Related papers: A guide to modeling plasmid co-infection dynamics
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows to introduce elements of novelty, while the latter is responsible for the motion of a system in its phase…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
Breaking a complex bio-social phenomenon (epidemic) into its components, considering the processes that determine its dynamics, formalizing the accepted hypotheses in mathematical equations, selecting appropriate experimental and…
In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed…
Infectious disease modeling is used to forecast epidemics and assess the effectiveness of intervention strategies. Although the core assumption of mass-action models of homogeneously mixed population is often implausible, they are…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
An adequate control of cell response in tissue engineering applications is of utmost importance to obtain products suitable to clinical practice. This paper is the first part of a series of two connected publications in which we study via…
Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
Mathematical modelling of epidemiological and coevolutionary dynamics is widely being used to improve disease management strategies of infectious diseases. Many diseases present some form of intra-host quiescent stage, also known as covert…
Nonlinear coupling between inter- and intra-element dynamics appears as a collective behaviour of elements. The elements in this paper denote symptoms such as a bacterium having an internal network of genes and proteins, a reactive droplet,…
We consider population dynamics on a network of patches, each of which has a the same local dynamics, with different population scales (carrying capacities). It is reasonable to assume that if the patches are coupled by very fast migration…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the…
Biological entities are inherently dynamic. As such, various ecological disciplines use mathematical models to describe temporal evolution. Typically, growth curves are modelled as sigmoids, with the evolution modelled by ordinary…
From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
Populations interact non-linearly and are influenced by environmental fluctuations. In order to have realistic mathematical models, one needs to take into account that the environmental fluctuations are inherently stochastic. Often,…