Related papers: An age-structured continuum model for myxobacteria
Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
Hydrodynamic interactions are transmitted by viscous diffusion and sound propagation: the temporal evolution of hydrodynamic interactions by both mechanisms is studied by direct numerical simulation in this paper. The hydrodynamic…
Microstructured materials, such as architected metamaterials and phononic crystals, exhibit complex wave propagation phenomena due to their internal structure. While full-scale numerical simulations can capture these effects, they are…
Motility is a fundamental survival strategy of bacteria to navigate porous environments. Swimming cells thrive in quiescent wetlands and sediments at the bottom of the marine water column, where they mediate many essential biogeochemical…
A new kinetic model for the dynamics of myxobacteria colonies on flat surfaces is derived formally, and first analytical and numerical results are presented. The model is based on the assumption of hard binary collisions of two different…
Near a solid boundary, E. coli swims in clockwise circular motion. We provide a hydrodynamic model for this behavior. We show that circular trajectories are natural consequences of force-free and torque-free swimming, and the hydrodynamic…
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.…
Collective motion is often modeled within the framework of active fluids, where the constituent active particles, when interactions with other particles are switched off, perform normal diffusion at long times. However, in biology,…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
The dynamic behaviour of glassy materials displays strong nonequilibrium effects, such as ageing in simple protocols, memory, rejuvenation and Kovacs effects in more elaborated experiments. We show that this phenomenology may be easily…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
We introduce and investigate a series of models for an infection of a diplodiploid host species by the bacterial endosymbiont \textit{Wolbachia}. The continuous models are characterized by partial vertical transmission, cytoplasmic…
The observed general time-asymmetric behavior of macroscopic systems -- embodied in the second law of thermodynamics -- arises naturally from time-symmetric microscopic laws due to the great disparity between macro and micro-scales. More…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be…
Models based on surfactant driven instabilities have been employed to describe pattern formation by swarming bacteria. However, by definition, such models cannot account for the effect of bacterial sensing and decision making. Here we…
Active Brownian motion with intermittent direction reversals are common in a class of bacteria like {\it Myxococcus xanthus} and {\it Pseudomonas putida}. We show that, for such a motion in two dimensions, the presence of the two time…
This paper deals with the numerical modeling of wave propagation in porous media described by Biot's theory. The viscous efforts between the fluid and the elastic skeleton are assumed to be a linear function of the relative velocity, which…
Liquid-liquid phase separation is important across biology, physics, and materials science. Although usually studied at equilibrium, active components - such as motor proteins, enzymes, and synthetic microswimmers - are increasingly…