

AML Publications, Images,
and Video 

Dynamic selfassembly 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, 45844589 (2016). Abstract: Biological systems often involve the selfassembly of basic components into complex and functioning structures. Artificial systems that mimic such processes can provide a wellcontrolled setting to explore the principles involved and also synthesize useful micromachines. Our experiments show that immotile, but active, components selfassemble into two types of structure that exhibit the fundamental forms of motility: translation and rotation. Specifically, micronscale 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 runandtumble motion.  
Linear drag law for highReynoldsnumber 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 highReynoldsnumber forcespeed 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 timeaveraged 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 dragspeed 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.
 
Actomyosindriven leftright 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 2016, 38:2430 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 molecularscale torque generation processes in the actomyosin cytoskeleton.  
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 selforganization 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 motordriven clustering of filament ends is a generic mechanism leading to contraction. Related: "Cytoskeleton: Largescale 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.  
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 flowmediated 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 wingwake 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 highfidelity 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 highspeed water flows. We find that different initial geometries are sculpted into a similar terminal form before ultimately vanishing, suggesting convergence to a stable shapeflow state. A model linking the flow and solute concentration shows how uniform boundarylayer 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.  
Stable hovering of a jellyfishlike flying machine
L. Ristroph and S. Childress Journal of the Royal Society Interface 11, 20130992 (2014). Abstract: Ornithopters, or flappingwing 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 selfrighting flight using flapping wings alone, without relying on additional aerodynamic surfaces and without feedback control. We design, construct and testfly 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 centreofmass location and the coupling of body translation and rotation. These results show the promise of flappingflight strategies beyond those that directly mimic the wing motions of flying animals. 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 surfacetension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. For a 3D diffusiondominated 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 KellerSegel model for the collective chemotactic aggregation of slime mold colonies. Mathematical analysis has established that the KellerSegel model can yield finitetime, finitemass concentration singularities. We show that such singular behavior occurs in our finitedepth system, and study the associated 3D flow structures. Hydrodynamic capture of microswimmers into spherebound orbits D. Takagi, J. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang Soft Matter 10, 17841789 (2014). Abstract: Selfpropelled particles can exhibit surprising nonequilibrium behaviors, and how they interact with obstacles remains an important open problem. We show experimentally that chemically propelled microrods can be captured, with little decrease in their speed, into close orbits around solid spheres resting on a horizontal plane. This shortrange interaction is consistent with a model, based on lubrication theory, of a force and torquefree swimmer driven by a surface slip and moving near a solid surface. This study reveals the crucial aspects of interactions of selfpropelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter. Selfsimilar 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 landforms, 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 selfsimilar evolution of the body, with an emerging quasitriangular 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 nonspherical 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, 497517 (2013). Abstract: Active suspensions, such as suspensions of selfpropelled 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 selfpropelled 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 largescale 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 microswimmers Lushi E and Peskin CS Computers and Structures 22, 239248 (2013). Abstract: We present a mathematical model and simulation method to compute the colonial dynamics of microswimmers that interact directly and through the fluid they are suspended in. The model uses the stress generated by each selfmotile particle for longrange interactions and includes shortrange steric effects between particles. The timestep 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 selfpropelling particles in three dimensions and with background flows. We show examples of collective behavior in suspensions of "pusher" and "puller" microswimmers. Optimization of chiral structures for microscale propulsion E. Keaveny, S. Walker, and M. Shelley Nanoletters 13, 531537 (2013). Abstract: Recent advances in micro and nanoscale fabrication techniques allow for the construction of rigid, helicallyshaped microswimmers that can be actuated using applied magnetic fields. These swimmers represent the first steps toward the development of microrobots 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 crosssections, 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 setup to investigate both the transient and longtime 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 OldroydB/NavierStokes 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 phaselocking. Dispersion of SelfPropelled Rods Undergoing FluctuationDriven 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 fluctuationdriven 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 longterm 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 IEEEASME 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 inhouse designed power electronics for lowfrequency 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 SelfGenerated 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 selfgenerated flows. A kinetic theory coupling runandtumble 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 longtime nonlinear dynamics show that hydrodynamic interactions can limit and modify chemotacticallydriven aggregation dynamics. In pusher suspensions chemotactic aggregation