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During drug development, evidence can emerge to suggest a treatment is more effective in a specific patient subgroup. Whilst early trials may be conducted in biomarker-mixed populations, later trials are more likely to enrol…
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…
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a…
There has been interest in the interactions between infectious disease dynamics and behaviour for most of the history of mathematical epidemiology. This has included consideration of which mathematical models best capture each phenomenon,…
We introduce a model called Host-Pathogen game for studying biological competitions. Notably, we focus on the invasive dynamics of external agents, like bacteria, within a host organism. The former are mapped to a population of defectors…
Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of…
Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We…
A mathematical model involving a syntrophic relationship between two populations of bacteria in a continuous culture is proposed. A detailed qualitative analysis is carried out. The local and global stability analysis of the equilibria are…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), linked with CRISPR associated (CAS) genes, play a profound role in the interactions between phage and their bacterial hosts. It is now well understood that CRISPR-CAS…
We studied the swimming of \textit{Escherichia coli} bacteria in the vicinity of the critical point in a solution of the non-ionic surfactant \chem{C_{12}E_{5}} in buffer solution. In phase contrast microscopy, each swimming cell produces a…
We investigate the structure and stability of the steady states for a bacterial colony model with density-suppressed motility. We treat the growth rate of bacteria as a bifurcation parameter to explore the local and global structure of the…
Infectious disease transmission in human populations has a complex two-way interaction with changes in host behaviour. It is increasingly recognised that incorporating adaptive behavioural change into epidemic models is important for…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
The role of activity on the hydrodynamic dispersion of bacteria in a model porous medium is studied by tracking thousands of bacteria in a microfluidic chip containing randomly placed pillars. We first evaluate the spreading dynamics of two…
The entrapment of bacteria near boundary surfaces is of biological and practical importance, yet the underlying physics is still not well understood. We demonstrate that it is crucial to include a commonly neglected entropic effect arising…
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…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…