Publications

Fish schools and bird flocks exhibit complex collective dynamics whose self-organization principles are largely unknown. The influence of hydrodynamics on such collectives has been relatively unexplored theoretically, in part due to the difficulty in modeling the temporally long-lived hydrodynamic interactions between many dynamic bodies. We address this through a novel discrete-time dynamical system (iterated map) that describes the hydrodynamic interactions between flapping swimmers arranged in one- and two-dimensional lattice formations. Our 1D results exhibit good agreement with previously published experimental data, in particular predicting the bistability of schooling states and new instabilities that can be probed in experimental settings. For 2D lattices, we determine the formations for which swimmers optimally benefit from hydrodynamic interactions. We thus obtain the following hierarchy: while a side-by-side single-row “phalanx” formation offers a small improvement over a solitary swimmer, 1D in-line and 2D rectangular lattice formations exhibit substantial improvements, with the 2D diamond lattice offering the largest hydrodynamic benefit. Generally, our self-consistent modeling framework may be broadly applicable to active systems in which the collective dynamics is primarily driven by a fluid-mediated memory.

We explore the behavior of micron-scale autophoretic Janus (Au / Pt) rods, having various Au / Pt length ratios, swimming near a wall in an imposed background flow. We find that their ability to robustly orient and move upstream, i.e., to rheotax, depends strongly on the Au / Pt ratio, which is easily tunable in synthesis. Numerical simulations of swimming rods actuated by a surface slip show a similar rheotactic tunability when varying the location of the surface slip versus surface drag. The slip location determines whether swimmers are pushers (rear actuated), pullers (front actuated), or in between. Our simulations and modeling show that pullers rheotax most robustly due to their larger tilt angle to the wall, which makes them responsive to flow gradients. Thus, rheotactic response infers the nature of difficult to measure flow fields of an active particle, establishes its dependence on swimmer type, and shows how Janus rods can be tuned for flow responsiveness.

We show that rotating membrane inclusions can crystallize due to combined hydrodynamic and steric interactions. Alone, steric repulsion of unconfined particles, even with thermal fluctuations, does not lead to crystallization, nor do rotational hydrodynamic interactions which allow only a marginally stable lattice. Hydrodynamic interactions enable particles to explore states inaccessible to a nonrotational system, yet, unlike Brownian motion, Hamiltonian conservation confines the ensemble which, when combined with steric interactions, anneals into a stable crystal state.

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

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

Cell biology has its beginnings in the first observations of cells through primitive microscopes and in the formulation of cell theory, which postulates that cells are the fundamental building blocks of life. Light microscopes showed that the insides of cells contained complex structures, such as nuclei, spindles, and chromosomes. The advent of electron microscopy in the mid 20th century brought the first truly detailed views of cell innards. Images revealed complexity at all observable scales, including cell-spanning networks of polymers, intricate organelles made of membranes, and a variety of micron- to nanometer-sized sacs and granules such as vesicles, lipid droplets, and ribosomes. (For a glossary of cellular components, see the Quick Study by Ned Wingreen, Physics Today, September 2006, page 80.) Those structures are immersed in or part of the aqueous cytoplasm—the cell’s fluidic medium.

Scientists have known for centuries that some plant and amoeboid cells have cytoplasmic flow inside them, as illustrated in figure 1a. Modern light microscopy has shown that such directed motions in cells are quite common. Researchers have studied those flows using such sophisticated methods as particle imaging velocimetry and simulations (see figures 1b and 1c). Such flows underlie the most basic biological functions of cells and can be a cause, an effect, or both. In any case, understanding them requires the study of forces and stresses that are created from activity inside the cell itself.

The organization of microtubules in spindles is complex and not fully understood. Here we report on current advances in generating 3D reconstructions of staged spindles by serial-section electron tomography, exemplified by the first mitotic spindle in early Caenorhabditis elegans embryo. We then review how advances in correlative light microscopy and quantitative electron tomography enable the development of theory and stochastic simulations, which describe how the microtubule organization in spindles emerges from their dynamics. We show how theory and simulations can be used to address long-standing questions in cell division research, advancing the field beyond a pure structural description of microtubules in spindles.

The macroscopic properties of polymeric fluids are inherited from the material properties of the fibers embedded in the solvent. The behavior of such passive fibers in flow has been of interest in a wide range of systems, including cellular mechanics, nutrient acquisition by diatom chains in the ocean, and industrial applications such as paper manufacturing. The rotational dynamics and shape evolution of fibers in shear depends upon the slenderness of the fiber and the non-dimensional “elasto-viscous” number that measures the ratio of the fluid’s viscous forces to the fiber’s elastic forces. For a small elasto-viscous number, the nearly-rigid fiber rotates in the shear, but when the elasto-viscous number reaches a threshold, buckling occurs. For even larger elasto-viscous numbers, there is a transition to a “snaking behavior” where the fiber remains aligned with the shear axis, but its ends curl in, in opposite directions. These experimentally-observed behaviors have recently been characterized computationally using slender-body theory and immersed boundary computations. However, classical experiments with nylon fibers and recent experiments with actin filaments have demonstrated that for even larger elasto-viscous numbers, multiple buckling sites and coiling can occur. Using a regularized Stokeslet framework coupled with a kernel independent fast multipole method, we present simulations that capture these complex fiber dynamics.

The Immersed Boundary (IB) method has been widely used to solve fluid-structure interaction problems, including those where the structure interacts with polymeric fluids. In this paper, we examine the convergence of one such scheme for a well known two-dimensional benchmark flow for the Oldroyd-B constitutive model, and we show that the traditional IB-based scheme fails to adequately capture the polymeric stress near to embedded boundaries. We analyze the reason for such failure, and we argue that this feature is not specific to the case study chosen, but a general feature of such methods due to lack of convergence in velocity gradients near interfaces. In order to remedy this problem, we build a different scheme for the Oldroyd-B system using the Immersed Boundary Smooth Extension (IBSE) scheme, which provides convergent viscous stresses near boundaries. We show that this modified scheme produces convergent polymeric stresses through the whole domain, including on embedded boundaries, and produces solutions in good agreement with known benchmarks.

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