can lead to destabilizing timedependent 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 pyramidshaped 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 bottomheavy flyers. Related: Simulations and Press A weakcoupling expansion for viscoelastic fluids applied to dynamic settling of a body M.N.J. Moore and M.J. Shelley Journal of NonNewtonian Fluid Mechanics 183184, 2536 (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 weakcoupling expansion that allows for semianalytical 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 OldroydB 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 weakcoupling expansion off ers information for orderone 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 timedependent bodyforce, and show how the introduction of the forcing timescale modi.fies the bodydynamics. Oscillations of a Layer of Viscoelastic Fluid under Steady Forcing B. Liu, M. Shelley, and J. Zhang Journal of NonNewtonian Fluid Mechanics 175176, 3843 (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 counterrotating 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, 7797 (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. FluidStructure Interactions: Research in the Courant Institute's Applied Mathematics Laboratory S. Childress, M. Shelley, and J. Zhang Communications in Pure and Applied Mathematics 65, 16971721 (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 LargeScale Flows in Motile Suspensions D. Saintillan and M. Shelley Journal of the Royal Society Interface 9, 571585 (2012). Abstract: The emergence of coherent structures, largescale flows, and correlated dynamics in suspensions of motile particles such as swimming microorganisms 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 largescale correlated motions in suspensions of rearactuated swimmers, or pushers, above a critical volume fraction and system size. This transition, which is not observed in suspensions of headactuated 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 meanfield 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 , 18091823 (2012). Abstract: Undulatory locomotion of microorganisms 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 fluidfilled arrays of micropillars 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 lifelike 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: Demo1LargeLatticeMovie Demo2SmallLatticeMovie 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 solidsolid friction is a classical subject, the mechanisms underlying frictionbased 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, JeanLuc Thiffeault and Jane Wang Physica D 240, 20, 15651684 (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 710th 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, 527556 (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 centreofmass and centreofvolume 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 50300. 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 SecondKind Boundary Integral Equation for Surface Tractions in Stokes Flow E. Keaveny and M. Shelley Journal of Computational Physics 230, 21412159 (2011). Abstract: A secondkind integral equation for the tractions on a rigid body moving in a Stokesian fluid is established using the Lorentz reciprocal theorem and a completed secondkind integral equation for a doublelayer density. A secondorder 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 nonlocal slender body theories. Motivated by the design of artificial microswimmers, similar simulations are performed on previously unstudied helices of noncircular crosssection to determine the dependence of the velocity and propulsion efficiency on the crosssection aspect ratio and orientation. Dynamics of Complex BioFluids 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. BenAmar, 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, 449465 (2011). Abstract: The flapping or bending of a flexible planar structure in a surrounding fluid flow, which includes the flapping of flags and the selfstreamlining of flexible bodies, constitutes a central problem in the field of fluidbody 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, 16021614 (2011). Abstract: To understand observations of low Reynolds number mixing and flow transitions in viscoelastic fluids, we study numerically the dynamics of the OldroydB viscoelastic fluid model. The fluid is driven by a simple timeindependent 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 smallscale vortices. This drives flow mixing, the details of which we closely examine. These new flow states are dominated by a singlequadrant 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 shearthickening 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 smallamplitude 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 underperformance relative to a rigid (nonpitching) 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 crosssection. 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 illposedness. Hence, we investigate the structure of this system linearized near a state of uniform isotropy. The linearized system is nonnormal and variable coefficient, and not wholly described by an eigenvalue problem, in particular at small lengthscales. Using a high wavenumber asymptotic analysis, we show that while longwave stability depends upon the particular swimming mechanism, shortwave 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 wellposed, 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 longwave instability in a Pusher suspension. We find reasonable agreement between the predictions of our theory and numerical simulations of rodlike 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, 415425 (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 quasisteady 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, 12601291 (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 NavierStokes 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 infinitedimensional 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 meritfunction 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 NavierStokes 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 fronttracking approach. In computing functional sensitivities with respect to shape, we use L^{2}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 steadystate 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 tophalf 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, 958977 (2010). Abstract: Motivated by the locomotion of flagellated microorganisms 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 mixedtype 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 secondorder accurate spatial and temporal discretizations. We find that the nearfield 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 micronscale particle clusters with helical symmetry. The basic building blocks of these aggregates are doublets composed of two micronscale beads of different radii bonded together by a magnetic cement. Such selfassembled 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 lowReynoldsnumber mixing and flow transitions in viscoelastic fluids, we simulate the dynamics of the OldroydB 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 smallerscale 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. TS2009Vort.mov: Movie of the dynamics of the vorticity. Note that there is a change in the scale of the axes at t=500. TS2009StrmLine.