arXiv subjects

Brato Chakrabarti

Publications and source records attributed to Brato Chakrabarti.

At least 19 recordsLinked to original sources

arXiv2026

Emergent odd response in active chiral films

Active chiral fluids can support a nondissipative transport coefficient known as odd (or Hall) viscosity. Hydrodynamic descriptions of such fluids typically introduce odd viscosity phenomenologically. How such a response emerges from specific microscopic interactions remains incompletely understood. Here, building on classical shear rheology, we microscopically derive an odd rheological response in active chiral films: thin layers of torque-exerting, elongated particles anchored to a no-slip surface. A canonical realization of such a film is the bacterial carpet, in which flagellated bacteria are tethered head-down to a solid surface while their flagella remain free to spin and inject angular momentum into the surrounding fluid. Using a kinetic theory for the orientational dynamics of these anchored particles, we derive their stress response to an imposed shear flow. We reveal that shear-induced reorientation leads to a flow-aligned polarization and a transverse surface traction from which the odd-viscosity tensor follows in closed form. Numerical solutions of the nonlinear kinetic theory further highlight saturation of the transverse traction at strong shear, driven by shear-induced orientation dynamics -- signaling departure from linear response. Our results demonstrate how odd viscosity can emerge self-consistently as a coarse-grained rheological signature of active fluid-structure interaction and establish active chiral films as a new controllable setting for odd hydrodynamics.

cond-mat.soft↗

arXiv2026

Growing, Buckling, and Swirling: motility from polymerization

Locomotion in low-Reynolds-number environments is achieved through a remarkable diversity of strategies, from flagellar rotation and ciliary beating to large-scale body deformations. A distinct and biologically important class of propulsion arises when surface-anchored filaments grow and collectively reorient - as seen in the cellulose-extruding bacterium Acetobacter xylinum and in recent experiments on actin-propelled synthetic colloids inspired by the motility of Listeria monocytogenes - suggesting that polymerization itself is a generic route to self-propulsion. Developing a theoretical framework for this class of problems requires simultaneously resolving filament kinetics, their orientational dynamics, and fluid-structure interactions - all self-consistently coupled to the resulting locomotion. To address this, we formulate a continuum framework in which the active forces driving locomotion emerge self-consistently from filament nucleation, growth, catastrophe, and hydrodynamic interactions. We show analytically that polymerization-induced compressive forces drive a long-wavelength buckling instability, leading to spontaneous symmetry breaking of the filament carpet and large-scale flows. In coupling this framework to a force- and torque-free motile spheroidal particle, a wide variety of behaviors emerge - this includes spontaneous spinning, directed motility, and chiral swimming - whose selection is governed by the spatial patterning of polymerizing filaments. These results establish a general theoretical foundation for motility, driven by collective dynamics of polymerizing filaments and point towards new design principles for synthetic micron-scale swimmers.

cond-mat.soft↗

arXiv2026

Reversibility, Chaos, and Attractors in Periodically Sheared Elastic Filaments

The dynamics of filaments in flow are central to understanding a wide range of biological and soft-matter systems, yet their behavior under time-dependent forcing remains poorly understood. Here, we investigate the long-time dynamics of Brownian inextensible elastic filaments subjected to strong uniform oscillatory shear by combining microfluidic experiments on actin filaments with numerical simulations based on a fluctuating Euler-Bernoulli elastica model in a viscous fluid. As the oscillation period increases, irreversibility emerges from the interplay of flow-induced deformations and thermal noise. This leads to a departure from reversible, deterministic rigid-body dynamics: in this regime, the filaments cycle between nearly straight, flow-aligned conformations at full periods and buckled shapes at half periods. Owing to the time-glide symmetry of the system, two such attracting states in fact coexist with a phase shift of half a period. The system spontaneously selects one, but occasionally switches between them as a result of noise, producing intermittent transitions between apparent order and disorder. This system constitutes an experimentally accessible realization of stochastic symmetry breaking, attractor hopping, and intermittency in a minimal nonequilibrium soft-matter system, with novel implications for the design and control of soft matter systems under time-dependent flows.

