arXiv subjects

Sho C. Takatori

Publications and source records attributed to Sho C. Takatori.

18 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.

cond-mat.soft↗

arXiv2026

Anisotropic Diffusion in Lyotropic Chromonic Liquid Crystal using Fluorescence Recovery After Photobleaching

Anisotropic diffusion governs transport in a wide range of soft and biological materials, where microstructure and molecular interactions jointly shape how matter moves. Here, we quantitatively investigate anisotropic molecular transport in lyotropic chromonic liquid crystals (LCLCs) using fluorescence recovery after photobleaching (FRAP). Disodium cromoglycate (DSCG) serves as a model LCLC system, and diffusion is measured across isotropic, nematic, and columnar phases as concentration and temperature are varied. To disentangle the roles of microstructure and molecular interactions, we employ two fluorescent tracers with distinct affinities for the LCLC aggregates: Acridine Orange (AO), which intercalates into DSCG aggregates, and Bodipy, which interacts weakly and remains largely in the aqueous phase. Fourier-space FRAP analysis independently resolves the parallel and perpendicular diffusion coefficients for both dyes relative to the liquid-crystal alignment. In the nematic phase, diffusion becomes anisotropic, with faster transport along the liquid-crystal director. As the DSCG concentration increases, AO dye molecules that are strongly coupled to the aggregates exhibit a slowdown in all directions, reflecting enhanced packing and steric confinement of the LC microstructure. In contrast, weakly interacting Bodipy dye molecules display enhanced transport along the alignment direction as the DSCG concentration increases in the nematic regime, suggesting the emergence of microscopic channels that guide motion, analogous to transport in oriented porous media. These results reveal how the evolving microstructure of LCLCs controls effective diffusion and provide a quantitative framework for understanding and designing anisotropic transport in aligned soft materials.

cond-mat.soft↗

arXiv2025

Colloidal hydrodynamic interactions in viscoelastic fluids

The motion of suspended colloidal particles generates fluid disturbances in the surrounding medium that create interparticle interactions. While such colloidal hydrodynamic interactions (HIs) have been extensively studied in viscous Newtonian media, comprehensive understanding of HIs in viscoelastic fluids is lacking. We develop a framework to quantify HIs in viscoelastic fluids with high spatiotemporal precision by trapping colloids and inducing translation-rotation hydrodynamic coupling. Using solutions of wormlike micelles (WLMs) as a case study, we discover that HIs are strongly time-dependent and depend on the structural memory generated in the viscoelastic fluid, in contrast to "instantaneous" HIs in viscous Newtonian fluids. We directly measure time-dependent HIs between a stationary probe and a driven particle during transient start-up, developing on the WLM relaxation timescale. Following the sudden cessation of the driven particle, we observe an intriguing flow reversal in the opposing direction, lasting for a time about ten times larger than the WLM relaxation time. We corroborate our observations with analytical microhydrodynamic theory, direct numerical solutions of a continuum model, and particle-based Stokesian dynamics simulations. We find that the structural recovery of the WLMs from a nonlinear strain can generate anisotropic and heterogeneous stresses that produce flow reversals and hydrodynamic attraction among colloids. Measured heterogeneities indicate a breakdown of standard continuum models for constitutive relations when the size of colloids is comparable to the length scales of the polymeric constituents and their entanglement lengths.

cond-mat.soft↗

arXiv2025

Learning Continuum-level Closures For Control of Interacting Active Particles

Active matter swarms -- collectives of self-propelled particles that could self-assemble, ferry microscopic cargo, or endow materials with dynamic properties -- remain hard to steer. In crowded systems, tracking or controlling individual agents becomes challenging, so strategies should operate on macroscopic fields like particle density. Yet predicting how density evolves is difficult due to inter-agent interactions. For model-based feedback control methods -- like Model Predictive Control (MPC) -- fast, accurate, and differentiable models are crucial. Detailed agent-based simulations are too slow, necessitating coarse-grained continuum models. However, constructing accurate closures -- approximations expressing the effect of unresolved microscopic states (e.g., agent positions) on continuum dynamics -- is challenging for active matter swarms. We present a learning-for-control framework that learns continuum closures from agent simulations, demonstrated with active Brownian particles under a controllable external field. Our Universal Differential Equation (UDE) framework represents the continuum as an advection-diffusion equation. A neural operator learns the advection term, providing closure relations for microscopic effects like self-propulsion, interactions, and external field responses. This UDE approach, embedding universal function approximators in differential equations, ensures adherence to physical laws (e.g., conservation) while learning complex dynamics directly from data. We embed this learned continuum model into MPC for precise agent simulation control. We demonstrate this framework's capabilities by dynamically exchanging particle densities between two groups, and simultaneously controlling particle density and mean flux to follow a prescribed sinusoidal profile. These results highlight the framework's potential to control complex active matter dynamics.

