Related papers: Statistical mechanics and thermodynamics of viral …
Superstatistics is a framework in nonequilibrium statistical mechanics that successfully describes a wide variety of complex systems, including hydrodynamic turbulence, weakly-collisional plasmas, cosmic rays, power grid fluctuations, among…
Phase transitions impose topological constraints on thermodynamic state variables, masking energetic fluctuations at the phase boundary. This constraint is most apparent in melting systems, where temperature remains pinned despite continued…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
Extrinsic environmental factors influence the distribution and population dynamics of many organisms, including insects that are of concern for human health and agriculture. This is particularly true for vector-borne infectious diseases,…
We present an analysis of six deterministic models for epidemic spreading. The evolution of the number of individuals of each class is given by ordinary differential equations of the first order in time, which are set up by using the laws…
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
We consider a nonlinear partial differential equation of conservation type to describe the dynamics of vesicular stomatitis virus observed in aliquots of fixed particle number taken from an evolving clone at periodic intervals of time…
In this work we to develop a general statistical mechanic formalism to study systems restricted to surfaces of revolution, these are a very well model to study the termodinamical properties of microbiological systems and macromolecules lies…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
We discuss the phase transition and critical exponents in the random allocation model (urn model) for different statistical ensembles. We provide a unified presentation of the statistical properties of the model in the thermodynamic limit,…
A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…
In this work we have investigated the evolutionary dynamics of a generalist pathogen, e.g. a virus population, that evolves towards specialisation in an environment with multiple host types. We have particularly explored under which…
RNA viruses exist as genetically diverse populations displaying different phenotypes, including diverse degrees of virulence. The evolution of virulence in viral populations is, however, poorly understood. Based on the experimental…
We consider the relationship between thermodynamics, fitness, and Darwinian selection in autocatalytic molecular replicators. We uncover a thermodynamic bound that relates fitness, replication rate, and thermodynamic affinity of…
Do negative absolute temperatures matter physics and specifically Statistical Physics? We provide evidence that we can certainly answer positively to this vexata quaestio. The great majority of models investigated by statistical mechanics…
Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for…