Related papers: Within-host bacterial growth dynamics with both mu…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…
The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…
In the framework of a 1D cyclic competition model, the Rock-Paper-Scissor model, where bacteria are allowed to mutate and move in space, we study the formation of stochastic patterns, where all the bacteria species do coexist. We modelled…
We study the growth of a population of bacteria in a dynamical hostile environment corresponding to the immune system of the colonised organism. The immune cells evolve as subcritical open clusters of oriented percolation and are…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…
Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…
In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in…
We present a mathematical model for within host viral infections that incorporates the Crowley Martin functional response, focusing on the dynamics influenced by periodic effects. This study establishes key properties of the model,…
Intraspecific trait variation has been increasingly recognized as an important factor in determining species interaction and diversity. Eco-evolutionary models have studied the distribution of trait values within a population that changes…
Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to…
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…
It is essential to understand the dynamics of epidemics in the presence of coexisting pathogens. There are various phenomenon that can effect the dynamics. In this paper, we formulate a mathematical model using different assumptions to…
The rise and spread of antibiotic resistance causes worsening medical cost and mortality especially for life-threatening bacteria infections, thereby posing a major threat to global health. Prescribing behavior of physicians is one of the…
When bacteria are grown on a mixture of two growth-limiting substrates, they exhibit a rich spectrum of substrate consumption patterns including diauxic growth, simultaneous consumption, and bistable growth. In previous work, we showed that…
It has long been known that antibiotic treatment will not completely kill off a bacteria population. For many species a small fraction of bacteria is not sensitive to antibiotics. These bacteria are said to persist. Recently it has been…
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…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…