Related papers: Quantifying Slow Evolutionary Dynamics in RNA Fitn…
We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to…
A fitness landscape is a genetic space -- with two genotypes adjacent if they differ in a single locus -- and a fitness function. Evolutionary dynamics produce a flow on this landscape from lower fitness to higher; reaching equilibrium only…
Phenotypic evolution implies sequential fixations of new genomic sequences. The speed at which these mutations fixate depends, in part, on the relative fitness (selection coefficient) of the mutant vs. the ancestor. Using a simple…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
A simple model of macroevolution is proposed exhibiting both the property of punctuated equilibrium and the dynamics of potentialities for different species to evolve towards increasingly higher complexity. It is based on the phenomenon of…
A simplified form of the time dependent evolutionary dynamics of a quasispecies model with a rugged fitness landscape is solved via a mapping onto a random flux model whose asymptotic behavior can be described in terms of a random walk. The…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
Populations of replicating entities frequently experience sudden or cyclical changes in environment. We explore the implications of this phenomenon via a environmental switching parameter in several common evolutionary dynamics models…
To our knowledge, the populations are generally assumed to be homogeneous in the traditional approach to evolutionary game dynamics. Here, we focus on the inhomogeneous populations. A simple model which can describe the inhomogeneity of the…
The rate of the trace distance is used to evaluate quantum speed-up for arbitrary mixed states. Compared with some present methods, the approach based on trace distance can provide an optimal bound to the speed of the evolution. The…
Information can evolve as a physical consequence of non-equilibrium dynamics, even in the absence of genes, replication, or predefined fitness functions. We present Stability-Driven Assembly (SDA), a framework in which stochastic assembly…
We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…
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 present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…