cond-mat.soft↗

arXiv2025

Hydrodynamic instabilities in driven chiral suspensions

Active Stokesian suspensions are conventionally understood to generate dipolar stresses that destabilize aligned states in the bulk and drive system-wide spatiotemporally chaotic flows. Here, we report dynamics in suspensions of torque-driven spinning chiral particles that exhibit a distinct and previously unrecognized route to collective dynamics. Using a mean-field kinetic theory, stability analysis, and nonlinear simulations, we demonstrate how flows driven by torque monopoles and self-propulsion resulting from microscopic chirality drive chaotic flows in three dimensions. Unlike the well-known alignment instability of dipolar active matter, the present dynamics is intrinsically tied to self-propulsion and relies on the emergent coupling between nematic and polar order. Our results establish a novel route to pattern formation, suggest strategies for designing torque-driven active suspensions, and provide a mechanistic framework to probe the rheology of chiral fluids.

cond-mat.soft↗

arXiv2025

The physical consequences of sperm gigantism

The male fruit fly produces ~1.8 mm long sperm, thousands of which can be stored until mating in a ~200 micron sac, the seminal vesicle. While the evolutionary pressures driving such extreme sperm (flagellar) lengths have long been investigated, the physical consequences of their gigantism are unstudied. Through high-resolution three-dimensional reconstructions of in vivo sperm morphologies and rapid live imaging, we discovered that stored sperm are organized into a dense and highly aligned state. The packed flagella exhibit system-wide collective 'material' flows, with persistent and slow-moving topological defects; individual sperm, despite their extraordinary lengths, propagate rapidly through the flagellar material, moving in either direction along material director lines. To understand how these collective behaviors arise from the constituents' nonequilibrium dynamics, we conceptualize the motion of individual sperm as topologically confined to a reptation-like tube formed by its neighbors. Therein, sperm propagate through observed amplitude-constrained and internally driven flagellar bending waves, pushing off counter-propagating neighbors. From this conception, we derive a continuum theory that produces an extensile material stress that can sustain an aligned flagellar material. Experimental perturbations and simulations of active elastic filaments verify our theoretical predictions. Our findings suggest that active stresses in the flagellar material maintain the sperm in an unentangled, hence functional state, in both sexes, and establish giant sperm in their native habitat as a novel and physiologically relevant active matter system.

cond-mat.soft↗

arXiv2024

Geometric Effects in Large Scale Intracellular Flows

This work probes the role of cell geometry in orienting self-organized fluid flows in the late stage Drosophila oocyte. Recent theoretical work has shown that a model, which relies only on hydrodynamic interactions of flexible, cortically anchored microtubules (MTs) and the mechanical loads from molecular motors moving upon them, is sufficient to generate observed flows. While the emergence of flows has been studied in spheres, oocytes change shape during streaming and it was unclear how robust these flows are to the geometry of the cell. Here we use biophysical theory and computational analysis to investigate the role of geometry and find that the axis of rotation is set by the shape of the domain and that the flow is robust to biologically relevant perturbations of the domain shape. Using live imaging and 3D flow reconstruction, we test the predictions of the theory/simulation, finding consistency between the model and live experiments, further demonstrating a geometric dependence on flow direction in late-stage Drosophila oocytes.

physics.bio-ph↗

arXiv2023

Cytoplasmic stirring by active carpets

Large cells often rely on cytoplasmic flows for intracellular transport, maintaining homeostasis, and positioning cellular components. Understanding the mechanisms of these flows is essential for gaining insights into cell function, developmental processes, and evolutionary adaptability. Here, we focus on a class of self-organized cytoplasmic stirring mechanisms that result from fluid-structure interactions between cytoskeletal elements at the cell cortex. Drawing inspiration from streaming flows in late-stage fruit fly oocytes, we propose an analytically tractable active carpet theory. This model deciphers the origins and three-dimensional spatio-temporal organization of such flows. Through a combination of simulations and weakly nonlinear theory, we establish the pathway of the streaming flow to its global attractor: a cell-spanning vortical twister. Our study reveals the inherent symmetries of this emergent flow, its low-dimensional structure, and illustrates how complex fluid-structure interaction aligns with classical solutions in Stokes flow. This framework can be easily adapted to elucidate a broad spectrum of self-organized, cortex-driven intracellular flows.