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. TS2009TrS.mov: Movie of the dynamics of the trace of the stress tensor. TS2009S12.mov: Movie of the dynamics of the shear stress S12. TS2009Vort_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 Shapechanging 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 shapechanging body can hover or ascend in an oscillating background flow. We study this ratcheting effect through numerical simulations of the twodimensional NavierStokes equations at intermediate Reynolds number. This effect could describe a viable means of locomotion or transport in such environments as a tidal pool with wavedriven 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 selfpropelled 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 nonlinear pattern formation in these systems. The evolution of a suspension of selfpropelled particles is modeled using a conservation equation for the particle configurations, coupled to a meanfield 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 selfpropelled 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. Nonlinear effects are also investigated using numerical simulations in two dimensions. These simulations confirm the results of the stability analysis, and the longtime nonlinear behavior is shown to be characterized by the formation of strong density fluctuations, which merge and break up in time in a quasiperiodic 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 swimmerdriven 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 nonNewtonian responses. Here, we present a numerical method for simulating an OldroydB fluid coupled to contractile, moving walls. A marker and cell gridbased 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 OldroydB 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) SelfInduced 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 largescale 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  Earthinabox 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 Tabletop experiment could explain why continents drift, June 24, 2008  (one must signin 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 nonlinear continuum simulations to study the collective dynamics in suspensions of selfpropelled 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, nonlinear effects are investigated, and the longtime 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 antiparallel vorticity in Euler flows Stephen Childress Physica D 237, 19211925 (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 antiparallel 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 finitetime 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 fullynonlinear 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, 53975425 (2008). Abstract: We test the efficacy of using a single Lagrangian point to represent a sphere, and a onedimensional 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 threedimensional 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 R^{3}. 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 shortpitched 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, 861870 (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 nematictoisotropic 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 nematictoisotropic 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 OldroydB 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 OldroydB 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 FENEP penalization appears to keep the stress bounded, but a cusp singularity is still approached exponentially in time. Orientational order and instabilities in suspensions of selflocomoting rods David Saintillan and Michael Shelley Physical Review Letters 99, 058102 (2007). Abstract: The orientational order and dynamics in suspensions of selflocomoting 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 largescale orientational disorder for particle dispersion are also discussed. Related: Click here to watch the dynamics of an active particle suspension StretchCoil Transition and Transport of Fibers in Cellular Flows YuanNan 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 "stretchcoil" 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 timeindependent closedstreamline 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 bucklingdriven transport Modeling the dynamics of a free boundary on turbulent thermal convection JinQiang Zhong and Jun Zhang Physical Review E 76, 016307 (2007). Abstract: Based on our previous experimental study, we present a onedimensional, 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 fullscale simulations. Dynamical states of a mobile heat blanket on a thermally convecting fluid JinQiang 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 largescale 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 lowdimensional 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 1065 Hz at amplitudes 15 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 selfsimilar 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 twodimensional flexible body interacting in a twodimensional flow. This coupled fluidstructure 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 AnnaKarin 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 inphase 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, 1116311166 (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 Jinqiang 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 selforganization. They range from smallscale thermal plumes that are produced near both the top and the bottom boundaries to largescale 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 selfsupporting sheet into flowing water, we study a heavy, streamlined 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 SaffmanTaylor Instability Petri Fast and Michael J. Shelley Journal of Computational Physics 212, 15 (2005). Abstract: Ten years ago Hou, Lowengrub and Shelley published a stateoftheart boundary integral simulation of a classical viscous fingering problem, the SaffmanTaylor 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 SaffmanTaylor 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, 393425 (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 twodimensional 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, 195212 (2005). Abstract: In this paper, we have used the immersed boundary method to solve the twodimensional NavierStokes equations for two immersed wings performing an idealized 'clap and fling' stroke and a 'fling' halfstroke. 