AML Publications, Images, and Video





Fast crystallization of rotating membrane proteins
N. Oppenheimer, D. B. Stein, and M. Shelley
arXiv, (2019).

Abstract: We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices. We show that crystallization is possible through a combination of hydrodynamic and repulsive interactions between the rotor proteins. In particular, hydrodynamic interactions induce rotational motion of the rotor protein assembly that, in the presence of repulsion, drives the system into a hexagonal lattice. The entire crystal rotates with an angular velocity which increases with motor density and decreases with lattice diameter — larger and sparser arrays rotate at a slower pace. The rotational interactions allow ensembles of proteins to sample configurations and reach an ordered steady state, which are inaccessible to the quenched nonrotational system. Rotational interactions thus act as a sort of temperature that removes disorder, except that actual thermal diffusion leads to expansion and loss of order. In contrast, the rotational interactions are bounded in space. Hence, once an ordered state is reached, it is maintained at all times.




A compact Eulerian representation of axisymmetric inviscid vortex sheet dynamics
A. I. Pesci, R. E. Goldstein, M. J. Shelley
to appear in Communications in Pure and Applied Mathematics, (2019).

Abstract: A classical problem in fluid mechanics is the motion of an axisymmetric vortex sheet evolving under the action of surface tension, surrounded by an inviscid fluid. Lagrangian descriptions of these dynamics are well-known, involving complex nonlocal expressions for the radial and longitudinal velocities in terms of elliptic integrals. Here we use these prior results to arrive at a remarkably compact and exact Eulerian evolution equation for the sheet radius r(z, t) in an explicit flux form associated with the conservation of enclosed volume. The flux appears as an integral involving the pairwise mutual induction formula for vortex loop pairs first derived by Helmholtz and Maxwell. We show how the well-known linear stability results for cylindrical vortex sheets in the presence of surface tension and streaming flows [A.M. Sterling and C.A. Sleicher, J. Fluid Mech. 68, 477 (1975)] can be obtained directly from this formulation. Furthermore, the inviscid limit of the empirical model of Eggers and Dupont [J. Fluid Mech. 262 205 (1994); SIAM J. Appl. Math. 60, 1997 (2000)], which has served as the basis for understanding singularity formation in droplet pinchoff, is derived within the present formalism as the leading order term in an asymptotic analysis for long slender axisymmetric vortex sheets, and should provide the starting point for a rigorous analysis of singularity formation.




Active matter invasion of a viscous fluid: Unstable sheets and a no-flow theorem
C. Miles, A. Evans, M. Shelley, and S. Spagnolie
Physical Review Letters, 122 098002 (2019).

Abstract: 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 that also describes the Saffman-Taylor instability in a Hele-Shaw cell, or the Rayleigh-Taylor instability in a 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 that is nonmonotonic 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.




Computing collision stress in assemblies of active spherocylinders: Applications of a fast and generic geometric method
W. Yan, H. Zhang, M. Shelley
Journal of Chemical Physics, 150 (2019).

Abstract: In this work, we provide a solution to the problem of computing collision stress in particle-tracking simulations. First, a formulation for the collision stress between particles is derived as an extension of the virial stress formula to general-shaped particles with uniform or non-uniform mass density. Second, we describe a collision-resolution algorithm based on geometric constraint minimization which eliminates the stiff pairwise potentials in traditional methods. The method is validated with a comparison to the equation of state of Brownian spherocylinders. Then we demonstrate the application of this method in several emerging problems of soft active matter.




Flow interactions between uncoordinated flapping swimmers give rise to group cohesion
J. W. Newbolt, J. Zhang, and L. Ristroph
Proc. of the National Academy of Sciences (PNAS), 116 2419-2424 (2019).

Abstract: Many species of fish and birds travel in groups, yet the role of fluid-mediated interactions in schools and flocks is not fully understood. Previous fluid-dynamical models of these collective behaviors assume that all individuals flap identically, whereas animal groups involve variations across members as well as active modifications of wing or fin motions. To study the roles of flapping kinematics and flow interactions, we design a minimal robotic “school” of two hydrofoils swimming in tandem. The flapping kinematics of each foil are independently prescribed and systematically varied, while the forward swimming motions are free and result from the fluid forces. Surprisingly, a pair of uncoordinated foils with dissimilar kinematics can swim together cohesively—without separating or colliding—due to the interaction of the follower with the wake left by the leader. For equal flapping frequencies, the follower experiences stable positions in the leader’s wake, with locations that can be controlled by flapping amplitude and phase. Further, a follower with lower flapping speed can defy expectation and keep up with the leader, whereas a faster-flapping follower can be buffered from collision and oscillate in the leader’s wake. We formulate a reduced-order model which produces remarkable agreement with all experimentally observed modes by relating the follower’s thrust to its flapping speed relative to the wake flow. These results show how flapping kinematics can be used to control locomotion within wakes, and that flow interactions provide a mechanism which promotes group cohesion.




Coarse-graining the dynamics of immersed and driven fiber assemblies
D. B. Stein and M. Shelley
arXiv, (2019).

Abstract:
An important class of fluid-structure problems involve the dynamics of ordered arrays of immersed, flexible fibers. While specialized numerical methods have been developed to study fluid-fiber systems, they become infeasible when there are many, rather than a few, fibers present, nor do these methods lend themselves to analytical calculation. Here, we introduce a coarse-grained continuum model, based on local-slender body theory, for elastic fibers immersed in a viscous Newtonian fluid. It takes the form of an anisotropic Brinkman equation whose skeletal drag is coupled to elastic forces. This model has two significant benefits: (1) the density effects of the fibers in a suspension become analytically manifest, and (2) it allows for the rapid simulation of dense suspensions of fibers in regimes inaccessible to standard methods. As a first validation, without fitting parameters, we achieve very reasonable agreement with 3D Immersed Boundary simulations of a bed of anchored fibers bent by a shear flow. Secondly, we characterize the effect of density on the relaxation time of fiber beds under oscillatory shear, and find close agreement to results from full numerical simulations. We then study buckling instabilities in beds of fibers, using our model both numerically and analytically to understand the role of fiber density and the structure of buckling transitions. We next apply our model to study the flow-induced bending of inclined fibers in a channel, as has been recently studied as a flow rectifier, examining the nature of the internal flows within the bed, and the emergence of inhomogeneous permeability. Finally, we extend the method to study a simple model of metachronal waves on beds of actuated fibers, as a model for ciliary beds. Our simulations reproduce qualitatively the pumping action of coordinated waves of compression through the bed.




Improving the propulsion speed of a heaving wing through artificial evolution of shape
S. Ramananarivo, T. Mitchel and L. Ristroph
Proc. R. Soc. A, 475 (2019).

Abstract: Aeronautical studies have shown that subtle changes in aerofoil shape substantially alter aerodynamic forces during fixed-wing flight. The link between shape and performance for flapping locomotion involves distinct mechanisms associated with the complex flows and unsteady motions of an air- or hydro-foil. Here, we use an evolutionary scheme to modify the cross-sectional shape and iteratively improve the speed of three-dimensional printed heaving foils in forward flight. In this algorithmicexperimental method, 'genes' are mathematical parameters that define the shape, 'breeding' is the combination of genes from parent wings to form a daughter, and a wing's measured speed is its 'fitness' that dictates its likelihood of breeding. Repeated over many generations, this process automatically discovers a fastest foil whose crosssection resembles a slender teardrop. We conduct an analysis that uses the larger population to identify what features of this shape are most critical, implicating slenderness, location of maximum thickness and fore-aft asymmetries in edge sharpness or bluntness. This analysis also reveals a tendency towards extremely thin and cusp-like trailing edges. These findings demonstrate artificial evolution in laboratory experiments as a successful strategy for tailoring shape to improve propulsive performance. Such a method could be used in related optimization problems, such as tuning kinematics or flexibility for flapping propulsion, and for flow–structure interactions more generally.




Dynamics of Flexible Fibers in Viscous Flows and Fluids
O. du Roure, A. Lindner, E. Nazockdast, M. Shelley
Annual Reviews of Fluid Mechanics, 51 539-572 (2019).

Abstract: The dynamics and deformations of immersed flexible fibers are at the heart of important industrial and biological processes, induce peculiar mechanical and transport properties in the fluids that contain them, and are the basis for novel methods of flow control. Here we focus on the low–Reynolds number regime where advances in studying these fiber–fluid systems have been especially rapid. On the experimental side, this is due to new methods of fiber synthesis, microfluidic flow control, and microscope-based tracking measurement techniques. Likewise, there have been continuous improvements in the specialized mathematical modeling and numerical methods needed to capture the interactions of slender flexible fibers with flows, boundaries, and each other.




From cytoskeletal assemblies to living materials
P. Foster, S. Fürthauer, M. Shelley, D. Needleman
Current Opinion in Cell Biology, 56 109-114 (2019).

Abstract: Many subcellular structures contain large numbers of cytoskeletal filaments. Such assemblies underlie much of cell division, motility, signaling, metabolism, and growth. Thus, understanding cell biology requires understanding the properties of networks of cytoskeletal filaments. While there are well established disciplines in biology dedicated to studying isolated proteins – their structure (Structural Biology) and behaviors (Biochemistry) – it is much less clear how to investigate, or even just describe, the structure and behaviors of collections of cytoskeletal filaments. One approach is to use methodologies from Mechanics and Soft Condensed Matter Physics, which have been phenomenally successful in the domains where they have been traditionally applied. From this perspective, collections of cytoskeletal filaments are viewed as materials, albeit very complex, `active' materials, composed of molecules which use chemical energy to perform mechanical work. A major challenge is to relate these material level properties to the behaviors of the molecular constituents. Here we discuss this materials perspective and review recent work bridging molecular and network scale properties of the cytoskeleton, focusing on the organization of microtubules by dynein as an illustrative example.




Actively crosslinked microtubule networks: mechanics, dynamics and filament sliding
S. Fürthauer, B. Lemma, P. Foster, S. Ems-McClung, C. Walczak, Z. Dogic, D. Needleman, M. Shelley
arXiv, (2018).

Abstract: Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and heavily crosslinked. Relating their large-scale dynamics to properties of their constituents remains an unsolved problem. Here we study an in vitro system made from microtubules and XCTK2 kinesin motors, which forms an aligned and active gel. Using photobleaching we demonstrate that the gel's aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local polarity. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using the microtubule-microtubule coupling, and force-velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain-rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.




The free surface of a colloidal chiral fluid: waves and instabilities from odd stress and Hall viscosity
V. Soni, E. Bililign, S. Magkiriadou, S. Sacanna, D. Bartolo, M. J. Shelley, and W. T. M. Irvine
arXiv (2018).

Abstract: In simple fluids, such as water, invariance under parity and time-reversal symmetry imposes that the rotation of constituent "atoms" are determined by the flow and that viscous stresses damp motion. Activation of the rotational degrees of freedom of a fluid by spinning its atomic building blocks breaks these constraints and has thus been the subject of fundamental theoretical interest across classical and quantum fluids [1–12]. However, the creation of a model liquid which isolates chiral hydrodynamic phenomena has remained experimentally elusive. Here we report the creation of a cohesive two-dimensional chiral liquid consisting of millions of spinning colloidal magnets and study its flows. We find that dissipative viscous edge pumping is a key and general mechanism of chiral hydrodynamics, driving uni-directional surface waves and instabilities, with no counterpart in conventional fluids. Spectral measurements of the chiral surface dynamics reveal the presence of Hall viscosity, an experimentally long sought property of chiral fluids [8, 13–15]. Precise measurements and comparison with theory demonstrate excellent agreement with a minimal but complete chiral hydrodynamic model, paving the way for the exploration of chiral hydrodynamics in experiment




Nonlinear concentration patterns and bands in autochemotactic suspensions
E. Lushi, R. Goldstein, M. Shelley
Physical Review E, 98 (2018).

Abstract: In suspensions of microorganisms, pattern formation can arise from the interplay of chemotaxis and the fluid flows collectively generated by the organisms themselves. Here we investigate the resulting pattern formation in square and elongated domains in the context of two distinct models of locomotion in which the chemoattractant dynamics is fully coupled to the fluid flows and swimmer motion. Analyses for both models reveal an aggregative instability due to chemotaxis, independent of swimmer shape and type, and a hydrodynamic instability for "pusher" swimmers. We discuss the similarities and differences between the models. Simulations reveal a critical length scale of the swimmer aggregates and this feature can be utilized to stabilize swimmer concentration patterns into quasi-one-dimensional bands by varying the domain size. These concentration bands transition to traveling pulses under an external chemoattractant gradient, as observed in experiments with chemotactic bacteria.




Directed migration of microscale swimmers by an array of shaped obstacles: modeling and shape optimization
J. Tong, M. J. Shelley
SIAM Journal of Applied Mathematics, 78 2370-2392 (2018).

Abstract: Achieving macroscopic directed migration of microscale swimmers in a fluid is an important step towards utilizing their autonomous motion. It has been experimentally shown that directed motion can be induced, without any external fields, by certain geometrically asymmetric obstacles due to interaction between their boundaries and the swimmers. In this paper, we propose a kinetic-type model to study swimming and directional migration of microscale bimetallic rods in a periodic array of posts with noncircular cross-sections. Both rod position and orientation are taken into account; rod trapping and release on the post boundaries are modeled by empirically characterizing curvature and orientational dependence of the boundary absorption and desorption. Intensity of the directed rod migration, which we call the normalized net flux, is then defined and computed given the geometry of the post array. We numerically study the effect of post spacings on the flux; we also apply shape optimization to find better post shapes that can induce stronger flux. Inspired by preliminary numerical results on two candidate posts, we perform an approximate analysis on a simplified model to show the key geometric features that a good post should have. Based on this, three new candidate shapes are proposed which give rise to large fluxes. This approach provides an effective tool and guidance for experimentally designing new devices that induce strong directed migration of microscale swimmers.




Extensile motor activity drives coherent motions in a model of interphase chromatin
D. Saintillan, M. J. Shelley, and A. Zidovska
Proc. of the National Academy of Sciences (PNAS), 115 11442–11447 (2018).

Abstract: The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin–the functional form of DNA in cells–fills the nucleus in its uncondensed polymeric form. Recent in vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of micrometers and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a coarse-grained active polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors that drive fluid flows by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing longranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.




Universal image systems for non-periodic and periodic Stokes flows above a no-slip wall
W. Yan, M. Shelley
Journal of Computational Physics, 375 263-270 (2018).

Abstract: It is well-known that by placing judiciously chosen image point forces and doublets to the Stokeslet above a flat wall, the no-slip boundary condition can be conveniently imposed on the wall Blake (1971) [8]. However, to further impose periodic boundary conditions on directions parallel to the wall usually involves tedious derivations because single or double periodicity in Stokes flow may require the periodic unit to have no net force, which is not satisfied by the well-known image system. In this work we present a force-neutral image system. This neutrality allows us to represent the Stokes image system in a universal formulation for non-periodic, singly periodic and doubly periodic geometries. This formulation enables the black-box style usage of fast kernel summation methods. We demonstrate the efficiency and accuracy of this new image method with the periodic kernel independent fast multipole method in both non-periodic and periodic geometries. We then extend this new image system to other widely used Stokes fundamental solutions, including the Laplacian of the Stokeslet and the Rotne–Prager–Yamakawa tensor.




Flexibly imposing periodicity in kernel independent FMM: A multipole-to-local operator approach
W. Yan and M. Shelley
Journal of Comp. Physics, 355 214-232 (2018).

