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Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…
The possibility of coexistence of two competing populations is a classical question which dates back to the earliest `predator-prey' models. In this paper we study this question in the context of a model for the spread of a virus infection…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
We investigate a time-delayed epidemic model for multi-strain diseases with temporary immunity. In the absence of cross-immunity between strains, dynamics of each individual strain exhibits emergence and anni- hilation of limit cycles due…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a…
We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work we also…
Understanding the interplay of different traits in a co-infection system with multiple strains has many applications in ecology and epidemiology. Because of high dimensionality and complex feedbacks between traits manifested in infection…
Understanding the spatio-temporal evolution of epidemics with multiple pathogens requires not only new theoretical models but also careful analysis of their practical consequences. Building on the Multiplex Bi-Virus Reaction-Diffusion…
We investigate a discrete-time two-strain symbiotic epidemic model on complex networks with both random and long-range interactions. Our analysis examines how the co-infection recovery rate ($\mu$), the long-range decay exponent ($\alpha$),…
Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is…
We introduce and investigate an SIS-type model for the spread of an infectious disease, where the infected population is structured with respect to the different strain of the virus/bacteria they are carrying. Our aim is to capture the…
Infectious diseases are practically represented by models with multiple states and complex transition rules corresponding to, for example, birth, death, infection, recovery, disease progression, and quarantine. In addition, networks…
We develop a new structured compartmental model for the coevolutionary dynamics between susceptible and infectious individuals in heterogeneous SI epidemiological systems. In this model, the susceptible compartment is structured by a…
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…
Multi-strain competition on networks is observed in many contexts, including infectious disease ecology, information dissemination or behavioral adaptation to epidemics. Despite a substantial body of research has been developed considering…
This study extends the SIS epidemic model for single virus propagation over an arbitrary graph to an SI1SI2S epidemic model of two exclusive, competitive viruses over a two-layer network with generic structure, where network layers…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here…
In this paper, a mathematical analysis of the global dynamics of a viral infection model in vivo is carried out. We study the dynamics of a hepatitis C virus (HCV) model, under therapy, that considers both extracellular and intracellular…