physics.flu-dyn↗

arXiv2023

Fluid circulation driven by collectively organized metachronal waves in swimming T. aceiti nematodes

Recent experiments have shown that the nematode {\it T. aceti} can assemble into collectively undulating groups at the edge of fluid drops. This coordinated state consists of metachronal waves and drives fluid circulation inside the drop. We find that the circulation velocity is about 2 mm/s and nearly half the speed of the metachronal wave. We develop a quasi two-dimensional hydrodynamics model using the Stokes flow approximation. The periodic motion of the nematodes constitute our moving boundary condition that drives the flow. Our model suggests that large amplitude excursions of the nematodes tails produce the fluid circulation. We discuss the constraints on containers that would enhance fluid motion, which could be used in the future design of on demand flow generating systems.

physics.flu-dyn↗

arXiv2022

A chemomechanical model of sperm locomotion reveals two modes of swimming

The propulsion of mammalian spermatozoa relies on the spontaneous periodic oscillation of their flagella. These oscillations are driven internally by the coordinated action of ATP-powered dynein motors that exert sliding forces between microtubule doublets, resulting in bending waves that propagate along the flagellum and enable locomotion. We present an integrated chemomechanical model of a freely swimming spermatozoon that uses a sliding-control model of the axoneme capturing the two-way feedback between motor kinetics and elastic deformations while accounting for detailed fluid mechanics around the moving cell. We develop a robust computational framework that solves a boundary integral equation for the passive sperm head alongside the slender-body equation for the deforming flagellum described as a geometrically nonlinear internally actuated Euler-Bernoulli beam, and captures full hydrodynamic interactions. Nonlinear simulations are shown to produce spontaneous oscillations with realistic beating patterns and trajectories, which we analyze as a function of sperm number and motor activity. Our results indicate that the swimming velocity does not vary monotonically with dynein activity, but instead displays two maxima corresponding to distinct modes of swimming, each characterized by qualitatively different waveforms and trajectories. Our model also provides an estimate for the efficiency of swimming, which peaks at low sperm number.

physics.flu-dyn↗

arXiv2022

Self-organized flows in phase-synchronizing active fluids

Many active biological particles, such as swimming microorganisms or motor-proteins, do work on their environment by going though a periodic sequence of shapes. Interactions between particles can lead to the phase-synchronization of their duty cycles. Here we consider collective dynamics in a suspension of such active particles coupled through hydrodynamics. We demonstrate that the emergent non-equilibrium states feature stationary patterned flows and robust unidirectional pumping states under confinement. Moreover the phase-synchronized state of the suspension exhibits spatially robust chimera patterns in which synchronized and phase-isotropic regions coexist within the same system. These findings demonstrate a new route to pattern formation and could guide the design of new active materials.

cond-mat.soft↗

arXiv2022

Dynamics of flexible filaments in oscillatory shear flows

The fluid-structure interactions between flexible fibers and viscous flows play an essential role in various biological phenomena, medical problems, and industrial processes. Of particular interest is the case of particles freely transported in time-dependent flows. This work elucidates the dynamics and morphologies of actin filaments under oscillatory shear flows by combining microfluidic experiments, numerical simulations, and theoretical modeling. Our work reveals that, in contrast to steady shear flows, in which small orientational fluctuations from a flow-aligned state initiate tumbling and deformations, the periodic flow reversal allows the filament to explore many different configurations at the beginning of each cycle. Investigation of filament motion during half time periods of oscillation highlights the critical role of the initial filament orientation on the emergent dynamics. This strong coupling between orientation and deformation results in new deformation regimes and novel higher-order buckling modes absent in steady shear flows. The primary outcome of our analysis is the possibility of suppression of buckling instabilities for certain combinations of the oscillation frequency and initial filament orientation, even in very strong flows. We explain this unusual behavior through a weakly nonlinear Landau theory of buckling, in which we treat the filaments as inextensible Brownian Euler-Bernoulli rods whose hydrodynamics are described by local slender-body theory.

