arXiv subjects

Zvonimir Dogic

Publications and source records attributed to Zvonimir Dogic.

At least 37 records · Page 2Linked to original sources

arXiv2021

Multiscale Microtubule Dynamics in Active Nematics

In microtubule-based active nematics, motor-driven extensile motion of microtubule bundles powers chaotic large-scale dynamics. We quantify the interfilament sliding motion both in isolated bundles and in a dense active nematic. The extension speed of an isolated microtubule pair is comparable to the molecular motor stepping speed. In contrast, the net extension in dense 2D active nematics is significantly slower; the interfilament sliding speeds are widely distributed about the average and the filaments exhibit both contractile and extensile relative motion. These measurements highlight the challenge of connecting the extension rate of isolated bundles to the multi-motor and multi-filament interactions present in a dense 2D active nematic. They also provide quantitative data that is essential for building multiscale models.

cond-mat.soft↗

arXiv2021

Active microphase separation in mixtures of microtubules and tip-accumulating molecular motors

Mixtures of microtubules and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents' molecular properties. We map the non-equilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulent-like extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous non-equilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work shows that the form of active stresses and phases in cytoskeletal networks are not solely dictated by the properties of individual motors and filaments, but are also contingent on the constituent's concentrations and spatial arrangement.

cond-mat.soft↗

arXiv2021

Active liquid crystals powered by force-sensing DNA-motor clusters

Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale non-equilibrium dynamics of active nematics.

cond-mat.soft↗

arXiv2021

Defect-mediated dynamics of coherent structures in active nematics

Active fluids, such as cytoskeletal filaments, bacterial colonies and epithelial cell layers, exhibit distinctive orientational coherence, often characterized by nematic order and topological defects. By contrast, little is known about positional coherence -- i.e., how a hidden dynamic skeleton organizes the underlying chaotic motion -- despite this being one of their most prominent and experimentally accessible features. Using a combination of dynamical systems theory, experiments on two-dimensional mixtures of microtubules and kinesin and hydrodynamic simulations, we characterize positional coherence in active nematics. These coherent structures can be identified in the framework of Lagrangian dynamics as moving attractors and repellers, which orchestrate complex motion. To understand the interaction of positional and orientational coherence on the dynamics of defects, we then analysed observations and simulations and see that +1/2 defects move and deform the attractors, thus functioning as control centers for collective motion. Additionally, we find that regions around isolated +1/2 defects undergo high bending and low stretching/shearing deformations, consistent with the local stress distribution. The stress is minimum at the defect, while high differential stress along the defect orientation induces folding. Our work offers a new perspective to describe self-organization in active fluids, with potential applications to multicellular systems.

cond-mat.soft↗

arXiv2021

Static adhesion hysteresis in elastic structures

Adhesive interactions between elastic structures such as graphene sheets, carbon nanotubes, and microtubules have been shown to exhibit hysteresis due to irrecoverable energy loss associated with bond breakage, even in static (rate-independent) experiments. To understand this phenomenon, we start with a minimal theory for the peeling of a thin sheet from a substrate, coupling the local event of bond breaking to the nonlocal elastic relaxation of the sheet and show that this can drive static adhesion hysteresis over a bonding/debonding cycle. Using this model we quantify hysteresis in terms of the adhesion and elasticity parameters of the system. This allows us to derive a scaling relation that preserves hysteresis at different levels of granularity while resolving a seeming paradox of lattice trapping in the continuum limit of a discrete fracture process. Finally, to verify our theory, we use new experiments to demonstrate and measure adhesion hysteresis in bundled microtubules.

physics.bio-ph↗

arXiv2020

Machine Learning Forecasting of Active Nematics

Active nematics are a class of far-from-equilibrium materials characterized by local orientational order of force-generating, anisotropic constitutes. Traditional methods for predicting the dynamics of active nematics rely on hydrodynamic models, which accurately describe idealized flows and many of the steady-state properties, but do not capture certain detailed dynamics of experimental active nematics. We have developed a deep learning approach that uses a Convolutional Long-Short-Term-Memory (ConvLSTM) algorithm to automatically learn and forecast the dynamics of active nematics. We demonstrate our purely data-driven approach on experiments of 2D unconfined active nematics of extensile microtubule bundles, as well as on data from numerical simulations of active nematics.

cond-mat.soft↗

arXiv2020

Confinement controlled bend instability of three-dimensional active fluids

Spontaneous growth of long-wavelength deformations is a defining feature of active fluids with orientational order. We investigate the effect of biaxial rectangular confinement on the instability of initially shear-aligned 3D isotropic active fluids composed of extensile microtubule bundles and kinesin molecular motors. Under confinement, such fluids exhibit finite-wavelength self-amplifying bend deformations which grow in the plane orthogonal to the direction of the strongest confinement. Both the instability wavelength and the growth rate increase with weakening confinement. These findings are consistent with a minimal hydrodynamic model, which predicts that the fastest growing deformation is set by a balance of active driving and elastic relaxation. Experiments in the highly confined regime confirm that the instability wavelength is set by the balance of active and elastic stresses, which are independently controlled by the concentration of motors and non-motile crosslinkers.