Abstract: An important but missing component in the application of the kernel independent fast multipole method (KIFMM) is the capability for flexibly and efficiently imposing singly, doubly, and triply periodic boundary conditions. In most popular packages such periodicities are imposed with the hierarchical repetition of periodic boxes, which may give an incorrect answer due to the conditional convergence of some kernel sums. Here we present an efficient method to properly impose periodic boundary conditions using a near-far splitting scheme. The near-field contribution is directly calculated with the KIFMM method, while the far-field contribution is calculated with a multipole-to-local (M2L) operator which is independent of the source and target point distribution. The M2L operator is constructed with the far-field portion of the kernel function to generate the far-field contribution with the downward equivalent source points in KIFMM. This method guarantees the sum of the near-field & far-field converge pointwise to results satisfying periodicity and compatibility conditions. The computational cost of the far-field calculation observes the same O(N) complexity as FMM and is designed to be small by reusing the data computed by KIFMM for the near-field. The far-field calculations require no additional control parameters, and observes the same theoretical error bound as KIFMM. We present accuracy and timing test results for the Laplace kernel in singly periodic domains and the Stokes velocity kernel in doubly and triply periodic domains.




Equilibrium Shapes and Their Stability for Liquid Films in Fast Flows
L. Ganedi, A. U. Oza, M. Shelley, and L. Ristroph
Phys. Rev. Lett., 121 (2018).



Abstract: We study how a suspended liquid film is deformed by an external flow en route to forming a bubble through experiments and a model. We identify a family of nonminimal but stable equilibrium shapes for flow speeds up to a critical value beyond which the film inflates unstably, and the model accounts for the observed nonlinear deformations and forces. A saddle-node or fold bifurcation in the solution diagram suggests that bubble formation at high speeds results from the loss of equilibrium and at low speeds from the loss of stability for overly inflated shapes.




Bistability in the rotational motion of rigid and flexible flyers
Y. Huang, L. Ristroph, M. Luhar and E. Kanso
J. Fluid Mech., 849 1043-1067 (2018).

Abstract: We explore the rotational stability of hovering flight in an idealized two-dimensional model. Our model is motivated by an experimental pyramid-shaped object (Weathers et al., J. Fluid Mech, vol. 650, 2010, pp. 415–425; Liu et al., Phys. Rev. Lett., vol. 108, 2012, 068103) and a computational ^ -shaped analogue (Huang et al., Phys. Fluids, vol. 27 (6), 2015, 061706; Huang et al., J. Fluid Mech., vol. 804, 2016, pp. 531–549) hovering passively in oscillating airflows; both systems have been shown to maintain rotational balance during free flight. Here, we attach the ^ -shaped flyer at its apex in oscillating flow, allowing it to rotate freely akin to a pendulum. We use computational vortex sheet methods and we develop a quasi-steady point-force model to analyse the rotational dynamics of the flyer. We find that the flyer exhibits stable concave-down (^) and concave-up (v) behaviour. Importantly, the down and up configurations are bistable and co-exist for a range of background flow properties. We explain the aerodynamic origin of this bistability and compare it to the inertia-induced stability of an inverted pendulum oscillating at its base. We then allow the flyer to flap passively by introducing a rotational spring at its apex. For stiff springs, flexibility diminishes upward stability but as stiffness decreases, a new transition to upward stability is induced by flapping. We conclude by commenting on the implications of these findings for biological and man-made aircraft.




Measuring and modeling polymer concentration profiles near spindle boundaries argues that spindle microtubules regulate their own nucleation
B. Kaye, O. Stiehl, P. J. Foster, M. J. Shelley, D. J. Needleman, and S. Fürthauer
New Journal of Physics, 838 (2018).

Abstract: Spindles are self-organized microtubule-based structures that segregate chromosomes during cell division. The mass of the spindle is controlled by the balance between microtubule turnover and nucleation. The mechanisms that control the spatial regulation of microtubule nucleation remain poorly understood. While previous work found that microtubule nucleators bind to pre-existing microtubules in the spindle, it is still unclear whether this binding regulates the activity of those nucleators. Here we use a combination of experiments and mathematical modeling to investigate this issue. We measured the concentration of microtubules and soluble tubulin in and around the spindle. We found a very sharp decay in the concentration of microtubules at the spindle interface. This is inconsistent with a model in which the activity of nucleators is independent of their association with microtubules but consistent with a model in which microtubule nucleators are only active when bound to pre-existing microtubules. This argues that the activity of microtubule nucleators is greatly enhanced when bound to pre-existing microtubules. Thus, microtubule nucleators are both localized and activated by the microtubules they generate.




Self-sculpting of a dissolvable body due to gravitational convection
M.S.D. Wykes, J.M. Huang, G.A. Hajjar and L. Ristroph
Phys. Rev. Fluids, 3 (2018).

Abstract: Natural sculpting processes such as erosion or dissolution often yield universal shapes that bear no imprint or memory of the initial conditions. Here we conduct laboratory experiments aimed at assessing the shape dynamics and role of memory for the simple case of a dissolvable boundary immersed in a fluid. Though no external flow is imposed, dissolution and consequent density differences lead to gravitational convective flows that in turn strongly affect local dissolving rates and shape changes, and we identify two distinct behaviors. A flat boundary dissolving from its lower surface tends to retain its overall shape (an example of near perfect memory) while bearing small-scale pits that reflect complex near-body flows. A boundary dissolving from its upper surface tends to erase its initial shape and form an upward spike structure that sharpens indefinitely. We propose an explanation for these different outcomes based on observations of the coupled shape dynamics, concentration fields, and flows.




Sculpting with flow
L. Ristroph
Journal of Fluid Mechanics, 838 1-4 (2018).

Abstract: Flowing air and water are persistent sculptors, gradually working stone, clay, sand and ice into landforms and landscapes. The evolution of shape results from a complex fluid-solid coupling that tends to produce stereotyped forms, and this morphology offers important clues to the history of a landscape and its development. Claudin et al. (J. Fluid Mech., vol. 832, 2017, R2) shed light on how we might read the rippled and scalloped patterns written into dissolving or melting solid surfaces by a flowing fluid. By better understanding the genesis of these patterns, we may explain why they appear in different natural settings, such as the walls of mineral caves dissolving in flowing water, ice caves in wind, and melting icebergs.





Bistability in the synchronization of actuated microfilaments
H. Guo, L. Fauci, M. Shelley, and E. Kanso
Journal of Fluid Mechanics, 836 304-323 (2018).

Abstract: Cilia and flagella are essential building blocks for biological fluid transport and locomotion at the micrometre scale. They often beat in synchrony and may transition between different synchronization modes in the same cell type. Here, we investigate the behaviour of elastic microfilaments, protruding from a surface and driven at their base by a configuration-dependent torque. We consider full hydrodynamic interactions among and within filaments and no slip at the surface. Isolated filaments exhibit periodic deformations, with increasing waviness and frequency as the magnitude of the driving torque increases. Two nearby but independently driven filaments synchronize their beating in-phase or anti-phase. This synchrony arises autonomously via the interplay between hydrodynamic coupling and filament elasticity. Importantly, in-phase and anti-phase synchronization modes are bistable and coexist for a range of driving torques and separation distances. These findings are consistent with experimental observations of in-phase and anti-phase synchronization in pairs of cilia and flagella and could have important implications on understanding the biophysical mechanisms underlying transitions between multiple synchronization modes.




Activity-induced instability of phonons in 1D microfluidic crystals
A. C. H. Tsang, M. J. Shelley, and E. Kanso
Soft Matter, 14 945 (2018).

Abstract: One-dimensional crystals of passively-driven particles in microfluidic channels exhibit collective vibrational modes reminiscent of acoustic ‘phonons’. These phonons are induced by the long-range hydrodynamic interactions among the particles and are neutrally stable at the linear level. Here, we analyze the effect of particle activity – self-propulsion – on the emergence and stability of these phonons. We show that the direction of wave propagation in active crystals is sensitive to the intensity of the background flow. We also show that activity couples, at the linear level, transverse waves to the particles’ rotational motion, inducing a new mode of instability that persists in the limit of large background flow, or, equivalently, vanishingly small activity. We then report a new phenomenon of phonons switching back and forth between two adjacent crystals in both passively-driven and active systems, similar in nature to the wave switching observed in quantum mechanics, optical communication, and density stratified fluids. These findings could have implications for the design of commercial microfluidic systems and the self-assembly of passive and active micro-particles into one-dimensional structures.




Connecting macroscopic dynamics with microscopic properties in active microtubule network contraction
P. J. Foster, W. Yan, S. Fürthauer, M. J. Shelley, and D. J. Needleman
New Journal of Physics, 19 125011 (2017).

Abstract: The cellular cytoskeleton is an active material, driven out of equilibrium by molecular motor proteins. It is not understood how the collective behaviors of cytoskeletal networks emerge from the properties of the network’s constituent motor proteins and filaments. Here we present experimental results on networks of stabilized microtubules in Xenopus oocyte extracts, which undergo spontaneous bulk contraction driven by the motor protein dynein, and investigate the effects of varying the initial microtubule density and length distribution.Wefind that networks contract to a similar final density, irrespective of the length of microtubules or their initial density, but that the contraction timescale varies with the average microtubule length. To gain insight into why this microscopic property influences the macroscopic network contraction time, we developed simulations where microtubules and motors are explicitly represented. The simulations qualitatively recapitulate the variation of contraction timescale with microtubule length, and allowed stress contributions from different sources to be estimated and decoupled.





Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid
T. Gao, M.D. Betterton, A. Jhang, and M. J. Shelley
Physical Review Fluids, 2 093302 (2017).

Abstract: We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile “extensor” particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several experimental systems, such as recently studied tripartite rods that create extensile flows by consuming a chemical fuel. We first describe the system through a Doi-Onsager kinetic theory based on microscopic modeling. This theory captures the active stresses produced by the particles that can drive hydrodynamic instabilities, as well as the steric interactions of rodlike particles that lead to nematic alignment. This active nematic system yields complex flows and disclination defect dynamics very similar to phenomenological Landau–deGennes Q-tensor theories for active nematic fluids, as well as by more complex Doi-Onsager theories for polar microtubule–motor-protein systems.We apply the quasiequilibrium Bingham closure, used to study suspensions of passive microscopic rods, to develop a nonstandard Q-tensor theory. We demonstrate through simulation that this BQ-tensor theory gives an excellent analytical and statistical accounting of the suspension’s complex dynamics, at a far reduced computational cost. Finally, we apply the BQ-tensor model to study the dynamics of extensor suspensions in circular and biconcave domains. In circular domains, we reproduce previous results for systems with weak nematic alignment, but for strong alignment we find unusual dynamics with activity-controlled defect production and absorption at the boundaries of the domain. In biconcave domains, a Fredericks-like transition occurs as the width of the neck connecting the two disks is varied.





C. elegans chromosomes connect to centrosomes by anchoring into the spindle network
S. Redemann, J. Baumgart, N. Lindow, M. Shelley, E. Nazockdast, A. Kratz, S. Prohaska, J. Brugués, S. Fürthauer, and T. Müller-Reichert
Nature Communications, 8 15288 (2017).

Abstract: The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.

Related:
"C. elegans chromosomes connect to centrosomes by anchoring into the spindle network" BioRxiv , 060855 (2016).




Cytoplasmic flows as signatures for the mechanics of mitotic positioning
E. Nazockdasta, A. Rahimian, D. Needleman, and M. Shelley
Molecular Biology of the Cell, 28 3261-3270 (2017).

Abstract: The proper positioning of mitotic spindle in the single-cell Caenorhabditis elegans embryo is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated astral microtubules (MTs). Pronuclear migration produces global cytoplasmic flows that couple the mechanics of all MTs, the PNC, and the cell periphery with each other through their hydrodynamic interactions (HIs). We present the first computational study that explicitly accounts for detailed HIs between the cytoskeletal components and demonstrate the key consequences of HIs for the mechanics of pronuclear migration. First, we show that, because of HIs between the MTs, the cytoplasm-filled astral MTs behave like a porous medium, with its permeability decreasing with increasing the number of MTs. We then directly study the dynamics of PNC migration under various force-transduction models, including the pushing or pulling of MTs at the cortex and the pulling of MTs by cytoplasmically bound force generators. Although achieving proper position and orientation on reasonable time scales does not uniquely choose a model, we find that each model produces a different signature in its induced cytoplasmic flow. We suggest that cytoplasmic flows can be used to differentiate between mechanisms.





A computational model of the flight dynamics and aerodynamics of a jellyfish-like flying machine
F. Fang, K. L. Ho, L. Ristroph, and M. J. Shelley
Journal of Fluid Mechanics, 819 621-655 (2017).

Abstract: We explore theoretically the aerodynamics of a recently fabricated jellyfish-like flying machine (Ristroph & Childress, J. R. Soc. Interface, vol. 11 (92), 2014, 20130992). This experimental device achieves flight and hovering by opening and closing opposing sets of wings. It displays orientational or postural flight stability without additional control surfaces or feedback control. Our model ‘machine’ consists of two mirror-symmetric massless flapping wings connected to a volumeless body with mass and moment of inertia. A vortex sheet shedding and wake model is used for the flow simulation. Use of the fast multipole method allows us to simulate for long times and resolve complex wakes. We use our model to explore the design parameters that maintain body hovering and ascent, and investigate the performance of steady ascent states. We find that ascent speed and efficiency increase as the wings are brought closer, due to a mirror-image ‘ground-effect’ between the wings. Steady ascent is approached exponentially in time, which suggests a linear relationship between the aerodynamic force and ascent speed. We investigate the orientational stability of hovering and ascent states by examining the flyer’s free response to perturbation from a transitory external torque. Our results show that bottom-heavy flyers (centre of mass below the geometric centre) are capable of recovering from large tilts, whereas the orientation of the top-heavy flyers diverges. These results are consistent with the experimental observations in Ristroph & Childress (J. R. Soc. Interface, vol. 11 (92), 2014, 20130992), and shed light upon future designs of flapping-wing micro aerial vehicles that use jet-based mechanisms.




Footprints of a flapping wing
J. Zhang
Journal of Fluid Mechanics, 818 1-4 (2017).

Abstract: Birds have to flap their wings to generate the needed thrust force, which powers them through the air. But how exactly do flapping wings create such force, and at what amplitude and frequency should they operate? These questions have been asked by many researchers. It turns out that much of the secret is hidden in the wake left behind the flapping wing. Exemplified by the study of Andersen et al. (J. Fluid Mech., vol. 812, 2017, R4), close examination of the flow pattern behind a flapping wing will inform us whether the wing is towed by an external force or able to generate a net thrust force by itself. Such studies are much like looking at the footprints of terrestrial animals as we infer their size and weight, figuring out their walking and running gaits. A map that displays the collection of flow patterns after a flapping wing, using flapping frequency and amplitude as the coordinates, offers a full picture of its flying ‘gaits’.




Guiding microscale swimmers using teardrop-shaped posts
M. S. D. Wykes, X. Zhong, J. Tong, T. Adachi, Y. Liu, L. Ristroph, M. D. Ward, M. J. Shelley, and J. Zhang
Soft Matter, 13 4681 (2017).

Abstract: The swimming direction of biological or artificial microscale swimmers tends to be randomised over long time-scales by thermal fluctuations. Bacteria use various strategies to bias swimming behaviour and achieve directed motion against a flow, maintain alignment with gravity or travel up a chemical gradient. Herein, we explore a purely geometric means of biasing the motion of artificial nanorod swimmers. These artificial swimmers are bimetallic rods, powered by a chemical fuel, which swim on a substrate printed with teardrop-shaped posts. The artificial swimmers are hydrodynamically attracted to the posts, swimming alongside the post perimeter for long times before leaving. The rods experience a higher rate of departure from the higher curvature end of the teardrop shape, thereby introducing a bias into their motion. This bias increases with swimming speed and can be translated into a macroscopic directional motion over long times by using arrays of teardrop-shaped posts aligned along a single direction. This method provides a protocol for concentrating swimmers, sorting swimmers according to different speeds, and could enable artificial swimmers to transport cargo to desired locations.




Fast accurate methods for simulating fiber suspensions applied to cellular mechanics
E. Nazockdast, A. Rahimian, D. Zorin, and M. Shelley
Journal of Computational Physics, 329 173-209 (2017).

Abstract: We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers...




The effect of microtubule-cytoplasm interactions on pronuclear migration
E. Nazockdast, A. Rahimian, D. Needleman, and M. Shelley
ArXiv (2017).

