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Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

Machine Learning · Statistics 2020-04-13 Travis E. Gibson , Georg K. Gerber

Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…

Soft Condensed Matter · Physics 2024-02-15 Scott Weady , David B. Stein , Alexandra Zidovska , Michael J. Shelley

Interaction of swimming bacteria with flows controls their ability to explore complex environments, crucial to many societal and environmental challenges and relevant for microfluidic applications as cell sorting. Combining experimental,…

Soft Condensed Matter · Physics 2020-09-03 Guangyin Jing , Andreas Zöttl , Éric Clément , Anke Lindner

To study the impact of active systems on their surroundings, we introduce a model that couples an active nematic fluid to an isotropic substrate fluid via friction. We numerically show that as the active layer develops turbulence, the…

Soft Condensed Matter · Physics 2025-12-01 Gianmarco Spera , Julia M. Yeomans , Sumesh P. Thampi

We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient reservoir (the blood), aimed at characterizing the role of…

Molecular Networks · Quantitative Biology 2017-06-09 Jorge Fernandez-de-Cossio-Diaz , Andrea De Martino , Roberto Mulet

We introduce a stochastic agent-based model for the flocking dynamics of self-propelled particles that exhibit velocity-alignment interactions with neighbours within their field of view. The stochasticity in the dynamics of the model arises…

Statistical Mechanics · Physics 2019-07-24 Trilochan Bagarti , Shakti N. Menon

Active matter systems provide fascinating examples of pattern formation and collective motility without counterparts in equilibrium systems. Here, we employ Brownian dynamics simulations to study the collective motion and self-organization…

Soft Condensed Matter · Physics 2021-12-20 Leila Abbaspour , Ali Malek , Stefan Karpitschka , Stefan Klumpp

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,…

Applications · Statistics 2017-11-17 Kris Sankaran , Susan P. Holmes

Active matter exhibits remarkable collective behavior in which flows, continuously generated by active particles, are intertwined with the orientational order of these particles. The relationship remains poorly understood as the activity…

Laminar-turbulent pattern formation is a distinctive feature of the intermittency regime in subcritical plane shear flows. By performing extensive numerical simulations of the plane channel flow, we show that the pattern emerges from a…

Fluid Dynamics · Physics 2022-12-16 Pavan V. Kashyap , Yohann Duguet , Olivier Dauchot

The locomotion of flexible membrane-like organisms on top of curved surfaces appears in different contexts and scales. Still, such dynamics have not yet been quantitatively modeled and no realization of such motion in manmade systems has…

Soft Condensed Matter · Physics 2024-02-27 Omri Y. Cohen , Yael Klein , Eran Sharon

Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior amongst the simplest…

The autonomous motion of liquid crystal oil droplets in micellar media arises from spontaneous breaking of time reversal symmetry via nonlinear coupling between Marangoni stresses and surfactant transport. While this phenomenon has been…

Soft Condensed Matter · Physics 2026-01-15 Salini Kar , Rohit V. Menon , Sanbed Das , Parth Pandya , Sayantan Dutta , Mithun Chowdhury

Bacterial swarms display intriguing dynamical states like active turbulence. Using a hydrodynamic model we now show that such dense active suspensions manifest super-diffusion, via L\'evy walks, which masquerades as a crossover from…

Soft Condensed Matter · Physics 2021-09-15 Siddhartha Mukherjee , Rahul K. Singh , Martin James , Samriddhi Sankar Ray

Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…

The fluid-structure interactions between flexible fibers and viscous flows play an essential role in various biological phenomena, medical problems, and industrial processes. Of particular interest is the case of particles freely…

Biofilms in porous media critically influence hydraulic properties in environmental and engineered systems. However, a mechanistic understanding of how microbial life controls permeability remains elusive. By combining microfluidics,…

Biological Physics · Physics 2026-05-29 Wenqiao Jiao , David Scheidweiler , Nolwenn Delouche , Alberto Guadagnini , Pietro de Anna

Modelling interfacial dynamics with soluble surfactants in a multiphase system is a challenging task. Here, we consider the numerical approximation of a phase-field surfactant model with fluid flow. The nonlinearly coupled model consists of…

Computational Physics · Physics 2020-03-02 Guangpu Zhu , Jisheng Kou , Shuyu Sun , Jun Yao , Aifen Li

A wide range of experimental systems including gliding, swarming and swimming bacteria, in-vitro motility assays as well as shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a…

Statistical Mechanics · Physics 2021-01-18 Markus Bär , Robert Großmann , Sebastian Heidenreich , Fernando Peruani

We consider a colony of point-like self-propelled surfactant particles (swimmers) without direct interactions that cover a thin liquid layer on a solid support. Although the particles predominantly swim normal to the free film surface,…

Soft Condensed Matter · Physics 2018-07-24 Andrey Pototsky , Uwe Thiele , Holger Stark