arXiv subjects

Zvonimir Dogic

Publications and source records attributed to Zvonimir Dogic.

At least 19 recordsLinked to original sources

arXiv2026

Mechanics of heterogeneous fiber networks

Internally generated active stresses drive soft materials into architectures inaccessible to thermal self-assembly. We use a microtubule-based active fluid to assemble and irreversibly restructure actin-fascin networks. Subsequently, we probe the mesoscale mechanics of such networks by combining active microrheology with fluorescence imaging of the strain field around the probe. Increasing motor concentration broadens the pore-size distribution and thickens load-bearing bundles, raising the mean local elastic modulus and its spatial variability. Displacement fields of actively-processed networks propagate over longer range when compared to unprocessed networks. At large strains, both networks strain soften and plastically restructure. The combined microrheology and strain-imaging approach show that tunable active stresses reprogram the structure and viscoelastic response of fiber networks at the scale of their structural heterogeneity.

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arXiv2026

Bicontinuity in active phase separation

We study phase separation between coexisting active and passive fluids in three-dimensions, using numerical simulation and experiments. Chaotic flows of the active phase drive giant interfacial deformations, causing the co-existing phases to interpenetrate and generate a continuously reconfiguring bicontinuous morphology which persists over the lifetime of the active fluid. Active bicontinuous structures are dominated by sheet-like interfaces, in marked difference from passive liquid-liquid phase separation which is controlled by saddle-like surfaces. Activity and surface tension control the length scale of the bicontinuous structure. These results demonstrate how active stresses suppress the coarsening of conventional phase separation, generating steady-state reconfigurable morphologies not accessible with conventional surface-modifying agents or through quenching of transient phase separated structures.

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arXiv2025

Mechanical instability generates monodisperse colloidosomes

Formation and rupture of vesicles is a fundamental process underlying diverse phenomena in biology, materials science, and biomedical applications. Vesicles form when the area of a growing disk-like membrane exceeds a critical value at which the edge and bending energies balance each other. Observing such topological transitions in lipid bilayers is a challenge because of their nanoscale dimensions and rapid dynamics. We study a scaled-up model of colloidal membranes assembled from rod-shaped colloidal particles. The unique features of colloidal membranes enable the real-time visualization of spontaneous closure driven by instability relevant to all membrane-based materials. First-principles theory quantitatively predicts the instability point for vesicle formation and intermediate membrane conformations during the disk-to-vesicle transition. The instability generates monodisperse, selectively permeable colloidosomes with size controlled by gravity and membrane thickness, providing a scalable and programmable platform for diverse applications.

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arXiv2025

Active assembly and non-reciprocal dynamics of elastic membranes

Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study adhesive non-thermal fibers immersed in an active fluid. Autonomous chaotic flows power non-equilibrium fiber dynamics, inducing their collisions, generating connections, and weaving a membrane-shaped elastic network. This active assembly generates a hierarchy of shapes, structures, and dynamical processes spanning nanometers to centimeters. Ultimately, it generates an active membrane that exhibits global limit cycles induced by a non-reciprocal coupling between the elastic membrane deformations and the alignment axis of the polar active fluid. Our work merges self-assembly with active matter, demonstrating self-processing materials wherein hierarchical life-like structures and dynamics emerge from an initially structureless suspension.

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arXiv2025

Topology and Kinetic Pathways of Colloidosome Assembly and Disassembly

Liquid shells, such as lipid vesicles and soap bubbles, are ubiquitous throughout biology, engineered matter, and everyday life. Their creation and disintegration are defined by a singularity that separates a topologically distinct extended liquid film from a boundary-free closed shell. Such topology-changing processes are essential for cellular transport and drug delivery. However, their studies are challenging because of the rapid dynamics and small length scale of conventional lipid vesicles. We develop fluid colloidosomes, micron-sized analogs of lipid vesicles. We study their stability close to their disk-to-sphere topological transition. Intrinsic colloidal length and time scales slow down the dynamics to reveal vesicle conformations in real time during their assembly and disassembly. Remarkably, the lowest-energy pathway by which a closed vesicle transforms into a disk involves a topologically distinct cylinder-like intermediate. These results reveal universal aspects of topological changes in all liquid shells and a robust platform for the encapsulation, transport, and delivery of nanosized cargoes.