Abstract: The proper positioning of the mitotic spindle is crucial for asymmetric cell division and generating cell diversity during development. Proper position in the single-cell embryo of Caenorhabditis elegans is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated centrosomal arrays of microtubules (MTs). We present here the first systematic theoretical study of how these O(1000) centrosomal microtubules (MTs) interact through the immersing cytoplasm, the cell periphery and PNC, and with each other, to achieve proper position. This study is made possible through our development of a highly efficient and parallelized computational framework that accounts explicitly for long-ranged hydrodynamic interactions (HIs) between the MTs, while also capturing their flexibility, dynamic instability, and interactions with molecular motors and boundaries. First, we show through direct simulation that previous estimates of the PNC drag coefficient, based on either ignoring or partially including HIs, lead to misprediction of the active forces and time-scales of migration. We then directly study the dynamics of PNC migration under various force-transduction models, including the pushing or pulling of MTs at the cortex, and the pulling of MTs by cytoplasmically-bound force generators. While achieving proper position and orientation on physiologically reasonable time-scales does not uniquely choose a model, we find that each model produces a different signature in its induced cytoplasmic flow and MT conformations. We suggest then that cytoplasmic flows and MT conformations can be used to differentiate between mechanisms and to determine their contribution to the migration process.




Flow interactions lead to orderly formations of flapping wings in forward flight
S. Ramananarivo, F. Fang, A. Oza, J. Zhang, and L. Ristroph
Physical Review Fluids, 1 071201(R) (2016).

Abstract: Classic models of fish schools and flying formations of birds are built on the hypothesis that the preferred locations of an individual are determined by the flow left by its upstream neighbor. Lighthill posited that arrangements may in fact emerge passively from hydro- or aerodynamic interactions, drawing an analogy to the formation of crystals by intermolecular forces. Here, we carry out physical experiments aimed at testing the Lighthill conjecture and find that self-propelled flapping wings spontaneously assume one of multiple arrangements due to flow interactions. Wings in a tandem pair select the same forward speed, which tends to be faster than a single wing, while maintaining a separation distance that is an integer multiple of the wavelength traced out by each body. When perturbed, these locomotors robustly return to the same arrangement, and direct hydrodynamic force measurements reveal springlike restoring forces that maintain group cohesion. We also use these data to construct an interaction potential, showing how the observed positions of the follower correspond to stable wells in an energy landscape. Flow visualization and vortex-based theoretical models reveal coherent interactions in which the follower surfs on the periodic wake left by the leader. These results indicate that, for the high-Reynolds-number flows characteristic of schools and flocks, collective locomotion at enhanced speed and in orderly formations can emerge from flow interactions alone. If true for larger groups, then the view of collectives as ordered states of matter may prove to be a useful analogy.




Forces positioning the mitotic spindle in the cell; Theories, and now experiments
H. Wu, E. Nazockdast, M. Shelley, and D. Needleman
BioEssays, 1600212 (2016).

Abstract: The position of the spindle determines the position of the cleavage plane, and is thus crucial for cell division. Although spindle positioning has been extensively studied, the underlying forces ultimately responsible for moving the spindle remain poorly understood. A recent pioneering study by Garzon-Coral et al. uses magnetic tweezers to perform the first direct measurements of the forces involved in positioning the mitotic spindle. Combining this with molecular perturbations and geometrical effects, they use their data to argue that the forces that keep the spindle in its proper position for cell division arise from astral microtubules growing and pushing against the cell's cortex. Here, we review these ground-breaking experiments, the various biomechanical models for spindle positioning that they seek to differentiate, and discuss new questions raised by these measurements.





Dynamic self-assembly of microscale rotors and swimmers
M.S.D. Wykes, J. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward, J. Zhang, and M.J. Shelley
Soft Matter 12, 4584-4589 (2016).

Abstract: Biological systems often involve the self-assembly of basic components into complex and functioning structures. Artificial systems that mimic such processes can provide a well-controlled setting to explore the principles involved and also synthesize useful micromachines. Our experiments show that immotile, but active, components self-assemble into two types of structure that exhibit the fundamental forms of motility: translation and rotation. Specifically, micron-scale metallic rods are designed to induce extensile surface flows in the presence of a chemical fuel; these rods interact with each other and pair up to form either a swimmer or a rotor. Such pairs can transition reversibly between these two configurations, leading to kinetics reminiscent of bacterial run-and-tumble motion.







Linear drag law for high-Reynolds-number flow past an oscillating body
N. Agre, S. Childress, J. Zhang and L. Ristroph
Physical Review Fluids 1, 033202 (2016).

Abstract: An object immersed in a fast flow typically experiences fluid forces that increase with the square of speed. Here we explore how this high-Reynolds-number force-speed relationship is affected by unsteady motions of a body. Experiments on disks that are driven to oscillate while progressing through air reveal two distinct regimes: a conventional quadratic relationship for slow oscillations and an anomalous scaling for fast flapping in which the time-averaged drag increases linearly with flow speed. In the linear regime, flow visualization shows that a pair of counterrotating vortices is shed with each oscillation and a model that views a train of such dipoles as a momentum jet reproduces the linearity. We also show that appropriate scaling variables collapse the experimental data from both regimes and for different oscillatory motions into a single drag-speed relationship. These results could provide insight into the aerodynamic resistance incurred by oscillating wings in flight and they suggest that vibrations can be an effective means to actively control the drag on an object.



Related:
"Comparative flow visualization for steady and unsteady motions of a disk through a fluid" AIP Physics of Fluids 27, 091103 (2015).
"Potrait of a flow in three colors" APS Division of Fluid Dynamics 67th annual meeting (2014): Gallery of Fluid Motion





Actomyosin-driven left-right asymmetry: from molecular torques to chiral self organization
S.R. Naganathan, T.C. Middelkoop, S. Fürthauer, and S.W. Grill
Current Opinion in Cell Biology, 38:24-30, (2016).

Abstract: Chirality or mirror asymmetry is a common theme in biology found in organismal body plans, tissue patterns and even in individual cells. In many cases the emergence of chirality is driven by actin cytoskeletal dynamics. Although it is well established that the actin cytoskeleton generates rotational forces at the molecular level, we are only beginning to understand how this can result in chiral behavior of the entire actin network in vivo. In this review, we will give an overview of actin driven chiralities across different length scales known until today. Moreover, we evaluate recent quantitative models demonstrating that chiral symmetry breaking of cells can be achieved by properly aligning molecular-scale torque generation processes in the actomyosin cytoskeleton.







Elastic fibers in flows
A. Lindner and M. Shelley
Fluid-structure interactions at low Reynolds numbers, Royal Society of Chemistry, (2016).

Abstract: A very common class of fluid-structure interaction problems involves the dynamics of flexible fibers immersed in a Stokesian fluid. In biology this arises in modeling the flagellae or cilia involved in micro-organismal locomotion and mucal transport, in determining the shape of biofilm streamers, and in understanding how biopolymers such as microtubules respond to the active coupling afforded by motor proteins. In engineering it arises in the paper processing industry, where wood pulp suspensions can show the abrupt appearance of normal stress differences, and in micro-fluidic engineering where flow control using flexible particles has lately been explored. Flow induced buckling of fibers is an important determinant on fiber transport in those flows, as well as for the fluid mechanical stresses that develop...





The dynamics of microtubule/motor-protein assemblies in biology and physics
M. Shelley
Annual Reviews of Fluid Mechanics 48, 487-506 (2016).

Abstract: Many important processes in the cell are mediated by stiff. microtubule polymers and the active motor proteins moving upon them. This includes the transport of subcellular structures (nuclei, chromosomes, organelles), and the self-assembly and positioning of the mitotic spindle. Very little is yet understood of these processes but they all present fascinating problems in fluid/structure interactions. Microtubules and motor proteins are also the building blocks of new "bio-synthetic" active suspensions driven by motor-protein activity. These reduced systems can probed, and modeled, more easily than the fully biological ones and show their own aspects of self-assembly and complex dynamics. I will review recent work modeling such systems as uid/structure interaction problems, and as multiscale complex fluids.





Active contraction of microtubule networks
P. J. Foster, S. Fürthauer, M. J. Shelley and D. J. Needleman
eLife 2015;10.7554/eLife.10837.

Abstract: Many cellular processes are driven by cytoskeletal assemblies. It remains unclear how cytoskeletal filaments and motor proteins organize into cellular scale structures and how molecular properties of cytoskeletal components affect the large scale behaviors of these systems. Here we investigate the self-organization of stabilized microtubules in Xenopus oocyte extracts and find that they can form macroscopic networks that spontaneously contract. We propose that these contractions are driven by the clustering of microtubule minus ends by dynein. Based on this idea, we construct an active fluid theory of network contractions which predicts a dependence of the timescale of contraction on initial network geometry, a development of density inhomogeneities during contraction, a constant final network density, and a strong influence of dynein inhibition on the rate of contraction, all in quantitative agreement with experiments. These results demonstrate that the motor-driven clustering of filament ends is a generic mechanism leading to contraction.






Related:
"Cytoskeleton: Large-scale microtubule networks contract quite well." J.M. Belmonte & F. Nédélec. eLife 2016;5:e14076
"Cell division: Microtubules, assemble!." Harvard School of Engineering and Applied Sciences. ScienceDaily, 28 January 2016.






Enhanced heat transport in partitioned thermal convection
Y. Bao, J. Chen, B.F. Liu, Z.S. She, J. Zhang, and Q. Zhou
Journal of Fluid Mechanics, 784 R5-1 (2015).

Abstract: Enhancement of heat transport across a fluid layer is of fundamental interest as well as great technological importance. For decades, Rayleigh-Bénard convection has been a paradigm for the study of convective heat transport, and how to improve its overall heat-transfer efficiency is still an open question. Here, we report an experimental and numerical study that reveals a novel mechanism that leads to much enhanced heat transport. When vertical partitions are inserted into a convection cell with thin gaps left open between the partition walls and the cooling/heating plates, it is found that the convective flow becomes self-organized and more coherent, leading to an unprecedented heat-transport enhancement. In particular, our experiments show that with six partition walls inserted, the heat flux can be increased by approximately 30 %. Numerical simulations show a remarkable heat-flux enhancement of up to 2.3 times (with 28 partition walls) that without any partitions.




Ratcheting fluid with geometric anisotropy
B. Thiria and J. Zhang
Applied Physics Letters, 106 054106 (2015).

Abstract: We investigate a mechanism that effectively transports fluids using vibrational motion imposed onto fluid boundary with anisotropy. In our experiment, two asymmetric, sawtooth-like structures are placed facing each other and form a corrugated fluid channel. This channel is then forced to open and close periodically. Under reciprocal motion, fluid fills in the gap during the expansion phase of the channel and is then forced out during contraction. Since the fluid experiences different impedances when flowing in different directions, the stagnation point that separates flows of two directions changes within each driving period. As a result, fluid is transported unidirectionally. This ratcheting effect of fluid is demonstrated through our measurements and its working principle discussed in some detail.




Multiscale modeling and simulation of microtubule motor-protein assemblies
T. Gao, R. Blackwell, M. Glaser, D. Betterton, and M. Shelley
Physical Review E, 92 062709 (2015).

Abstract: Microtubules and motor proteins self-organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by adenosine triphosphate?consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield such larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation.








Hydrodynamic schooling of flapping swimmers
A. D. Becker, H. Masoud, J. W. Newbolt, M. Shelley and L. Ristroph
Nature Communications 6, 8514 (2015).

Abstract: Fish schools and bird flocks are fascinating examples of collective behaviours in which many individuals generate and interact with complex flows. Motivated by animal groups on the move, here we explore how the locomotion of many bodies emerges from their flow-mediated interactions. Through experiments and simulations of arrays of flapping wings that propel within a collective wake, we discover distinct modes characterized by the group swimming speed and the spatial phase shift between trajectories of neighbouring wings. For identical flapping motions, slow and fast modes coexist and correspond to constructive and destructive wing-wake interactions. Simulations show that swimming in a group can enhance speed and save power, and we capture the key phenomena in a mathematical model based on memory or the storage and recollection of information in the flow field. These results also show that fluid dynamic interactions alone are sufficient to generate coherent collective locomotion, and thus might suggest new ways to characterize the role of flows in animal groups.





Lateral line layout correlates with the differential hydrodynamic pressure on swimming fish
L. Ristroph, J. C. Liao and J. Zhang
Physical Review Letters 114, 018102 (2015).

Abstract: The lateral line of fish includes the canal subsystem that detects hydrodynamic pressure gradients and is thought to be important in swimming behaviors such as rheotaxis and prey tracking. Here, we explore the hypothesis that this sensory system is concentrated at locations where changes in pressure are greatest during motion through water. Using high-fidelity models of rainbow trout, we mimic the flows encountered during swimming while measuring pressure with fine spatial and temporal resolution. The variations in pressure for perturbations in body orientation and for disturbances to the incoming stream are seen to correlate with the sensory network. These findings support a view of the lateral line as a "hydrodynamic antenna" that is configured to retrieve flow signals and also suggest a physical explanation for the nearly universal sensory layout across diverse species.





Shape dynamics and scaling laws for a body dissolving in a fluid flow
J. M. Huang, M. N. J. Moore and L. Ristroph
Journal of Fluid Mechanics 765, R3 (2015).

Abstract: While fluid flows are known to promote dissolution of materials, such processes are poorly understood due to the coupled dynamics of the flow and the receding surface. We study this moving boundary problem through experiments in which hard candy bodies dissolve in laminar high-speed water flows. We find that different initial geometries are sculpted into a similar terminal form before ultimately vanishing, suggesting convergence to a stable shape-flow state. A model linking the flow and solute concentration shows how uniform boundary-layer thickness leads to uniform dissolution, allowing us to obtain an analytical expression for the terminal geometry. Newly derived scaling laws predict that the dissolution rate increases with the square root of the flow speed and that the body volume vanishes quadratically in time, both of which are confirmed by experimental measurements.





Multiscale polar theory of Microtubule and Motor-Protein Assemblies
T. Gao, R. Blackwell, M. Glaser, M. Betterton, and M. Shelley
Physical Review Letters, 114 048101 (2015).

Abstract: Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new ?bioactive? liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics. It is not yet well understood how microscopic activity, which involves polarity dependent interactions between motor proteins and microtubules, yields such larger-scale dynamical structures. In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by cross-linking motors allow us to study microscopic organization and stresses. Polarity sorting and crosslink relaxation emerge as two polar-specific sources of active destabilizing stress. On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses. The results connect local polar structure to flow structures and defect dynamics.





Transport and buckling dynamics of an elastic fiber in in a viscous cellular flow
N. Quennouz, M. Shelley, O. du Roure, and A. Lindner
Journal of Fluid Mechanics, 769 387-402 (2015).

Abstract: We study, using both experiment and theory, the coupling of transport and shape dynamics for elastomeric fibres moving through an inhomogeneous flow. The cellular flow, created electromagnetically in our experiment, comprises many identical cells of counter-rotating vortices, with a global flow geometry characterized by a backbone of stable and unstable manifolds connecting hyperbolic stagnation points. Our mathematical model is based upon slender-body theory for the Stokes equations, with the fibres modelled as inextensible elastica. Above a certain threshold of the control parameter, the elasto-viscous number, transport of fibres is mediated by their episodic buckling by compressive stagnation point flows, lending an effectively chaotic component to their dynamics. We use simulations of the model to construct phase diagrams of the fibre state (buckled or not) near stagnation points in terms of two variables that arise in characterizing the transport dynamics. We show that this reduced statistical description quantitatively captures our experimental observations. By carefully reproducing the experimental protocols and time scales of observation within our umerical simulations, we also quantitatively explain features of the measured buckling probability curve as a function of the effective flow forcing. Finally, we show within both experiment and simulation the existence of short and long time scales in the evolution of fibre conformation.





Theory of Active Suspensions
D. Saintillan and M. Shelley
Complex Fluids in Biological Systems, S. Spagnolie (ed.), Springer-Verlag (2015).

