相关论文: Microbial metabolism: optimal control of uptake ve…
The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry…
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…
Local perturbations of individual metabolic reactions may result in different levels of lethality, depending on their roles in metabolism and the size of subsequent cascades induced by their failure. Moreover, essentiality of individual…
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 ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Microbes constantly interact with their environment by depleting and transforming food sources. Theoretical studies have mainly focused on Lotka-Volterra models, which do not account for food source dynamics. In contrast, consumer-resource…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant…
Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using game theory with parameters renormalized by diffusion. Contrary to…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptake measurements of Synechocystis sp. PCC6803 with a…
Life relies on a sophisticated metabolic molecular machinery that turns over high-energy molecules to evolve complex macromolecules and assemblies. At the molecular origin of life, such machinery was absent, implying the need for simple yet…