Publications

47. Geometric dependence of curvature-induced rigidity

H. Mao, T. G. J. Chandler, M. Han, and S.E. Spagnolie (submitted) 2024.

Bending the edge of a thin elastic material promotes rigidity far from its clamped boundary. However, this curvature-induced rigidity can be overwhelmed by gravity or other external loading, resulting in elastic buckling and large deformations. We consider the role of body geometry on this competition using experiments, numerical simulations, and reduced-order models. Finite element simulations are performed using a model nonlinear hyperelastic material, and a theoretical framework is proposed that incorporates small lateral curvatures, large longitudinal rotations, and a varying cross-sectional width. A particular focus is on the comparison between rectangular and triangular sheets, and trapezoidal sheets in between. Sheet geometry affects downward tip deflection by changing the relative importance of the sheet's weight and the rigidity provided by curvature, often in subtle ways. In extreme cases, non-monotonic deflection is observed with increasing sheet length, and a region of hysteretic bistability emerges, becoming more pronounced with rectangular sheets and large imposed curvatures. These findings demonstrate the profound impact of geometry on the competition between curvature-induced rigidity and gravity-induced deformation in thin elastic materials.

• S1: Relaxation of random initial data to equilibrium for sufficiently small active Ericksen number [via kinetic theory].
• S2: The first flowing arrested state for immotile particles, emerging beyond a critical active Ericksen number (or particle concentration) [kinetic theory].
• S3: A fully two-dimensional flowing arrested state at larger active Ericksen number [kinetic theory].
• S4: A higher wavenumber dynamics and arrested state for of immotile particles at yet larger active Ericksen number [kinetic theory].
• S5: Traveling concentration wave for motile particles [via moment equations].
• S6: A retrograde traveling concentration wave with motile particles at larger active Ericksen number [moment equations].
• S7: A traveling periodic 'thrashing' mode emerges at larger swimming speeds [moment equations].

46. Arrested development and traveling waves of active suspensions in nematic liquid crystals

J. Li, L. Ohm, and S.E. Spagnolie (submitted) 2024.

Active particles in anisotropic, viscoelastic fluids experience competing stresses which guide their trajectories. An aligned suspension of particles can trigger a hydrodynamic bend instability, but the elasticity of the fluid can drive particle orientations back towards alignment. To study these competing effects, we examine a dilute suspension of active particles in an Ericksen-Leslie model nematic liquid crystal. For small active Ericksen number, the suspension settles to an equilibrium state with uniform alignment. Beyond a critical active Ericksen number, the suspension instead can buckle into a steady flowing state. Rather than entering the fully developed roiling state observed in isotropic fluids, however, the development is arrested by fluid elasticity. A secondary instability is observed at higher values of active Ericksen number, leading to arrested states of higher wavenumber. If the active particles are motile, traveling waves emerge, including a traveling, oscillatory 'thrashing' state. Moment equations based on kinetic theory are derived and solved numerically, and are analyzed in asymptotic limits which admit exact expressions for the traveling wave speed and both particle orientation and director fields in the arrested state.

45. Active nematic response to a deformable body or boundary: elastic deformations and anchoring-induced flow

T. G. J. Chandler and S.E. Spagnolie (submitted) 2024.

A body immersed in a nematic liquid crystal disturbs the fluid's preferred molecular configuration and increases its stored elastic energy. In an active nematic, the fluid components also generate a stress in the bulk fluid. By introducing either an immersed body or boundary, a fluid flow can be triggered due to anchoring boundary conditions. The fluid imposes elastic, viscous, and active stresses on such surfaces, which, if compliant, may result in a surface deformation. We study the deformations and stress in a linearly elastic body placed in an active nematic in two-dimensions. Using complex variables techniques, exact expressions for the fluid flow, director field, surface tractions, and body deformation are derived. Qualitative differences between elastic and active stress-driven deformations are identified, depending on an active Ericksen number, anchoring conditions, and body material properties, thereby suggesting a new method for measuring the active stresses in active anisotropic biological systems. Flow profiles, external confinement, and anchoring-induced stirring are also addressed.

44. The hydrodynamics of marbling art

Y. Sun, J.W.M. Bush, S.E. Spagnolie, and C.H. Rycroft, Physical Review Fluids 9, 110506 (2024).

This paper is associated with a video winner of a 2023 American Physical Society's Division of Fluid Dynamics (DFD) Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion. The original video is available online at the Gallery of Fluid Motion:

43. Rigid and deformable bodies in nematic liquid crystals

T. G. J. Chandler and S.E. Spagnolie, Physical Review Fluids, 9, 110511 (2024).

A nematic liquid crystal, a phase of matter composed of rod-like molecules, exhibits a tendency towards uniform molecular alignment. Bodies inserted into such a fluid can disturb this orientational order, resulting in elastic stresses bound in the bulk fluid and exerted on the body surfaces, even at equilibrium. One avenue of energy relaxation is by a change in the immersed particle positions and orientations, leading to elastic forces and torques that bodies exert on each other through the fluid. Soft particles offer an additional means of relaxation, deformation, which in turn can modify particle interactions through the LC medium. We review classical work on rigid particles and their interactions in nematic liquid crystals, and more recent work on the shapes and interactions of deformable bodies in LCs. In addition to experimental findings, a number of common mathematical modeling techniques, both in terms of a director field n and a second-order tensor field Q, are introduced throughout, including derivations of body forces and torques, and, of particular use in the study of deformable media in LCs, surface tractions and moments.

42. Exact and approximate solutions for elastic interactions in a nematic liquid crystal

T. G. J. Chandler and S.E. Spagnolie, SIAM J. Appl. Math., 84, 2476-2501 (2024).

Anisotropic fluids appear in a diverse array of systems, from liquid-crystal displays to bacterial swarms, and are characterized by orientational order. Large colloidal particles immersed in such environments disturb the medium's orientational order, however, resulting in a stored elastic energy within the bulk. As a consequence, multiple immersed bodies interact at equilibrium through fluid-mediated forces and torques, which depend on the bodies' positions, orientations, and shapes. We provide the equilibrium configuration of a model nematic liquid crystal with multiple immersed bodies or inclusions in two-dimensions, as well as the associated body forces, torques, and surface tractions. A complex variables approach is taken which leans on previous work by Crowdy for describing solutions with multiply-connected domains. Free periods of a complex director field, which correspond to topological defect positioning and net topological charge, are determined numerically to minimize a global stored elastic energy, including a contribution of a weak (finite) anchoring strength on the body surfaces. Finally, a general and analytical description of two-body far-field interactions is provided, along with examples using two cylindrical inclusions of arbitrary position and size, and two triangles of arbitrary position and orientation.

• S1: Sunmaid raisins in a glass container, filled with Klarbrunn carbonated water, perform vertical dancing and wobbling.
• S2: Bubble growth and coalescence, and arrival at a fluctuating steady state, on a fixed 3D-printed sphere, at an early insertion time (1 min. after opening).
• S3: Same, at an intermediate insertion time (10 min. after opening).
• S4: For bodies with a dense array of surface bubbles, rotational freedom can be of critical importance for vertical dancing. When the body rotates at the fluid-air interface, the surface is cleared of a larger number of buoyancy-conferring bubbles, and a vertical excursion becomes far more likely.
• S5: The motion of nearby bodies can provide a perturbation, nudging the body to rotate and plummet.
• S6: The 3D-printed body dancing in carbonated water for two hours, at 4x speed.
• S7: Numerical simulations using the discrete bubble model explore the role of the number of bubbles, the dimensionless bubble growth rate, Λ, and the dimensionless maximum lifting force, β. (C. Grote)
• S8: Bubble growth on a skewer of raisins, at 100x speed.

