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David J. Smith

Publications and source records attributed to David J. Smith.

At least 37 records · Page 2Linked to original sources

Sharp quadrature error bounds for the nearest-neighbor discretization of the regularized stokeslet boundary integral equation

The method of regularized stokeslets is a powerful numerical method to solve the Stokes flow equations for problems in biological fluid mechanics. A recent variation of this method incorporates a nearest-neighbor discretization to improve accuracy and efficiency while maintaining the ease-of-implementation of the original meshless method. This method contains three sources of numerical error, the regularization error associated from using the regularized form of the boundary integral equations (with parameter $\varepsilon$), and two sources of discretization error associated with the force and quadrature discretizations (with lengthscales $h_f$ and $h_q$). A key issue to address is the quadrature error: initial work has not fully explained observed numerical convergence phenomena. In the present manuscript we construct sharp quadrature error bounds for the nearest-neighbor discretisation, noting that the error for a single evaluation of the kernel depends on the smallest distance ($δ$) between these discretization sets. The quadrature error bounds are described for two cases: with disjoint sets ($δ>0$) being close to linear in $h_q$ and insensitive to $\varepsilon$, and contained sets ($δ=0$) being quadratic in $h_q$ with inverse dependence on $\varepsilon$. The practical implications of these error bounds are discussed with reference to the condition number of the matrix system for the nearest-neighbor method, with the analysis revealing that the condition number is insensitive to $\varepsilon$ for disjoint sets, and grows linearly with $\varepsilon$ for contained sets. Error bounds for the general case ($δ\geq 0$) are revealed to be proportional to the sum of the errors for each case.

physics.flu-dyn↗

Meshfree and efficient modelling of swimming cells

Locomotion in Stokes flow is an intensively-studied problem because it describes important biological phenomena such as the motility of many species' sperm, bacteria, algae and protozoa. Numerical computations can be challenging, particularly in three dimensions, due to the presence of moving boundaries and complex geometries; methods which combine ease-of-implementation and computational efficiency are therefore needed. A recently-proposed method to discretise the regularised Stokeslet boundary integral equation without the need for a connected 'mesh' is applied to the inertialess locomotion problem in Stokes flow. The mathematical formulation and key aspects of the computational implementation in MATLAB/GNU Octave are described, followed by numerical experiments with biflagellate algae and multiple uniflagellate sperm swimming between no-slip surfaces, for which both swimming trajectories and flow fields are calculated. These computational experiments required minutes of time on modest hardware; an extensible implementation is provided in a github repository. The nearest neighbour discretisation dramatically improves convergence and robustness, a key challenge in extending the regularised Stokeslet method to complicated, three dimensional, biological fluid problems.

physics.flu-dyn↗

Biological Fluid Mechanics Under the Microscope: A Tribute to John Blake

John Blake (1947--2016) was a leader in fluid mechanics, his two principal areas of expertise being biological fluid mechanics on microscopic scales and bubble dynamics. He produced leading research and mentored others in both Australia, his home country, and the UK, his adopted home. This article reviews John Blake's contributions in biological fluid mechanics, as well as giving the author's personal viewpoint as one of the many graduate students and researchers who benefitted from his supervision, guidance and inspiration. The key topics from biological mechanics discussed are: `squirmer' models of protozoa, the method of images in Stokes flow and the `blakelet' solution, discrete cilia modelling via slender body theory, physiological flows in respiration and reproduction, blinking stokeslets in microorganism feeding, human sperm motility, and embryonic nodal cilia.

physics.flu-dyn↗

A nearest-neighbour discretisation of the regularized stokeslet boundary integral equation

