Related papers: Simulating short- and long-term evolutionary dynam…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
This study focuses on open quasispecies systems with competition and death flow, described by modified Eigen and Crow-Kimura models. We examine the evolutionary adaptation process as a reaction to changes in rates. One of the fundamental…
We consider a continuous-time random walk which is the generalization, by means of the introduction of waiting periods on sites, of the one-dimensional nonhomogeneous random walk with a position-dependent drift known in the mathematical…
Migration between different habitats is ubiquitous among biological populations. In this Letter, we study a simple quasispecies model for evolution in two different habitats, with different fitness landscapes, coupled through one-way…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
A discrete binomial random-walk description of molecular collisions is used to quantify the variance of coarse-grained velocity fields arising solely from collision-induced momentum exchange. Closed-form expressions for the growth of…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
In this paper, we show that different types of evolutionary game dynamics are, in principle, special cases of a dynamical system model based on our previously reported framework of generalized growth transforms. The framework shows that…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
This thesis investigates critical phenomena and equilibrium states in various stochastic models through three interconnected studies. In the first chapter, we analyze the Activated Random Walk model on a one-dimensional ring in the…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Robots are still poor at traversing cluttered large obstacles required for important applications like search and rescue. By contrast, animals are excellent at doing so, often using direct physical interaction with obstacles rather than…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
We develop quantum electrodynamics into a kinetic-theory-like evolution equation for electrons, positrons and photons. To keep the "collision rules" simple, we make use of longitudinal and temporal photons in addition to the usual…
We study the effect that disturbances in the ecological landscape exert on the spatial distribution of a population that evolves according to the nonlocal FKPP equation. Using both numerical and analytical techniques, we explore the three…
We perform simulations for one dimensional continuous-time random walks in two dynamic random environments with fast (independent spin-flips) and slow (simple symmetric exclusion) decay of space-time correlations, respectively. We focus on…
A single-column model is used to investigate regime transitions within the stable atmospheric boundary layer, focusing on the role of small-scale fluctuations in wind and temperature dynamics and of turbulence intermittency as triggers for…