Related papers: Evolutionary features in a minimal physical system…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
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…
Cellular development follows a stochastic yet rule-governed trajectory, though the underlying principles remain elusive. Here, we propose that cellular development follows paths of least action, aligning with foundational physical laws that…
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
The purpose of this roadmap article is to draw attention to a paradigm shift in our understanding of evolution towards a perspective of ecological-evolutionary feedback, highlighted through two recent highly simplified examples of rapid…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
The coupling between evolutionary and ecological changes (eco-evolutionary dynamics) has been shown to be relevant among diverse species, and is also of interest outside of ecology, i.e. in cancer evolution. These dynamics play an important…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…
Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
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.…
This paper explores the idea that information is an essential and distinctive feature of living systems. Unlike non-living systems, living systems actively acquire, process, and use information about their environments to respond to…
We propose a model for the growth of weighted networks that couples the establishment of new edges and vertices and the weights' dynamical evolution. The model is based on a simple weight-driven dynamics and generates networks exhibiting…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
We study several approaches for constructing a minimal model of Universe evolution by matching different stages of scale factor laws. We discuss the continuity in the transitions among the stages and the time variables involved. We develop…
Natural selection successfully explains how organisms accumulate adaptive change despite that traits acquired over a lifetime are eliminated at the end of each generation. However, in some domains that exhibit cumulative, adaptive change --…