Related papers: Interaction between directional epistasis and aver…

Models in evolutionary game theory traditionally assume symmetric interactions in homogeneous environments. Here, we consider populations evolving in a heterogeneous environment, which consists of patches of different qualities that are…

Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…

The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…

We study an abstract model for the co-evolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit…

Depletion interactions are thought to significantly contribute to the organization of intracellular structures in the crowded cytosol. The strength of depletion interactions depends on physical parameters like the depletant number density…

The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…

Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression.…

Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…

Traditional approaches to ecosystem modelling have relied on spatially homogeneous approximations to interaction, growth and death. More recently, spatial interaction and dispersal have also been considered. While these leads to certain…

While Neutral Theory famously describes the number of discrete genetic differences in populations, we consider the number of genetic backgrounds under which such differences are observed - setting limits to the generalizability of their…

We show that, during adiabatic evolution, any changes in entanglement can be attributed to a succession of avoided energy level crossings at which eigenvalues swap their eigenvectors. These swaps mediate the generation and redistribution of…

Gene-environment interactions have important implications to elucidate the genetic basis of complex diseases beyond the joint function of multiple genetic factors and their interactions (or epistasis). In the past, G$\times$E interactions…

RNA protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation. We investigate the…

Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…

For two genotypes that have the same mean number of offspring but differ in the variance in offspring number, natural selection will favor the genotype with lower variance. The concept of fitness becomes cloudy under these conditions…

This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating…

In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data.…

Fitness consequence of dispersal depends on property of the entire landscape, which patches are available and what are the cost of moving. These are information that are not available locally when an organism make the decision to disperse.…

In battery modeling, the electrode is discretized at the macroscopic scale with a single representative particle in each volume. This lacks the accurate physics to describe interparticle interactions in electrodes. To remedy this, we…

The mutation process in evolution strategies has been interlinked with the normal distribution since its inception. Many lines of reasoning have been given for this strong dependency, ranging from maximum entropy arguments to the need for…