Abstract: Active suspensions, of which a bath of swimming microorganisms is a paradigmatic example, denote large collections of individual particles or macromolecules capable of converting fuel into mechanical work and microstructural stresses. Such systems, which have excited much research in the last decade, exhibit complex dynamical behaviors such as large-scale correlated motions and pattern formation due to hydrodynamic interactions. In this chapter, we summarize efforts to model these systems using particle simulations and continuum kinetic theories. After reviewing results from experiments and simulations, we present a general kinetic model for a suspension of self-propelled rod-like particles and discuss its stability and nonlinear dynamics. We then address extensions of this model that capture the effect of steric interactions in concentrated systems, the impact of confinement and interactions with boundaries, and the effect of the suspending medium rheology. Finally, we discuss new active systems such as those that involve the interactions of biopolymers with immersed motor proteins, and surface-bound suspensions of chemically-powered particles.





Stable hovering of a jellyfish-like flying machine
L. Ristroph and S. Childress
Journal of the Royal Society Interface 11, 20130992 (2014).

Abstract: Ornithopters, or flapping-wing aircraft, offer an alternative to helicopters in achieving manoeuvrability at small scales, although stabilizing such aerial vehicles remains a key challenge. Here, we present a hovering machine that achieves self-righting flight using flapping wings alone, without relying on additional aerodynamic surfaces and without feedback control. We design, construct and test-fly a prototype that opens and closes four wings, resembling the motions of swimming jellyfish more so than any insect or bird. Measurements of lift show the benefits of wing flexing and the importance of selecting a wing size appropriate to the motor. Furthermore, we use highspeed video and motion tracking to show that the body orientation is stable during ascending, forward and hovering flight modes. Our experimental measurements are used to inform an aerodynamic model of stability that reveals the importance of centre-of-mass location and the coupling of body translation and rotation. These results show the promise of flapping-flight strategies beyond those that directly mimic the wing motions of flying animals.

Related:
Patented design:
L. Ristroph, S. Childress. Flapping-wing device. U.S. Provisional Patent, No. 61/814,031 (April 19, 2013).
Some of the press coverage of this research:
New Scientist Tech, Four-winged robot flies like a jellyfish, Sandrine Ceurstemont, 25 Nov. 2013
The New York Times, With Math as Inspiration, a New Form of Flyer, James Gorman, Jan. 15, 2014
The Washington Post, Meet the flying machine that was inspired by a jellyfish, Max Ehrenfreund, Nov. 25, 2013
The Economist, Ornithopters - Aerial Jellyfish, Jan. 17, 2014
Nature, Robot jellyfish takes to the air, Philip Ball, 15 Jan. 2014
The Royal Society, News, Miniature machine glides through air like a jellyfish through water, News, 15 Jan. 2014
BBC News, Flying drone inspired by swimming jellyfish, 14 Jan. 2014
National Geographics Daily News, Tiny Drone Flies Like A... Jellyfish?, Jane J. Lee, Nov. 26, 2013
Nature World News, Researchers Create Robot that 'Flies' Like a Jellyfish, Nov. 25, 2013
The Japan Times, First jellyfish aircraft simple yet efficient, Jan. 19, 2014
Washington Square News, Courant Professors create Flying Robot, Nicole Del Mauro, Dec. 10, 2013
National Public Radio - The Two-Way, VIDEO: A Tiny Mechanical 'Jellyfish' That Flies, by Mark Memmott, Nov. 25, 2014
Science Daily, A new, flying jellyfish-like machine, Nov. 24, 2013





Collective Surfing of Chemically Active Particles
H. Masoud and M. J. Shelley
Physical Review Letters 112, 128304 (2014).

Abstract: We study theoretically the collective dynamics of immotile particles bound to a 2D surface atop a 3D fluid layer. These particles are chemically active and produce a chemical concentration field that creates surface-tension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. For a 3D diffusion-dominated concentration field and Stokesian fluid we show that the surface dynamics of active particle density can be determined using nonlocal 2D surface operators. Remarkably, we also show that for both deep or shallow fluid layers this surface dynamics reduces to the 2D Keller-Segel model for the collective chemotactic aggregation of slime mold colonies. Mathematical analysis has established that the Keller-Segel model can yield finite-time, finite-mass concentration singularities. We show that such singular behavior occurs in our finite-depth system, and study the associated 3D flow structures.





Hydrodynamic capture of microswimmers into sphere-bound orbits
D. Takagi, J. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang
Soft Matter 10, 1784-1789 (2014).

Abstract: Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles remains an important open problem. We show experimentally that chemically propelled micro-rods can be captured, with little decrease in their speed, into close orbits around solid  spheres resting on a horizontal plane. This short-range interaction is consistent with a model, based  on lubrication theory, of a force- and torque-free swimmer driven by a surface slip and moving near  a solid surface. This study reveals the crucial aspects of interactions of self-propelled particles with  passive objects, and brings into question the use of colloidal tracers as probes of active matter.





Self-similar Evolution of a Body eroding in a Fluid Flow
M. Moore, L. Ristroph, S. Childress, J. Zhang, and M. Shelley
Physics of Fluids 25, 116602 (2013).

Abstract: Erosion of solid material by flowing fluids plays an important role in shaping land-forms, and in this natural context is often dictated by processes of high complexity. Here, we examine the coupled evolution of solid shape and fluid flow within the idealized setting of a cylindrical body held against a fast, unidirectional flow, and eroding under the action of fluid shear stress. Experiments and simulations both show self-similar evolution of the body, with an emerging quasi-triangular geometry that is an attractor of the shape dynamics. Our fluid erosion model, based on Prandtl boundary layer theory, yields a scaling law that accurately predicts the body's vanishing rate. Further, a class of exact solutions provides a partial prediction for the body's terminal form as one with a leading surface of uniform shear stress. Our simulations show this predicted geometry to emerge robustly from a range of different initial conditions, and allow us to explore its local stability. The sharp, faceted features of the terminal geometry defy the intuition of erosion as a globally smoothing process.





On the Rotation of Porous Ellipsoids in Simple Shear Flows
H. Masoud, H. A. Stone, and M. J. Shelley
Journal of Fluid Mechanics 733, R6 (2013).

Abstract: We study theoretically the dynamics of porous ellipsoids rotating in simple shear flows. We use the Brinkman-Debye-Bueche (BDB) model to simulate flow within and through particles and solve the coupled Stokes-BDB equations to calculate the overall flow field and the rotation rate of porous ellipsoids. Our results show that the permeability has little effect on the rotational behaviour of particles, and that Jeffery's prediction of the angular velocity of impermeable ellipsoids in simple shear flows (Proc. R. Soc. Lond. A, vol. 102, 1922, pp. 161-179) remains an excellent approximation, if not an exact one, for porous ellipsoids. Employing an appropriate scaling, we also present approximate expressions for the torque exerted on ellipses and spheroids rotating in a quiescent fluid. Our findings can serve as the basis for developing a suspension theory for non-spherical porous particles, or for understanding the orientational diffusion of permeable ellipses and spheroids.





Active Suspensions and Their Nonlinear Models
D. Saintillan and M. Shelley
Comptes Rendes Physique 14, 497-517 (2013).

Abstract: Active suspensions, such as suspensions of self-propelled microorganisms and related synthetic microswimmers, are known to undergo complex dynamics and pattern formation as a result of hydrodynamic interactions. In this review, we summarize recent e fforts to model these systems using continuum  kinetic theories. We first derive a basic kinetic model for a suspension of self-propelled rodlike particles and discuss its stability and nonlinear dynamics. We then present extensions of this model to analyze the e ffective rheology of active suspensions in external flows, the eff ect of steric interactions in concentrated systems, and the dynamics of chemotactically responsive suspensions in chemical fields.





Instabilities and nonlinear dynamics of concentrated active suspensions
B. Ezhilan, M. J. Shelley, D. Saintillan
Physics of Fluids 25, 070607 (2013).

Abstract: Suspensions of active particles, such as motile microorganisms and artificial microswimmers, are known to undergo a transition to complex large-scale dynamics at high enough concentrations. While a number of models have demonstrated that hydrodynamic interactions can in some cases explain these dynamics, collective motion in experiments is typically observed at such high volume fractions that steric interactions between nearby swimmers are significant and cannot be neglected. This raises the question of the respective roles of steric vs hydrodynamic interactions in these dense systems, which we address in this paper using a continuum theory and numerical simulations...





Modeling and simulation of active suspensions containing large numbers of interacting micro-swimmers
Lushi E and Peskin CS
Computers and Structures 22, 239-248 (2013).

Abstract: We present a mathematical model and simulation method to compute the colonial dynamics of micro-swimmers that interact directly and through the fluid they are suspended in. The model uses the stress generated by each self-motile particle for long-range interactions and includes short-range steric effects between particles. The time-step computational cost is O(N logN + M), with N the total number of mesh points, and M the number of swimmers. This fast method enables us to efficiently simulate many thousands of interacting self-propelling particles in three dimensions and with background flows. We show examples of collective behavior in suspensions of "pusher" and "puller" micro-swimmers.





Optimization of chiral structures for micro-scale propulsion
E. Keaveny, S. Walker, and M. Shelley
Nanoletters 13, 531-537 (2013).

Abstract: Recent advances in micro- and nano-scale fabrication techniques allow for the construction of rigid, helically-shaped micro-swimmers that can be actuated using applied magnetic fields. These swimmers represent the first steps toward the development of micro-robots for targeted drug delivery and minimally invasive surgical procedures. To assess the performance of these devices and improve on their design, we perform shape optimization computations to determine swimmer geometries that maximize speed in the direction of a given applied magnetic torque. We directly assess aspects of swimmer shapes that have been developed in previous experimental studies, including helical propellers with elongated cross-sections, and attached payloads. From these optimizations, we identify key improvements to existing designs that result in swimming speeds that are 250 - 470% of their original values.





An actuated elastic sheet interacting with passive and active structures in a viscoelastic fluid
J. Chrispell, M. Shelley, L. Fauci
Physics of Fluids 25, 013103 (2013).

Abstract: We adapt the classic Taylor swimming sheet set-up to investigate both the transient and long-time dynamics of an actuated elastic sheet immersed in a viscoelastic fluid as it interacts with neighboring structures. While the preferred kinematics of the sheet are specied, the flexible sheet interacts with the surrounding fluid and other structures, and its realized kinematics emerges from this coupling. We use an immersed boundary framework to evolve the Oldroyd-B/Navier-Stokes equations and capture the spatial and temporal development of viscoelastic stresses and sheet shape. We compare the dynamics when the actuated sheet swims next to a free elastic membrane, with and without bending rigidity, and next to a xed wall. We demonstrate that the sheets can exploit the neighboring structures to enhance their swimming speed and efficiency, and also examine how this depends upon fluid viscoelasticity. When the neighboring structure is likewise an actuated elastic sheet, we investigate the viscoelastic dynamics of phase-locking.





Dispersion of Self-Propelled Rods Undergoing Fluctuation-Driven Flips
D. Takagi, A. Braunschweig, J. Zhang, and M. Shelley
Phys. Rev. Lett. 110, 038301 (2013).

Abstract: Synthetic microswimmers may someday perform medical and technological tasks, but predicting their motion and dispersion is challenging. Here we show that chemically propelled rods tend to move on a surface along large circles but curiously show stochastic changes in the sign of the orbit curvature. By accounting for fluctuation-driven flipping of slightly curved rods, we obtain analytical predictions for the ensemble behavior in good agreement with our experiments. This shows that minor defects in swimmer shape can yield major long-term effects on macroscopic dispersion.





Sculpting of an erodible body by flowing water
L. Ristroph, N. Moore, S. Childress, M. Shelley, and J. Zhang
PNAS 109, 19606 (2012).

Abstract: Erosion by flowing fluids carves striking landforms on Earth and also provides important clues to the past and present environments of other worlds. In these processes, solid boundaries both influence and are shaped by the surrounding fluid, but the emergence of morphology as a result of this interaction is not well understood. We study the coevolution of shape and flow in the context of erodible bodies molded from clay and immersed in a fast, unidirectional water flow. Although commonly viewed as a smoothing process, We find that erosion sculpts pointed and cornerlike features that persist as the solid shrinks. We explain these observations using flow visualization and a fluid mechanical model in which the surface shear stress dictates the rate of material removal. Experiments and simulations show that this interaction ultimately leads to selfsimilarly receding boundaries and a unique front surface characterized by nearly uniform shear stress. This tendency toward conformity of stress offers a principle for understanding erosion in more complex geometries and flows, such as those present in nature.





Wireless powering of ionic polymer metal composites toward howering microswimmers
K. Abdelnour, A. Stinchcombe, M. Porfiri, J. Zhang, and S. Childress
IEEE-ASME Transactions on Mechatronics 17, 924 (2012).

Abstract: In this paper, we present the design of a wireless powering system for ionic polymer metal composites (IPMCs). The system design is motivated by the need for enabling technologies to replicate hovering flight and swimming in biological systems. IPMC wireless powering is achieved by using radio frequency magnetically coupled coils and in-house designed power electronics for low-frequency IPMC actuation. Parameters of the circuit components describing the resonantly coupled coils and the IPMC are experimentally identified. The power transfer from the external power source to the receiver at the IPMC is experimentally analyzed for a broad range of system parameters. Flow visualization and particle image velocimetry are used to ascertain the system capabilities. Moreover, the IPMC vibration in the wireless and wired configurations is compared.





Collective Chemotactic Dynamics in the Presence of Self-Generated Fluid Flows
E. Lushi, R. Goldstein, and M. Shelley
Rapid Communications, Physical Review E 86, 040902 (2012).

Abstract: In suspensions of flagellated microorganisms cellular locomotion necessarily generates fluid motion, and it is known that such flows can lead to collective behavior from unbiased swimming. We examine the complementary problem of how chemotaxis is a ffected by self-generated flows. A kinetic theory coupling run-and-tumble chemotaxis to the flows of collective swimming shows separate branches of chemotactic and hydrodynamic instability for isotropic suspensions, the first driving aggregation, the second producing increased orientational order in suspensions of "pushers". Simulations of the long-time nonlinear dynamics show that hydrodynamic interactions can limit and modify chemotactically-driven aggregation dynamics. In pusher suspensions chemotactic aggregation can lead to destabilizing time-dependent flows with fragmented regions of accumulation.





Intrinsic Stability of a Body Hovering in an Oscillating Airflow
Bin Liu, Leif Ristroph, Annie Weathers, Stephen Childress, and Jun Zhang
Physical Review Letters 108, 068103 (2012).

Abstract: We explore the stability of flapping flight in a model system that consists of a pyramid-shaped object hovering in a vertically oscillating airflow. Such a flyer not only generates sufficient aerodynamic force to keep aloft but also robustly maintains balance during free flight. Flow visualization reveals that both weight support and orientational stability result from the periodic shedding of vortices. We explain these findings with a model of the flight dynamics, predict increasing stability for higher center of mass, and verify this counterintuitive fact by comparing top- and bottom-heavy flyers.

Related:
Simulations and Press





A weak-coupling expansion for viscoelastic  fluids applied to dynamic settling of a body
M.N.J. Moore and M.J. Shelley
Journal of Non-Newtonian Fluid Mechanics 183-184, 25-36 (2012).

Abstract: The flow of viscoelastic fluids is an area in which analytical results are difficult to attain, yet can provide invaluable information. We present a weak-coupling expansion that allows for semi-analytical computations of viscoelastic fluid flows coupled to immersed structures. We apply the expansion to the transient benchmark problem of a rigid sphere settling from rest through a viscoelastic fluid using the Oldroyd-B model, and we recover the previously observed transient behavior. The theory presented here is in contrast to the retarded motion, or low Weissenberg number, expansions that have received much attention, and one advantage is that the weak-coupling expansion off ers information for order-one Weissenberg number. The expansion's limit of validity is closely related to the diluteness criterion for a Boger fluid. We extend the classical settling problem to include a time-dependent body-force, and show how the introduction of the forcing time-scale modi.fies the body-dynamics.





Oscillations of a Layer of Viscoelastic Fluid under Steady Forcing
B. Liu, M. Shelley, and J. Zhang
Journal of Non-Newtonian Fluid Mechanics 175-176, 38-43 (2012).