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arXiv2024

Closed-loop control of active nematic flows

Living things enact control of non-equilibrium, dynamical structures through complex biochemical networks, accomplishing spatiotemporally-orchestrated physiological tasks such as cell division, motility, and embryogenesis. While the exact minimal mechanisms needed to replicate these behaviors using synthetic active materials are unknown, controlling the complex, often chaotic, dynamics of active materials is essential to their implementation as engineered life-like materials. Here, we demonstrate the use of external feedback control to regulate and control the spatially-averaged speed of a model active material with time-varying actuation through applied light. We systematically vary the controller parameters to analyze the steady-state flow speed and temporal fluctuations, finding the experimental results in excellent agreement with predictions from both a minimal coarse-grained model and full nematohydrodynamic simulations. Our findings demonstrate that proportional-integral control can effectively regulate the dynamics of active nematics in light of challenges posed by the constituents, such as sample aging, protein aggregation, and sample-to-sample variability. As in living things, deviations of active materials from their steady-state behavior can arise from internal processes and we quantify the important consequences of this coupling on the controlled behavior of the active nematic. Finally, the interaction between the controller and the intrinsic timescales of the active material can induce oscillatory behaviors in a regime of parameter space that qualitatively matches predictions from our model. This work underscores the potential of feedback control in manipulating the complex dynamics of active matter, paving the way for more sophisticated control strategies in the design of responsive, life-like materials.

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arXiv2024

Asymmetric fluctuations and self-folding of active interfaces

We study the structure and dynamics of the interface separating a passive fluid from a microtubule-based active fluid. Turbulent-like active flows power giant interfacial fluctuations, which exhibit pronounced asymmetry between regions of positive and negative curvature. Experiments, numerical simulations, and theoretical arguments reveal how the interface breaks up the spatial symmetry of the fundamental bend instability to generate local vortical flows that lead to asymmetric interface fluctuations. The magnitude of interface deformations increases with activity: In the high activity limit, the interface self-folds invaginating passive droplets and generating a foam-like phase, where active fluid is perforated with passive droplets. These results demonstrate how active stresses control the structure, dynamics, and break-up of soft, deformable, and reconfigurable liquid-liquid interfaces.

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arXiv2024

Deep-learning Optical Flow Outperforms PIV in Obtaining Velocity Fields from Active Nematics

Deep learning-based optical flow (DLOF) extracts features in adjacent video frames with deep convolutional neural networks. It uses those features to estimate the inter-frame motions of objects at the pixel level. In this article, we evaluate the ability of optical flow to quantify the spontaneous flows of MT-based active nematics under different labeling conditions. We compare DLOF against the commonly used technique, particle imaging velocimetry (PIV). We obtain flow velocity ground truths either by performing semi-automated particle tracking on samples with sparsely labeled filaments, or from passive tracer beads. We find that DLOF produces significantly more accurate velocity fields than PIV for densely labeled samples. We show that the breakdown of PIV arises because the algorithm cannot reliably distinguish contrast variations at high densities, particularly in directions parallel to the nematic director. DLOF overcomes this limitation. For sparsely labeled samples, DLOF and PIV produce results with similar accuracy, but DLOF gives higher-resolution fields. Our work establishes DLOF as a versatile tool for measuring fluid flows in a broad class of active, soft, and biophysical systems.

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arXiv2023

Light-activated microtubule-based 2D active nematic

We characterize two-dimensional (2D) microtubule-based active nematics driven by light-responsive kinesin motor clusters. We assess two constructs of optogenetic kinesin: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors. Focusing on opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light and examine the transient behavior between steady-states. The steady-state nematic flow and defect densities are set by the applied light intensity across centimeter-sized samples, independent of initial conditions. Although nematic flow reaches steady-state within tens of seconds, the defect density exhibits transient behavior for 4 to 10 minutes, showing a separation between small-scale active reorganization and system-scale structural states. This work establishes an experimental platform to test theoretical frameworks which exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.

