Regularized representation of bacterial hydrodynamics

Ishimoto, Kenta; Gaffney, Eamonn A.; Walker, Benjamin J.

doi:10.1103/physrevfluids.5.093101

Cited by 12 publications

(8 citation statements)

References 52 publications

(69 reference statements)

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“…2020). Facilitating many of the control modalities explored in this work, hydrodynamic interactions between particles have also been studied in various biophysical contexts, such as the enhancement of hydrodynamic capturing of swimming sperm near an egg (Ishimoto, Cosson & Gaffney 2016), the colonisation of bacteria near a nutrient source (Desai, Shaik & Ardekani 2019) and bacterial predator–prey dynamics (Ishimoto, Gaffney & Walker 2020). Further, flow-mediated particle control has been discussed in the context of nutrition uptake in microorganisms and ciliated cells (Riisgård & Larsen 2010; Kiørboe et al.…”

Section: Discussionmentioning

confidence: 99%

The control of particles in the Stokes limit

et al. 2022

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There are numerous ways to control objects in the Stokes regime, with microscale examples ranging from the use of optical tweezers to the application of external magnetic fields. In contrast, there are relatively few explorations of theoretical controllability, which investigate whether or not refined and precise control is indeed possible in a given system. In this work, seeking to highlight the utility and broad applicability of such rigorous analysis, we recount and illustrate key concepts of geometric control theory in the context of multiple particles in Stokesian fluids interacting with each other, such that they may be readily and widely applied in this largely unexplored fluid-dynamical setting. Motivated both by experimental and abstract questions of control, we exemplify these techniques by explicit and detailed application to multiple problems concerning the control of two particles, such as the motion of tracers in flow and the guidance of one sphere by another. Further, we showcase how this analysis of controllability can directly lead to the construction of schemes for control, in addition to facilitating explorations of mechanical efficiency and contributing to our overall understanding of non-local hydrodynamic interactions in the Stokes limit.

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Section: Discussionmentioning

confidence: 99%

The control of particles in the Stokes limit

et al. 2022

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“…However, the error introduced by this approximation becomes non-negligible in the near field, as shown in Ref. [57].…”

Section: Coarse Graining the Flow Fieldmentioning

confidence: 96%

“…A more comprehensive approach to coarse-grain the flow field is to approximate the complex system of forces that the swimmer exerts on the surrounding fluid [19,57]. From a physical perspective, these are described by the traction f at the swimmer boundary-recall the balance equations ( 3)and can be computed using the BEM mentioned in Sec.…”

Section: Coarse Graining the Flow Fieldmentioning

confidence: 99%

HowEuglena gracilisswims: Flow field reconstruction and analysis

et al. 2021

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Euglena gracilis is a unicellular organism that swims by beating a single anterior flagellum. We study the nonplanar waveforms spanned by the flagellum during a swimming stroke and the three-dimensional flows that they generate in the surrounding fluid. Starting from a small set of time-indexed images obtained by optical microscopy on a swimming Euglena cell, we construct a numerical interpolation of the stroke. We define an optimal interpolation (which we call synthetic stroke) by minimizing the discrepancy between experimentally measured velocities (of the swimmer) and those computed by solving numerically the equations of motion of the swimmer driven by the trial interpolated stroke. The good match we obtain between experimentally measured and numerically computed trajectories provides a first validation of our synthetic stroke. We further validate the procedure by studying the flow velocities induced in the surrounding fluid. We compare the experimentally measured flow fields with the corresponding quantities computed by solving numerically the Stokes equations for the fluid flow, in which the forcing is provided by the synthetic stroke, and find good matching. Finally, we use the synthetic stroke to derive a coarse-grained model of the flow field resolved in terms of a few dominant singularities. The far field is well approximated by a time-varying Stresslet, and we show that the average behavior of Euglena during one stroke is that of an off-axis puller. The reconstruction of the flow field closer to the swimmer body requires a more complex system of singularities. A system of two Stokeslets and one Rotlet, that can be loosely associated with the force exerted by the flagellum, the drag of the body, and a torque to guarantee rotational equilibrium, provides a good approximation.

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“…The microswimmers are described in a coarse-grained manner applying the squirmer model [57][58][59][60][61]. Particular attention is paid to the influence of the microswimmers' hydrodynamic flow field on their collective behavior, i.e, the active stress and the rotlet dipole resulting from the rotating of a flagella (bundles) and the counterrotating cell body in flagellated bacteria [62][63][64][65]. In general, hydrodynamics plays a decisive role in the collective behavior of microswimmers.…”

Section: Introductionmentioning

confidence: 99%

Active turbulence in microswimmer suspensions | the role of active hydrodynamic stress and volume exclusion

Westphal

Gompper

et al. 2021

Preprint

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Microswimmers exhibit an intriguing, highly-dynamic collective motion with large-scale swirling and streaming patterns, denoted as active turbulence — reminiscent of classical high-Reynolds-number hydrodynamic turbulence. Various experimental, numerical, and theoretical approaches have been applied to elucidate similarities and differences to inertial hydrodynamic and active turbulence. These studies reveal a wide spectrum of possible structural and dynamical behaviors of active mesoscale systems, not necessarily consistent with the predictions of the Kolmogorov-Kraichnan theory of turbulence. We use squirmers embedded in a mesoscale fluid, modeled by the multiparticle collision dynamics (MPC) approach, to explore the collective behavior of bacteria-type microswimmers. Our model includes the active hydrodynamic stress generated by propulsion, and a rotlet dipole characteristic for flagellated bacteria. We find emergent clusters, activity-induced phase separation, and swarming, depending on density, active stress, and the rotlet dipole strength. The analysis of the squirmer dynamics in the swarming phase yields Kolomogorov-Kraichnan-type hydrodynamic turbulence and energy spectra for sufficiently high concentrations and strong rotlet dipoles. This emphasizes the paramount importance of the hydrodynamic flow field for swarming and bacterial turbulence.

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Regularized representation of bacterial hydrodynamics

Cited by 12 publications

References 52 publications

The control of particles in the Stokes limit

The control of particles in the Stokes limit

HowEuglena gracilisswims: Flow field reconstruction and analysis

Active turbulence in microswimmer suspensions | the role of active hydrodynamic stress and volume exclusion

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