种群与进化
In Part 1, we introduced a stochastic model of an infectious disease, based on the BDI (birth and death with immigration) process. We showed that random processes defined by this model can capture the essence of the stochastic, often…
We consider certain analytical features of a stochastic model that can explain among other things competition among species and simultaneous predation on the competing species from a geometric perspective which allows for a systematic…
Predation driven Allee effects play an important role in the dynamics of small population, however, such predation-driven Allee effects cannot occur for the model with type I functional response. It generally occurs when a generalist…
We generalize the Susceptible-Infected-Removed model for epidemics to take into account generic effects of heterogeneity in the degree of susceptibility to infection in the population. We introduce a single new parameter corresponding to a…
In the article a virus transmission model is constructed on a simplified social network. The social network consists of more than 2 million nodes, each representing an inhabitant of Slovenia. The nodes are organised and interconnected…
The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level…
State government-mandated social distancing measures have helped to slow down the growth of the COVID-19 pandemic in the United States. Current predictive models of the development of COVID-19, especially after mitigation efforts, are…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
Background: Rapid testing for an infection is paramount during a pandemic to prevent continued viral spread and excess morbidity and mortality. This study aimed to determine whether alternative testing strategies based on sample pooling can…
Collective behavior, and swarm formation in particular, has been studied from several perspectives within a large variety of fields, ranging from biology to physics. In this work, we apply Projective Simulation to model each individual as…
A hybrid network--deterministic model for simulation of multiresistant pathogen spread in a healthcare system is presented. The model accounts for two paths of pathogen transmission between the healthcare facilities: inter-hospital patient…
The World Health Organization describes zoonotic diseases as a major pandemic threat, and modeling the behavior of such diseases is a key component of their control. Many emerging zoonoses, such as SARS, Nipah, and Hendra, mutated from…
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…
Without a cure, vaccine, or proven long-term immunity against SARS-CoV-2, test-trace-and-isolate (TTI) strategies present a promising tool to contain its spread. For any TTI strategy, however, mitigation is challenged by pre- and…
As the interactions between people increases, the impending menace of COVID-19 outbreaks materialize, and there is an inclination to apply lockdowns. In this context, it is essential to have easy-to-use indicators for people to use as a…
The Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model is one of the standard models of disease spreading. Here we analyse an extended SEIR model that accounts for asymptomatic carriers, believed to play an important role…
Exploiting the SIQR model for COVID-19, I show that the wavy infection curve in Japan is the result of fluctuation of policy on isolation measure imposed by the government and obeyed by citizens. Assuming the infection coefficient be a…
The infection fatality rate (IFR) of the Coronavirus Disease 2019 (COVID-19) is one of the most discussed figures in the context of this pandemic. Using German COVID-19 surveillance data and age-group specific IFR estimates from multiple…
Seasonal influenza presents an ongoing challenge to public health. The rapid evolution of the flu virus necessitates annual vaccination campaigns, but the decision to get vaccinated or not in a given year is largely voluntary, at least in…
We study the evolutionary dynamics of the prisoner's dilemma game in which cooperators and defectors interact with another actor type called exiters. Rather than being exploited by defectors, exiters exit the game in favour of a small…