Related papers: Formation and Dissolution of Bacterial Colonies
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a…
Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…
We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining…
The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of…
Bacteria frequently colonize natural microcavities such as gut crypts, plant apoplasts, and soil pores. Recent studies have shown that the physical structure of these spaces plays a crucial role in shaping the stability and resilience of…
Anaerobic processes (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is…
It has been proposed that during the early steps in the origin of life, small droplets could have formed via the segregation of molecules from complex mixtures by phase separation. These droplets could have provided chemical reaction…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
Bacteria on surfaces exhibit collective behaviors, such as active turbulence and active stresses, which result from their motility, growth, and interactions with their local surroundings. However, interfacial deformations on soft surfaces…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
A diffusion-reaction model for the growth of bacterial colonies is presented. The often observed cooperative behavior developed by bacteria which increases their motility in adverse growth conditions is here introduced as a nonlinear…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…
The transition from localized to systemic spreading of bacteria, viruses and other agents is a fundamental problem that spans medicine, ecology, biology and agriculture science. We have conducted experiments and simulations in a simple…
Densely packed, motile bacteria can adopt collective states not seen in conventional, passive materials. These states remain in many ways mysterious, and their physical characterization can aid our understanding of natural bacterial…
This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…