The method of regularized stokeslets is extensively used in biological fluid dynamics due to its conceptual simplicity and meshlessness. This simplicity carries a degree of cost in computational expense and accuracy because the number of degrees of freedom used to discretise the unknown surface traction is generally significantly higher than that required by boundary element methods. We describe a meshless method based on nearest-neighbour interpolation that significantly reduces the number of degrees of freedom required to discretise the unknown traction, increasing the range of problems that can practically solved, without excessively complicating the task of the modeller. The nearest-neighbour technique is tested against the classical problem of rigid body motion of a sphere immersed in very viscous fluid, then applied to the more complex biophysical problem of calculating the diffusion timescales of a macromolecular structure modelled by three closely-spaced non-slender rods. A heuristic for finding the required density of force and quadrature points by numerical refinement is suggested. Matlab/GNU Octave code for the key steps of the algorithm are given, which predominantly use basic linear algebra operations, with a full implementation being provided on github. Compared with the standard Nyström discretisation more accurate and substantially more efficient results can be obtained by de-refining the force discretisation relative to the quadrature discretisation: a cost reduction of over 10 times with improved accuracy is observed. This improvement comes at minimal additional technical complexity. Future avenues to develop the algorithm are then discussed.

physics.flu-dyn↗

Linear Rayleigh-Bénard stability of a transversely-isotropic fluid

Suspended fibres significantly alter fluid rheology, as exhibited in for example solutions of DNA, RNA and synthetic biological nanofibres. It is of interest to determine how this altered rheology affects flow stability. Motivated by the fact thermal gradients may occur in biomolecular analytic devices, and recent stability results, we examine the problem of Rayleigh-Bénard convection of the transversely-isotropic fluid of Ericksen. A transversely-isotropic fluid treats these suspensions as a continuum with an evolving preferred direction, through a modified stress tensor incorporating four viscosity-like parameters. We consider the linear stability of a stationary, passive, transversely-isotropic fluid contained between two parallel boundaries, with the lower boundary at a higher temperature than the upper. To determine the marginal stability curves the Chebyshev collocation method is applied, and we consider a range of initially uniform preferred directions, from horizontal to vertical, and three orders of magnitude in the viscosity-like anisotropic parameters. Determining the critical wave and Rayleigh numbers we find that transversely-isotropic effects delay the onset of instability; this effect is felt most strongly through the incorporation of the anisotropic shear viscosity, although the anisotropic extensional viscosity also contributes. Our analysis confirms the importance of anisotropic rheology in the setting of convection.

physics.flu-dyn↗

Influences of transversely-isotropic rheology and translational diffusion on the stability of active suspensions

Suspensions of self-motile, elongated particles are a topic of significant current interest, exemplifying a form of `active matter'. Examples include self-propelling bacteria, algae and sperm, and artificial swimmers. Ericksen's model of a transversely-isotropic fluid [J. L. Ericksen, Colloid Polym. Sci. 173(2):117-122 (1960)] treats suspensions of non-motile particles as a continuum with an evolving preferred direction; this model describes fibrous materials as diverse as extracellular matrix, textile tufts and plant cell walls. Director-dependent effects are incorporated through a modified stress tensor with four viscosity-like parameters. By making fundamental connections with recent models for active suspensions, we propose a modification to Ericksen's model, mainly the inclusion of self motility; this can be considered the simplest description of an oriented suspension including transversely-isotropic effects. Motivated by the fact that transversely-isotropic fluids exhibit modified flow stability, we conduct a linear stability analysis of two distinct cases, aligned and isotropic suspensions of elongated active particles. Novel aspects include the anisotropic rheology and translational diffusion. In general anisotropic effects increase the instability of small perturbations, whilst translational diffusion stabilises a range of wave-directions and, in some cases, a finite range of wave-numbers, thus emphasising that both anisotropy and translational diffusion can have important effects in these systems.

physics.bio-ph↗

Above 400 K Robust Perpendicular Ferromagnetic Phase in a Topological Insulator

The quantum anomalous Hall effect (QAHE) that emerges under broken time-reversal symmetry in topological insulators (TI) exhibits many fascinating physical properties for potential applications in nano-electronics and spintronics. However, in transition-metal doped TI, the only experimentally demonstrated QAHE system to date, the effect is lost at practically relevant temperatures. This constraint is imposed by the relatively low Curie temperature (Tc) and inherent spin disorder associated with the random magnetic dopants. Here we demonstrate drastically enhanced Tc by exchange coupling TI to Tm3Fe5O12, a high-Tc magnetic insulator with perpendicular magnetic anisotropy. Signatures that the TI surface states acquire robust ferromagnetism are revealed by distinct squared anomalous Hall hysteresis loops at 400 K. Point-contact Andreev reflection spectroscopy confirms that the TI surface is indeed spin-polarized. The greatly enhanced Tc, absence of spin disorder, and perpendicular anisotropy are all essential to the occurrence of the QAHE at high temperatures.