41. Levitation and dynamics of bodies in supersaturated fluids

S.E. Spagnolie, S. Christianson, and C. Grote, Nature Communications, 15, 3910 (2024).

A body immersed in a supersaturated fluid like carbonated water can accumulate a dynamic field of bubbles upon its surface. The bubbles grow and coalesce as gas is continually pulled from the environment. If the body is mobile, the attached bubbles can lift it upward against gravity, but arrival at a free surface can clean the body of these lifting agents, upon which the body may plummet. The process then begins anew, and continues for as long as the concentration of gas in the fluid supports it. Experiments using fixed and free immersed bodies reveal fundamental features of force development. A continuum model which incorporates the dynamics of a surface buoyancy field is used to predict the ranges of body mass and size, and fluid properties, for which the system is most dynamic, and those for which body excursions are suppressed. Simulations are used to probe systems which are dominated by a small number of large bubbles. Body rotations at the surface are found to be critical for driving periodic vertical motions of large bodies, which in turn can produce body wobbling, rolling, and damped surface 'bouncing' dynamics.

40. A nematic liquid crystal with an immersed body: equilibrium, stress, and paradox

T. G. J. Chandler and S.E. Spagnolie, J. Fluid Mech., 967, A19 (2023).

We examine the equilibrium configurations of a nematic liquid crystal with an immersed body in two-dimensions. A complex variables formulation provides a means for finding analytical solutions in the case of strong anchoring. Local tractions, forces, and torques on the body are discussed in a general setting. For weak (finite) anchoring strengths, an effective boundary technique is proposed which is used to determine asymptotic solutions. The energy-minimizing locations of topological defects on the body surface are also discussed. A number of examples are provided, including circular and triangular bodies, and a Janus particle with hybrid anchoring conditions. Analogues to classical results in fluid dynamics are identified, including d'Alembert's paradox, Stokes' paradox, and the Kutta condition for circulation selection.

• S1: Self-bending of a swarmer P. mirabilis cell (Weibel lab).
• S2: Pinwheeling P. mirabilis cell (Weibel lab).
• S3: Twisted swimming of a P. mirabilis cell (Weibel lab).
• S4: P. mirabilis swimming with substantial self-winding (Weibel lab).
• S5: Model swimmer dynamics, and projection onto a low-order configuration space (W. Lough).
• S6: Different bending/twisting moduli can produce more complex swimming modes (W. Lough).
• S7: A comparison of swimming speeds across bending/twisting moduli (W. Lough).
• S8: Slight variations in bending stiffness can have an outsized effect (non-interacting swimmers) (W. Lough).

39. Self-buckling and self-writhing of semi-flexible microorganisms

W. Lough, D.B. Weibel and S.E. Spagnolie, Soft Matter, 19, 7349-7357 (2023).

Multi-flagellated microorganisms can buckle and writhe under their own activity as they swim through a viscous fluid. New equilibrium configurations and steady-state dynamics then emerge which depend on the organism's mechanical properties and on the oriented distribution of flagella along its surface. Modeling the cell body as a semi-flexible Kirchhoff rod and coupling the mechanics to a dynamically evolving flagellar orientation field, we derive the Euler-Poincare' equations governing dynamics of the system, and rationalize experimental observations of buckling and writhing of elongated swarmer P. mirabilis cells. A sequence of bifurcations is identified as the body is made more compliant, due to both buckling and torsional instabilities. The results suggest that swarmer cells invest no more resources in maintaining membrane integrity than is necessary to prevent self-buckling.

38. Swimming in Complex Fluids

S.E. Spagnolie and P.T. Underhill, Annu. Rev. Condens. Matter Phys., 14, 381-415 (2023).

We review the literature on swimming in complex fluids. A classification is proposed by comparing the length and time scales of a swimmer with those of nearby obstacles, interpreted broadly, extending from rigid or soft confining boundaries to molecules which confer the bulk fluid with complex stresses. A third dimension in the classification is the concentration of swimmers, which incorporates fluids whose complexity arises purely by the collective motion of swimming organisms. For each of the eight system classes which we identify we provide a background and describe modern research findings. While some classes have seen a great deal of attention for decades, others remain uncharted waters still open and awaiting exploration.

• Increasing the contrast of spatially varying bending stiffness or spontaneous curvature: a bifurcation is revealed!
• Parity matters...
• Same as above, but with a larger material property contrast

37. Swinging and tumbling of multicomponent vesicles in flow

P. Gera, D. Salac, and S.E. Spagnolie, J. Fluid Mech., 935, A39 (2022).

Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and rich dynamics when placed into a flow. Under the assumption of small deformations and a two-dimensional system, we develop a reduced-order model to describe the fluid-structure interaction between a viscous background shear flow and an inextensible membrane with spatially varying bending stiffness and spontaneous curvature. Material property variations of a critical magnitude, relative to the flow rate and internal/external viscosity contrast, can set off a qualitative change in the vesicle dynamics. A membrane of nearly constant bending stiffness or spontaneous curvature undergoes a small amplitude swinging motion (which includes tangential tank-treading), while for large enough material variations the dynamics pass through a regime featuring tumbling and periodic phase-lagging of the membrane material, and ultimately for very large material variation to a rigid-body tumbling behaviour. Distinct differences are found for even and odd spatial modes of domain distribution. Full numerical simulations are used to probe the theoretical predictions, which appear valid even when studying substantially deformed membranes.

36. Helical trajectories of swimming cells with a flexible flagellar hook

Z. Zou, W. Lough, and S.E. Spagnolie, Phys. Rev. Fluids, 6, 103102 (2021).

The flexibility of the bacterial flagellar hook is believed to have substantial consequences for microorganism locomotion. Using a simplified model of a rigid flagellum and a flexible hook, we show that the paths of axisymmetric cell bodies driven by a single flagellum are generically helical. Phase-averaged resistance and mobility tensors are produced to describe the flagellar hydrodynamics, and a helical rod model which retains a coupling between translation and rotation is identified as a distinguished asymptotic limit. A supercritical Hopf bifurcation in the flagellar orientation beyond a critical ratio of flagellar motor torque to hook bending stiffness, which is set by the spontaneous curvature of the flexible hook, the shape of the cell body, and the flagellum geometry, can have a dramatic effect on the cell's trajectory through the fluid. Although the equilibrium hook angle can result in a wide variance in the trajectory's helical pitch, we find a very consistent prediction for the trajectory's helical amplitude using parameters relevant to swimming P. aeruginosa cells.

