Related papers: Maximum principle and mutation thresholds for four…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
We study a novel model for evolution of complex networks. We introduce information filtering for reduction of the number of available nodes to a randomly chosen sample, as stochastic component of evolution. New nodes are attached to the…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
Kingman's model describes the evolution of a one-locus haploid population of infinite size and discrete generations under the competition of selection and mutation. A random generalisation has been made in a previous paper which assumes all…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
We reconsider the Eigen's quasi-species model for competing self-reproductive macromolecules in populations characterized by a single-peaked fitness landscape. The use of ideas and tools borrowed from polymers theory and statistical…
The dynamics of quantum phase transitions are inevitably accompanied by the formation of defects when crossing a quantum critical point. For a generic class of quantum critical systems, we solve the problem of minimizing the production of…
Competitions can occur on an absolute scale, to be faster or more efficient, or they can occur on a relative scale, to "beat" one's competitor in a zero-sum game. Ecological models have focused on absolute competitions, in which optima…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
We pursue the task of developing a finite population counterpart to Eigen's model. We consider the classical Wright-Fisher model describing the evolution of a population of size $m$ of chromosomes of length $\ell$ over an alphabet of…
We present stochastic, finite-population formulations of the Crow-Kimura and Eigen models of quasispecies theory, for fitness functions that depend in an arbitrary way on the number of mutations from the wild type. We include back mutations…
The quantum error threshold is the highest (model-dependent) noise rate which we can tolerate and still quantum-compute to arbitrary accuracy. Although noise thresholds are frequently estimated for the Steane seven-qubit, distance-three…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
We analyze the force-extension curve for a general class of systems, which are described at the mesoscopic level by a free energy depending on the extension of its components. Similarly to what is done in real experiments, the total length…
We consider a model of a population with fixed size $N$, which is subjected to an unlimited supply of beneficial mutations at a constant rate $\mu_N$. Individuals with $k$ beneficial mutations have the fitness $(1+s_N)^k$. Each individual…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
Crossover and mutation are the two main operators that lead to new solutions in evolutionary approaches. In this article, a new method of performing the crossover phase is presented. The problem of choice is evolutionary decision tree…
New experimental methods make it possible to measure the expression levels of many genes, simultaneously, in snapshots from thousands or even millions of individual cells. Current approaches to analyze these experiments involve clustering…