cond-mat.mtrl-sci↗

Nanoscale Magnetic Compasses

We have synthesized nanoscale magnetic compasses with high yield. These ferromagnetic iron carbide nano-particles, which are encapsulated in a pair of parallel carbon needles, change their direction in response to an external magnetic field. Electron holography reveals magnetic fields confined to the vicinity of the bicone-shaped particles, which are composed of few ferromagnetic domains. Aligned magnetically and encapsulated in an acrylate polymer matrix, these nanocompasses exhibit anisotropic bulk magnetic permeability with an easy axis normal to the needle direction, that can be understood as a result of the anisotropic demagnetizing field of a nonspherical single-domain particle. This novel material with orthogonal magnetic and structural axes could be highly useful as magnetic components in electromagnetic wave absorbent materials and magnetorheological fluids.

cond-mat.mes-hall↗

Viscous propulsion in active transversely-isotropic media

Taylor's swimming sheet is a classical model of microscale propulsion and pumping. Many biological fluids and substances are fibrous, having a preferred direction in their microstructure; for example cervical mucus is formed of polymer molecules which create an oriented fibrous network. Moreover, suspensions of elongated motile cells produce a form of active oriented matter. To understand how these effects modify viscous propulsion, we extend Taylor's classical model of small-amplitude zero-Reynolds-number propulsion of a 'swimming sheet' via the transversely-isotropic fluid model of Ericksen, which is linear in strain rate and possesses a distinguished direction. The energetic costs of swimming are significantly altered by all rheological parameters and the initial fibre angle. Propulsion in a passive transversely-isotropic fluid produces an enhanced mean rate of working, independent of the initial fibre orientation, with an approximately linear dependence of energetic cost on the extensional and shear enhancements to the viscosity caused by fibres. In this regime the mean swimming velocity is unchanged from the Newtonian case. The effect of the constant term in Ericksen's model for the stress, which can be identified as a fibre tension or alternatively a stresslet characterising an active fluid, is also considered. This stress introduces an angular dependence and dramatically changes the streamlines and flow field; fibres aligned with the swimming direction increase the energetic demands of the sheet. The constant fibre stress may result in a reversal of the mean swimming velocity and a negative mean rate of working if sufficiently large relative to the other rheological parameters.

physics.flu-dyn↗

Three-dimensional flow in Kupffer's Vesicle

Whilst many vertebrates appear externally left-right symmetric, the arrangement of internal organs is asymmetric. In zebrafish, the breaking of left-right symmetry is organised by Kupffer's Vesicle (KV): an approximately spherical, fluid-filled structure that begins to form in the embryo 10 hours post fertilisation. A crucial component of zebrafish symmetry breaking is the establishment of a cilia-driven fluid flow within KV. However, it is still unclear (a) how dorsal, ventral and equatorial cilia contribute to the global vortical flow, and (b) if this flow breaks left-right symmetry through mechanical transduction or morphogen transport. Fully answering these questions requires knowledge of the three-dimensional flow patterns within KV, which have not been quantified in previous work. In this study, we calculate and analyse the three-dimensional flow in KV. We consider flow from both individual and groups of cilia, and (a) find anticlockwise flow can arise purely from excess of cilia on the dorsal roof over the ventral floor, showing how this vortical flow is stabilised by dorsal tilt of equatorial cilia, and (b) show that anterior clustering of dorsal cilia leads to around 40% faster flow in the anterior over the posterior corner. We argue that these flow features are supportive of symmetry breaking through mechano-sensory cilia, and suggest a novel experiment to test this hypothesis. From our new understanding of the flow, we propose a further experiment to reverse the flow within KV to potentially induce situs inversus.

