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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…
Vector-borne diseases often infect multiple host species, increasing the likelihood of disease persistence due to the presence of multiple reservoirs. Vector biting patterns and feeding preferences can shift in response to selective…
Antimicrobial resistance is a silent pandemic that is being exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
We consider a branching random walk in a random space-time environment of disasters where each particle is killed when meeting a disaster. This extends the model of the "random walk in a disastrous random environment" introduced by [15]. We…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of…
We apply optimal control theory to a tuberculosis model given by a system of ordinary differential equations. Optimal control strategies are proposed to minimize the cost of interventions, considering reinfection and post-exposure…
In the Staged Progression (SP) epidemic models, infected individuals are classified into a suitable number of states. The goal of these models is to describe as closely as possible the effect of differences in infectiousness exhibited by…
Antimicrobial resistance (AMR) poses a global health threat, reducing the effectiveness of antibiotics and complicating clinical decision-making. To address this challenge, we introduce abx_amr_simulator, a Python-based simulation package…
Inspired by DNA data of the human cytomegalovirus we propose a model of a two-type parasite population distributed over its hosts. The parasite is capable to persist in its host till the host dies, and to reinfect other hosts. To maintain…
Motivated by a model of an area-wide integrated pest management, we develop an interacting particle system evolving in a random environment. It is a generalised contact process in which the birth rate takes two possible values, determined…
Sexually transmitted infections (STIs) continue to present a complex and costly challenge to public health programs. The preferences and social dynamics of a population can have a large impact on the course of an outbreak as well as the…
Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix.…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
We extend our BDI (birth-death-immigration) process based stochastic model of an infectious disease to time-nonhomogeneous cases. First, we discuss the deterministic model, and derive the expected value of the infection process. Then as an…
Persistence is an important characteristic of many complex systems in nature, related to how long the system remains at a certain state before changing to a different one. The study of complex systems' persistence involves different…
Purpose: Antimicrobial resistance is a major global health concern, affecting hospital admissions and treatment success. This study aims to introduce an experimental setup for monitoring bacterial activity over time using image-based…
Microbial communities routinely have several possible species compositions or community states observed for the same environmental parameters. Changes in these parameters can trigger abrupt and persistent transitions (regime shifts) between…
We consider active Brownian particles that intermittently switch between active and inactive states. Such behavior is ubiquitous at all scales, from bacteria to animals and in artificial active systems. We derive exact expressions for key…