• LC stretching of a RBC using experimental parameters
• Extremely stiff red blood cell
• 3D reconstruction of the z-stack images obtained through confocal microscopy (K. Nayani)

35. Dynamic and reversible shape response of red blood cells in synthetic liquid crystals

K. Nayani, A. Evans, S.E. Spagnolie, and N.L. Abbott, PNAS, 117, 26083-26090 (2020).

Mammalian cells are soft, and correct functioning requires that cells undergo dynamic shape changes in vivo. Although a range of diseases are associated with stiffening of red blood cells (RBCs; e.g., sickle cell anemia or malaria), the mechanical properties and thus shape responses of cells to complex viscoelastic environments are poorly understood. We use vapor pressure measurements to identify aqueous liquid crystals (LCs) that are in osmotic equilibrium with RBCs and explore mechanical coupling between RBCs and LCs. When transferred from an isotropic aqueous phase into a LC, RBCs exhibit complex yet reversible shape transformations, from initially biconcave disks to elongated and folded geometries with noncircular cross-sections. Importantly, whereas the shapes of RBCs are similar in isotropic fluids, when strained by LC, a large variance in shape response is measured, thus unmasking cell-to-cell variation in mechanical properties. Numerical modeling of LC and cell mechanics reveals that RBC shape responses occur at constant cell membrane area but with membrane shear moduli that vary between cells from 2 to 16 x 1e-6 N/m. Temperature-dependent LC elasticity permits continuous tuning of RBC strains, and chemical cross-linking of RBCs, a model for diseased cells, leads to striking changes in shape responses of the RBCs. Overall, these results provide insight into the coupling of strain between soft mammalian cells and synthetic LCs, and hint at new methods for rapidly characterizing mechanical properties of single mammalian cells in a population and thus cell-to-cell variance.

• Bacterial chain in a shear flow stretching of a RBC using experimental parameters

34. Shaving and breaking bacterial chains with a viscous flow

F. Gomand, F. Borges, J. Burgain, W.H. Mitchell, J. Petit, S.E. Spagnolie, and C. Gaiani,

Soft Matter, 16, 9273-9291 (2020).

Some food and ferment manufacturing steps such as spray-drying result in the application of viscous stresses to bacteria. This study explores how a viscous flow impacts both bacterial adhesion functionality and bacterial cell organization using a combined experimental and modeling approach. As a model organism we study Lactobacillus rhamnosus GG (LGG) "wild type" (WT), known to feature strong adhesive affinities towards beta-lactoglobulin thanks to pili produced by the bacteria on cell surfaces, along with three cell-surface mutant strains. Applying repeated flows with high shear-rates reduces bacterial adhesive abilities up to 20\% for LGG WT. Bacterial chains are also broken by this process, into 2-cell chains at low industrial shear rates, and into single cells at very high shear rates. To rationalize the experimental observations we study numerically and analytically the Stokes equations describing viscous fluid flow around a chain of elastically connected spheroidal cell bodies. In this model setting we examine the relationship between surface traction, a proxy for pili removal rate, and bacterial chain length (number of cells). Longer chains result in higher maximal surface tractions, particularly at the chain extremities, while inner cells enjoy a small protection from surface tractions due to hydrodynamic interactions with their neighbors. Chain rupture therefore may act as a mechanism to preserve surface adhesive functionality in bacteria.

33. Programming van der Waals interactions with complex symmetries into microparticles using liquid crystallinity

H.A. Fuster, X. Wang, X.-G. Wang, E. Bukusoglu, S.E. Spagnolie, and N.L. Abbott,

Science Advances, 6, eabb1327 (2020).

Asymmetric interactions such as entropic (e.g., encoded by nonspherical shapes) or surface forces (e.g., encoded by patterned surface chemistry or DNA hybridization) provide access to functional states of colloidal matter, but versatile approaches for engineering asymmetric van der Waals interactions have the potential to expand further the palette of materials that can be assembled through such bottom-up processes. We show that polymerization of liquid crystal (LC) emulsions leads to compositionally homogeneous and spherical microparticles that encode van der Waals interactions with complex symmetries (e.g., quadrupolar and dipolar) that reflect the internal organization of the LC. Experiments performed using kinetically controlled probe colloid adsorption and complementary calculations support our conclusion that LC ordering can program van der Waals interactions by ~20 kBT across the surfaces of microparticles. Because diverse LC configurations can be engineered by confinement, these results provide fresh ideas for programming van der Waals interactions for assembly of soft matter.

32. Molecular simulation of mechanical properties and membrane activities of the ESCRT-III complexes

T. Mandal, W. Lough, S. Spagnolie, A. Audhya, and Q. Cui, Biophys. J., 118, 1333-1343 (2020).

The endosomal sorting complex required for transport (ESCRT) machinery carries out the membrane scission reactions that are required for many biological processes throughout cells. How ESCRTs bind and deform cellular membranes and ultimately produce vesicles has been a matter of active research in recent years. In this study, we use fully atomistic molecular dynamics simulations to scrutinize the structural details of a filament composed of Vps32 protomers, a major component of ESCRT-III complexes. The simulations show that both hydrophobic and electrostatic interactions between monomers help maintain the structural stability of the filament, which exhibits an intrinsic bend and twist. Our findings suggest that the accumulation of bending and twisting stresses as the filament elongates on the membrane surface likely contribute to the driving force for membrane invagination. The filament exposes a large cationic surface that senses the negatively charged lipids in the membrane, and the N-terminal amphipathic helix of the monomers not only acts as a membrane anchor but also generates significant positive membrane curvature. Taking all results together, we discuss a plausible mechanism for membrane invagination driven by ESCRT-III.

31. Swimming with small and large amplitude waves in a confined liquid crystal

M.S. Krieger, S.E. Spagnolie, and T.R. Powers J. Non-Newtonian Fluid Mech., 273,104185 (2019).

Boundaries can have a significant impact on the physics of microorganism locomotion. Here we examine the effects of confinement by a rigid boundary or symmetric channel on undulatory locomotion in an anisotropic fluid, treated as a nematic liquid crystal. The competition between hydrodynamics, fluid elasticity, and anchoring conditions results in a complex locomotion problem with unique transport properties. We examine this problem analytically using a classical mathematical model, an infinite swimming sheet with small wave amplitude, and numerically for large amplitude waves using a modification of the immersed boundary method. For a prescribed stroke and strong planar anchoring in a narrow channel, we demonstrate that the swimming speed approaches its Newtonian value, though the power required to maintain the swimmer's speed depends on the properties of the liquid crystal. We show that an unusual prograde swimming (in the direction of transverse wave propagation) theorized to exist at small wave amplitude persists at large amplitude, and that the presence of a sufficiently close boundary returns the swimming behavior to the more standard retrograde motion (opposite the direction of the traveling wave).

• Initially polarized Gaussian colonies
• A thin band of aligned pushers
• A thin band of aligned pullers
• Initially isotropic in orientation: a no-flow theorem
• Swim for the gold

30. Active matter invasion of a viscous fluid: Unstable sheets and a no-flow theorem

C.J. Miles, A.A. Evans, M.J. Shelley, and S.E. Spagnolie, Phys. Rev. Lett., 222, 098002 (2019).

We investigate the dynamics of a dilute suspension of hydrodynamically interacting motile or immotile stress-generating swimmers or particles as they invade a surrounding viscous fluid. Colonies of aligned pusher particles are shown to elongate in the direction of particle orientation and undergo a cascade of transverse concentration instabilities, governed at small times by an equation which also describes the Saffman-Taylor instability in a Hele-Shaw cell, or Rayleigh-Taylor instability in two-dimensional flow through a porous medium. Thin sheets of aligned pusher particles are always unstable, while sheets of aligned puller particles can either be stable (immotile particles), or unstable (motile particles) with a growth rate which is non-monotonic in the force dipole strength. We also prove a surprising "no-flow theorem": a distribution initially isotropic in orientation loses isotropy immediately but in such a way that results in no fluid flow everywhere and for all time.

