Related papers: Evolutionary dynamics determines adaptation to ina…
The biological theory of adaptive dynamics proposes a description of the long-term evolution of a structured asexual population. It is based on the assumptions of large population, rare mutations and small mutation steps, that lead to a…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
Hundreds of Evolutionary Computation approaches have been reported. From an evolutionary perspective they focus on two fundamental mechanisms: cultural inheritance in Swarm Intelligence and genetic inheritance in Evolutionary Algorithms.…
We study a complex formation between the DNA and cationic amphiphilic molecules. As the amphiphile is added to the solution containing DNA, a cooperative binding of surfactants to the DNA molecules is found. This binding transition occurs…
The observed cooperation on the level of genes, cells, tissues, and individuals has been the object of intense study by evolutionary biologists, mainly because cooperation often flourishes in biological systems in apparent contradiction to…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through…
We consider an unpinned chain of harmonic oscillators with periodic boundary conditions, whose dynamics is perturbed by a random flip of the sign of the velocities. The dynamics conserves the total volume (or elongation) and the total…
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Complex change is often described as "evolutionary" in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary…
In multicellular organisms, cells differentiate into several distinct types during early development. Determination of each cellular state, along with the ratio of each cell type, as well as the developmental course during cell…
Large language models produce repetitive output when prompted independently across many batches, a phenomenon we term cross-batch mode collapse: the progressive loss of output diversity when a language model is prompted repeatedly without…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
The extent of parallel evolution at the genotypic level is quantitatively linked to the distribution of beneficial fitness effects (DBFE) of mutations. The standard view, based on light-tailed distributions (i.e. distributions with finite…
Symbiotic interactions between microbes and their multicellular hosts have manifold impacts on molecular, cellular and organismal biology. To identify candidate bacterial genes involved in maintaining endosymbiotic associations with insect…
We propose a minimal off-lattice model of living organisms where just a very few dynamical rules of growth are assumed. The stable coexistence of many clusters is detected when we replace the global restriction rule by a locally applied…
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…