physics.flu-dyn↗

arXiv2021

A multiscale biophysical model gives quantized metachronal waves in a lattice of cilia

Motile cilia are slender, hair-like cellular appendages that spontaneously oscillate under the action of internal molecular motors and are typically found in dense arrays. These active filaments coordinate their beating to generate metachronal waves that drive long-range fluid transport and locomotion. Until now, our understanding of their collective behavior largely comes from the study of minimal models that coarse-grain the relevant biophysics and the hydrodynamics of slender structures. Here we build on a detailed biophysical model to elucidate the emergence of metachronal waves on millimeter scales from nanometer scale motor activity inside individual cilia. Our study of a 1D lattice of cilia in the presence of hydrodynamic and steric interactions reveals how metachronal waves are formed and maintained. We find that in homogeneous beds of cilia these interactions lead to multiple attracting states, all of which are characterized by an integer charge that is conserved. This even allows us to design initial conditions that lead to predictable emergent states. Finally, and very importantly, we show that in nonuniform ciliary tissues, boundaries and inhomogeneities provide a robust route to metachronal waves.

cond-mat.soft↗

arXiv2021

Signatures of elastoviscous buckling in the dilute rheology of stiff polymers

As a stiff polymer tumbles in shear flow, it experiences compressive viscous forces that can cause it to buckle and undergo a sequence of morphological transitions with increasing flow strength. We use numerical simulations to uncover the effects of these transitions on the steady shear rheology of a dilute suspension of stiff polymers. Our results agree with classic scalings for Brownian rods in relatively weak flows but depart from them above the buckling threshold. Signatures of elastoviscous buckling include enhanced shear thinning and an increase in the magnitude of normal stress differences. We discuss our findings in the light of past work on rigid Brownian rods and non-Brownian elastic fibers and highlight the subtle role of thermal fluctuations in triggering instabilities.

physics.flu-dyn↗

arXiv2020

Trapping, gliding, vaulting: Transport of semiflexible polymers in periodic post arrays

The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the dynamics of semiflexible polymers under the influence of an imposed flow in a structured two-dimensional lattice serving as an idealization of a porous medium. This problem has received much attention in the limit of reptation and for long-chain polymer molecules such as DNA that are transported through micropost arrays for electrophoretic chromatographic separation. In contrast to long entropic molecules, the dynamics of elastic polymers results from a combination of scattering with the obstacles and flow-induced buckling instabilities. We identify three dominant modes of transport that involve trapping, gliding and vaulting of the polymers around the obstacles, and we reveal their essential features using tools from dynamical systems theory. The interplay of these scattering dynamics with transport and deformations in the imposed flow results in the long-time asymptotic dispersion of the center of mass, which we quantify in terms of a hydrodynamic dispersion tensor. We then discuss a simple yet efficient chromatographic device that exploits the competition between different modes of transport to sort filaments in a dilute suspension according to their lengths.

cond-mat.soft↗

arXiv2019

Hydrodynamic synchronization of spontaneously beating filaments

Using a geometric feedback model of the flagellar axoneme accounting for dynein motor kinetics, we study elastohydrodynamic phase synchronization in a pair of spontaneously beating filaments with waveforms ranging from sperm to cilia and Chlamydomonas. Our computations reveal that both in-phase and anti-phase synchrony can emerge for asymmetric beats while symmetric waveforms go in-phase, and elucidate the mechanism for phase slips due to biochemical noise. Model predictions agree with recent experiments and illuminate the crucial roles of hydrodynamics and mechanochemical feedback in synchronization.

