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Cellular metabolism is globally regulated by various currency metabolites such as ATP, GTP, and NAD(P)H. These metabolites cycle between charged (high-energy) and uncharged (low-energy) states to mediate energy transfer. While distinct…
Photosynthetic microbes have evolved and successfully adapted to the ever-changing environmental conditions in complex microhabitats throughout almost all ecosystems on Earth. In the absence of light, they can sustain their biological…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
As urbanization and climate change progress, urban heat becomes a priority for climate adaptation efforts. High temperatures concentrated in urban heat can drive increased risk of heat-related death and illness as well as increased energy…
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
In nature, objects which are in thermal contact with each other, usually approach the same temperature, unless a heat source (or sink) cherishes a persistent flow of heat. Accordingly, in a well-isolated apartment flat, most items are at a…
Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
Situations where a spontaneous process of energy or matter transfer is enhanced by an external device are widespread in nature (human sweating system, enzyme catalysis, facilitated diffusion across bio-membranes, industrial heat…
An approximate many-body theory has been used to calculate the heat capacity and the condensate fraction of a BEC with effective repulsive interaction. The effect of interactions has been analyzed and compared with the non-interacting case.…
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…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…
Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over non-motile cells. Since motility is energetically costly, cells must optimize their swimming speed and…