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Nitrogen (N) removal from estuaries is driven in part by sedimentary microbial processes. The processes of denitrification and anaerobic ammonium oxidation (anammox) remove N from estuaries by producing di-nitrogen gas, and each can be…
Nitrous oxide (N2O) is a potent greenhouse gas emitted during biological wastewater treatment. A pseudo-mechanistic model describing three biological pathways for nitric oxide (NO) and N2O production was calibrated for mixed culture biomass…
Wastewater treatment plants are increasingly recognized as promising candidates for machine learning applications, due to their societal importance and high availability of data. However, their varied designs, operational conditions, and…
Dynamics of adsorption and desorption of (4S)-N on amorphous solid water are analyzed using molecular dynamics simulations. The underlying potential energy surface was provided by machine-learned interatomic potentials. Binding energies…
Subsurface flows, particularly hyporheic exchange fluxes, driven by streambed topography, permeability, channel gradient and dynamic flow conditions provide prominent ecological services such as nitrate removal from streams and aquifers.…
The striking variety of macroscopic morphologies displayed by bacterial colonies depends on microscopic environmental and behavioural details in a manner that is currently not well understood. A surprising example is sibling inhibition,…
Anaerobic digestion enables the water industry to treat wastewater as a resource for generating energy and recovering valuable by-products. The complexity of the anaerobic digestion process has motivated the development of complex models.…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
Understanding how pore structure influences flow and transport behaviour in granular materials is essential for addressing a wide range of geotechnical, hydraulic, and environmental challenges. These processes are largely shaped by the…
Microbial interactions regulate their spread and survival in competitive environments. It is not clear if the physical parameters of the environment regulate the outcome of these interactions. In this work, we show that the opportunistic…
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…
Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive mechanism are expected to speculate a novel rule in wood biomass…
Nitrogen (N) deposition is a primary driver of species loss in plant communities globally. However, the mechanisms by which high N availability causes species loss remain unclear. Many hypotheses for species loss with increasing N…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Bacteria at fluid interfaces endure physical and chemical stresses unique to these highly asymmetric environments. The responses of Pseudomonas aeruginosa PAO1 and PA14 to a hexadecane-water interface are compared. PAO1 cells form elastic…
The NDHA model comprehensively describes nitrous oxide (N2O) producing pathways by both autotrophic ammonium oxidizing and heterotrophic bacteria. The model was calibrated via a set of targeted extant respirometric assays using enriched…
Networks are ubiquitous in biology where they encode connectivity patterns at all scales of organization, from molecular to the biome. However, biological networks are noisy due to the limitations of measurement technology and inherent…
We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory…
The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. Modelling these reactions is however difficult when water directly participates in…
Dictyostelium discoideum is an ideal organism to test the pathogenicity of Pseudomonas aeruginosa, since its eukaryote nature allows for comparisons to be made to human health. Additionally, D. discoideum naturally feeds on bacteria and has…