种群与进化
This review article is the second part of the project ``Selected Topics of Social Physics". The first part has been devoted to equilibrium systems. The present part considers nonequilibrium systems. The style of the paper combines the…
Compartmental models are valuable tools for investigating infectious diseases. Researchers building such models typically begin with a simple structure where compartments correspond to individuals with different epidemiological statuses,…
In the study of cancer evolution and therapeutic strategies, scientific evidence shows that a key dynamics lies in the tumor-environment interaction. In particular, oxygen concentration plays a central role in the determination of the…
In the study of therapeutic strategies for the treatment of cancer, eco-evolutionary dynamics are of particular interest, since characteristics of the tumour population, interaction with the environment and effects of the treatment,…
We introduce an individual-based model of a complex ecological community with random interactions. The model contains a large number of species, each with a finite population of individuals, subject to discrete reproduction and death…
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of. moving throughout the high-dimensional space of trees. However, hyperbolic space offers a low…
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…
In the long run, the eventual extinction of any biological population is an inevitable outcome. While extensive research has focused on the average time it takes for a population to go extinct under various circumstances, there has been…
Symmetry arguments are frequently used -- often implicitly -- in mathematical modeling of natural selection. Symmetry simplifies the analysis of models and reduces the number of distinct population states to be considered. Here, I introduce…
Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) models, describing the interactions between phytoplankton, zooplankton systems, and their ecosystem, are used to predict their ecological and evolutionary population dynamics. These…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
In the world of epidemics, the mathematical modeling of disease co-infection is gaining importance due to its contributions to mathematics and public health. Because the co-infection may have a double burden on families, countries, and the…
A very large class of ODE epidemic models (2.2) discussed in this paper enjoys the property of admitting also an integral renewal formulation, with respect to an "age of infection kernel" a(t) which has a matrix exponential form (3.2). We…
In models for the evolution of predation from initially purely competitive species interactions, the propensity of predation is most often assumed to be a direct consequence of the relative morphological and physiological traits of…
The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely…
Digital contact tracing/notification was initially hailed as a promising strategy to combat SARS-CoV-2, but in most jurisdictions it did not live up to its promise. To avert a given transmission event, both parties must have adopted the…
Ecosystems dynamics is often considered as driven by a coupling of species' resource consumption and its population size dynamics. Such resource-population dynamics is captured by MacArthur-type models. One biologically relevant feature…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
We study the stochastic spatial Lotka-Volterra (LV) model for predator-prey interaction subject to a periodically varying carrying capacity. The LV model with on-site lattice occupation restrictions that represent finite food resources for…
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…