A 'suspension' of spotted jellyfish (Mastigias papua) at the Vancouver Aquarium

• Spotted jellyfish at the Vancouver Aquarium

29. Velocity fluctuations in a dilute suspension of viscous vortex rings

T. Morrell, S.E. Spagnolie, and J.-L. Thiffeault, Phys. Rev. Fluids, 4, 044501 (2019).

We explore the velocity fluctuations in a fluid due to a dilute suspension of randomly-distributed vortex rings at moderate Reynolds number, for instance those generated by a large colony of jellyfish. Unlike previous analysis of velocity fluctuations associated with gravitational sedimentation or suspensions of microswimmers, here the vortices have a finite lifetime and are constantly being produced. We find that the net velocity distribution is similar to that of a single vortex, except for the smallest velocities which involve contributions from many distant vortices; the result is a truncated 5/3-stable distribution with variance (and mean energy) linear in the vortex volume fraction φ. The distribution has an inner core with a width scaling as φ^(3/5), then long tails with power law |u|^(-8/3), and finally a fixed cutoff (independent of φ) above which the probability density scales as |u|^(-5), where u is a component of the velocity. We argue that this distribution is robust in the sense that the distribution of any velocity fluctuations caused by random forces localized in space and time has the same properties, except possibly for a different scaling after the cutoff.

From Hewitt & Balmforth (J. Fluid Mech., 856, 2018)

Dropping slender-body theory into the mud

S.E. Spagnolie, J. Fluid Mech. (Focus on Fluids), 862, 1-4 (2019).

The equations describing classical viscous fluid flow are notoriously challenging to solve, even approximately, when the flow is host to one or many immersed bodies. When an immersed body is slender, the smallness of its aspect ratio can sometimes be used as a basis for a 'slender-body theory' describing its interaction with the surrounding environment. If the fluid is complex, however, such classical theories are generally invalid and efforts to understand the dynamics of immersed bodies are almost entirely numerical in nature. In a valiant effort, Hewitt & Balmforth (J. Fluid Mech., vol. 856, 2018, pp. 870-897) have unearthed a theory to describe the motion of slender bodies in a viscoplastic fluid, 'fluids' such as mud or toothpaste which can be coaxed to flow, but only with a sufficiently large amount of forcing. Mathematical theories for some tremendously complicated physical systems might now be within reach.

• Pointwise traction on a prolate ellipsoid moving parallel to a wall, while slowly decreasing the separation distance.
• Erosion of a body in a constant flow
• Erosion in a shear flow
• Erosion in a shear flow near a wall

28. A generalized traction integral equation for Stokes flow, with applications to near-wall particle mobility and viscous erosion

W.H. Mitchell and S.E. Spagnolie, J. Comput. Phys., 333, 462-482 (2017).

A double-layer integral equation for the surface tractions on a body moving in a viscous fluid is derived, allowing for the incorporation of a background flow and/or the presence of a plane wall. The Lorentz reciprocal theorem is used to link the surface tractions on the body to integrals involving the background velocity and stress fields on an imaginary bounding sphere (or hemisphere for wall-bounded flows). The derivation requires the velocity and stress fields associated with numerous fundamental singularity solutions which we provide for free-space and wall-bounded domains. Two sample applications of the method are discussed: we study the tractions on an ellipsoid moving near a plane wall, which provides a more detailed understanding of the well-studied glancing and reversing trajectories, and we explore a new problem, erosion of bodies by a viscous flow, in which the surface is ablated at a rate proportional to the local viscous shear stress. Simulations and analytical estimates suggest that a spherical body in a uniform flow first reduces to nearly (but not exactly) the drag minimizing profile of a body in a Stokes flow and then vanishes in finite time. The shape dynamics of an eroding body in a shear flow and near a wall are also investigated. Stagnation points of the flow on the body lead generically to the formation of cusps, whose number depends on the flow configuration and/or the presence of a nearby wall.

• Passive sorting of swimmers with different wall departure angles

27. Microorganism Billiards

S.E. Spagnolie, C. Wahl, J. Lukasic, and J.-L. Thiffeault, Physica D., 341, 33-44 (2017).

Recent experiments and numerical simulations have shown that certain types of microorganisms "reflect" off of a flat surface at a critical angle of departure, independent of the angle of incidence. The nature of the reflection may be active (cell and flagellar contact with the surface) or passive (hydrodynamic) interactions. We explore the billiard-like motion of such a body inside a regular polygon and show that the dynamics can settle on a stable periodic orbit, or can be chaotic, depending on the swimmer's departure angle and the domain geometry. The dynamics are often found to be robust to the introduction of weak random fluctuations. The Lyapunov exponent of swimmer trajectories can be positive or negative, can have extremal values, and can have discontinuities depending on the degree of the polygon. A passive sorting device is proposed that traps swimmers of different departure angles into separate bins. We also study the external problem of a microorganism swimming in a patterned environment of square obstacles, where the departure angle dictates the possibility of trapping or diffusive trajectories.

26. A locally gradient-preserving reinitialization for level set functions

L. Li, X. Xu, and S.E. Spagnolie, J. Sci. Comput., 341, 274-302 (2017).

The level set method commonly requires a reinitialization of the level set function due to interface motion and deformation. We extend the traditional technique for reinitializing the level set function to a method that preserves the interface gradient. The gradient of the level set function represents the stretching of the interface, which is of critical importance in many physical applications. The proposed locally gradient-preserving reinitialization (LGPR) method involves the solution of three PDEs of Hamilton-Jacobi type in succession; first the signed distance function is found using a traditional reinitialization technique, then the interface gradient is extended into the domain by a transport equation, and finally the new level set function is achieved with the solution of a generalized reinitialization equation. We prove the well-posedness of the Hamilton-Jacobi equations, with possibly discontinuous Hamiltonians, and propose numerical schemes for their solutions. A subcell resolution technique is used in the numerical solution of the transport equation to extend data away from the interface directly with high accuracy. The reinitialization technique is computationally inexpensive if the PDEs are solved only in a small band surrounding the interface. As an important application, the LGPR method will enable the application of the local level set approach to the Eulerian Immersed boundary method.

• Bright-field and polarized microscopy videos

25. Straining soft colloids in aqueous nematic liquid crystals

P.C. Mushenheim, J.S. Pendery, D.B. Weibel, S.E. Spagnolie, and N.L. Abbott, Proc. Natl. Acad. Sci. USA, 113, 5564-5569 (2016).

Liquid crystals (LCs) are anisotropic, viscoelastic fluids that can be used to direct colloids (e.g., metallic nanorods) into organized assemblies with unusual optical, mechanical, and electrical properties. In past studies, the colloids have been sufficiently rigid that their individual shapes and properties have not been strongly coupled to elastic stresses imposed by the LCs. Herein, we explore how soft colloids (micrometer-sized shells formed from phospholipids) behave in LCs. We reveal a sharing of strain between the LC and shells, resulting in formation of spindle-like shells and other complex shapes and also, tuning of properties of the shells (e.g., barrier properties). These results hint at previously unidentified designs of reconfigurable soft materials with applications in sensing and biology.

