Jeffery's orbits and microswimmers in flows: A theoretical review

In this review, we provide a theoretical introduction to Jeffery's equations for the orientation dynamics of an axisymmetric object in a flow at low Reynolds number, and review recent theoretical extensions and applications to the motions of self-propelled particles, so-called microswimmers, in external flows. Bacteria colonize human organs and medical devices even with flowing fluid, microalgae occasionally cause huge harmful toxic blooms in lakes and oceans, and recent artificial microrobots can migrate in flows generated in well-designed microfluidic chambers. The Jeffery equations, a simple set of ordinary differential equation, provide a useful building block in modeling, analyzing, and understanding these microswimmer dynamics in a flow current, in particular when incorporating the impact of the swimmer shape since the equations contain a shape parameter as a single scalar, known as the Bretherton parameter. The particle orientation forms a closed orbit when situated in a simple shear, and this non-uniform periodic rotational motion, referred to as Jeffery's orbits, is due to a constant of motion in the non-linear equation. After providing a theoretical introduction to microswimmer hydrodynamics and a derivation of the Jeffery equations, we discuss possible extensions to more general shapes, including those with rapid deformation. In the latter part of this review, simple mathematical models of microswimmers in different types of flow fields are described, with a focus on constants of motion and their relation to periodic motions in phase space, together with a breakdown of degenerate orbits, to discuss the stable, unstable, and chaotic dynamics of the system. The discussion in this paper will provide a comprehensive theoretical foundation for Jeffery's orbits and will be useful to understand the motions of microswimmers under various flows.Comment: 26 pages, 13 figures. To appear in the Journal of the Physical Society of Japa

Helicoidal particles and swimmers in a flow at low Reynolds number

In this paper, we consider the dynamics of a helicoidal object, which can be either a passive particle or an active swimmer, with an arbitrary shape in a linear background flow at low Reynolds number, and derive a generalized version of the Jeffery equations for the angular dynamics of the object, including a new constant from the chirality of the object as well as the Bretherton constant. The new constant appears from the inhomogeneous chirality distribution along the axis of the helicoidal symmetry, whereas the overall chirality of the object contributes to the drift velocity. Further investigations are made for an object in a simple shear flow, and it is found that the chirality effects generate non-closed trajectories of the director vector which will be stably directed parallel or anti-parallel to the background vorticity vector depending on the sign of the chirality. A bacterial swimmer is considered as an example of a helicoidal object, and we calculate the values of the constants in the generalized Jeffery equations for a typical morphology of Escherichia coli. Our results provide useful expressions for the studies of microparticles and biological fluids, and emphasize the significance of the symmetry of an object on its motion at low Reynolds number

Most probable path of an active Brownian particle

In this study, we investigate the transition path of a free active Brownian particle (ABP) on a two-dimensional plane between two given states. The extremum conditions for the most probable path connecting the two states are derived using the Onsager--Machlup integral and its variational principle. We provide explicit solutions to these extremum conditions and demonstrate their nonuniqueness through an analogy with the pendulum equation indicating possible multiple paths. The pendulum analogy is also employed to characterize the shape of the globally most probable path obtained by explicitly calculating the path probability for multiple solutions. We comprehensively examine a translation process of an ABP to the front as a prototypical example. Interestingly, the numerical and theoretical analyses reveal that the shape of the most probable path changes from an I to a U shape and to the $\ell$ shape with an increase in the transition process time. The Langevin simulation also confirms this shape transition. We also discuss further method applications for evaluating a transition path in rare events in active matter

Generalised Taylor dispersion of chiral microswimmers

Transport phenomena of microswimmers in fluid flows play a crucial role in various biological processes, including bioconvection and cell sorting. In this paper, we investigate the dispersion behavior of chiral microswimmers in a simple shear flow utilizing the generalized Taylor dispersion (GTD) theory, motivated by biased locomotion of bacterial swimmers known as bacterial rheotaxis. We thus focus on the influence of shear-induced torque effects due to particle chirality, employing an extended Jeffery equation for individual deterministic dynamics. We then numerically calculate macroscopic parameters including averaged swimming velocity and effective diffusion tensor using spherical harmonic expansion, and argue the obtained results based on the fixed points and their stability of the orientational dynamical systems. Our results reveal that chiral effects induce biased locomotion and we observe qualitative transitions in the orientational distribution with increasing Pecl\'et number, aligning with previous experimental findings. The diffusion tensor analysis highlights significant reduction in the diffusion coefficient perpendicular to the flow plane due to chirality. This suggests potential applications in flow-mediated cell separation and we numerically demonstrate such chirality-induced fluid transportation. The presented methods will be useful in predicting and controlling dispersion behaviors of such chiral microswimmers.Comment: 15 pages, 8 figure

Filament mechanics in a half-space via regularised Stokeslet segments

We present a generalisation of efficient numerical frameworks for modelling fluid-filament interactions via the discretisation of a recently-developed, non-local integral equation formulation to incorporate regularised Stokeslets with half-space boundary conditions, as motivated by the importance of confining geometries in many applications. We proceed to utilise this framework to examine the drag on slender inextensible filaments moving near a boundary, firstly with a relatively-simple example, evaluating the accuracy of resistive force theories near boundaries using regularised Stokeslet segments. This highlights that resistive force theories do not accurately quantify filament dynamics in a range of circumstances, even with analytical corrections for the boundary. However, there is the notable and important exception of movement in a plane parallel to the boundary, where accuracy is maintained. In particular, this justifies the judicious use of resistive force theories in examining the mechanics of filaments and monoflagellate microswimmers with planar flagellar patterns moving parallel to boundaries. We proceed to apply the numerical framework developed here to consider how filament elastohydrodynamics can impact drag near a boundary, analysing in detail the complex responses of a passive cantilevered filament to an oscillatory flow. In particular, we document the emergence of an asymmetric periodic beating in passive filaments in particular parameter regimes, which are remarkably similar to the power and reverse strokes exhibited by motile 9+2 cilia. Furthermore, these changes in the morphology of the filament beating, arising from the fluid-structure interactions, also induce a significant increase in the hydrodynamic drag of the filament.Comment: 21 pages, 9 figures. Supplementary Material available upon reques

The mechanics clarifying counterclockwise rotation in most IVF eggs in mice

Ishimoto, K., Ikawa, M. & Okabe, M. The mechanics clarifying counterclockwise rotation in most IVF eggs in mice. Sci Rep 7, 43456 (2017). https://doi.org/10.1038/srep4345

Odd elastohydrodynamics: non-reciprocal living material in a viscous fluid

Motility is a fundamental feature of living matter, encompassing single cells and collective behavior. Such living systems are characterized by non-conservativity of energy and a large diversity of spatio-temporal patterns. Thus, fundamental physical principles to formulate their behavior are not yet fully understood. This study explores a violation of Newton's third law in motile active agents, by considering non-reciprocal mechanical interactions known as odd elasticity. By extending the description of odd elasticity to a nonlinear regime, we present a general framework for the swimming dynamics of active elastic materials in low-Reynolds-number fluids, such as wave-like patterns observed in eukaryotic cilia and flagella. We investigate the non-local interactions within a swimmer using generalized material elasticity and apply these concepts to biological flagellar motion. Through simple solvable models and the analysis of {\it Chlamydomonas} flagella waveforms and experimental data for human sperm, we demonstrate the wide applicability of a non-local and non-reciprocal description of internal interactions within living materials in viscous fluids, offering a unified framework for active and living matter physics.Comment: 18 pages, 9 figure

In the name of ‘war’: Buhari’s national re- orientation campaign

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The control of particles in the Stokes limit

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