Abstract: We study the dynamics of a layer of viscoelastic fluid, in the Stokesian regime, that is driven from below by a 4 x 4 checkerboard pattern of rotating and counter-rotating disks. At low disk rotation rate (low Weissenberg number) the fluid flow response is slaved to the geometry of this forcing and divides into many steadily rotating cells, each contained within invariant manifolds issuing from hyperbolic stagnation points. As the rotation rate increases these fluid cells begin to oscillate periodically in a synchronized fashion. At a yet higher rotation rate, this temporally periodic flow disappears and is replaced by a richer, "turbulent" dynamics where the flow is delocalized from the forcing and has fluid cells that are continuously destroyed and reformed.





A thermodynamic efficiency for Stokesian swimming
Stephen Childress
Journal of Fluid Mechanics 705, 77-97 (2012).

Abstract: Since free Stokesian swimming does no work external to fluid and body, the classical thermodynamic efficiency of this activity is zero. This paper introduces a potential thermodynamic efficiency by partially tethering the body so that work is done externally and instantaneously. We compare the resulting efficiency with other definitions utilized in Stokes flow, extend the instantaneous definition to encompass a full swimming stroke, and compute it for propulsion of a spherical body by a helical flagellum.





Fluid-Structure Interactions: Research in the Courant Institute's Applied Mathematics Laboratory
S. Childress, M. Shelley, and J. Zhang
Communications in Pure and Applied Mathematics 65, 1697-1721 (2012).

Abstract: Applied Mathematics Laboratory is a research laboratory within the Mathematics Department of the Courant Institute. It was established to carry out physical experiments, modeling, and associated numerical studies in a variety of problems of interest to Courant faculty, postdocs, and graduate and undergraduate students. Most of the research to date has involved fluid mechanics, and we focus in this paper on the work that relates to the interaction of fluids with rigid, moveable, or flexible bodies.





Emergence of Coherent Structures and Large-Scale Flows in Motile Suspensions
D. Saintillan and M. Shelley
Journal of the Royal Society Interface 9, 571-585 (2012).

Abstract: The emergence of coherent structures, large-scale flows, and correlated dynamics in suspensions of motile particles such as swimming micro-organisms or artificial microswimmers is studied using direct particle simulations. Simulations are performed with periodic boundary conditions for various system sizes and suspension volume fractions, and clearly demonstrate a transition to large-scale correlated motions in suspensions of rear-actuated swimmers, or pushers, above a critical volume fraction and system size. This transition, which is not observed in suspensions of head-actuated swimmers, or pullers, is characterized by a sudden and sharp increase in fluid velocity correlation lengths, number density fluctuations, particle velocities, mixing efficiency, and passive tracer diffusivities. These observations are all consistent with and confirm for the first time a prediction from our previous mean-field kinetic theory, which states that instabilities will arise in uniform isotropic suspensions of pushers when the product of the linear system size with the suspension volume fraction exceeds a given threshold. Good quantitative agreement is found between the theoretically predicted threshold and its measured value in our simulations.





Experiments and theory of undulatory locomotion in a simple structured medium
T. Majmudar, E. Keaveny, J. Zhang and M. Shelley
Journal of the Royal Society Interface 9 , 1809-1823 (2012).

Abstract: Undulatory locomotion of micro-organisms through geometrically complex, fluidic environments is ubiquitous in nature and requires the organism to negotiate both hydrodynamic effects and geometrical constraints. To understand locomotion through such media, we experimentally investigate swimming of the nematode Caenorhabditis elegans through fluid-filled arrays of micro-pillars and conduct numerical simulations based on a mechanical model of the worm that incorporates hydrodynamic and contact interactions with the lattice. We show that the nematode's path, speed and gait are significantly altered by the presence of the obstacles and depend strongly on lattice spacing. These changes and their dependence on lattice spacing are captured, both qualitatively and quantitatively, by our purely mechanical model. Using the model, we demonstrate that purely mechanical interactions between the swimmer and obstacles can produce complex trajectories, gait changes and velocity fluctuations, yielding some of the life-like dynamics exhibited by the real nematode. Our results show that mechanics, rather than biological sensing and behaviour, can explain some of the observed changes in the worm's locomotory dynamics.

Related:
Published online, Feb. 9, 2012
Supplemental Material: The Mechanical Worm Model
New Scientist, Best of the Web 2010, Swimming Worms
Supplemental Movies:
Experimental:    Movie 1    Movie 2    Movie 3
Simulations:    Movie 4    Movie 5    Movie 6    Movie 7
DFD Gallery of Fluid Motion Movie:    Locomotion of C. elegans in Structured Media
Extra Movie Files:    Demo-1-Large-Lattice-Movie    Demo-2-Small-Lattice-Movie    Worms in a Sessile Drop





Slithering Locomotion
David Hu and Michael Shelley
Natural Locomotion: Swimming, Flying, and Sliding, edited by S. Childress, A. Hosoi, W. Schultz, and J. Wang, Springer, New York (2012).

Abstract: Limbless terrestrial animals propel themselves by sliding their bellies along the ground. Although the study of dry solid-solid friction is a classical subject, the mechanisms underlying friction-based limbless propulsion have received little attention. We review and expand upon our previous work on the locomotion of snakes, who are expert sliders. We show that snakes use two principal mechanisms to slither on at surfaces. First, their bellies are covered with scales that catch upon ground asperities, providing frictional anisotropy. Second, they are able to lift parts of their body slightly off the ground when moving. This reduces undesired frictional drag and applies greater pressure to the parts of the belly that are pushing the snake forwards. We review a theoretical framework that may be adapted by future investigators to understand other kinds of limbless locomotion.





From Theory to Experiment, special issue in honor of Steve Childress
Edited by Andrew Gilbert, Isaac Klapper, Jean-Luc Thiffeault and Jane Wang
Physica D 240, 20, 1565-1684 (1 October 2011).

From the Preface by the Editors:
This Special Issue of Physica D is dedicated to Steve Childress in celebration of his scientific work, and is linked to a conference on 'Fluid Dynamics: from Theory to Experiment', held at Montana State University, Bozeman, USA, from 7-10th June 2010. Steve's long and distinguished career spans a wide range of areas of fluid mechanics. His work is characterised by novel and rigorous mathematical analysis of fluid systems, from the practical to the idealized, often closely linked to experiments, observations and numerical simulations. Steve was one of the pioneers in the area of biological fluid mechanics, and in particular how animals can swim and fly. At large Reynolds number inertial processes such as vortex shedding are important; but at tiny scales, where viscosity is dominant, very different strategies must be adopted. Steve's book is a classic reference in what continues to be a lively, interdisciplinary scientific field. When a fluid contains a suspension of many microscopic swimmers, moving in concert towards a source of light or nutrients, macroscopic cellular motions may be driven. .......





A bug on a raft: recoil locomotion in a viscous fluid
Stephen Childress, Saverio E. Spagnolie, Tadashi Tokieda
Journal of Fluid Mechanics 669, 527-556 (2011).

Abstract: 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.

Related:
Movies of the Simulations:
Recoil locomotion at frequency Reynolds number 16
Recoil locomotion at frequency Reynolds number 256





Applying a Second-Kind Boundary Integral Equation for Surface Tractions in Stokes Flow
E. Keaveny and M. Shelley
Journal of Computational Physics 230, 2141-2159 (2011).

Abstract: A second-kind integral equation for the tractions on a rigid body moving in a Stokesian fluid is established using the Lorentz reciprocal theorem and a completed second-kind integral equation for a double-layer density. A second-order collocation method based on the trapezoidal rule is applied to the integral equation after appropriate singularity reduction. For translating prolate spheriods with various aspect ratios, the scheme is used to explore the effects of the choice of completion flow on the error in the numerical solution, as well as the condition number of the discretized integral operator. The approach is applied to obtain the velocity and viscous dissipation of rotating helices of circular cross section. These results are compared with both local and non-local slender body theories. Motivated by the design of artificial micro-swimmers, similar simulations are performed on previously unstudied helices of non-circular cross-section to determine the dependence of the velocity and propulsion efficiency on the cross-section aspect ratio and orientation.





Dynamics of Complex Bio-Fluids
C. Hohenegger and M. Shelley
in Lecture Notes for the 2009 Ecole de Physique des Houches: New Trends in the Physics and Mechanics of Biological Systems.
Edited by M. Ben-Amar, A. Goriely, M. Muller, and L. Cugliandolo, Oxford University Press, (2011)





Flapping and Bending Bodies Interacting with Fluid Flows
M. Shelley, and J. Zhang
Annual Review of Fluid Mechanics 43, 449-465 (2011).

Abstract: The flapping or bending of a flexible planar structure in a surrounding fluid flow, which includes the flapping of flags and the self-streamlining of flexible bodies, constitutes a central problem in the field of fluid-body interactions. Here we review recent, highly detailed experiments that reveal new nonlinear phenomena in these systems, as well advances in theoretical understanding, resulting in large part from the rapid development of new simulational methods that fully capture the mutual coupling of fluids and flexible solids.





A Stokesian Viscoelastic Flow: Transition to Oscillations and Mixing
B. Thomases, M. Shelley, and J.-L. Thiffeault
Physica D 240, 1602-1614 (2011).

Abstract: To understand observations of low Reynolds number mixing and flow transitions in viscoelastic fluids, we study numerically the dynamics of the Oldroyd-B viscoelastic fluid model. The fluid is driven by a simple time-independent forcing that, in the absence of viscoelastic stresses, creates a cellular flow with extensional stagnation points. We find that at O(1) Weissenberg number these flows lose their slaving to the forcing geometry of the background force, become oscillatory with multiple frequencies, and show continual formation and destruction of small-scale vortices. This drives flow mixing, the details of which we closely examine. These new flow states are dominated by a single-quadrant vortex, which may be stationary or cycle persistently from cell to cell.





Focused Force Transmission through an Aqueous Suspension of Granules
B. Liu, M. Shelley, and J. Zhang
Physical Review Letters 105, 188301 (2010).

Abstract: We investigate force transmission through a layer of shear-thickening fluid, here a concentrated aqueous cornstarch suspension. When a solid body is pushed through this complex fluid and approaches its containing wall, a hardened volume of the suspension is observed that adds to the leading side of the body. This volume leads to an imprint on the wall which is made of molding clay. By studying the geometry of the hardened volume, inferred by the imprint shapes, we find that its geometry is determined by the size and speed of the body. By characterizing the response of the clay to deformation we show that the force transmitted through the suspension to the wall is localized. We also study other aspects of this dynamical hardening of the suspension, such as the effect of the substrate and body shape, and its relaxation as the imposed straining is stopped.

Related:
Science News, Science Daily, Corn Starch Solution Can Help Shape Solid Materials, Nov. 4, 2010
National Science Foundation, News from the Field, NYU Researchers Find Corn Starch Solution Can Help Shape Solid Materials, Nov. 4, 2010





Viscoelastic fluid response can increase the speed and efficiency of a free swimmer
J. Teran, L. Fauci, and M. Shelley
Physical Review Letters 104, 038101 (2010).

Abstract: Microorganisms navigate through complex environments such as biofilms and mucosal tissues and tracts. To understand the effect of a complex media upon their locomotion, we investigate numerically the effect of fluid viscoelasticity on the dynamics of an undulating swimming sheet. First, we recover recent small-amplitude results for infinite sheets that suggest that viscoelasticity impedes locomotion. We find the opposite result when simulating free swimmers with large tail undulations, with both velocity and mechanical efficiency peaking for Deborah numbers near one. We associate this with regions of highly stressed fluid aft of the undulating tail.





Surprising Behaviors in Flapping Locomotion with Passive Pitching
S. Spagnolie, L. Moret, J. Zhang, and M. Shelley
Physics of Fluids 22, 041903 (2010).

Abstract: 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 heaved in a fluid. We observe a range of  flapping frequencies corresponding to very efficient locomotion, a regime of under-performance relative to a rigid (non-pitching) 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). Unlike for the rigid 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.

Related:
Movies of the Experiments and Simulations:
"Forward" flapping locomotion (experiment)
"Forward" flapping locomotion (simulation)
"Backward" flapping locomotion (experiment)
"Backward" flapping locomotion (simulation)
Why nature doesn't use fat flapping wings





Stability of Active Suspensions
C. Hohenegger and M. Shelley
Physical Review E 81, 046311 (2010).

Abstract: We study theoretically the stability of "active suspensions", modeled here as a Stokesian fluid in which are suspended motile particles. The basis of our study is a kinetic model recently posed by Saintillan & Shelley (2008) where the motile particles are either ``Pushers'' or ``Pullers''. General considerations suggest that, in the absence of diffusional processes, perturbations from uniform isotropy will decay for Pullers, but grow unboundedly for Pushers, suggesting a possible ill-posedness. Hence, we investigate the structure of this system linearized near a state of uniform isotropy. The linearized system is non-normal and variable coefficient, and not wholly described by an eigenvalue problem, in particular at small length-scales. Using a high wave-number asymptotic analysis, we show that while long-wave stability depends upon the particular swimming mechanism, short-wave stability does not, and that the growth of perturbations for Pusher suspensions is associated not with concentration fluctuations, as we show these generally decay, but with a proliferation of oscillations in swimmer orientation. These results are also confirmed through numerical simulation, and suggest that the basic model is well-posed, even in the absence of translational and rotational diffusion effects. We also consider the influence of diffusional effects in the case where the rotational and translational diffusion coefficients are proportional and inversely proportional respectively to the volume fraction and predict the existence of a critical volume fraction or system size for the onset of the long-wave instability in a Pusher suspension. We find reasonable agreement between the predictions of our theory and numerical simulations of rod-like swimmers by Saintillan & Shelley (2007).





Hovering of a rigid pyramid in an oscillatory airflow
Annie Weathers, Brendan Folie, Bin Liu, Stephen Childress and Jun Zhang
Journal of Fluid Mechanics 650, 415-425 (2010).

Abstract: We investigate the dynamics of rigid bodies (hollow 'pyramids') placed within a background airflow, oscillating with zero mean. The asymmetry of the body introduces a net upward force. We find that when the amplitude of the airflow is above a threshold, the net lift exceeds the weight and the object starts to hover. Our results show that the objects hover at far smaller air amplitudes than would be required by a quasi-steady theory, although this theory accounts qualitatively for the behaviour of the system as the body mass becomes small.




Shape Optimization of Peristaltic Pumping
S. Walker and M. Shelley
Journal of Computational Physics 229, 1260-1291 (2010).

Abstract: Transport is a fundamental aspect of biology and peristaltic pumping is a fundamental mechanism to accomplish this; it is also important to many industrial processes. We present a variational method for optimizing the wave shape of a peristaltic pump. Specifically, we optimize the wave profile of a two dimensional channel containing a Navier-Stokes fluid with no assumption on the wave profile other than it is a traveling wave (e.g. we do not assume it is the graph of a function). Hence, this is an infinite-dimensional optimization problem. The optimization criteria consists of minimizing the input fluid power (due to the peristaltic wave) subject to constraints on the average flux of fluid and area of the channel. Sensitivities of the cost and constraints are computed variationally via shape differential calculus and we use a sequential quadratic programming (SQP) method to find a solution of the first order KKT conditions.  We also use a merit-function based line search in order to balance between decreasing the cost and keeping the constraints satisfied when updating the channel shape. Our numerical implementation uses a finite element method for computing a solution of the Navier-Stokes equations, adjoint equations, as well as for the SQP method when computing perturbations of the channel shape. The walls of the channel are deformed by an explicit front-tracking approach. In computing functional sensitivities with respect to shape, we use L2-type projections for computing boundary stresses and for geometric quantities such as the tangent field on the channel walls and the curvature; we show error estimates for the boundary stress and tangent field approximations. As a result, we find optimized shapes that are not obvious and have not been previously reported in the peristaltic pumping literature. Specifically, we see highly asymmetric wave shapes that are far from being sine waves. Many examples are shown for a range of fluxes and Reynolds numbers up to Re = 500 which illustrate the capabilities of our method.