• P. mirabilis pushing a non-motile C. albicans cell
• P. mirabilis pushing cargo along a specified LC director field

24. Bacterial transport of colloids in liquid crystalline environments

R.R. Trivedi, R. Maeda, N.L. Abbott, S.E. Spagnolie, and D.B. Weibel, Soft Matter, 11, 8404 - 8408 (2015).

We describe the controlled transport and delivery of polymer microparticles and non-motile eukaryotic cells by swimming bacteria suspended in nematic liquid crystals. The bacteria are shown to push reversibly attached cargo in a stable, unidirectional path (or along a complex patterned director field) over exceptionally long distances. Numerical simulations and an analytical prediction for swimming speeds provide a mechanistic insight into the hydrodynamics of the system. This study lays the foundation for using cargo-carrying bacteria in engineering applications and for understanding interspecies interactions in polymicrobial communities.

23. Microscale locomotion in a nematic liquid crystal

M.S. Krieger, S.E. Spagnolie, and T.R. Powers, Soft Matter, 11, 9115 - 9125 (2015).

Microorganisms often encounter anisotropy, for example in mucus and biofilms. We study how anisotropy and elasticity of the ambient fluid affects the speed of a swimming microorganism with a prescribed stroke. Motivated by recent experiments on swimming bacteria in anisotropic environments, we extend a classical model for swimming microorganisms, the Taylor swimming sheet, actuated either by transverse or longitudinal traveling waves in a three-dimensional nematic liquid crystal without twist. We calculate the swimming speed and entrained volumetric flux as a function of the swimmer's stroke properties as well as the elastic and rheological properties of the liquid crystal. The behavior is quantitatively and qualitatively well-approximated by a hexatic liquid crystal except in the cases of small Ericksen number and in a nematic fluid with tumbling parameter near the transition to a flow-aligning nematic, where anisotropic effects dominate. We also propose a novel method of swimming or pumping in a nematic fluid by passing a traveling wave of director oscillation along a flat rigid wall.

• Glancing, reversing, and tumbling
(W. H. Mitchell)

22. Sedimentation of ellipsoidal particles near walls in viscous fluids: glancing, reversing, tumbling, and sliding

W.H. Mitchell and S.E. Spagnolie, J. Fluid Mech., 772, 600 - 629 (2015).

The sedimentation of a rigid particle near a wall in a viscous fluid has been studied numerically by many authors, but analytical solutions have been derived only for special cases such as the motion of spherical particles. In this paper the method of images is used to derive simple ordinary differential equations describing the sedimentation of arbitrarily oriented prolate and oblate spheroids at zero Reynolds number near a vertical or inclined plane wall. The reduced order system may be solved analytically in many situations, and full trajectories are predicted which compare favorably with complete numerical simulations, performed using a novel double layer boundary integral formulation, a method of stresslet images. The conditions under which the glancing and reversing trajectories, first observed by Russel et al. (1977), occur are studied for bodies of arbitrary aspect ratio. Several additional trajectories are also described: a periodic tumbling trajectory for nearly spherical bodies, a linearly stable sliding trajectory which appears when the wall is slightly inclined, and three-dimensional glancing, reversing, and wobbling.

21. Geometric capture and escape of a microswimmer colliding with an obstacle

S.E. Spagnolie, G. Moreno-Flores, D. Bartolo and E. Lauga, Soft Matter, 11, 3396 - 3411 (2015).

Motivated by recent experiments, we consider the hydrodynamic capture of a microswimmer near a stationary spherical obstacle. Simulations of model equations show that a swimmer approaching a small spherical colloid is simply scattered. In contrast, when the colloid is larger than a critical size it acts as a passive trap: the swimmer is hydrodynamically captured along closed trajectories and endlessly orbits around the colloidal sphere. In order to gain physical insight into this hydrodynamic scattering problem, we address it analytically. We provide expressions for the critical trapping radius, the depth of the "basin of attraction," and the scattering angle, which show excellent agreement with our numerical findings. We also demonstrate and rationalize the strong impact of swimming-flow symmetries on the trapping efficiency. Finally, we give the swimmer an opportunity to escape the colloidal traps by considering the effects of Brownian, or active, diffusion. We show that in some cases the trapping time is governed by an Ornstein-Uhlenbeck process, which results in a trapping time distribution that is well-approximated as inverse-Gaussian. The predictions again compare very favorably with the numerical simulations. We envision applications of the theory to bioremediation, microorganism sorting techniques, and the study of bacterial populations in heterogeneous or porous environments.

20. Stability and dynamics of magnetocapillary interactions

R. Chinomona, J. Lajeunesse, W.H. Mitchell, Y. Yao and S.E. Spagnolie, Soft Matter, 11, 1828 - 1838 (2015).

Recent experiments have shown that floating paramagnetic beads, under the influence of an oscillating background magnetic field, can move along a liquid-air interface in a sustained periodic locomotion. The locomotion arises from a periodically induced dipole-dipole repulsion between the beads acting in concert with a capillary attraction. We investigate analytically and numerically the stability and dynamics of this magnetocapillary swimming, and explore other related topics including the steady and periodic equilibrium configurations of two and three beads. The swimming speed and system stability depend on a dimensionless measure of the relative repulsive and attractive forces which we term the magnetocapillary number. An oscillatory magnetic field may stabilize an otherwise unstable collinear configuration, and striking behaviors are observed in fast transitions to and from locomotory states, offering insight into the behavior and self-assembly of interface-bound micro-particles.

19. Swimming and pumping by helical waves in viscous and viscoelastic fluids

L. Li and S.E. Spagnolie, Phys. Fluids, 27, 021902 (2015).

We study helical bodies of arbitrary cross-sectional profile as they swim or transport fluid by the passage of helical waves. Many cases are explored: the external flow problem of swimming in a cylindrical tube or an infinite domain, the internal fluid pumping problem, and confined/unconfined swimming and internal pumping in a viscoelastic (Oldroyd-B) fluid. A helical coordinate system allows for the analytical calculation of swimming and pumping speeds and fluid velocities in the asymptotic regime of nearly-cylindrical bodies. In a Newtonian flow, a matched asymptotic analysis results in corrections to the swimming speed accurate to fourth-order in the small wave amplitude, and the results compare favorably with full numerical simulations. We find that the torque-balancing rigid body rotation generally opposes the direction of wave passage, but not always. Confinement can result in local maxima and minima of the swimming speed in the helical pitch, and the effects of confinement decrease exponentially fast with the diameter of the tube. In a viscoelastic fluid, we find that the effects of fluid elasticity on swimming and internal pumping modify the Newtonian results through the mode-dependent complex viscosity, even in a confined domain.

Complex Fluids in Biological Systems: Experiment, Theory, and Computation

S.E. Spagnolie (Ed.), (2015).

