Related papers: Endogenous viral mutations, evolutionary selection…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
We propose a simple SIR model in order to investigate the impact of various confinement strategies on a most virulent epidemic. Our approach is motivated by the current COVID-19 pandemic. The main hypothesis is the existence of two…
A current challenge for disease modeling and public health is understanding pathogen dynamics across scales since their ecology and evolution ultimately operate on several coupled scales. This is particularly true for vector-borne diseases,…
The rapid spread of the Coronavirus SARS-2 is a major challenge that led almost all governments worldwide to take drastic measures to respond to the tragedy. Chief among those measures is the massive lockdown of entire countries and cities,…
Previous evolutionary studies demonstrated how evaluating evolving agents in variable environmental conditions enable them to develop solutions that are robust to environmental variation. We demonstrate how the robustness of the agents can…
Most research on adaptive decision-making takes a strategy-first approach, proposing a method of solving a problem and then examining whether it can be implemented in the brain and in what environments it succeeds. We present a method for…
Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the…
Understanding dynamics of an outbreak like that of COVID-19 is important in designing effective control measures. This study aims to develop an agent based model that compares changes in infection progression by manipulating different…
We consider the effect of network structure on the evolution of a population. Models of this kind typically consider a population of fixed size and distribution. Here we consider eco-evolutionary dynamics where population size and…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
We examine the feasibility of predicting and subsequently managing the future evolution of a Complex Adaptive System. Our archetypal system mimics a competitive population of mechanical, biological, informational or human objects. We show…
In this work, we introduce a quantum-inspired epidemic model to study the dynamics of an infectious disease in a population divided into compartments. By treating the healthy population as a large reservoir, we construct a framework based…
We study a bi-virus susceptible-infected-susceptible (SIS) epidemic model in which individuals are either susceptible or infected with one of two virus strains, and consider mutation-driven transitions between strains. The general case of…
We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the…
We investigate a cyclic game system where organisms face an epidemic beyond being threatened by natural enemies. As a survival strategy, individuals of one out of the species usually safeguard themselves by approaching the enemies of their…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
We develop a simulation tool to support policy-decisions about healthcare for chronic diseases in defined populations. Incident disease-cases are generated in-silico from an age-sex characterised general population using standard…
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…
This paper studies a distributed continuous-time bi-virus model in which two competing viruses spread over a network consisting of multiple groups of individuals. Limiting behaviors of the network are characterized by analyzing the…
We argue that the phenomenon of symmetry breaking in genetics can enhance the adaptability of a species to changes in the environment. In the case of a virus, the claim is that the codon bias in the neutralization epitope improves the…