Related papers: Bacterial self-organisation and computation
We discuss recent progress in the theoretical description of chemotaxis by coupling the diffusion equation of a chemical species to equations describing the motion of sensing microorganisms. In particular, we discuss models for…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
The purpose of this work is the study of \textit{chemotaxis} and how to model it through the equations of Keller-Segel. \textit{Chemotaxis} is a natural process which induces the organisms to direct their movement according to certain…
In our article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
The optimal use of resources has motivated the engineering community to employ controlled distribution of material within their structural designs, often relying on cellular and lattice porous structures. In this research work, a…
Collective migration -- the directed, coordinated motion of many self-propelled agents -- is a fascinating emergent behavior exhibited by active matter that has key functional implications for biological systems. Extensive studies have…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
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…
Motile bacteria can migrate along chemical gradients in a process known as chemotaxis. When exposed to uniform environmental stress, Escherichia coli cells coordinate their chemotactic responses to form millimeter-sized condensates…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Chemotaxis is the physical phenomenon that bacteria adjust their motions according to chemical stimulus. A classical model for this phenomenon is a kinetic equation that describes the velocity jump process whose tumbling/transition kernel…
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…
In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and…
Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering…
Bacteria seem masters of chemotaxis, yet recent work suggests otherwise. Henry Mattingly and colleagues (Nature Physics, 2026) argue that Escherichia coli uses only a small fraction of the sensory information available at its surface,…