This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history-dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world's foremost experts explore key topics such as:

• Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation
• Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood
• Experiments and theory of active suspensions, and the motility of microorganisms in complex fluids
• Challenges and solutions in the numerical simulation of biologically relevant complex fluid flows

18. Introduction to complex fluids

A. Morozov and S.E. Spagnolie, Complex Fluids in Biological Systems, Springer, (2015)

In this chapter we introduce the fundamental concepts in Newtonian and complex fluid mechanics, beginning with the basic underlying assumptions in continuum mechanical modeling. The equations of mass and momentum conservation are derived, and the Cauchy stress tensor makes its first of many appearances. The Navier-Stokes equations are derived, along with their inertialess limit, the Stokes equations. Models used to describe complex fluid phenomena such as shear-dependent viscosity and viscoelasticity are then discussed, beginning with generalized Newtonian fluids. The Carreau-Yasuda and power-law fluid models receive special attention, and a mechanical instability is shown to exist for highly shear-thinning fluids. Differential constitutive models of viscoelastic flows are then described, beginning with the Maxwell fluid and Kelvin-Voigt solid models. After providing the foundations for objective (frame-independent) derivatives, the linear models are extended to mathematically sound nonlinear models including the upper-convected Maxwell and Oldroyd-B models, and others. A derivation of the upper-convected Maxwell model from the kinetic theory perspective is also provided. Finally, normal stress differences are discussed, and the reader is warned about common pitfalls in the mathematical modeling of complex fluids.

17. Locomotion and transport in a hexatic liquid crystal

M.S. Krieger, S.E. Spagnolie, and T.R. Powers, Phys. Rev. E., 90, 052503 (2014).

The swimming behavior of bacteria and other microorganisms is sensitive to the physical properties of the fluid in which they swim. Mucus, biofilms, and artificial liquid-crystalline solutions are all examples of fluids with some degree of anisotropy that are also commonly encountered by bacteria. In this paper, we study how liquid-crystalline order affects the swimming behavior of a model swimmer. The swimmer is a one-dimensional version of G. I. Taylor's swimming sheet: an infinite line undulating with small-amplitude transverse or longitudinal traveling waves. The fluid is a two-dimensional hexatic liquid-crystalline film. We calculate the power dissipated, swimming speed, and flux of fluid entrained as a function of the swimmer's waveform as well as properties of the hexatic film, such as the rotational and shear viscosity, the Frank elastic constant, and the anchoring strength. The departure from isotropic behavior is greatest for large rotational viscosity and weak anchoring boundary conditions on the orientational order at the swimmer surface. We even find that if the rotational viscosity is large enough, the transverse-wave swimmer moves in the opposite direction relative to a swimmer in an isotropic fluid.

16. The instability of a sedimenting suspension of weakly flexible fibres

H. Manikantan, L. Li, S.E. Spagnolie, and D. Saintillan, J. Fluid Mech., 756, 935-964 (2014).

Suspensions of sedimenting slender fibres in a viscous fluid are known to be unstable to fluctuations of concentration. In this paper we develop a theory for the role of fibre flexibility in sedimenting suspensions in the asymptotic regime of weakly-flexible bodies (large elasto-gravitation number). Unlike the behaviour of straight fibres, individual flexible filaments rotate as they sediment, leading to an anisotropic base-state of fibre orientations in an otherwise homogeneous suspension. A mean-field theory is derived to describe the evolution of fibre concentration and orientation fields, and we explore the stability of the base-state to perturbations of fibre concentration. We show that fibre flexibility affects suspension stability in two distinct and competing ways: the anisotropy of the base-state renders the suspension more unstable to perturbations, while individual particle self-rotation acts to prevent clustering and stabilizes the suspension. In the presence of thermal noise, the dominant effect depends critically upon the relative scales of flexible fibre self-rotation compared to rotational Brownian motion.

15. Swimming and pumping of rigid helical bodies in viscous fluids

L. Li and S.E. Spagnolie, Phys. Fluids, 26, 041901 (2014).

Editor's pick

Rotating helical bodies of arbitrary cross-sectional profile and infinite length are explored as they swim through or transport a viscous fluid. The Stokes equations are studied in a helical coordinate system, and closed form analytical expressions for the force-free swimming speed and torque are derived in the asymptotic regime of nearly cylindrical bodies. High-order accurate expressions for the velocity field and swimming speed are derived for helical bodies of finite pitch angle through a double series expansion. The analytical predictions match well with the results of full numerical simulations, and accurately predict the optimal pitch angle for a given cross-sectional profile. This work may improve the modeling and design of helical structures used in microfluidic manipulation, synthetic microswimmer engineering, and the transport and mixing of viscous fluids

• Trajectories, Particle Clouds, and Buckling of Flexible Filaments
(H. Manikantan)

14. The sedimentation of flexible filaments

L. Li, H. Manikantan, D. Saintillan, and S.E. Spagnolie, J. Fluid Mech., 735, 705-736 (2013).

The dynamics of a flexible filament sedimenting in a viscous fluid are explored analytically and numerically. Compared with the well-studied case of sedimenting rigid rods, the introduction of filament compliance is shown to cause a significant alteration in the long-time sedimentation orientation and filament geometry. A model is developed by balancing viscous, elastic and gravitational forces in a slender-body theory for zero-Reynolds-number flows, and the filament dynamics are characterized by a dimensionless elasto-gravitation number. Filaments of both non-uniform and uniform cross-sectional thickness are considered. In the weakly flexible regime, a multiple-scale asymptotic expansion is used to obtain expressions for filament translations, rotations and shapes. These are shown to match excellently with full numerical simulations. Furthermore, we show that trajectories of sedimenting flexible filaments, unlike their rigid counterparts, are restricted to a cloud whose envelope is determined by the elasto-gravitation number. In the highly flexible regime we show that a filament sedimenting along its long axis is susceptible to a buckling instability. A linear stability analysis provides a dispersion relation, illustrating clearly the competing effects of the compressive stress and the restoring elastic force in the buckling process. The instability travels as a wave along the filament opposite the direction of gravity as it grows and the predicted growth rates are shown to compare favourably with numerical simulations. The linear eigenmodes of the governing equation are also studied, which agree well with the finite-amplitude buckled shapes arising in simulations

13. Locomotion of helical bodies in viscoelastic fluids: enhanced swimming at large helical amplitudes

S.E. Spagnolie, B. Liu, and T.R. Powers, Phys. Rev. Lett., 111, 068101 (2013).

See also: Physics Focus article by Philip Ball and ScienceDaily.

The motion of a rotating helical body in a viscoelastic fluid is considered. In the case of force-free swimming, the introduction of viscoelasticity can either enhance or retard the swimming speed and locomotive efficiency, depending on the body geometry, fluid properties, and the body rotation rate. Numerical solutions of the Oldroyd-B equations show how previous theoretical predictions break down with increasing helical radius or with decreasing filament thickness. Helices of large pitch angle show an increase in swimming speed to a local maximum at a Deborah number of order unity. The numerical results show how the small-amplitude theoretical calculations connect smoothly to the large-amplitude experimental measurements.

• Standard buckling of a floating filament
• Buckling with endpoints pulled by external forces
• Collapse of a hairpin shape to a racquet shape, and a folding cascade
• Period doubling (sinusoidal initial configuration)

12. Elastocapillary self-folding: buckling, wrinkling, and collapse of floating filaments

A.Evans, S.E. Spagnolie, D. Bartolo, and E. Lauga, Soft Matter, 9, 1711-1720 (2013).

When a flexible filament is confined to a fluid interface, the balance between capillary attraction, bending resistance, and tension from an external source can lead to a self-buckling instability. We perform an analysis of this instability and provide analytical formulae that compare favorably with the results of detailed numerical computations. The stability and long-time dynamics of the filament are governed by a single dimensionless elastocapillary number quantifying the ratio between capillary to bending stresses. Complex, folded filament configurations such as loops, needles, and racquet shapes may be reached at longer times, and long filaments can undergo a cascade of self-folding events.