cond-mat.soft↗

arXiv2020

Machine learning active-nematic hydrodynamics

Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more apparent than in active matter where the energy cascade mechanisms responsible for autonomous large-scale dynamics are poorly understood. Here, we use active nematics to demonstrate that neural networks can extract the spatio-temporal variation of hydrodynamic parameters directly from experiments. Our algorithms analyze microtubule-kinesin and actin-myosin experiments as computer vision problems. Unlike existing methods, neural networks can determine how multiple parameters such as activity and elastic constants vary with ATP and motor concentration. In addition, we can forecast the evolution of these chaotic many-body systems solely from image-sequences of their past by combining autoencoder and recurrent networks with residual architecture. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems even when no knowledge of the underlying dynamics exists.

cond-mat.soft↗

arXiv2020

Shear-induced gelation of self-yielding active networks

Molecular-motor generated active stresses drive the cytoskeleton away from equilibrium, endowing it with tunable mechanical properties that are essential for diverse functions such as cell division and motility[1-5]. Designing analogous biomimetic systems is a key prerequisite for creating active matter that can emulate cellular functions[6-7]. These long-term goals requires understanding of how motor-generated stresses tune the mechanics of filamentous networks[8-11]. In microtubule-based active matter, kinesin motors generate extensile motion that leads to persistent breaking and reforming of the network links[12]. We study how such microscopic dynamics modifies the network's mechanical properties, uncovering that the network viscosity first increases with the imposed shear rate before transitioning back to a low-viscosity state. The non-monotonic shear-dependent viscosity can be controlled by tuning the speed of molecular motors. A two-state phenomenological model that incorporates liquid- and solid-like elements quantitatively relates the non-monotonic shear-rate-dependent viscosity to locally-measured flows. These studies show that rheology of extensile networks are different from previously studied active gels[13], where contractility enhances mechanical stiffness. Moreover, the flow induced gelation is not captured by continuum models of hydrodynamically interacting swimmers[14-21]. Observation of activity-dependent viscoelasticity necessitates the development of models for self-yielding of soft active solids whose intrinsic active stresses fluidize or stiffen the network.

cond-mat.soft↗

arXiv2019

Statistical Properties of Autonomous Flows in 2D Active Nematics

We study the dynamics of a tunable 2D active nematic liquid crystal composed of microtubules and kinesin motors confined to an oil-water interface. Kinesin motors continuously inject mechanical energy into the system through ATP hydrolysis, powering the relative microscopic sliding of adjacent microtubules, which in turn generates macroscale autonomous flows and chaotic dynamics. We use particle image velocimetry to quantify two-dimensional flows of active nematics and extract their statistical properties. In agreement with the hydrodynamic theory, we find that the vortex areas comprising the chaotic flows are exponentially distributed, which allows us to extract the characteristic system length scale. We probe the dependence of this length scale on the ATP concentration, which is the experimental knob that tunes the magnitude of the active stress. Our data suggest a possible mapping between the ATP concentration and the active stress that is based on the Michaelis-Menten kinetics that governs motion of individual kinesin motors.

cond-mat.soft↗

arXiv2019

Topological structure and dynamics of three dimensional active nematics

Point-like motile topological defects control the universal dynamics of diverse two-dimensional active nematics ranging from shaken granular rods to cellular monolayers. A comparable understanding in higher dimensions has yet to emerge. We report the creation of three-dimensional active nematics by dispersing extensile microtubule bundles in a passive colloidal liquid crystal. Light-sheet microscopy reveals the millimeter-scale structure of active nematics with a single bundle resolution and the temporal evolution of the associated nematic director field. The dominant excitations of three-dimensional active nematics are extended charge-neutral disclination loops that undergo complex dynamics and recombination events. These studies introduce a new class of non-equilibrium systems whose turbulent-like dynamics arises from the interplay between internally generated active stresses, the chaotic flows and the topological structure of the constituent defects.

cond-mat.soft↗

arXiv2019

All twist and no bend makes raft edges splay: Spontaneous curvature of domain edges in colloidal membranes

Using a combination of theory and experiments we study the interface between two immiscible domains in a colloidal membrane composed of rigid rods of different lengths. Geometric considerations of rigid rod packing imply that a domain of sufficiently short rods in a background membrane of long rods is more susceptible to twist than the inverse structure, a long-rod domain in a short-rod membrane background. The tilt at the inter-domain edge forces splay, which in turn manifests as a spontaneous edge curvature whose energetics are controlled by the length asymmetry of constituent rods. A thermodynamic model of such tilt-curvature coupling at inter-domain edges explains a number of experimental observations, including a non-monotonic dependence of the edge twist on the domain radius, and annularly shaped domains of long rods. Our work shows how coupling between orientational and compositional degrees of freedom in two-dimensional fluids give rise to complex shapes and thermodynamics of domains, analogous to shape transitions in 3D fluid vesicles.

cond-mat.soft↗

arXiv2019

Structure, dynamics and phase behavior of short rod inclusions dissolved in a colloidal membrane