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arXiv2023

Rectified Rotational Dynamics of Mobile Inclusions in Two-Dimensional Active Nematics

We investigate the dynamics of mobile inclusions embedded in 2D active nematics. The interplay between the inclusion shape, the boundary-induced nematic order, and the autonomous flow powers the inclusion motion. Disks and achiral gears exhibit unbiased rotational motion, but with distinct dynamics. In comparison, chiral gear-shaped inclusions exhibit long-term rectified rotation, which is correlated with dynamics and polarization of nearby +1/2 topological defects. The chirality of defect polarities and the active nematic texture around the inclusion correlate with the inclusion's instantaneous rotationr ate. Inclusions provide a promising tool for probing the rheological properties of active nematics and extracting ordered motion from the inherently chaotic motion of active nematics.

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arXiv2022

Bonded straight and helical flagellar filaments form ultra-low-density glasses

We study how the three-dimensional shape of rigid filaments determines the microscopic dynamics and macroscopic rheology of entangled semi-dilute Brownian suspensions. To control the filament shape we use bacterial flagella, which are micron-long helices assembled from flagellin monomers. We compare the dynamics of straight rods, helical filaments, and shape diblock copolymers composed of seamlessly joined straight and helical segments. Caged by their neighbors, straight rods preferentially diffuse along their long axis, but exhibit significantly suppressed rotational diffusion. Entangled helical filaments escape their confining tube by corkscrewing through the dense obstacles created by other filaments. By comparison, the adjoining segments of the rod-helix shape-diblocks suppress both the translation and the corkscrewing dynamics, so that shape-diblocks become permanently jammed at exceedingly low densities. We also measure the rheological properties of semi-dilute suspensions and relate their mechanical properties to the microscopic dynamics of constituent filaments. In particular, rheology shows that an entangled suspension of shape rod-helix copolymers forms a low-density glass whose elastic modulus can be estimated by accounting for how shear deformations reduce the entropic degrees of freedom of constrained filaments. Our results demonstrate that the three-dimensional shape of rigid filaments can be used to design rheological properties of semi-dilute fibrous suspensions.

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arXiv2022

Structure and dynamics of motor-driven microtubule bundles

Connecting the large-scale emergent behaviors of active materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by studying the impact of polyethylene glycol, a crowding agent, on bundles of microtubules and kinesin-14 molecular motors. Bundles assembled in the presence of either low or high concentrations of polyethylene glycol generate similar net extensile behaviors. However, as polyethylene glycol concentration is increased, the motion of microtubules in the bundles transition from bi-directional sliding with extension to pure extension with no sliding. Small-angle X-ray scattering shows that the transition in microtubule dynamics is concomitant with a rearrangement of microtubules in the bundles from an open hexagonal to a compressed rectangular lattice. These results demonstrate that bundles of microtubules and molecular motors can display similar mesoscopic extensile behaviors despite having very different internal structures and dynamics.

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arXiv2022

Spatiotemporal patterning of extensile active stresses in microtubule-based active fluids

Active stresses, which are collectively generated by the motion of energy-consuming rod-like constituents, generate chaotic autonomous flows. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering, and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend-instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

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arXiv2022

Controlling liquid-liquid phase behavior with an active fluid

Demixing of binary liquids is a ubiquitous transition, which is explained using a well-established thermodynamic formalism that requires equality of intensive thermodynamics parameters across the phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, for example, by external shear flow. Predicting demixing transition under non-equilibrium non-potential conditions remains, however, a challenge. We drive liquid-liquid phase separation (LLPS) of attractive DNA nanostar molecules away from equilibrium using an internally driven microtubule-based active fluid. Activity lowers the critical temperature and narrows the coexistence concentrations, but only when there are mechanical bonds between the liquid droplets and the reconfiguring active fluid. Similar behaviors are observed in numerical simulations, suggesting that activity suppression of liquid-liquid phase separation is a generic feature of active LLPS. Our work describes a platform for building soft active materials with feedback control while also providing insight into cell biology, where phase separation emerged as a ubiquitous self-organizational principle.