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 twowinged case than in the onewinged case. This differs from threedimensional insect flight where the leading edge vortices remain attached to the wing throughout each halfstroke. 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 twowinged fling during the translational phase are also enhanced when compared to the onewinged case. Indeed, they begin about 70% higher than the onewinged case during pure translation. When averaged over the entire translational part of the stroke, lift coefficients per wing are 35% higher for the twowinged case during a 4.5 chord translation following fling. In addition, lift enhancement increases with decreasing Re. This result suggests that the WeisFogh mechanism of lift generation has greater benefit to insects flying at lower Re. Drag coefficients produced during fling are also substantially higher for the twowinged case than the onewinged 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, 147155 (2004). Abstract: Flapping flight is ubiquitous in Nature, yet cilia and flagella, not wings, prevail in the world of microorganisms. 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 symmetrybreaking 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 flappingbased locomotion of swimming and flying animals. Related: Click here to see a video of coherent locomotion resulting from a symmetrybreaking instability How flexibility induces streamlining in a twodimensional flow. Silas Alben, Michael Shelley, and Jun Zhang Physics of Fluids 16, 16941713 (2004). Abstract: Recent work in biofluid 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 soapfilm 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 freestreamline models that couple fluid and elastic forces and solve them in an efficient numerical scheme. Shape selfsimilarity 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 U^{2} drag scaling of rigid bodies to a U^{4/3} 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 farfield 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 Re_{ω} Stephen Childress and Robert Dudley Journal of Fluid Mechanics 498, 257288 (2004). Abstract: From observations of swimming of the shellless 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 520. We test the hypothesis that Re ≈ 520 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 Re_{ω} = ω L^{2}/ν. For a selfsimilar 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 U_{f} obtained at the instability is determined by the mechanics of a viscous fluid at a value of Re_{f}=U_{f} 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), 20662083 (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. 1623]. 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 NavierStokes 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 AnnaKarin Tornberg and Michael J. Shelley Journal of Computational Physics 196 840 (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 nonlocal 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 EulerBernoulli theory to model bending and tensile forces yields an integral expression for the velocity of the filament centerlines, coupled to auxiliary integrodifferential 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 timestepping 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 fiascoelastic 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 NonNewtonian HeleShaw 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 longtime simulation of an air bubble displacing a nonNewtonian fluid in the prototypical thin film device, the Helehaw cell. We use a twodimensional generalization of Darcy's law that accounts for shear thinning of a nonNewtonian 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 bodyconforming grids reduces grid anisotropy effects and allows the accurate modeling of boundary conditions. Chaotic mixing in a torus map JeanLuc Thiffeault and Stephen Childress Chaos 13, (2), 502507 (2003). Abstract: The advection and diffusion of a passive scalar is investigated for a map of the 2torus. The map is chaotic, and the limit of almostuniform 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 advectiondiffusion operator, in which most of the scalar variance is concentrated at small scales, even though a largescale 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 selfsimilar bending of a flexible body. Silas Alben, Michael Shelley, and Jun Zhang Nature 420, 479481 (2002). Abstract: The classical theory of highspeed 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 selfsimilar; for such configurations, the drag scales with the length of selfsimilarity, 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 NaicaLoebell, Telepolis, 11.12.2002 Dynamic Patterns and SelfKnotting 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 wellknown 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 secondorder 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 secondorder accurate version of the immersed boundary method and its application to the computer simulation of blood flow in a threedimensional model of the human heart. Related: Click here for heart animations computed by the immersed boundary method Twodimensional simulations of valveless pumping using the immersed boundary method Eunok Jung and Charles S. Peskin SIAM J. Sci. Comput. 23, 1945 (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 onedimensional flags in a twodimensional wind. Jun Zhang, Stephen Childress, Albert Libchaber, and Michael Shelley Nature 408, 835839 (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 stretchedstraight 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 largescale flows in systems driven by concentrated Archimedean forces is considered. A twodimensional 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 freefloating 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 quasiperiodic fashion. NonBoussinesq 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 topbottom 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 sublayers, through measurements derived from the power spectrum of temperature timeseries. 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. NonBoussinesq 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 (10^{6}10^{9}) and large Prandtl number (10^{2}10^{3}) 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 socalled nonBoussinesq 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 twodimensional 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. 