Related:
Each frame of the movies show the current shape with the steady-state flow field illustrated by streamlines. Everything is plotted with respect to the wave frame of the traveling wave. Periodic boundary conditions are imposed on the left and right ends of the channel. The Reynolds number is Re = 500.
- Asymmetry Allowed
In these movies, both top and bottom walls are independent but each moves with the same wave speed.
Asymmetric: Medium Flux Constraint (MPG)
Asymmetric: Large Flux Constraint (MPG)
- Symmetry Enforced
In these movies, the bottom wall corresponds to a line of symmetry. Only the top-half of the domain is shown.
Symmetric: Medium Flux Constraint (MPG)
Symmetric: Large Flux Constraint (MPG)




Modeling simple locomotors in Stokes flow
A. Kanevsky, M. Shelley and A.-K. Tornberg
Journal of Computational Physics 229, 958-977 (2010).

Abstract: Motivated by the locomotion of flagellated micro-organisms and by recent experiments of chemically driven nanomachines, we study the dynamics of bodies of simple geometric shape that are propelled by specified tangential surface stresses. We develop a mathematical description of the body dynamics based on a mixed-type boundary integral formulation. We also derive analytic axisymmetric solutions for the case of a single locomoting sphere and ellipsoid based on spherical and ellipsoidal harmonics, and compare our numerical results to these. The hydrodynamic interactions between two spherical and ellipsoidal swimmers in an infinite fluid are then simulated using second-order accurate spatial and temporal discretizations. We find that the near-field interactions result in complex and interesting changes in the locomotors' orientations and trajectories. Stable as well as unstable pairwise swimming motions are observed, similar to the recent findings of Pooley et al.




Hydrodynamic mobility of Chiral colloidal aggregates
Eric E. Keaveny and Michael J. Shelley
Physical Review E79, 051405 (2009).

Abstract: A recent advance in colloidal technology [Zerrouki et al., Nature 455, 380 (2008)] uses magnetic aggregation to enable the formation of micron-scale particle clusters with helical symmetry. The basic building blocks of these aggregates are doublets composed of two micron-scale beads of different radii bonded together by a magnetic cement. Such self-assembled structures offer potential for controllable transport and separation in a low Reynolds number environment using externally applied magnetic or electric fields. Establishing the hydrodynamic properties of the aggregates, in particular the coupling between rotation and translation afforded by the cluster geometry, is an essential initial step toward the design of microfluidic devices employing these aggregates. To quantify this coupling, we first determine parameterized expressions that describe the positions of the beads in an aggregrate as a function of size ratio of the two beads composing the doublets. With the geometry of the structure known, we perform hydrodynamic calculations to ascertain entries of the mobility matrix for the aggregate and establish the relationship between the applied torque about the helical axis and translations parallel to this direction. We find that for larger values of the particle radius ratio the coupling between rotations and translations changes sign as the number of doublets in the aggregate increases. This feature indicates that the clusters possess a more complex superhelical structure.




Transition to mixing and oscillations in a Stokesian viscoelastic flow
Becca Thomases and Michael Shelley
Physical Review Letters 103, 094501 (2009).

Abstract: In seeking to understand experiments on low-Reynolds-number mixing and flow transitions in viscoelastic fluids, we simulate the dynamics of the Oldroyd-B model, with a simple background force driving the flow. We find that at small Weissenberg number, flows are "slaved" to the extensional geometry imposed by forcing. For large Weissenberg number, such solutions become unstable and transit to a structurally dissimilar state dominated by a single large vortex. This new state can show persistent oscillatory behavior with the production and destruction of smaller-scale vortices that drive mixing.

Related:
These movies show the dynamics of the flow and stress tensor for the Weissenberg 10 simulations and run for t=0 to 2000. They correspond with Figures 1 and 2 in the paper.
TS2009-Vort.mov: Movie of the dynamics of the vorticity. Note that there is a change in the scale of the axes at t=500.
TS2009-StrmLine.mov: Movie of the dynamics of the streamlines of the flow. At each time step, streamlines are calculated and these are then animated over time.
TS2009-TrS.mov: Movie of the dynamics of the trace of the stress tensor.
TS2009-S12.mov: Movie of the dynamics of the shear stress S12.
TS2009-Vort_2.mov: Movie of the dynamics of the vorticity in the case referred to at the end of the paper where the vortex does not relax to a single quadrant, but instead switches dynamically and persistently from quadrant to quadrant.




The mechanics of slithering locomotion
David L. Hu, Jasmine Nirody, Terri Scott, and Michael J. Shelley
Proceedings of the National Academy of Science (USA) doi:10.1073/pnas.0812533106 (2009).

Abstract: In this experimental and theoretical study, we investigate the slithering of snakes on flat surfaces. Previous studies of slithering have rested on the assumption that snakes slither by pushing laterally against rocks and branches. In this study, we develop a theoretical model for slithering locomotion by observing snake motion kinematics and experimentally measuring the friction coefficients of snakeskin. Our predictions of body speed show good agreement with observations, demonstrating that snake propulsion on flat ground, and possibly in general, relies critically on the frictional anisotropy of their scales. We have also highlighted the importance of weight distribution in lateral undulation, previously difficult to visualize and hence assumed uniform. The ability to redistribute weight, clearly of importance when appendages are airborne in limbed locomotion, has a much broader generality, as shown by its role in improving limbless locomotion.

Related:
Click here for images and videos of Limbless Locomotion
Snakes use scales to slither: Mathematical model suggests 'sideways' friction is key, Roberta Kwok, NatureNews, 8 June 2009
Snakes' Locomotion Appears a Matter of Scales, Henry Fountain, Observatory, The New York Times, June 06, 2009




Shape-changing bodies in fluid: Hovering, ratcheting, and bursting
Saverio E. Spagnolie and Michael J. Shelley
Physics of Fluids 21, 013103 (2009).

Abstract: 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.

Related:
Click here for video of "Ratcheting Upward Against Gravity"




Instabilities, pattern formation and mixing in active suspensions
D. Saintillan and M. Shelley
Physics of Fluids 20, 123304 (2008).

Abstract: Suspensions of self-propelled particles, such as swimming microorganisms, are known to undergo complex dynamics as a result of hydrodynamic interactions. To elucidate these dynamics, a kinetic theory is developed and applied to study the linear stability and the non-linear pattern formation in these systems. The evolution of a suspension of self-propelled particles is modeled using a conservation equation for the particle configurations, coupled to a mean-field description of the flow arising from the stress exerted by the particles on the fluid. Based on this model, we first investigate the stability of both aligned and isotropic suspensions. In aligned suspensions, an instability is shown to always occur at finite wavelengths, a result that extends previous predictions by Simha and Ramaswamy [Hydrodynamic fluctuations and instabilities in ordered suspensions of self-propelled particles," Phys. Rev. Lett. 89, 058101 (2002)]. In isotropic suspensions, we demonstrate the existence of an instability for the active particle stress, in which shear stresses are eigenmodes and grow exponentially at long scales. Non-linear effects are also investigated using numerical simulations in two dimensions. These simulations confirm the results of the stability analysis, and the long-time non-linear behavior is shown to be characterized by the formation of strong density fluctuations, which merge and break up in time in a quasi-periodic fashion. These complex motions result in very efficient fluid mixing, which we quantify by means of a multiscale mixing norm.

Related:
Click here to see a movie of swimmer-driven mixing




Anomalous Hydrodynamic Drafting of Interacting Flapping Flags
Leif Ristroph and Jun Zhang
Physical Review Letters 101, 194502 (2008).

Abstract: In aggregates of objects moving through a fluid, bodies downstream of a leader generally experience reduced drag force. This conventional drafting holds for objects of fixed shape, but interactions of deformable bodies in a flow are poorly understood, as in schools of fish. In our experiments on "schooling" flapping flags we find that it is the leader of a group who enjoys a significant drag reduction (of up to 50 %), while the downstream flag suffers a drag increase. This counterintuitive inverted drag relationship is rationalized by dissecting the mutual influence of shape and flow in determining drag. Inverted drafting has never been observed with rigid bodies, apparently due to the inability to deform in response to the altered flow field of neighbors.

Related:
Wired Science, The Weird and Beautiful World of Fluid Dynamics: Inverted Drafting, Jane J. Lee, June 22, 2011
NewsDay.com, Health, Kathy Wollard, How Come?: Why do flags flap in the wind?, March 29, 2009
Nature Physics, Research Highlights, Follow the Leader, Dec. 2008
Physics Today, back scatter Flapping flags in tandem, p. 108, November, 2008
Nature, Research Highlights - physics Flags and drag, v456, p284, 2008
The Economist, Science & Technology, Aerodynamics Blowin' in the wind, Flapping flags may shed light on how fish school and birds flock, Nov. 27th, 2008




Peristaltic pumping and irreversibility of a Stokesian viscoelastic fluid
J. Teran, L. Fauci, and M. Shelley
Physics of Fluids 20, 073101 (2008).

Abstract: Peristaltic pumping by wavelike contractions is a fundamental biomechanical mechanism for fluid and material transport and is used in the esophagus, intestine, oviduct, and ureter. While peristaltic pumping of a Newtonian fluid is well understood, in many important settings, as in the fluid dynamics of reproduction, the fluids have non-Newtonian responses. Here, we present a numerical method for simulating an Oldroyd-B fluid coupled to contractile, moving walls. A marker and cell grid-based projection method is used for the fluid equations and an immersed boundary method is used for coupling to a Lagrangian representation of the deforming walls. We examine numerically the peristaltic transport of a highly viscous Oldroyd-B fluid over a range of Weissenberg numbers and peristalsis wavelengths and amplitudes.

Related:
Click here to see a movie demonstrating irreversibility of Stokesian viscoelastic flows
or Click here for a quicktime movie of the above (for Linux, MacOSX)




Self-Induced Cyclic Reorganization of Free Bodies through Thermal Convection
Bin Liu and Jun Zhang
Physical Review Letters 100, 244501 (2008).

Abstract: We investigate the dynamics of a thermally convecting fluid as it interacts with freely moving solid objects. This is a previously unexplored paradigm of interactions between many free bodies mediated by thermal convection, which gives rise to surprising robust oscillations between different large-scale circulations. Once begun, this process repeats cyclically, with the collection of objects (solid spheres) entrained and packed from one side of the convection cell to the other. The cyclic frequency is highest when the spheres occupy about half of the cell bottom and their size coincides with the thickness of the thermal boundary layer. Our work shows that a deformable mass stimulates a thermally convecting fluid into oscillation, a collective behavior that may be found in nature.

Related:
Click here for New Scientist Video of the Experiment -- Earth-in-a-box may explain continental drift (on youTube)
New Scientist Environment -- Why continents split up and get back together, by Devin Powell, 02 July 2008
Physical Review Focus -- Desktop Continental Drift, 12 June 2008 (contains videos from the experiment)
physicsworld.com Table-top experiment could explain why continents drift, June 24, 2008 - (one must sign-in to read article).




Instabilities and pattern formation in active particle suspensions: Kinetic theory and continuum simulations
David Saintillan and Michael J. Shelley
Physical Review Letters 100, 178103 (2008).

Abstract: We use kinetic theory and non-linear continuum simulations to study the collective dynamics in suspensions of self-propelled particles. The stability of aligned suspensions is first analyzed, and we demonstrate that such suspensions are always unstable to fluctuations, a result that generalizes previous predictions by Simha and Ramaswamy (2002). Isotropic suspensions are also considered, and it is shown that an instability for the particle stress occurs in that case. Using simulations, non-linear effects are investigated, and the long-time behavior of the suspensions is observed to be characterized by the formation of strong density fluctuations, resulting in efficient fluid mixing.




An experimental investigation and a simple model of a valveless pump
Thomas T. Bringley, Stephen Childress, Nicolas Vandenberghe, and Jun Zhang
Physics of Fluids 20, 033602 (2008).

Abstract: We construct a valveless pump consisting of a section of elastic tube and a section of rigid tube connected in a closed loop and filled with water. By periodically squeezing the elastic tube at an asymmetric location, a persistent flow around the tubes is created. This effect, called the Liebau phenomenon or valveless pumping, has been known for some time but is still not completely understood. We study the flow rates for various squeezing locations, frequencies, and elastic tube rigidities. To understand valveless pumping, we formulate a simple model that can be described by ordinary differential equations. The time series of flow velocities generated by the model are qualitatively and quantitatively similar to those seen in the experiment. The model provides a physical explanation of valveless pumping, and it allows us to identify the essential pumping mechanisms.




Growth of anti-parallel vorticity in Euler flows
Stephen Childress
Physica D 237, 1921-1925 (2008).

Abstract: In incompressible Euler flows, vorticity is intensified by line stretching, a process that can come either from the action of shear, or from advection with curvature. Focusing on the latter process, we derive some estimates on the maximal growth of vorticity in axisymmetric flow without swirl, given that vorticity support volume or kinetic energy is fixed. This leads to consideration of locally 2D anti-parallel vortex structures in three dimensions. We exhibit a class of line motions which lead to infinite vorticity in a finite time, with only a finite total line stretching. If the line is replaced by a locally 2D Euler flow, we obtain a class of models of vorticity growth which are similar to the paired vortex structures studied by Pumir and Siggia. We speculate on the mechanisms which can suppress the nonlinear effects necessary for the finite-time singularity exhibited by the moving line problem.




Flapping states of a flag in an inviscid fluid: bistability and the transition to chaos
Silas Alben and Michael J. Shelley
Physical Review Letters 100, 074301 (2008).

Abstract: We investigate the "flapping flag" instability through a model for an inextensible flexible sheet in an inviscid 2D flow with a free vortex sheet. We solve the fully-nonlinear dynamics numerically and find a transition from a power spectrum dominated by discrete frequencies to an apparently continuous spectrum of frequencies. We compute the linear stability domain which agrees with previous approximate models in scaling but differs by large multiplicative factors. We also find hysteresis, in agreement with previous experiments.

Related:
Erratum: correction of parameters and Fig. 2
Movies (avi):
First Periodic State
Second Periodic State
Third Periodic State
Chaotic State




Validation of a simple method for representing spheres and slender bodies in an immersed boundary method for Stokes flow on an unbounded domain
Thomas T. Bringley, Charles S. Peskin
Journal of Computational Physics 227, 5397-5425 (2008).

Abstract: We test the efficacy of using a single Lagrangian point to represent a sphere, and a one-dimensional array of such points to represent a slender body, in a new immersed boundary method for Stokes flow. A numerical parameter, the spacing of the Eulerian grid, is used to determine the effective radius of the immersed sphere or slender body. Such representations are much less expensive computationally than those with two or three-dimensional meshes of Lagrangian points. To perform this test, we develop a numerical method to solve the discretized Stokes equations on an unbounded Eulerian grid which contains an arbitrary configuration of Lagrangian points that apply force to the fluid and that move with the fluid. We compare results computed with this new immersed boundary method to known results for spheres and rigid cylinders in Stokes flow in R3. We find that, for certain choices of parameters, the interactions with the fluid of a single Lagrangian point accurately replicate those of a sphere of some particular radius, independent of the location of the point with respect to the Eulerian grid. The interactions of a linear array of Lagrangian points, for certain choices of parameters, accurately replicate those of a cylinder of some particular radius, independent of the position and orientation of the array with respect to the Eulerian grid. The effective radius of the sphere and the effective radius of the cylinder turn out to be related in a simple and natural way. Our results suggest recipes for choosing parameters that should be useful to practitioners. One surprising result is that one must not use too many Lagrangian points in an array. Another is that the approximate delta functions traditionally used in the immersed boundary method perform much better than higher order delta functions with the same support.




Rotational dynamics of a superhelix towed in a Stokes fluid
Sunghwan Jung, Kathleen Mareck, Lisa Fauci, and Michael J. Shelley
Physics of Fluids 19, 103105 (2007).