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arXiv2022

Dynamics of active liquid interfaces

Controlling interfaces of phase separating fluid mixtures is key to creating diverse functional soft materials. Traditionally, this is accomplished with surface-modifying chemical agents. Using experiment and theory, we study how mechanical activity shapes soft interfaces that separate an active and a passive fluid. Chaotic flows in the active fluid give rise to giant interfacial fluctuations and non-inertial propagating active waves. At high activities, stresses disrupt interface continuity and drive droplet generation, producing an emulsion-like active state comprised of finite-sized droplets. When in contact with a solid boundary, active interfaces exhibit non-equilibrium wetting transitions, wherein the fluid climbs the wall against gravity. These results demonstrate the promise of mechanically driven interfaces for creating a new class of soft active matter.

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arXiv2022

Controlling the shape and topology of two-component colloidal membranes

Changes in the geometry and topology of self-assembled membranes underlie diverse processes across cellular biology and engineering. Similar to lipid bilayers, monolayer colloidal membranes have in-plane fluid-like dynamics and out-of-plane bending elasticity. Their open edges and micron length scale provide a tractable system to study the equilibrium energetics and dynamic pathways of membrane assembly and reconfiguration. Here, we find that doping colloidal membranes with short miscible rods transforms disk-shaped membranes into saddle-shaped surfaces with complex edge structures. The saddle-shaped membranes are well-approximated by Enneper's minimal surfaces. Theoretical modeling demonstrates that their formation is driven by increasing positive Gaussian modulus, which in turn is controlled by the fraction of short rods. Further coalescence of saddle-shaped surfaces leads to diverse topologically distinct structures, including catenoids, tri-noids, four-noids, and higher order structures. At long time scales, we observe the formation of a system-spanning, sponge-like phase. The unique features of colloidal membranes reveal the topological transformations that accompany coalescence pathways in real time. We enhance the functionality of these membranes by making their shape responsive to external stimuli. Our results demonstrate a novel pathway towards control of thin elastic sheets' shape and topology -- a pathway driven by the emergent elasticity induced by compositional heterogeneity.

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arXiv2022

Data-driven discovery of active nematic hydrodynamics

Two-dimensional active nematics are often modeled using phenomenological continuum theories that describe the dynamics of the nematic director and fluid velocity through partial differential equations (PDEs). While these models provide a statistically accurate description of the experiments, the identification of the relevant terms in the PDEs and their parameters is usually indirect. Here, we adapt a recently developed method to automatically identify optimal continuum models for active nematics directly from the spatio-temporal director and velocity data, via sparse fitting of the coarse-grained fields onto generic low order PDEs. We test the method extensively on computational models, and then apply it to data from experiments on microtubule-based active nematics. Thereby, we identify the optimal models for microtubule-based active nematics, along with the relevant phenomenological parameters. We find that the dynamics of the orientation field are largely governed by its coupling to the underlying flow, with free-energy gradients playing a negligible role. Furthermore, by fitting the flow equation to experimental data, we estimate a key parameter quantifying the `activity' of the nematic.

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arXiv2021

Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes

We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing viscoelasticity of the F-actin network controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate F-actin concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. The self-regulating layered organization survives aster merging events, which are reminiscent of droplet coalescence, and suggest the presence of effective surface tension. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. Taken together, these results challenge the current models of active matter. They demonstrate that the self-organized dynamical states and patterns, which are evocative of those observed in the cytoskeleton, do not require precise biochemical regulation but can arise due to purely mechanical interactions of actively driven filamentous materials.

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