arXiv subjects

Kenta Ishimoto

Publications and source records attributed to Kenta Ishimoto.

43 records · Page 3Linked to original sources

arXiv2020

Efficient simulation of filament elastohydrodynamics in three dimensions

Fluid-structure simulations of slender inextensible filaments in a viscous fluid are often plagued by numerical stiffness. Recent coarse-graining studies have reduced the computational requirements of simulating such systems, though have thus far been limited to the motion of planar filaments. In this work we extend such frameworks to filament motion in three dimensions, identifying and circumventing coordinate-system singularities introduced by filament parameterisation via repeated changes of basis. The resulting methodology enables efficient and rapid study of the motion of flexible filaments in three dimensions, and is readily extensible to a wide range of problems, including filament motion in confined geometries, large-scale active matter simulations, and the motility of mammalian spermatozoa.

physics.flu-dyn↗

arXiv2019

The pairwise hydrodynamic interactions of synchronized spermatozoa

The journey of mammalian spermatozoa in nature is well-known to be reliant on their individual motility. Often swimming in crowded microenvironments, the progress of any single swimmer is likely dependent on their interactions with other nearby swimmers. Whilst the complex dynamics of lone spermatozoa have been well-studied, the detailed effects of hydrodynamic interactions between neighbors remain unclear, with inherent nonlinearity in the governing hydrodynamics and potential dependence on the details of swimmer morphology. In this study we will attempt to elucidate the pairwise swimming behaviors of virtual spermatozoa, forming a computational representation of an unbound swimming pair and evaluating the details of their interactions via a high-accuracy boundary element method. We have explored extensive regions of parameter space to determine the pairwise interactions of synchronized spermatozoa, with synchronized swimmers often being noted in experimental observations, and have found that two-dimensional reduced autonomous dynamical systems capture the anisotropic nature of the swimming speed and stability arising from near-field hydrodynamic interactions. Focusing on two configurations of spermatozoa, namely those with swimmers located side-by-side or above and below one another, we have found that side-by-side cells attract each other, and the trajectories in the phase plane are well captured by a recently-proposed coarse-graining method of microswimmer dynamics via superposed regularised Stokeslets. In contrast, the above-below pair exhibit a remarkable stable pairwise swimming behavior, corresponding to a stable configuration of the plane autonomous system with swimmers lying approximately parallel to one another....

physics.flu-dyn↗

arXiv2019

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.

physics.flu-dyn↗

arXiv2019

The N-flagella problem: Elastohydrodynamic motility transition of multi-flagellated bacteria

Peritrichous bacteria such as Escherichia coli swim in viscous fluids by forming a helical bundle of flagellar filaments. The filaments are spatially distributed around the cell body to which they are connected via a flexible hook. To understand how the swimming direction of the cell is determined, we theoretically investigate the elastohydrodynamic motility problem of a multi-flagellated bacterium. Specifically, we consider a spherical cell body with a number N of flagella which are initially symmetrically arranged in a plane in order to provide an equilibrium state. We analytically solve the linear stability problem and find that at most 6 modes can be unstable and that these correspond to the degrees of freedom for the rigid-body motion of the cell body. Although there exists a rotation-dominated mode that generates negligible locomotion, we show that for the typical morphological parameters of bacteria the most unstable mode results in linear swimming in one direction accompanied by rotation around the same axis, as observed experimentally.

physics.bio-ph↗

arXiv2019

Automated identification of flagella from videomicroscopy via the medial axis transform

Ubiquitous in eukaryotic organisms, the flagellum is a well-studied organelle that is well-known to be responsible for motility in a variety of organisms. Commonly necessitated in their study is the capability to image and subsequently track the movement of one or more flagella using videomicroscopy, requiring digital isolation and location of the flagellum within a sequence of frames. Such a process in general currently requires some researcher input, providing some manual estimate or reliance on an experiment-specific heuristic to correctly identify and track the motion of a flagellum. Here we present a fully-automated method of flagellum identification from videomicroscopy based on the fact that the flagella are of approximately constant width when viewed by microscopy. We demonstrate the effectiveness of the algorithm by application to captured videomicroscopy of Leishmania mexicana, a parasitic monoflagellate of the family Trypanosomatidae. ImageJ Macros for flagellar identification are provided, and high accuracy and remarkable throughput are achieved via this unsupervised method, obtaining results comparable in quality to previous studies of closely-related species but achieved without the need for precursory measurements or the development of a specialised heuristic, enabling in general the automated generation of digitised kinematic descriptions of flagellar beating from videomicroscopy.

q-bio.QM↗

arXiv2018

Boundary behaviours of Leishmania mexicana: a hydrodynamic simulation study

It is well established that the parasites of the genus Leishmania exhibit complex surface interactions with the sandfly vector midgut epithelium, but no prior study has considered the details of their hydrodynamics. Here, the boundary behaviours of motile Leishmania mexicana promastigotes are explored in a computational study using the boundary element method, with a model flagellar beating pattern that has been identified from digital videomicroscopy. In particular a simple flagellar kinematics is observed and quantified using image processing and mode identification techniques, suggesting a simple mechanical driver for the Leishmania beat. Phase plane analysis and long-time simulation of a range of Leishmania swimming scenarios demonstrate an absence of stable boundary motility for an idealised model promastigote near passive or repulsive surfaces, with behaviours ranging from boundary capture to deflection into the bulk. Indeed, the inclusion of a repulsive surface force results in the deflection of all surface-bound promastigotes, suggesting that the documented surface detachment of infective metacyclic promastigotes may be the result of morphological adaptation and simple hydrodynamics. Further, simulation elucidates a remarkable morphology-dependent hydrodynamic mechanism of boundary approach, hypothesised to be the cause of the well-established phenomenon of tip-first epithelial attachment of Leishmania promastigotes to the sandfly vector midgut.

physics.bio-ph↗

arXiv2011

A rigorous proof of the scallop theorem and a finite mass effect of a microswimmer

We reconsider fluid dynamics for a self-propulsive swimmer in Stokes flow. With an exact definition of deformation of a swimmer, a proof is given to Purcell's scallop theorem including the body rotation. The breakdown of the theorem due to a finite Stokes number is discussed by using a perturbation expansion method and it is found that the breakdown generally occurs at the first order of the Stokes number. In addition, employing the Purcell's "scallop" model, we show that the theorem holds up to a higher order if the strokes of the swimmer has some symmetry.

physics.flu-dyn↗