an important role in models of elementary particle physics. We discuss the origin of such symmetries in the framework of consistent ultraviolet completions of the standard model in field and string…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…