Related papers: A Growth Model for Dna Evolution (submitted to Nat…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
We present the first example where length scale for the growth of ordered regions and the correlation length for the two point correlations of persistent sites scale differently with time. We do so by studying a global spin exchange…
In this paper, we propose a method to study the nature of resonant relaxation in near-Keplerian systems. Our technique is based on measuring the fractal dimension of the angular momentum trails and we use it to analyze the outcome of N-body…
We briefly review some of the models used to describe DNA denaturation dynamics, focusing on the value of the dynamical exponent $z$, which governs the scaling of the characteristic time $\tau\sim L^z$ as a function of the sequence length…
We propose a minimal model of the dynamics of diversity -- replicator equations with extinction, invasion and mutation. We numerically study the behavior of this simple model and show that it displays completely different behavior from the…
In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
By means of the concept of factorial moment the charge transfer rates in DNA segments with fractal structures are investigated. An analytical form for the electron transfer rate is obtained.
We consider a branching model in discrete time where each individual has a trait in some general state space. Both the reproduction law and the trait inherited by the offsprings may depend on the trait of the mother and the environment. We…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Growth-fragmentation processes describe the evolution of systems in which cells grow slowly and fragment suddenly. Despite originating as a way to describe biological phenomena, they have recently been found to describe the lengths of…