Abstract: Motivated by the intriguing motility of spirochetes of helically shaped bacteria that screw through viscous fluids due to the action of internal periplasmic flagella, we examine the fundamental fluid dynamics of superhelices translating and rotating in a Stokes fluid. A superhelical structure may be thought of as a helix whose axial centerline is not straight, but also a helix. We examine the particular case in which these two superimposed helices have different handedness, and employ a combination of experimental, analytic, and computational methods to determine the rotational velocity of superhelical bodies being towed through a very viscous fluid. We find that the direction and rate of the rotation of the body is a result of competition between the two superimposed helices; for small axial helix amplitude, the body dynamics is controlled by the short-pitched helix, while there is a crossover at larger amplitude to control by the axial helix.We find far better, and excellent, agreement of our experimental results with numerical computations based upon the method of Regularized Stokeslets than upon the predictions of classical resistive force theory.




Liquid crystal droplet production in a microfluidic device
B. Hamlington, B. Steinhaus, J. Feng, D. Link, A.-Q. Shen, and M. Shelley
Liquid Crystals 34, 861-870 (2007).

Abstract: Liquid crystal drops dispersed in a continuous phase of silicone oil are generated with a narrow distribution in droplet size in microfluidic devices both above and below the nematic-to-isotropic transition temperature. Our experiments show that the surface properties of the channels can be critical for droplet formation. We observe different dynamics in liquid crystal droplet generation and coalescence, and distinct droplet morphology on altering the microchannel surface energy. This is explained by the thermodynamic description of the wetting dynamics of the system. The effect of the nematic-to-isotropic transition on the formation of liquid crystal droplets is also observed and related to the capillary number. We also investigate how the nematic droplet size varies with the flow rate ratio and compare this behaviour with a Newtonian reference system. The effect of the defect structures of the nematic liquid crystal can lead to distinctly different scaling of droplet size in comparison with the Newtonian system. When the nematic liquid crystal phase is stretched into a thin filament before entering the orifice, different defect structures and numbers of defect lines can introduce scatter in the drop size. Capillary instabilities in thin nematic liquid crystal filament have an additional contribution from anisotropic effects such as surface gradients of bending stress, which can provide extra instability modes compared with that of isotropic fluids.




Emergence of singular structures in Oldroyd-B fluids
Becca Thomases and Michael Shelley
Physics Of Fluids 19, 103103 (2007).

Abstract: Numerical simulations reveal the formation of singular structures in the polymer stress field of a viscoelastic fluid modeled by the Oldroyd-B equations driven by a simple body force. These singularities emerge exponentially in time at hyperbolic stagnation points in the flow and their algebraic structure depends critically on the Weissenberg number. Beyond a first critical Weissenberg number the stress field approaches a cusp singularity, and beyond a second critical Weissenberg number the stress becomes unbounded exponentially in time. A local approximation to the solution at the hyperbolic point is derived from a simple ansatz, and there is excellent agreement between the local solution and the simulations. Although the stress field becomes unbounded for a sufficiently large Weissenberg number, the resultant forces of stress grow subexponentially. Enforcing finite polymer chain lengths via a FENE-P penalization appears to keep the stress bounded, but a cusp singularity is still approached exponentially in time.




Orientational order and instabilities in suspensions of self-locomoting rods
David Saintillan and Michael Shelley
Physical Review Letters 99, 058102 (2007).

Abstract: The orientational order and dynamics in suspensions of self-locomoting slender rods are investigated numerically. In agreement with previous theoretical predictions, nematic suspensions of swimming particles are found to be unstable at long wavelengths as a result of hydrodynamic fluctuations. Nevertheless, a local nematic ordering is shown to persist over short length scales and to have a significant impact on the mean swimming speed. Consequences of the large-scale orientational disorder for particle dispersion are also discussed.

Related:
Click here to watch the dynamics of an active particle suspension




Stretch-Coil Transition and Transport of Fibers in Cellular Flows
Yuan-Nan Young and Michael Shelley
Physical Review Letters 99, 058303 (2007).

Abstract: It is shown that a slender elastic fiber moving in a Stokesian fluid can be susceptible to a buckling instability -- termed the "stretch-coil" instability -- when moving in the neighborhood of a hyperbolic stagnation point of the flow.  When the stagnation point is embedded in an extended cellular flow, it is found that immersed fibers can move as random walkers across time-independent closed-streamline flows.  It is also found that the flow is segregated into transport regions around hyperbolic stagnation points and their manifolds, and closed entrapment regions around elliptic points.

Related:
Click here to see a simulation of buckling-driven transport




Modeling the dynamics of a free boundary on turbulent thermal convection
Jin-Qiang Zhong and Jun Zhang
Physical Review E 76, 016307 (2007).

Abstract: Based on our previous experimental study, we present a one-dimensional, phenomenological model of a thermal blanket floating on the upper surface of a thermally convecting fluid. The model captures the most important interactions between the floating solid and the fluid underneath. By the thermal blanketing effect, the presence of the solid plate modifies the flow structure below; in turn, the flow exerts a viscous drag that causes the floating boundary to move. An oscillatory state and a trapped state are found in this model, which is in excellent agreement with experimental observations. The model also offers details on the transition between the states, and gives useful insights on this coupled system without the need for full-scale simulations.




Dynamical states of a mobile heat blanket on a thermally convecting fluid
Jin-Qiang Zhong and Jun Zhang
Physical Review E 75, 055301(R) (2007).

Abstract: We experimentally study the dynamical states of a freely moving, floating heat blanket that is coupled with a thermally convecting fluid. This floating boundary modifies the large-scale flow pattern in the bulk and destabilizes the coupled system, leading to spontaneous oscillations. As the moving boundary exceeds a critical size, the system makes a transition from an oscillatory state to a weakly confined state, in which the moving boundary executes only small excursions in response to random bypassing thermal plumes. To explain the observed states and transition, we provide a low-dimensional model that appears to capture the underlying mechanism of this coupled system.




Surface waves on a semitoroidal water ring
Sungwhan Jung, Erica Kim, Michael Shelley and Jun Zhang
Physics of Fluids 19, 058105 (2007).

Abstract: We study the dynamics of surface waves on a semitoroidal ring of water that is excited by vertical vibration. We create this specific fluid volume by patterning a glass plate with a hydrophobic coating, which confines the fluid to a precise geometric region. To excite the system, the supporting plate is vibrated up and down, thus accelerating and decelerating the fluid ring along its toroidal axis. When the driving acceleration is sufficiently high, the surface develops a standing wave, and at yet larger accelerations, a traveling wave emerges. We also explore frequency dependencies and other geometric shapes of confinement.

Related:
Click here for a movie from the experiment
Instructions to view this movie on Windows, MacOSX, and Linux platforms




Hovering of a passive body in an oscillating airflow
Stephen Childress, Nicolas Vandenberghe and Jun Zhang
Physics of Fluids 18, 117103 (2006).

Abstract: Small flexible bodies are observed to hover in an oscillating air column. The air is driven by a large speaker at frequencies in the range 10-65 Hz at amplitudes 1-5 cm. The bodies are made of stiffened tissue paper, bent to form an array of four wings, symmetric about a vertical axis. The flapping of the wings, driven by the oscillating flow, leads to stable hovering. The hovering position of the body is unstable under free fall in the absence of the airflow. Measurements of the minimum flow amplitude as a function of flow frequency were performed for a range of self-similar bodies of the same material. The optimal frequency for hovering is found to vary inversely with the size. We suggest, on the basis of flow visualization, that hovering of such bodies in an oscillating flow depends upon a process of vortex shedding closely analogous to that of an active flapper in otherwise still air. A simple inviscid model is developed illustrating some of the observed properties of flexible passive hoverers at high Reynolds number.

Related:
Click here for a movie from experiment 1 - divX avi movie
Click here for a movie from experiment 2 - wmv3 movie
The video frame rate here is close to the flapping frequency so the bug does not seem to be flapping, but it is.
Instructions to view these movies on Windows, MacOSX, and Linux platforms




Dynamics of a Deformable Body in a Fast Flowing Soap Film
Sungwhan Jung, Kathleen Mareck, Michael Shelley, and Jun Zhang
Physical Review Letters 97, 134502 (2006).

Abstract: We study the behavior of an elastic loop embedded in a flowing soap film. This deformable loop is wetted into the film and is held fixed at a single point against the oncoming flow. We interpret this system as a two-dimensional flexible body interacting in a two-dimensional flow. This coupled fluid-structure system shows bistability, with both stationary and oscillatory states. In its stationary state, the loop remains essentially motionless and its wake is a von Kármán vortex street. In its oscillatory state, the loop sheds two vortex dipoles, or more complicated vortical structures, within each oscillation period. We find that the oscillation frequency of the loop is linearly proportional to the flow velocity, and that the measured Strouhal numbers can be separated based on wake structure.

Related:
Click here for a movie from the experiment




Periodic sedimentation in a Stokesian fluid
Sungwhan Jung, Saverio Spagnolie, Karishma Parikh, Michael Shelley, and Anna-Karin Tornberg
Physical Review E 74, 035302(R) (2006)

Abstract: We study the sedimentation of two identical but nonspherical 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.

Related:
Movies of the Experiments and Simulations:
Sedimenting disks (experiment)
Periodic Tumbling: Three disks
Instability of three (initially perturbed) sedimenting bodies
Two meandering disks
APS/DFD 2005, Video Presentation - Periodic Parachutes




On Unidirectional Flight of a Free Flapping Wing
Nicolas Vandenberghe, Stephen Childress and Jun Zhang
Physics of Fluids 18, 014102 (2006)

Abstract: We study the dynamics of a rigid, symmetric wing that is flapped vertically in a fluid. The motion of the wing in the horizontal direction is not constrained. Above a critical flapping frequency, forward flight arises as the wing accelerates to a terminal state of constant speed. We describe a number of measurements which supplement our previous work. These include (a) a study of the initial transition to forward flight near the onset of the instability, (b) the separate effects of flapping amplitude and frequency, (c) the effect of wing thickness, (d) the effect of asymmetry of the wing planform, and (e) the response of the wing to an added resistance. Our results emphasize the robustness of the mechanisms determining the forward flight speed as observed in our previous study.




Coherent Locomotion as an Attracting State for a Free Flapping Body
S. Alben and M. Shelley
Proceedings of the National Academy of Science (USA) 102, 11163-11166 (2005)

Abstract: A common strategy for locomotion through a fluid uses appendages, such as wings or fins, flapping perpendicularly to the direction of travel. This is in marked difference to strategies using propellers or screws, ciliary waves, or rowing with limbs or oars which explicitly move fluid in the direction opposite to travel. Flapping locomotion is also never observed for microorganisms moving at low Reynolds number. To understand the nature of flapping locomotion we study numerically the dynamics of a simple body, flapped up and down within a viscous fluid and free to move horizontally. We show here that, at sufficiently large frequency Reynolds number, unidirectional locomotion emerges as an attracting state for an initially nonlocomoting body. Locomotion is generated in two stages: first, the fluid field loses symmetry by the classical von Karman instability; and second, precipitous interactions with vortical structures shed in previous flapping cycles push the body into locomotion. Body mass and slenderness play central and unexpected roles in each stage. Conceptually, this work demonstrates how locomotion can be transduced from the simple oscillations of a body through an interaction with its fluid environment.

Related:
Click here for movies referenced in the publication




Thermal convection with a freely moving top boundary
Jin-qiang Zhong and Jun Zhang
Physics of Fluids 17, 115105 (2005).

Abstract: In thermal convection, coherent flow structures emerge at high Rayleigh numbers as a result of intrinsic hydrodynamic instability and self-organization. They range from small-scale thermal plumes that are produced near both the top and the bottom boundaries to large-scale circulations across the entire convective volume. These flow structures exert viscous forces upon any boundary. Such forces will affect a boundary which is free to deform or change position. In our experiment, we study the dynamics of a free boundary that floats on the upper surface of a convective fluid. This seemingly passive boundary is subjected solely to viscous stress underneath. However, the boundary thermally insulates the fluid, modifying the bulk flow. As a consequence, the interaction between the free boundary and the convective flows results in a regular oscillation. We report here some aspects of the fluid dynamics and discuss possible links between our experiment and continental drift.




Heavy flags undergo spontaneous oscillations in flowing water
M. Shelley, N. Vandenberghe, and J. Zhang
Physical Review Letters 94, 094302 (2005).

Abstract: By immersing a compliant yet self-supporting sheet into flowing water, we study a heavy, stream-lined and elastic body interacting with a fluid. We find that above a critical flow velocity a sheet aligned with the flow begins to flap with a Strouhal frequency consistent with animal locomotion. This transition is subcritical. Our results agree qualitatively with a simple fluid dynamical model that predicts linear instability at a critical flow speed. Both experiment and theory emphasize the importance of body inertia in overcoming the stabilizing effects of finite rigidity and fluid drag.

Related:
Click here for a movie from the experiment




Moore's Law and the Saffman-Taylor Instability
Petri Fast and Michael J. Shelley
Journal of Computational Physics 212, 1-5 (2005).

Abstract: Ten years ago Hou, Lowengrub and Shelley published a state-of-the-art boundary integral simulation of a classical viscous fingering problem, the Saffman-Taylor instability. In terms of complexity and level of detail, those computations are still among the most ramified and accurately computed interfacial instability patterns that have appeared in the literature. Since 1994, the computational power of a standard workstation has increased a hundredfold as predicted by Moore's law. The purpose of this Note is to consider Moore's law and its consequences in computational science, and in particular, its impact on studying the Saffman-Taylor instability. We illustrate Moore's law and fast algorithms in action by presenting the worlds largest viscous fingering simulation to date.

Related:
Click here for an animation from the data
Instructions to view this movie on Windows, MacOSX, and Linux platforms




Falling Cards
Marvin A. Jones and Michael J. Shelley
Journal of Fluid Mechanics 540, 393-425 (2005).

Abstract: In this study we consider the unsteady separated flow of an inviscid fluid around a falling flat plate of small thickness and high aspect ratio. The motion of the plate, which is initially released from rest, is unknown in advance and is determined as part of the solution. The flow solution is assumed two-dimensional and to consist of a bound vortex sheet coincident with the plate and two free vortex sheets that emanate from each of the plate's two sharp edges. Throughout its motion, the plate continually sheds vorticity from each of its two sharp edges and the unsteady Kutta condition, which states the fluid velocity must be bounded everywhere, is applied at each edge. The coupled equations of motion for the plate and its trailing vortex wake are derived and are shown to depend only on a modified Froude number.




A computational fluid dynamics of 'clap and fling' in the smallest insects
Laura A. Miller and Charles S. Peskin
The Journal of Experimental Biology 208, 195-212 (2005).

Abstract: In this paper, we have used the immersed boundary method to solve the two-dimensional Navier-Stokes equations for two immersed wings performing an idealized 'clap and fling' stroke and a 'fling' half-stroke. We calculated lift coefficients as functions of time per wing for a range of Reynolds numbers (Re) between 8 and 128. We also calculated the instantaneous streamlines around each wing throughout the stroke cycle and related the changes in lift to the relative strength and position of the leading and trailing edge vortices. Our results show that lift generation per wing during the 'clap and fling' of two wings when compared to the average lift produced by one wing with the same motion falls into two distinct patterns. For Re=64 and higher, lift is initially enhanced during the rotation of two wings when lift coefficients are compared to the case of one wing. Lift coefficients after fling and during the translational part of the stroke oscillate as the leading and trailing edge vortices are alternately shed. In addition, the lift coefficients are not substantially greater in the two-winged case than in the one-winged case. This differs from three-dimensional insect flight where the leading edge vortices remain attached to the wing throughout each half-stroke. For Re=32 and lower, lift coefficients per wing are also enhanced during wing rotation when compared to the case of one wing rotating with the same motion. Remarkably, lift coefficients following two-winged fling during the translational phase are also enhanced when compared to the one-winged case. Indeed, they begin about 70% higher than the one-winged case during pure translation. When averaged over the entire translational part of the stroke, lift coefficients per wing are 35% higher for the two-winged case during a 4.5 chord translation following fling. In addition, lift enhancement increases with decreasing Re. This result suggests that the Weis-Fogh mechanism of lift generation has greater benefit to insects flying at lower Re. Drag coefficients produced during fling are also substantially higher for the two-winged case than the one-winged case, particularly at lower Re.