physics.flu-dyn↗

Spermatozoa scattering by a microchannel feature: an elastohydrodynamic model

Sperm traverse their microenvironment through viscous fluid by propagating flagellar waves; the waveform emerges as a consequence of elastic structure, internal active moments, and low Reynolds number fluid dynamics. Engineered microchannels have recently been proposed as a method of sorting and manipulating motile cells; the interaction of cells with these artificial environments therefore warrants investigation. A numerical method is presented for the geometrically nonlinear elastohydrodynamic interaction of active swimmers with domain features. This method is employed to examine hydrodynamic scattering by a model microchannel backstep feature. Scattering is shown to depend on backstep height and the relative strength of viscous and elastic forces in the flagellum. In a 'high viscosity' parameter regime corresponding to human sperm in cervical mucus analogue, this hydrodynamic contribution to scattering is comparable in magnitude to recent data on contact effects, being of the order of 5-10 degrees. Scattering can be positive or negative depending on the relative strength of viscous and elastic effects, emphasising the importance of viscosity on the interaction of sperm with their microenvironment. The modulation of scattering angle by viscosity is associated with variations in flagellar asymmetry induced by the elastohydrodynamic interaction with the boundary feature.

physics.flu-dyn↗

Domain structure and perpendicular magnetic anisotropy in CoFe/Pd multilayers using off-axis electron holography

Multilayers of Co90Fe10/Pd with different bilayer thicknesses, have been deposited by dc-magnetron sputtering on thermally oxidized Si wafers. Transmission electron microscopy showed that the highly textured crystalline films had columnar structure, while scanning transmission electron microscopy and atomic force microscopy respectively indicated some layer waviness and surface roughness. The magnetic domain structure and perpendicular magnetic anisotropy (PMA) of the Co90Fe10/Pd multilayers were investigated by off-axis electron holography and magnetic force microscopy. The Co90Fe10 layer thickness was the primary factor determining the magnetic domain size and the perpendicular magnetization: both decreased as the thickness increased. The strongest PMA was observed in the sample with the thinnest magnetic layer of 0.45 nm.

cond-mat.mtrl-sci↗

Symmetry breaking cilia-driven flow in the zebrafish embryo

Fluid mechanics plays a vital role in early vertebrate embryo development, an example being the establishment of left-right asymmetry. Following the dorsal-ventral and anterior-posterior axes, the left-right axis is the last to be established; in several species it has been shown that an important process involved with this is the production of a left-right asymmetric flow driven by 'whirling' cilia. It has previously been established in experimental and mathematical models of the mouse ventral node that the combination of a consistent rotational direction and posterior tilt creates left-right asymmetric flow. The zebrafish organising structure, Kupffer's vesicle, has a more complex internal arrangement of cilia than the mouse ventral node; experimental studies show the flow exhibits an anticlockwise rotational motion when viewing the embryo from the dorsal roof, looking in the ventral direction. Reports of the arrangement and configuration of cilia suggest two possible mechanisms for the generation of this flow from existing axis information: (1) posterior tilt combined with increased cilia density on the dorsal roof, and (2) dorsal tilt of 'equatorial' cilia. We develop a mathematical model of symmetry breaking cilia-driven flow in Kupffer's vesicle using the regularized Stokeslet boundary element method. Computations of the flow produced by tilted whirling cilia in an enclosed domain suggest that a possible mechanism capable of producing the flow field with qualitative and quantitative features closest to those observed experimentally is a combination of posteriorly tilted roof and floor cilia, and dorsally tilted equatorial cilia.

physics.flu-dyn↗

Physics of Rheologically-Enhanced Propulsion: Different Strokes in Generalized Stokes

