Related papers: Functional universality in slow-growing microbial …

Interactions in natural communities can be highly heterogeneous, with any given species interacting appreciably with only some of the others, a situation commonly represented by sparse interaction networks. We study the consequences of…

We introduce the logistic model of consumption growth, which captures a negative feedback loop preventing an unlimited growth of consumption due to finite biophysical resources of our planet. This simple dynamic model allows for derivation…

Assessing quantitatively the state and dynamics of a social system is a very difficult problem. It is of great importance for both practical and theoretical reasons such as establishing the efficiency of social action programs, detecting…

Hypotheses: Quantitative molecular-thermodynamic theory of the growth of giant wormlike micelles in mixed nonionic surfactant solutions can be developed on the basis of a generalized model, which includes the classical phase separation and…

Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…

Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…

Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…

The rise of trait-based ecology has led to an increased focus on the distribution and dynamics of traits in communities. However, a general theory of trait-based ecology, that can apply across different scales (e.g., species that differ in…

Species interactions through cross-feeding via leakage and uptake of chemicals are important in microbial communities, and play an essential role in the coexistence of diverse species. Here, we study a simple dynamical model of a microbial…

Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…

Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…

We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…

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.…

Recent studies show that the microbial communities inhabiting the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Based on…

The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…

System-level properties of metabolic networks may be the direct product of natural selection or arise as a by-product of selection on other properties. Here we study the effect of direct selective pressure for growth or viability in…

The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…

Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…

The dynamics governing the evolution of a many body system is constrained by a nonabelian local symmetry. We obtain explicit forms of the global macroscopic condition assuring that at the microscopic level the evolution respects the overall…

The deep connection between thermodynamics, computation, and information is now well established both theoretically and experimentally. Here, we extend these ideas to show that thermodynamics also places fundamental constraints on…