Related papers: A Point Process Model for Generating Biofilms with…
Spatial profiling technologies in biology, such as imaging mass cytometry (IMC) and spatial transcriptomics (ST), generate high-dimensional, multi-channel data with strong spatial alignment and complex inter-channel relationships.…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
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…
The fields of mechanobiology and biomechanics are expanding our understanding of the complex behavior of soft biological tissues across multiple scales. Given the intricate connection between tissue microstructure and its macroscale…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
We investigate a mathematical model for a bacterial population in a continuously stirred tank reactor with wall attachment. The model couples a free-boundary value problem for substrate diffusion in the one-dimensional biofilm with a system…
Microcrystals deform very differently from their macroscopic counterparts, displaying a size-dependent yield stress and intermittent plastic strain bursts. Here we demonstrate that size effects and strain bursts may be just two different…
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Directed growth, anisotropic cell shapes, and confinement drive self-organization in multicellular systems. We investigate the influence of particle shape on the distribution and dynamics of nematic microdomains in a minimal in-silico model…
A challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately…
We propose a model for the mechanical behavior of protein materials. Based on a limited number of experimental macromolecular parameters (persistence and contour lengths, rate of unfolding dissipation) we obtain the macroscopic behavior of…
This fluid dynamics video presents three-dimensional kinetic simulations of the dynamics in suspensions of oxytactic bacteria confined in thin liquid film surrounded by air. At the initial time, the bacterial concentration is uniform and…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
Growth in bacterial populations generally depends on the environment (availability and quality of nutrients, presence of a toxic inhibitor, product inhibition..). Here, we build a model to describe the action of a bacteriostatic antibiotic,…
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the…
Propagating spiral waves have been discovered in various chemical, biological and physical systems. Spiral waves in multicellular organisms are often associated with essential living functions. Although certain eukaryotic microorganisms…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Biological systems commonly exhibit complex spatiotemporal patterns whose underlying generative mechanisms pose a significant analytical challenge. Traditional approaches to spatiodynamic inference rely on dimensionality reduction through…
Purpose: From the myofibrils to the whole muscle scale, muscle micro-constituents exhibit passive and active mechanical properties, potentially coupled to electrical, chemical, and thermal properties. Experimental characterization of some…