Related papers: A Growth Model for Dna Evolution (submitted to Nat…
One of the properties that make ecological systems so unique is the range of complex behavioural patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Concentrations of matter, such as galaxies and galactic clusters, originated as very small density fluctuations in the early universe. The existence of galaxy clusters and super-clusters suggests that a natural scale for the matter…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
For taxonomic levels higher than species, the abundance distributions of number of subtaxa per taxon tend to approximate power laws, but often show strong deviationns from such a law. Previously, these deviations were attributed to…
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some initial time. We deduce the time translational matrix for…
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…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Recently Storm and Nelson [1] (Phys.Rev. E67, 51906 (2003)) introduced the discrete persistent chain model which contains both features of the freely jointed chain (FJC) and the wormlike chain (WLC) models. Equation (20) of their paper is…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally…
An analytic model of long string network evolution, recently developed by the authors, is presented in detail, and modified to describe string loop evolution. By treating the average string velocity, as well as the characteristic…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
Analysis of experimental kinetic dependences and results of the computer modeling of pairwise interactions in the heterogeneous system have shown that a character of its fractal property variation in the evolution process would be different…