• Wall interaction redirects a ciliated body (potential flow "squirmer")
• Hydrodynamic entrapment (with nose pitched up) of a spherical cell driven by a short flagellum
• A different initial distance leads to escape in the same swimmer
• Hydrodynamic entrapment (with nose pitched down) of a spherical cell driven by a longer flagellum

11. Hydrodynamics of self-propulsion near boundaries: predictions and accuracy of far-field approximations

S.E. Spagnolie and E. Lauga, J. Fluid Mech., 700, 105-147 (2012).

The swimming trajectories of self-propelled organisms or synthetic devices in a viscous fluid can be altered by hydrodynamic interactions with nearby boundaries. We explore a multipole description of swimming bodies and provide a general framework for studying the fluid-mediated modifications to swimming trajectories. A general axisymmetric swimmer is described as a linear combination of fundamental solutions to the Stokes equations: a Stokeslet dipole, a source dipole, a Stokeslet quadrupole, and a rotlet dipole. The effects of nearby walls or stress-free surfaces on swimming trajectories are described through the contribution of each singularity, and we address the question of how accurately this multipole approach captures the wall effects observed in full numerical solutions of the Stokes equations. The reduced model is used to provide simple but accurate predictions of the wall-induced attraction and pitching dynamics for model Janus particles, ciliated organisms, and bacteria-like polar swimmers. Transitions in attraction and pitching behaviour as functions of body geometry and propulsive mechanism are described. The reduced model may help to explain a number of recent experimental results.

10. The hydrodynamics of the double-wave structure of insect spermatozoa

O.S. Pak, S.E. Spagnolie, and E. Lauga, J. R. Soc. Interface, 9, 1908-1924 (2012).

In addition to conventional planar and helical flagellar waves, insect sperm flagella have also been observed to display a double-wave structure characterized by the presence of two super- imposed helical waves. In this paper, we present a hydrodynamic investigation of the locomotion of insect spermatozoa exhibiting the double-wave structure, idealized here as superhelical waves. Resolving the hydrodynamic interactions with a non-local slender body theory, we predict the swimming kinematics of these superhelical swimmers based on experimentally collected geometric and kinematic data. Our consideration provides insight into the relative contributions of the major and minor helical waves to swimming; namely, propulsion is owing primarily to the minor wave, with negligible contribution from the major wave. We also explore the dependence of the propulsion speed on geometric and kinematic parameters, revealing counterintuitive results, particularly for the case when the minor and major helical structures are of opposite chirality.

9. Comparative hydrodynamics of bacterial polymorphism

S.E. Spagnolie and E. Lauga, Phys. Rev. Lett., 106, 058103 (2011).

Most bacteria swim through fluids by rotating helical flagella which can take one of 12 distinct polymorphic shapes, the most common of which is the normal form used during forward swimming runs. To shed light on the prevalence of the normal form in locomotion, we gather all available experimental measurements of the various polymorphic forms and compute their intrinsic hydrodynamic efficiencies. The normal helical form is found to be the most efficient of the 12 polymorphic forms by a significant margin - a conclusion valid for both the peritrichous and polar flagellar families, and robust to a change in the effective flagellum diameter or length. Hence, although energetic costs of locomotion are small for bacteria, fluid mechanical forces may have played a significant role in the evolution of the flagellum.

• Recoil locomotion at frequency Reynolds number 16
• Recoil locomotion at frequency Reynolds number 256

8. A bug on a raft: Recoil locomotion in a viscous fluid

S. Childress, S.E. Spagnolie, and T. Tokieda, J. Fluid Mech., 669, 527-556 (2011).

The locomotion of a body through an inviscid incompressible fluid, such that the flow remains irrotational everywhere, is known to depend on inertial forces and on both the shape and the mass distribution of the body. In this paper we consider the influence of fluid viscosity on such inertial modes of locomotion. In particular we consider a free body of variable shape and study the centre-of-mass and centre-of-volume variations caused by a shifting mass distribution. We call this recoil locomotion. Numerical solutions of a finite body indicate that the mechanism is ineffective in Stokes flow but that viscosity can significantly increase the swimming speed above the inviscid value once Reynolds numbers are in the intermediate range 50-300. To study the problem analytically, a model which is an analogue of Taylor's swimming sheet is introduced. The model admits analysis at fixed, arbitrarily large Reynolds number for deformations of sufficiently small amplitude. The analysis confirms the significant increase of swimming velocity above the inviscid value at intermediate Reynolds numbers.

7. Jet propulsion without inertia

S.E. Spagnolie and E. Lauga, Phys. Fluids, 22, 081902 (2010).

Phys. Fluids "Research Highlights."

A body immersed in a highly viscous fluid can locomote by drawing in and expelling fluid through pores at its surface. We consider this mechanism of jet propulsion without inertia in the case of spheroidal bodies and derive both the swimming velocity and the hydrodynamic efficiency. Elementary examples are presented and exact axisymmetric solutions for spherical, prolate spheroidal, and oblate spheroidal body shapes are provided. In each case, entirely and partially porous i.e., jetting surfaces are considered and the optimal jetting flow profiles at the surface for maximizing the hydrodynamic efficiency are determined computationally. The maximal efficiency which may be achieved by a sphere using such jet propulsion is 12.5%, a significant improvement upon traditional flagella-based means of locomotion at zero Reynolds number, which corresponds to the potential flow created by a source dipole at the sphere center. Unlike other swimming mechanisms which rely on the presentation of a small cross section in the direction of motion, the efficiency of a jetting body at low Reynolds number increases as the body becomes more oblate and limits to approximately 162% in the case of a flat plate swimming along its axis of symmetry. Our results are discussed in the light of slime extrusion mechanisms occurring in many cyanobacteria.

• Spontaneous curvature swimmer (slow)
• Spontaneous curvature swimmer (fast)
• Bilayer coupling swimmer

6. Stokesian jellyfish: Locomotion of a bilayer vesicle

A. Evans, S.E. Spagnolie, and E. Lauga, Soft Matter, 6, 1737-1747, (2010).

Selected to appear in the Virtual Journal of Biological Physics Research, April 15, 2010.

Motivated by recent advances in vesicle engineering, we consider theoretically the locomotion of shape-changing bilayer vesicles at low Reynolds number. By modulating their volume and membrane composition, the vesicles can be made to change shape quasi-statically in thermal equilibrium. When the control parameters are tuned appropriately to yield periodic shape changes, which are not time- reversible, the result is a net swimming motion over one cycle of shape deformation. For two classical vesicle models (spontaneous curvature and bilayer coupling), we numerically determine the sequence of vesicle shapes through an enthalpy minimization, as well as the fluid-body interactions by solving a boundary integral formulation of the Stokes equations. For both models, net locomotion can be obtained either by continuously modulating fore-aft asymmetric vesicle shapes or by crossing a continuous shape-transition region and alternating between fore-aft asymmetric and fore-aft symmetric shapes. The obtained hydrodynamic efficiencies are similar to those of other low Reynolds number biological swimmers and suggest that shape-changing vesicles might provide an alternative to flagella-based synthetic microswimmers.