physics.flu-dyn↗

arXiv2019

Flexible filaments buckle into helicoidal shapes in strong compressional flows

The occurrence of coiled or helical morphologies is common in nature, from plant roots to DNA packaging into viral capsids, as well as in applications such as oil drilling processes. In many examples, chiral structures result from the buckling of a straight fiber either with intrinsic twist or to which end moments have been applied in addition to compression forces. Here, we elucidate a generic way to form regular helicoidal shapes from achiral straight filaments transported in viscous flows with free ends. Through a combination of experiments using fluorescently labeled actin filaments in microfluidic divergent flows and of two distinct sets of numerical simulations, we demonstrate the robustness of helix formation. A nonlinear stability analysis is performed and explains the emergence of such chiral structures from the nonlinear interaction of perpendicular planar buckling modes, an effect that solely requires a strong compressional flow, independent of the exact nature of the fiber or type of flow field. The fundamental mechanism for the uncovered morphological transition and characterization of the emerging conformations advance our understanding of several biological and industrial processes and can also be exploited for the controlled microfabrication of chiral objects.

physics.flu-dyn↗

arXiv2019

Transport and dispersion of active particles in periodic porous media

The transport of self-propelled particles such as bacteria and phoretic swimmers through crowded heterogeneous environments is relevant to many natural and engineering processes, from biofilm formation and contamination processes to transport in soils and biomedical devices. While there has been experimental progress, a theoretical understanding of mean transport properties in these systems has been lacking. In this work, we apply generalized Taylor dispersion theory to analyze the long-time statistics of an active self-propelled Brownian particle transported under an applied flow through the interstices of a periodic lattice that serves as an idealization of a porous medium. Our theoretical model, which we validate against Brownian dynamics simulations, is applied to unravel the roles of motility, fluid flow, and lattice geometry on asymptotic mean velocity and dispersivity. In weak flows, transport is dominated by active dispersion, which results from self-propulsion in the presence of noise and is hindered by the obstacles that act as entropic barriers. In strong flows, shear-induced Taylor dispersion becomes the dominant mechanism for spreading, with pillars now acting as regions of shear production that enhance dispersion. The interplay of these two effects leads to complex and unexpected trends, such as a non-monotonic dependence of axial dispersivity on flow strength and a reduction in dispersion due to swimming activity in strong flows. Brownian dynamics are used to cast light on the pre-asymptotic regime, where tailed distributions are observed in agreement with recent experiments on motile micro-organisms. Our results also highlight the subtle effects of pillar shape, which can be used to control the magnitude of dispersion and to drive a net particle migration in quiescent systems.

physics.flu-dyn↗

arXiv2018

Morphological transitions of elastic filaments in shear flow

The morphological dynamics, instabilities and transitions of elastic filaments in viscous flows underlie a wealth of biophysical processes from flagellar propulsion to intracellular streaming, and are also key to deciphering the rheological behavior of many complex fluids and soft materials. Here, we combine experiments and computational modeling to elucidate the dynamical regimes and morphological transitions of elastic Brownian filaments in a simple shear flow. Actin filaments are employed as an experimental model system and their conformations are investigated through fluorescence microscopy in microfluidic channels. Simulations matching the experimental conditions are also performed using inextensible Euler-Bernoulli beam theory and non-local slender-body hydrodynamics in the presence of thermal fluctuations, and agree quantitatively with observations. We demonstrate that filament dynamics in this system is primarily governed by a dimensionless elasto-viscous number comparing viscous drag forces to elastic bending forces, with thermal fluctuations only playing a secondary role. While short and rigid filaments perform quasi-periodic tumbling motions, a buckling instability arises above a critical flow strength. A second transition to strongly-deformed shapes occurs at a yet larger value of the elasto-viscous number and is characterized by the appearance of localized high-curvature bends that propagate along the filaments in apparent "snaking" motions. A theoretical model for the so far unexplored onset of snaking accurately predicts the transition and explains the observed dynamics. For the first time, we present a complete characterization of filament morphologies and transitions as a function of elasto-viscous number and scaled persistence length and demonstrate excellent agreement between theory, experiments and simulations.

physics.flu-dyn↗