Related:
Click here for articles and simulations of Tiny Insect Flight.




Symmetry Breaking Leads to Forward Flapping Flight
Nicolas Vandenberghe, Jun Zhang, and Stephen Childress
Journal of Fluid Mechanics 506, 147-155 (2004).

Abstract: Flapping flight is ubiquitous in Nature, yet cilia and flagella, not wings, prevail in the world of micro-organisms. This paper addresses this dichotomy. We investigate experimentally the dynamics of a wing, flapped up and down and free to move horizontally. The wing begins to move forward spontaneously as a critical frequency is exceeded, indicating that 'flapping flight' occurs as a symmetry-breaking bifurcation from a pure flapping state with no horizontal motion. A dimensionless parameter, the Reynolds number based on the flapping frequency, characterizes the point of bifurcation. Above this bifurcation, we observe that the forward speed increases linearly with the flapping frequency. Visualization of the flow field around the heaving and plunging foil shows a symmetric pattern below transition. Above threshold, an inverted von Kármán vortex street is observed in the wake of the wing. The results of our model experiment, namely the critical Reynolds number and the behaviour above threshold, are consistent with observations of the flapping-based locomotion of swimming and flying animals.

Related:
Click here to see a video of coherent locomotion resulting from a symmetry-breaking instability




How flexibility induces streamlining in a two-dimensional flow.
Silas Alben, Michael Shelley, and Jun Zhang
Physics of Fluids 16, 1694-1713 (2004).

Abstract: Recent work in bio-fluid dynamics has studied the relation of fluid drag to flow speed for flexible organic structures, such as tree leaves, seaweed, and coral beds, and found a reduction in drag growth due to body reconfiguration with increasing flow speed. Our theoretical and experimental work isolates the role of elastic bending in this process. Using a flexible glass fibre wetted into a vertical soap-film tunnel, we identify a transition in flow speed beyond which fluid forces dominate the elastic response, and yield large deformation of the fibre that greatly reduce drag. We construct free-streamline models that couple fluid and elastic forces and solve them in an efficient numerical scheme. Shape self-similarity emerges, with a scaling set by the balance of forces in a small "tip region" about the flow's stagnation point. The result is a transition from the classical U2 drag scaling of rigid bodies to a U4/3 drag law. The drag scaling is derived from an asymptotic expansion in the length scale of similarity, and it is found that the tip region induces the far-field behavior. The drag law persists, with a simple modification, under variations of the model suggested by the experiment, such as the addition of flow tunnel walls, and a back pressure in the wake.




Transition from ciliary to flapping mode in a swimming mollusc: flapping flight as a bifurcation in Reω
Stephen Childress and Robert Dudley
Journal of Fluid Mechanics 498, 257-288 (2004).

Abstract: From observations of swimming of the shell-less pteropod mollusc Clione antarctica we compare swimming velocities achieved by the organism using ciliated surfaces alone with velocities achieved by the same organism using a pair of flapping wings. Flapping dominates locomotion above a swimming Reynolds number Re in the range 5-20. We test the hypothesis that Re ≈ 5-20 marks the onset of 'flapping flight' in these organisms. We consider the proposition that forward, reciprocal flapping flight is impossible for locomoting organisms whose motion is fully determined by a body length L and a frequency ω below some finite critical value of the Reynolds number Reω = ω L2. For a self-similar family of body shapes, the critical Reynolds number should depend only upon the geometry of the body and the cyclic movement used to locomote. We give evidence of such a critical Reynolds number in our data, and study the bifurcation in several simplified theoretical models. We argue further that this bifurcation marks the departure of natural locomotion from the low Reynolds number or Stokesian realm and its entry into the high Reynolds number or Eulerian realm. This occurs because the equilibrium swimming or flying speed Uf obtained at the instability is determined by the mechanics of a viscous fluid at a value of Ref=Uf L/ν that is not small.

Related:
Click here for videos of the Antarctic Pteropods
Research at McMurdo Station, Antarctica. - Steve Childress' journal, photo gallery, research notes




Simulations of the whirling instability by the immersed boundary method
Sookkyung Lim and Charles S. Peskin
Siam J. Sci. Comput. 25, (6), 2066-2083 (2004).

Abstract: When an elastic filament spins in a viscous incompressible fluid it may undergo a whirling instability, as studied asymptotically by Wolgemuth, Powers, and Goldstein [Phys. Rev. Lett., 84 (2000), pp. 16-23]. We use the immersed boundary (IB) method to study the interaction between the elastic filament and the surrounding viscous fluid as governed by the incompressible Navier-Stokes equations. This allows the study of the whirling motion when the shape of the filament is very different from the unperturbed straight state.

Related:
Click here for animations of twirling and overwhirling motions.




Simulating the dynamics and interactions of flexible fibers in Stokes flows
Anna-Karin Tornberg and Michael J. Shelley
Journal of Computational Physics 196 8-40 (2004).

Abstract: The dynamics of slender filaments or fibers suspended in Stokesian fluids are fundamental to understanding many flows arising in physics, biology and engineering. Such filaments can have aspect ratios of length to radius ranging from a few tens to several thousands. Full discretizations of such 3D flows are very costly. Instead, we employ a non-local slender body theory that yields an integral equation, along the filament centerline, relating the force exerted on the body to the filament velocity. This hydrodynamical description takes into account the effect of the filament on the fluid, and is extended to capture the interaction of multiple filaments as mediated by the intervening fluid. We consider filaments that are inextensible and elastic. Replacing the force in the slender body integral equation by an explicit expression that uses Euler-Bernoulli theory to model bending and tensile forces yields an integral expression for the velocity of the filament centerlines, coupled to auxiliary integro-differential equations for the filament tensions. Based on a regularized version of these slender body equations that is asymptotically equivalent to the original formulation, we construct a numerical method which uses a combination of finite differences, implicit time-stepping to avoid severe stability constraints, and special quadrature methods for nearly singular integrals. We present simulations of single flexible filaments, as well as multiple interacting filaments, evolving in a background shear flow. These simulations show shear induced buckling and relaxation of the filaments, leading to the storage and release of elastic energy. These dynamics are responsible for the development of positive first normal stress differences, commonly associated with fiasco-elastic fluids that are suspensions of microscopic elastic fibers.

Related:
Click here for animations of the simulation
Instability of Semiflexible Filaments in Shear Flow Yields First Normal Stress Difference by Leif Becker and Michael Shelley, Physical Review Letters 87, 198301 (2001)
The Growth and Buckling of Smectic Liquid Crystal Filaments, Michael Shelley and Tetsuji Ueda




A Moving Overset Grid Method for Interface Dynamics applied to Non-Newtonian Hele-Shaw Flow
Petri Fast and Michael J. Shelley
Journal of Computational Physics 195, 117 (2004).

Abstract: We present a novel moving overset grid scheme for the accurate and efficient long-time simulation of an air bubble displacing a non-Newtonian fluid in the prototypical thin film device, the Helehaw cell. We use a two-dimensional generalization of Darcy's law that accounts for shear thinning of a non-Newtonian fluid. In the limit of weak shear thinning, the pressure is found from a ladder of two linear elliptic boundary value problems, each to be solved in the whole fluid domain. A moving body fitted grid is used to resolve the flow near the interface, while most of the fluid domain is covered with a fixed Cartesian grid. Our use of body-conforming grids reduces grid anisotropy effects and allows the accurate modeling of boundary conditions.




Chaotic mixing in a torus map
Jean-Luc Thiffeault and Stephen Childress
Chaos 13, (2), 502-507 (2003).

Abstract: The advection and diffusion of a passive scalar is investigated for a map of the 2-torus. The map is chaotic, and the limit of almost-uniform stretching is considered. This allows an analytic understanding of the transition from a phase of constant scalar variance (for short times) to exponential decay (for long times). This transition is embodied in a short superexponential phase of decay. The asymptotic state in the exponential phase is an eigenfunction of the advection-diffusion operator, in which most of the scalar variance is concentrated at small scales, even though a large-scale mode sets the decay rate. The duration of the superexponential phase is proportional to the logarithm of the exponential decay rate; if the decay is slow enough then there is no superexponential phase at all.




Drag reduction through self-similar bending of a flexible body.
Silas Alben, Michael Shelley, and Jun Zhang
Nature 420, 479-481 (2002).

Abstract: The classical theory of high-speed flow predicts that a moving rigid object experiences a drag proportional to the square of its speed. However, this reasoning does not apply if the object in the flow is flexible, because its shape then becomes a function of its speed -- for example, the rolling up of broad tree leaves in a stiff wind. The reconfiguration of bodies by fluid forces is common in nature, and can result in a substantial drag reduction that is beneficial for many organisms. Experimental studies of such flow structure interactions generally lack a theoretical interpretation that unifies the body and flow mechanics. Here we use a flexible fibre immersed in a flowing soap film to measure the drag reduction that arises from bending of the fibre by the flow. Using a model that couples hydrodynamics to bending, we predict a reduced drag growth compared to the classical theory. The fibre undergoes a bending transition, producing shapes that are self-similar; for such configurations, the drag scales with the length of self-similarity, rather than the fibre profile width. These predictions are supported by our experimental data.

Related:
Nature News and Views -- Bend and Survive, by Victor Steinberg
Nature's Secret to Building for Strength: Flexibility, Kenneth Chang, The New York Times, December 17,2002
Stark durch Nachgeben, Andrea Naica-Loebell, Telepolis, 11.12.2002




Dynamic Patterns and Self-Knotting of a Driven Hanging Chain
Andrew Belmonte, Shaden Eldakar, Michael Shelley, and Chris Wiggins
Physical Review Letters 87, (11), 114301 (2001).

Abstract: When shaken vertically, a hanging chain displays a startling variety of distinct behaviors. We find experimentally that instabilities occur in tonguelike bands of parameter space, to swinging or rotating pendular motion, or to chaotic states. Mathematically, the dynamics are described by a nonlinear wave equation. A linear stability analysis predicts instabilities within the well-known resonance tongues; their boundaries agree very well with experiment. Full simulations of the 3D dynamics reproduce and elucidate many aspects of the experiment. The chain is also observed to tie knots in itself, some quite complex. This is beyond the reach of the current analysis and simulations.

Related:
Click here for movies of the experiment
Click here for movies of the simulation
Maths helps magicians knot, NatureNews, 11 Sept. 2001




Heart simulation by an immersed boundary method with formal second-order accuracy and reduced numerical viscosity
David M. McQueen and Charles S. Peskin
Mechanics for a New Millennium, Proceedings of the International Conference on Theoretical and Applied Mechanics (ICTAM) 2000, (H. Aref and J.W. Phillips, eds.) Kluwer Academic Publishers, (2001).

Abstract: This paper describes a formally second-order accurate version of the immersed boundary method and its application to the computer simulation of blood flow in a three-dimensional model of the human heart.

Related:
Click here for heart animations computed by the immersed boundary method




Two-dimensional simulations of valveless pumping using the immersed boundary method
Eunok Jung and Charles S. Peskin
SIAM J. Sci. Comput. 23, 19-45 (2001).

Abstract: Flow driven by pumping without valves is examined, motivated by biomedical applications: cardiopulmonary resuscitation (CPR) and the human fetus before the development of the heart valves. The direction of flow inside a loop of tubingwhic h consists of (almost) rigid and flexible parts is investigated when the boundary of one end of the flexible segment is forced periodically in time. Despite the absence of valves, net flow around the loop may appear in these simulations. The magnitude and even the direction of this flow depend on the driving frequency of the periodic forcing.

Related:
An experiment on valveless pumping - AML experiment




Flexible filaments in a flowing soap film as a model for one-dimensional flags in a two-dimensional wind.
Jun Zhang, Stephen Childress, Albert Libchaber, and Michael Shelley
Nature 408, 835-839 (2000).

Abstract: The dynamics of swimming fish and flapping flags involves a complicated interaction of their deformable shapes with the surrounding fluid flow. Even in the passive case of a flag, the flag exerts forces on the fluid through its own inertia, elastic responses, and is likewise acted on by hydrodynamic pressure and drag. But such couplings are not well understood. Here we study these interactions experimentally, using an analogous system of flexible filaments in flowing soap films. We find that, for a single filament (or 'flag') held at its upstream end and otherwise unconstrained, there are two distinct, stable dynamical states. The first is a stretched-straight state: the filament is immobile and aligned in the flow direction. The existence of this state seems to refute the common belief that a flag is always unstable and will flap. The second is the flapping state: the filament executes a sinuous motion in a manner akin to the flapping of a flag in the wind. We study further the hydrodynamically coupled interaction between two such filaments, and demonstrate the existence of four different dynamical states.

Related:
Click here for ABC News video, March 2003. The late Mr. Peter Jennings reported about the work in the AML on flapping flags. - video
Online articles related to this research




Eulerian mean flow from an instability of convective plumes.
S. Childress
Chaos 10, 1054 (2000).

Abstract: The origin of large-scale flows in systems driven by concentrated Archimedean forces is considered.  A two-dimensional model  of plumes, such as those observed in thermal convection at large Rayleigh and Prandtl numbers, is introduced. From this model, we deduce the onset of mean flow as an instability of a convective state consisting of parallel vertical flow supported by buoyancy forces.  The form of the linear equation governing the instability is derived and two modes of instability are discussed, one of which leads to the onset of steady Eulerian mean flow in the system. We are thus able to link the origin of the mean flow precisely to the profiles of the unperturbed plumes. The form of the nonlinear  partial differential equation governing the Eulerian mean flow , including nonlinear effects, is derived in one special case.  The extension to three dimensions is outlined.




Periodic boundary motion in thermal turbulence
Jun Zhang, Albert Libchaber
Phys. Rev. Lett. 84, 4361 (2000).

Abstract: A free-floating plate is introduced in a Bénard convection cell with an open surface. It covers partially the cell and distorts the local heat flux, inducing a coherent flow that in turn moves the plate. Remarkably, the plate can be driven to a periodic motion even under the action of a turbulent fluid. The period of the oscillation depends on the coverage ratio, and on the Rayleigh number of the convective system. The plate oscillatory behavior observed in this experiment, may be related to a geological model, in which continents drift in a quasi-periodic fashion.




Non-Boussinesq effect: asymmetric velocity profiles in thermal convection
Jun Zhang, S. Childress, and A. Libchaber
Physics of Fluids 10, 1534 (1998).

Abstract: In thermal convection at high Rayleigh numbers, in the hard turbulent regime, a large scale flow is present. When the viscosity of the fluid strongly depends on temperature, the top-bottom symmetry is broken. In addition to the asymmetric temperature profile across the convection cell, the velocity profiles near the plate boundaries show dramatic differences from the symmetric case. We report here that the second derivative of the velocity profiles are of opposite signs in the thermal sub-layers, through measurements derived from the power spectrum of temperature time-series. As a result, the stress rate applied at the plates is maintained constant within a factor of 3, while the viscosity changes by a factor of 53, in qualitative agreement with previous theory.




Non-Boussinesq effect: thermal convection with broken symmetry
Jun Zhang, S. Childress, and A. Libchaber
Physics of Fluids 9, (4)a, 1034 (1997).

Abstract: We investigate large Rayleigh number (106-109) and large Prandtl number (102-103) thermal convection in glycerol in an aspect ratio one cubic cell. The kinematic viscosity of the fluid strongly depends upon the temperature. The symmetry between the top and bottom boundary layers is thus broken, the so-called non-Boussinesq regime. In a previous paper Wu and Libchaber have proposed that in such a state the two thermal boundary layers adjust their length scales so that the mean hot and cold temperature fluctuations are equal in the center of the cell. We confirm this equality. A simplified two-dimensional model for the mean center temperature based on an equation for the thermal boundary layer is presented and compared with the experimental results. The conclusion is that the central temperature adjusts itself so that the heat fluxes from the boundary layers are equal, temperature fluctuations at the center symmetrical, at a cost of very different temperature drops and Rayleigh number for each boundary.