Inclusions dissolved in an anisotropic quasi-2D membrane acquire new types of interactions that can drive assembly of complex structures and patterns. We study colloidal membranes composed of a binary mixture of long and short rods, such that the length ratio of the long to short rods is approximately two. At very low volume fractions, short rods dissolve in the membrane of long rods by strongly anchoring to the membrane polymer interface. At higher fractions, the dissolved short rods phase separate from the background membrane, creating a composite structure comprised of bilayer droplets enriched in short rods that coexist with the background monolayer membrane. These results demonstrate that colloidal membranes serve as a versatile platform for assembly of soft materials, while simultaneously providing new insight into universal membrane-mediated interactions.

cond-mat.soft↗

arXiv2019

Equation of State of Colloidal Membranes

In the presence of a non-adsorbing polymer, monodisperse rod-like colloids assemble into one-rod-length thick liquid-like monolayers, called colloidal membranes. The density of the rods within a colloidal membrane is determined by a balance between the osmotic pressure exerted by the enveloping polymer suspension and the repulsion between the colloidal rods. We developed a microfluidic device for continuously observing an isolated membrane while dynamically controlling the osmotic pressure of the polymer suspension. Using this technology we measured the membrane rod density over a range of osmotic pressures than is wider that what is accessible in equilibrium samples. With increasing density we observed a first-order phase transition, in which the in-plane membrane order transforms from a 2D fluid into a 2D solid. In the limit of low osmotic pressures, we measured the rate at which individual rods evaporate from the membrane. The developed microfluidic technique could have wide applicability for in situ investigation of various soft materials and how their properties depend on the solvent composition.

cond-mat.soft↗

arXiv2019

Force induced formation of twisted chiral ribbons

We study the emergence of helical structures subjected to a stretching force, demonstrating that the force transforms disk-shaped colloidal membranes into twisted chiral ribbons of predetermined handedness. Using an experimental technique that enforces torque-free boundary conditions we simultaneously measure the force-extension curve and quantify the shape of emergent ribbons. An effective theory that accounts for the membrane bending energy and uses geometric properties of the edge to model the internal liquid crystalline degrees of freedom explains both the measured force-extension curve and shape of the twisted ribbons in response to an applied force.

cond-mat.soft↗

arXiv2019

Conformational switching of chiral colloidal rafts regulates raft-raft attractions and repulsions

Membrane-mediated particle interactions depend both on the properties of the particles themselves and the membrane environment in which they are suspended. Experiments have shown that chiral rod-like inclusions dissolved in a colloidal membrane of opposite handedness assemble into colloidal rafts, which are finite-sized reconfigurable droplets consisting of a large but precisely defined number of rods. Here, we systematically tune the chirality of the background membrane, and find that in the achiral limit colloidal rafts acquire fundamentally new structural properties and interactions. In particular, rafts can switch between two chiral states of opposite handedness, which dramatically alters the nature of the membrane-mediated raft-raft interactions. Rafts with the same chirality have long-ranged repulsions, while those with opposite chirality acquire attractions with a well-defined minimum. Both attractive and repulsive interactions are explained by a continuum model that accounts for the coupling between the membrane thickness and the local tilt of the constituent rods. These switchable interactions enable assembly of colloidal rafts into intricate higher-order architectures with unusual symmetries, including stable tetrameric clusters and "ionic crystallites" of counter-twisting domains organized on a binary square lattice. Furthermore, the properties of individual rafts, such as their sizes, are controlled by their complexation with other rafts. The emergence of these complex behaviors can be rationalized purely in terms of generic couplings between compositional and orientational order of fluids of rod-like elements. Thus, the uncovered principles might have relevance for conventional lipid bilayers, in which the assembly of higher-order structures is also mediated by complex membrane-mediated interactions.

cond-mat.soft↗

arXiv2019

Self-organized dynamics and the transition to turbulence of confined active nematics

We study how confinement transforms the chaotic dynamics of bulk microtubule-based active nematics into regular spatiotemporal patterns. For weak confinements, multiple continuously nucleating and annihilating topological defects self-organize into persistent circular flows of either handedness. Increasing confinement strength leads to the emergence of distinct dynamics, in which the slow periodic nucleation of topological defects at the boundary is superimposed onto a fast procession of a pair of defects. A defect pair migrates towards the confinement core over multiple rotation cycles, while the associated nematic director field evolves from a distinct double spiral towards a nearly circularly symmetric configuration. The collapse of the defect orbits is punctuated by another boundary-localized nucleation event, that sets up long-term doubly-periodic dynamics. Comparing experimental data to a theoretical model of an active nematic, reveals that theory captures the fast procession of a pair of $+\frac{1}{2}$ defects, but not the slow spiral transformation nor the periodic nucleation of defect pairs. Theory also fails to predict the emergence of circular flows in the weak confinement regime. The developed confinement methods are generalized to more complex geometries, providing a robust microfluidic platform for rationally engineering two-dimensional autonomous flows.

cond-mat.soft↗

arXiv2018

Actively crosslinked microtubule networks: mechanics, dynamics and filament sliding

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

cond-mat.soft↗