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Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
As antibiotic resistance continues to pose a significant threat to public health, alternative treatments are urgently needed. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
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…
We explore the potential multistability of the climate for a planet around the habitable zone. We focus on conditions reminiscent to those of the Earth system, but our investigation aims at presenting a general methodology for dealing with…
As the impending consequences of climate change loom over the Earth, it has become vital for researchers to understand the role microorganisms play in this process. In this paper, we examine how environmental factors, including moisture…
Environmental and mental conditions are known risk factors for dermatitis and symptoms of skin inflammation, but their interplay is difficult to quantify; epidemiological studies rarely include both, along with possible confounding factors.…
The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…
The factors contributing to the persistence and stability of life are fundamental for understanding complex living systems. Organisms are commonly challenged by harsh and fluctuating environments that are suboptimal for growth and…
This paper studies a two microbial species model in competition for a single resource in the chemostat including general interspecific density-dependent growth rates with distinct removal rates for each species. We give the necessary and…
In a wide variety of natural systems, closely-related microbial strains coexist stably, resulting in high levels of fine-scale biodiversity. However, the mechanisms that stabilize this coexistence are not fully understood. Spatial…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ``probiotic" treatments intended to alter the…
The main purpose of this paper is to study the existence of periodic solutions for a nonautonomous differential-difference system describing the dynamics of hematopoietic stem cell (HSC) population under some external periodic regulatory…
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…
Equilibrium statistical mechanics is intended to link the microscopic dynamics of particles to the thermodynamic laws for macroscopic quantities. However, the modern statistical theory is faced with significant difficulties, as applied to…
Under low concentrations of antibiotics causing DNA damage, \textit{Escherichia coli} bacteria can trigger stochastically a stress response known as the SOS response. While the expression of this stress response can make individual cells…
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…