Shear-thinning is an important rheological property of many biological fluids, such as mucus, whereby the apparent viscosity of the fluid decreases with shear. Certain microscopic swimmers have been shown to progress more rapidly through shear-thinning fluids, but is this behavior generic to all microscopic swimmers, and what are the physics through which shear-thinning rheology affects a swimmer's propulsion? We examine swimmers employing prescribed stroke kinematics in two-dimensional, inertialess Carreau fluid: shear-thinning "Generalized Stokes" flow. Swimmers are modeled, using the method of femlets, by a set of immersed, regularized forces. The equations governing the fluid dynamics are then discretized over a body-fitted mesh and solved with the finite element method. We analyze the locomotion of three distinct classes of microswimmer: (1) conceptual swimmers comprising sliding spheres employing both one- and two-dimensional strokes, (2) slip-velocity envelope models of ciliates commonly referred to as "squirmers" and (3) monoflagellate pushers, such as sperm. We find that morphologically identical swimmers with different strokes may swim either faster or slower in shear-thinning fluids than in Newtonian fluids. We explain this kinematic sensitivity by considering differences in the viscosity of the fluid surrounding propulsive and payload elements of the swimmer, and using this insight suggest two reciprocal sliding sphere swimmers which violate Purcell's Scallop theorem in shear-thinning fluids. We also show that an increased flow decay rate arising from shear-thinning rheology is associated with a reduction in the swimming speed of slip-velocity squirmers. For sperm-like swimmers, a gradient of thick to thin fluid along the flagellum alters the force it exerts upon the fluid, flattening trajectories and increasing instantaneous swimming speed.

physics.flu-dyn↗

Modelling the Fluid Mechanics of Cilia and Flagella in Reproduction and Development

Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscous-dominated microscale flow, including time-reversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higher order multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: (1) left-right symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and (2) motility of microswimmers through non-Newtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a body-conforming finite element framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a three-sphere model swimmer and a model sperm are similarly affected by shear-thinning; in both cases swimming due to a prescribed beat is enhanced by shear-thinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shear-thickening hindering cell progress.

q-bio.QM↗

Negative tunneling magnetoresistance by canted magnetization in MgO/NiO tunnel barriers

The influence of insertion of an ultra-thin NiO layer between the MgO barrier and ferromagnetic electrode in magnetic tunnel junctions has been investigated by measuring the tunneling magnetoresistance and the X-ray magnetic circular dichroism (XMCD). The magnetoresistance shows a high asymmetry with respect to bias voltage, giving rise to a negative value of -16% at 2.8 K. We attribute this to the formation of non-collinear spin structures in the NiO layer as observed by XMCD. The magnetic moments of the interface Ni atoms tilt from the easy axis due to exchange interaction and the tilting angle decreases with increasing the NiO thickness. The experimental observations are further support by non-collinear spin density functional theory.

cond-mat.mtrl-sci↗

A boundary element regularised Stokeslet method applied to cilia and flagella-driven flow

A boundary element implementation of the regularised Stokeslet method of Cortez is applied to cilia and flagella-driven flows in biology. Previously-published approaches implicitly combine the force discretisation and the numerical quadrature used to evaluate boundary integrals. By contrast, a boundary element method can be implemented by discretising the force using basis functions, and calculating integrals using accurate numerical or analytic integration. This substantially weakens the coupling of the mesh size for the force and the regularisation parameter, and greatly reduces the number of degrees of freedom required. When modelling a cilium or flagellum as a one-dimensional filament, the regularisation parameter can be considered a proxy for the body radius, as opposed to being a parameter used to minimise numerical errors. Modelling a patch of cilia, it is found that: (1) For a fixed number of cilia, reducing cilia spacing reduces transport. (2) For fixed patch dimension, increasing cilia number increases the transport, up to a plateau at $9\times 9$ cilia. Modelling a choanoflagellate cell it is found that the presence of a lorica structure significantly affects transport and flow outside the lorica, but does not significantly alter the force experienced by the flagellum.

physics.flu-dyn↗

Surface accumulation of spermatozoa: a fluid dynamic phenomenon

Recent mathematical fluid dynamics models have shed light into an outstanding problem in reproductive biology: why do spermatozoa cells show a 'preference' for swimming near to surfaces? In this paper we review quantitative approaches to the problem, originating with the classic paper of Lord Rothschild in 1963. A recent 'boundary integral/slender body theory' mathematical model for the fluid dynamics is described, and we discuss how it gives insight into the mechanisms that may be responsible for the surface accumulation behaviour. We use the simulation model to explore these mechanisms in more detail, and discuss whether simplified models can capture the behaviour of sperm cells. The far-field decay of the fluid flow around the cell is calculated, and compared with a stresslet model. Finally we present some new findings showing how, despite having a relatively small hydrodynamic drag, the sperm cell 'head' has very significant effects on surface accumulation and trajectory.

physics.flu-dyn↗