Related papers: A model of hydrodynamic interaction between swimmi…
Using a fluid-particle dynamics approach, we numerically study the effects of hydrodynamic interactions on the collective dynamics of active suspensions within a simple model for bacterial motility: each microorganism is modeled as a…
The swimming properties of an E. coli-type model bacterium are investigated by mesoscale hy- drodynamic simulations, combining molecular dynamics simulations of the bacterium with the multiparticle particle collision dynamics method for the…
In the present work we simulate the basic two-dimensional dynamics of swarming E. coli bacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with…
Active matter exhibits various forms of non-equilibrium states in the absence of external forcing, including macroscopic steady-state currents. Such states are often too complex to be modelled from first principles and our understanding of…
Cells swimming in confined environments are attracted by surfaces. We measure the steady-state distribution of smooth-swimming bacteria (Escherichia coli) between two glass plates. In agreement with earlier studies, we find a strong…
We numerically study the dynamics of run-and-tumble particles confined in two chambers connected by thin channels. Two dominant dynamical behaviors emerge: (i) an oscillatory pumping state, in which particles periodically fill the two…
Collective motion is a phenomenon observed across length scales in nature, from bacterial swarming and tissue migration to the flocking of animals. The mechanisms underlying this behavior vary significantly depending on the biological…
Flagellated bacteria are hydrodynamically attracted to rigid walls, yet past work shows a 'hovering' state where they swim stably at a finite height above surfaces. We use numerics and theory to reveal the physical origin of hovering.…
Microswimmers exhibit more diverse behavior in quasi-two dimensions than in three dimensions. Such behavior remains elusive due to the analytical difficulty of dealing with two parallel solid boundaries. The existence of additional…
Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with…
The sedimentation process in a suspension of bacteria is the result of the competition between gravity and the intrinsic motion of the microorganisms. We perform simulations of run-and-tumble "squirmers" that move in a fluid medium,…
Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling and particle-based simulations to investigate…
{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
The hydrodynamic interactions of a suspension of self-propelled particles are studied using a direct numerical simulation method which simultaneously solves for the host fluid and the swimming particles. A modified version of the "Smoothed…
We employ computer simulations to unveil the translational and rotational dynamics of the self-driven chemically symmetric and asymmetric rigid dumbbells in two-dimensional polymer gel. Our results show that activity or the self-propulsion…
We present a joint experimental and computational study of the effect of bacterial motion on micron-scale colloids contained in a two-dimensional suspension of Bacillus subtilis. With respect to previous work using E. coli, here we…
Swimming micro-organisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where…
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…
Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and…