• The optimal elastic flagellum
• Numerical C. elegans

5. The optimal elastic flagellum

S.E. Spagnolie and E. Lauga, Phys. Fluids, 22, 031901, (2010).

Selected to appear in the Virtual Journal of Biological Physics Research, March 15, 2010.

Motile eukaryotic cells propel themselves in viscous fluids by passing waves of bending deformation down their flagella. An infinitely long flagellum achieves a hydrodynamically optimal low-Reynolds number locomotion when the angle between its local tangent and the swimming direction remains constant along its length. Optimal flagella therefore adopt the shape of a helix in three dimensions
smooth and that of a sawtooth in two dimensions
nonsmooth. Physically, biological organisms
or engineered microswimmers must expend internal energy in order to produce the waves of deformation responsible for the motion. Here we propose a physically motivated derivation of the optimal flagellum shape. We determine analytically and numerically the shape of the flagellar wave which leads to the fastest swimming for a given appropriately defined energetic expenditure. Our novel approach is to define an energy which includes not only the work against the surrounding fluid, but also
(1) the energy stored elastically in the bending of the flagellum, (
2) the energy stored elastically in the internal sliding of the polymeric filaments which are responsible for the generation of the bending waves
microtubules, and (
3) the viscous dissipation due to the presence of an internal fluid. This approach regularizes the optimal sawtooth shape for two-dimensional deformation at the expense of a small loss in hydrodynamic efficiency. The optimal waveforms of finite-size flagella are shown to depend on a competition between rotational motions and bending costs, and we observe a surprising bias toward half-integer wave numbers. Their final hydrodynamic efficiencies are above 6%, significantly larger than those of swimming cells, therefore indicating available room for further biological tuning.

• "Forward" flapping locomotion (experiment)
• "Forward" flapping locomotion (simulation)
• "Backward" flapping locomotion (experiment)
• "Backward" flapping locomotion (simulation)
• Why nature doesn't use fat flapping wings

4. Surprising behaviors in flapping locomotion with passive pitching

S.E. Spagnolie, L. Moret, M.J. Shelley, and J. Zhang, Phys. Fluids, 22, 041903 (2010).

To better understand the role of wing and fin flexibility in flapping locomotion, we study through experiment and numerical simulation a freely moving wing that can pitch passively as it is actively heaved in a fluid. We observe a range of flapping frequencies corresponding to large horizontal velocities, a regime of underperformance relative to a clamped (non-pitching) flapping wing, and a surprising, hysteretic regime in which the flapping wing can move horizontally in either direction !despite left/right symmetry being broken by the specific mode of pitching". The horizontal velocity is shown to peak when the flapping frequency is near the immersed system's resonant frequency. Unlike for the clamped wing, we find that locomotion is achieved by vertically flapped symmetric wings with even the slightest pitching flexibility, and the system exhibits a continuous departure from the Stokesian regime. The phase difference between the vertical heaving motion and consequent pitching changes continuously with the flapping frequency, and the direction reversal is found to correspond to a critical phase relationship. Finally, we show a transition from coherent to chaotic motion by increasing the wing's aspect ratio, and then a return to coherence for flapping bodies with circular cross section.

• Optimal biflagellar locomotion

3. Rehinging bi-flagellar locomotion in a viscous fluid

S.E. Spagnolie, Phys. Rev. E, 80, 046323 (2009).

A means of swimming in a viscous fluid is presented, in which a swimmer with only two links rotates around a joint and then rehinges in a periodic fashion in what is here termed rehinging locomotion. This two-link rigid swimmer is shown to locomote with an efficiency similar to that of Purcell's well-studied three-link swimmer, but with a simpler morphology. The hydrodynamically optimal stroke of an analogous flexible biflagellated swimmer is also considered. The introduction of flexibility is found to increase the swimming efficiency by up to 520% as the body begins to exhibit wavelike dynamics, with an upper bound on the efficiency determined by a degeneracy in the limit of infinite flexibility

• Ratcheting upward against gravity

2. Shape-changing bodies in fluid: Hovering, ratcheting, and bursting

S.E. Spagnolie and M.J. Shelley, Phys. Fluids, 21, 013103 (2009).

Featured in "Outside JEB", J. Exp. Biol., 2009.

Motivated by recent experiments on the hovering of passive bodies, we demonstrate how a simple shape-changing body can hover or ascend in an oscillating background flow. We study this ratcheting effect through numerical simulations of the two-dimensional Navier-Stokes equations at intermediate Reynolds number. This effect could describe a viable means of locomotion or transport in such environments as a tidal pool with wave-driven sloshing. We also consider the velocity burst achieved by a body through a rapid increase in its aspect ratio, which may contribute to the escape dynamics of such organisms as jellyfish.

• Sedimenting disks (experiment)
• Periodic tumbling: three disks
• Instability of three (perturbed) sedimenting bodies
• Two meandering disks
• APS-DFD 2005, video presentation

1. Periodic sedimentation in a Stokesian Fluid

S.Jung, S.E. Spagnolie, K. Parikh, M. Shelley, and A-K. Tornberg, Phys. Rev. E, 74, 035302 (2006).

We study the sedimentation of two identical but non-spherical particles sedimenting in a Stokesian fluid. Experiments and numerical simulations reveal periodic orbits wherein the bodies mutually induce an in-phase rotational motion accompanied by periodic modulations of sedimentation speed and separation distance. We term these "tumbling orbits" and find that they appear over a broad range of body shapes

Vijayanagara: The Deccan Empires of Medieval India, 1290-1398

S.E. Spagnolie, M. Johnson, C. Graham, and A. Matthews, GMT Games (2023).

It is 1290, and the Indian subcontinent finds itself under the authoritative sway of the Delhi Sultanate. The Sultan’s dominion stretches across vast expanses, from the northern realms of Punjab to the Tamilakam region far to the south. Deeply entrenched in their pursuit of power and prosperity, Delhi’s rulers have for generations gazed with ambitious intent upon the affluent kingdoms of the Deccan Plateau, beyond the impassable Vindhya Range. Among these kingdoms are the Yadavas in the natural stronghold of Devagiri; the Kakatiyas ruling from Warangal, a capital city surrounded by three great concentric walls; and the Hoysalas and Pandyas further south in Karnataka and Tamilakam.

The Sultan’s quest for riches comes with some urgency and is not without purpose. Ever-looming is the threat of Mongol invasions from the northwestern frontier, requiring the continual purchase of warhorses from afar and the maintenance of a standing army. Although the Sultan periodically sends his armies to attack and plunder the southern kingdoms, the Sultanate cannot afford to maintain its military presence in the south. Instead, after demanding obedience and collecting tribute, these armies will retreat to Delhi. Local rulers, amirs and rajas, are left intact to pay annual tributes again in the future – but are also left with a smoldering desire to cast off Delhi’s oppression once and for all...

Vijayanagara is a 1-3 player board game depicting the dynamics of the Indian subcontinent during the years 1290-1398. The game spans the Khalji (1290-1320) and most of the Tughlaq (1320-1413) dynasties of the Delhi Sultanate, while showing the birth of two upstart powers in the Deccan Plateau, the Bahmani Kingdom and the Vijayanagara Empire. The game closes with the historical invasion of Delhi by Timur in 1398, though a careful Delhi Sultanate player might be able to avoid this fate.