Related papers: Stochastic Modeling and Simulation of Viral Evolut…
We develop a stochastic two-patch epidemic model with nonlinear recidivism to investigate infectious disease dynamics in heterogeneous populations. Extending a deterministic framework, we introduce stochasticity to account for random…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
Multispecies ecosystems modelled by generalized Lotka-Volterra equations exhibit stationary population abundances, where large number of species often coexist. Understanding the precise conditions under which this is at all feasible and…
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…
In a wide variety of natural systems, closely-related microbial strains coexist stably, resulting in high levels of fine-scale biodiversity. However, the mechanisms that stabilize this coexistence are not fully understood. Spatial…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
We investigate the long-time dynamics of a SIR epidemic model with infinitely many pathogen variants infecting a homogeneous host population. We show that the basic reproduction number $\mathcal{R}_0$ of the pathogen can be defined in that…
The coexistence between different informational molecules has been the preferred mode to circumvent the limitation posed by imperfect replication on the amount of information stored by each of these molecules. Here we reexamine a classic…
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…
When mutations are rampant, quasispecies theory or Eigen's model predicts that the fittest type in a population may not dominate. Beyond a critical mutation rate, the population may even be delocalized completely from the peak of the…
Some populations, such as red blood cells (RBCs), exhibit a pattern of population decline that is closer to linear rather than exponential, which has proven to be unexpectedly challenging to describe with a single simple mathematical model.…
The quasispecies theory is studied for dynamic replication landscapes. A meaningful asymptotic quasispecies is defined for periodic time dependencies. The quasispecies' composition is constantly changing over the oscillation period. The…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
A branching process in varying environment with generation-dependent immigration is a modification of the standard branching process in which immigration is allowed and the reproduction and immigration laws may vary over the generations.…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
The paper studies multi-competitive continuous-time epidemic processes in the presence of a shared resource. We consider the setting where multiple viruses are simultaneously prevalent in the population, and the spread occurs due to not…