Related papers: Studying viral populations with tools from quantum…
We pursue the task of developing a finite population counterpart to Eigen's model. We consider the classical Wright-Fisher model describing the evolution of a population of size $m$ of chromosomes of length $\ell$ over an alphabet of…
We study a susceptible-vaccinated--infected--recovered (SVIR) epidemic-spreading model with diversity of infection rate of the individuals. By means of analytical arguments as well as extensive computer simulations, we demonstrate that the…
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…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…
Reliable estimation of spatio-temporal trends in population-level HIV incidence is becoming an increasingly critical component of HIV prevention policy-making. However, direct measurement is nearly impossible. Current, widely used models…
We study the early stages of viral infection, and the distribution of times to obtain a persistent infection. The virus population proliferates by entering and reproducing inside a target cell until a sufficient number of new virus…
Compartmental epidemic models with dynamics that evolve over a graph network have gained considerable importance in recent years but analysis of these models is in general difficult due to their complexity. In this paper, we develop two…
The susceptible-infectious-recovered (SIR) model describes the evolution of three species of individuals which are subject to an infection and recovery mechanism. A susceptible $S$ can become infectious with an infection rate $\beta$ by an…
Two simple agent based models are often employed in epidemic studies: the susceptible-infected (SI) and the susceptible-infected-susceptible (SIS). Both models describe the time evolution of infectious diseases in networks in which vertices…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have…
IBM quantum computers are used to simulate the dynamics of small systems of interacting quantum spins. For time-independent systems with fewer than three spins, we compute the exact time evolution at arbitrary times and measure spin…
We investigate Eigen's model for the evolution of the genetic code of microorganisms using a novel method based on population dynamics analysis. This model, for a given number of offspring, determines long-term survival as a function of the…
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…
Epidemiological processes are studied within a recently proposed hierarchical network model using the susceptible-infected-refractory dynamics of an epidemic. Within the network model, a population may be characterized by $H$ independent…
This survey concerns the study of quasi-stationary distributions with a specific focus on models derived from ecology and population dynamics. We are concerned with the long time behavior of different stochastic population size processes…
We discuss a population of sequences subject to mutations and frequency-dependent selection, where the fitness of a sequence depends on the composition of the entire population. This type of dynamics is crucial to understand the evolution…
One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status,…
We propose to use quantum computers to simulate infection spreading in networks. We first show the analogy between the infection distribution and spin-lattice configurations with Ising-type interactions. Then, since the spreading process…
The study of social networks, and in particular the spread of disease on networks, has attracted considerable recent attention in the physics community. In this paper, we show that a large class of standard epidemiological models, the…