种群与进化
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
With growing exchanges of people and merchandise between countries, epidemics have become an issue of increasing importance and huge amounts of data are being collected every day. Hence, analyses that were usually run in personal computers…
We model and calculate the fraction of infected population necessary to reach herd immunity, taking into account the heterogeneity in infectiousness and susceptibility, as well as the correlation between those two parameters. We show that…
A great issue of discussion of an infectious disease is its basic reproduction number R0, which provides an estimation of the contagiousness of the disease. When R0 > 1, the disease spread will potentially lead to an outbreak, such that of…
A fractional compartmental mathematical model for the spread of the COVID-19 disease is proposed. Special focus has been done on the transmissibility of super-spreaders individuals. Numerical simulations are shown for data of Galicia,…
Increasing number in global COVID-19 cases demands for mathematical model to analyze the interaction between the virus dynamics and the response of innate and adaptive immunity. Here, based on the assumption of a weak and delayed response…
We demonstrate that a simple model based on reaction-diffusion-advection (RDA) equation forced by realistic surface velocities and nutrients is skilled in reproducing the distributions of the surface phytoplankton chlorophyll in the…
Understanding the dynamics of the COVID-19 pandemic is crucial for improved control and social distancing strategies. To that effect, we have employed the susceptible-exposed-infectious-recovered model, refined by contact tracing and…
In this paper, we propose a two-group SIR epidemic model to simulate the outcome of stay-at-home policy and wearing face masks during the first COVID-19 epidemic wave in the United States. Based on our proposed model, we further use the…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
By fitting a compartment ODE model for Covid-19 propagation to cumulative case and death data for US states and European countries, we find that the case mortality rate seems to have decreased by at least 80% in most of the US and at least…
Without vaccines and treatments, societies must rely on non-pharmaceutical intervention strategies to control the spread of emerging diseases such as COVID-19. Though complete lockdown is epidemiologically effective, because it eliminates…
We address a novel approach for stochastic individual-based modelling of a single species population. Individuals are distinguished by their remaining lifetimes, which are regulated by the interplay between the inexorable running of time…
The current COVID-19 pandemic is affecting different countries in different ways. The assortment of reporting techniques alongside other issues, such as underreporting and budgetary constraints, makes predicting the spread and lethality of…
We have learned to live with many potentially deadly viruses for which there is no vaccine, no immunity, and no cure. We do not live in constant fear of these viruses, instead, we have learned how to outsmart them and reduce the harm they…
The SIR(D) epidemiological model is defined through a system of transcendental equations, not solvable by elementary functions. In the present paper those equations are successfully replaced by approximate ones, whose solutions are given…
The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many…
An essential feature of the adaptive immune system is the proliferation of antigen-specific lymphocytes during an immune reaction to form a large pool of effector cells. This proliferation must be regulated to ensure an effective response…
The transmission of COVID-19 is dependent on social contacts, the rate of which have varied during the pandemic due to mandated and voluntary social distancing. Changes in transmission dynamics eventually affect hospital admissions and we…
In this paper, we investigate a novel 3-compartment model of HIV infection of CD4$^+$ T-cells with a mass action term by including two versions: one baseline ODE model and one delay-differential equation (DDE) model with a constant discrete…