Related papers: Evolutionary comparison between viral lysis rate a…
Delayed processes are ubiquitous in biological systems and are often characterized by delay differential equations (DDEs) and their extension to include stochastic effects. DDEs do not explicitly incorporate intermediate states associated…
In this paper, we extend the demographic eco-evolutionary game approach, based on explicit birth and death dynamics instead of abstract "fitness" interpreted as an abstract "Malthusian parameter", by the introduction of the delay resulting…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
We consider the rates of noise-induced switching between the stable states of dissipative dynamical systems with delay and also the rates of noise-induced extinction, where such systems model population dynamics. We study a class of systems…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
Many socio-economic and biological processes can be modeled as systems of interacting individuals. The behaviour of such systems can be often described within game-theoretic models. In these lecture notes, we introduce fundamental concepts…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
Many studies have been performed to characterize the dynamics and stability of the microbiome across a range of environmental contexts [Costello et al., 2012, Faust et al., 2015]. For example, it is often of interest to identify time…
Traveling waves are analyzed in a model of the Hantavirus infection of deer mice. The existence of two kinds of wave phenomena is predicted. An environmental parameter governs a transition between two regimes of propagation. In one of them…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…
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…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
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…
The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
The evolutionary spread of cheater strategies can destabilize populations engaging in cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for populations dynamics. At the same time, the…
Malware detection and classification into families are critical tasks in cybersecurity, complicated by the continual evolution of malware to evade detection. This evolution introduces concept drift, in which the statistical properties of…
This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…