Related papers: Multi-lineage evolution in viral populations drive…
Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
Levels of sociality in nature vary widely. Some species are solitary; others live in family groups; some form complex multi-family societies. Increased levels of social interaction can allow for the spread of useful innovations and…
Asymptomatic infection has gained notoriety as an important feature of infectious disease dynamics. Despite increasing attention, there have been few rigorous examinations of how asymptomatic transmission influences pathogen evolution. In…
The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of…
We propose a physical theory underlying the temporal evolution of competing virus variants that relies on the existence of (quasi) fixed points capturing the large time scale invariance of the dynamics. To motivate our result we first…
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when…
Organisms from microbes to humans engage in a variety of social behaviors, which affect fitness in complex, often nonlinear ways. The question of how these behaviors evolve has consequences ranging from antibiotic resistance to human…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
Infectious diseases outbreaks are often characterized by a spatial component induced by hosts' distribution, mobility, and interactions. Spatial models that incorporate hosts' movements are being used to describe these processes, to…
Immunological systems have been an abundant inspiration to contemporary computer scientists. Problem solving strategies, stemming from known immune system phenomena, have been successfully applied to challenging problems of modern computing…
We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios,…
In this paper we study a two-level branching model for virus populations under cell division. We assume that the cells are carrying virus populations which evolve as a branching particle system with competition, while the cells split…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to…
Population structure induced by both spatial embedding and more general networks of interaction, such as model social networks, have been shown to have a fundamental effect on the dynamics and outcome of evolutionary games. These effects…
Epidemic spreading over populations networks has been an important subject of research for several decades, and especially during the Covid-19 pandemic. Most epidemic outbreaks are likely to create multiple mutations during their spreading…
An interesting inference drawn by some Covid-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection -- even at the start of the current pandemic. This paper introduces a model of…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…