cond-mat.soft↗

arXiv2025

Phase field model for viscous inclusions in anisotropic networks

The growth of viscous two-dimensional lipid domains in contact with a viscoelastic actin network was recently shown to exhibit unusual lipid domain ripening due to the geometry and anisotropy of the actin network [Arnold & Takatori. Langmuir. 40, 26570-26578 (2024)]. In this work, we interpret previous experimental results on lipid membrane-actin composites with a theoretical model that combines the Cahn-Hilliard and Landau-de Gennes liquid crystal theory. In our model, we incorporate fiber-like characteristics of actin filaments and bundles through a nematic order parameter, and elastic anisotropy through cubic nematic gradients. Numerical simulations qualitatively agree with experimental observations, by reproducing the competition between the thermodynamic forces that coarsen lipid domains versus the elastic forces generated by the surrounding actin network that resist domain coarsening. We observe a decrease in the growth of domain sizes, finding $R(t) \sim t^α$ with $α< 1/4$ for different actin network stiffnesses, in sharp contrast to the $\sim t^{1/3}$ scaling for diffusive growth of domains in the absence of the actin network. Our findings may serve as a foundation for future developments in modeling elastic ripening in complex systems.

cond-mat.soft↗

arXiv2025

Direct experimental measurement of many-body hydrodynamic interactions with optical tweezers

Many-body hydrodynamic interactions (HIs) play an important role in the dynamics of fluid suspensions. While many-body HIs have been studied extensively using particle simulations, there is a dearth of experimental frameworks with which to quantify fluid-mediated multi-body interactions. To address this, we design an experimental method that utilizes optical laser tweezers for quantifying fluid-mediated colloidal interactions with exquisite precision and control. By inducing translation-rotation hydrodynamic coupling between trapped fluorescently-labeled colloids, we obtain a direct reporter of few- to many-body HIs experimentally. We leverage the torque-free nature of laser tweezers to enable sensitive measurements of signals between trapped colloids. First, we measure the pair HI between a stationary tracer probe and a translating particle as a function of their separation distance. We discover that our technique can precisely quantify distant fluid disturbances that are generated by ~2 pN of hydrodynamic force at 12 particle radii of separation. To study the effect of many-body HIs, we measure the rotational mobility of a probe in a three-particle setup and in a model material, a two-dimensional hexagonally-close-packed lattice, that undergoes oscillatory strain. Respectively, we discover that the probe's rotation can reverse in certain three-body configurations, and we find that rotational mobility in the crystalline array is strongly attenuated by particle rigidity. Experimental measurements are corroborated by microhydrodynamic theory and Stokesian Dynamics simulations with excellent agreement, highlighting our ability to measure accurately many-body HIs. Lastly, we extend our theoretical framework to manipulate colloidal-scale fluid flows. With experimental validation, we compute the required trajectory of a moving particle to induce a desired angular velocity of a probe.

cond-mat.soft↗

arXiv2024

Motility Modulates the Partitioning of Bacteria in Aqueous Two-Phase Systems

We study the partitioning of motile bacteria in an aqueous two-phase mixture of dextran (DEX) and polyethylene glycol (PEG), which can phase separate into DEX-rich and PEG-rich phases. While non-motile bacteria partition exclusively into the DEX-rich phase in all conditions tested, we observed that motile bacteria penetrate the soft DEX/PEG interface and partition variably among the two phases. For our model organism \textit{Bacillus subtilis}, the fraction of motile bacteria in the DEX-rich phase increased from 0.58 to 1 as we increased DEX composition within the two-phase region. We hypothesized that the chemical affinity between DEX and the bacteria cell wall acts to weakly confine the bacteria within the DEX-rich phase; however, motility can generate sufficient mechanical forces to overcome the soft confinement and propel the bacteria into the PEG-rich phase. Using optical tweezers to drag a bacterium across the DEX/PEG interface, we demonstrate that the overall bacteria partitioning is determined by a competition between the interfacial forces and bacterial propulsive forces. Our measurements are supported by a theoretical model of dilute active rods embedded within a periodic soft confinement potential.

cond-mat.soft↗

arXiv2024

Lipid membrane domains control actin network viscoelasticity

The mammalian cell membrane is embedded with biomolecular condensates of protein and lipid clusters, which interact with an underlying viscoelastic cytoskeleton network to organize the cell surface and mechanically interact with the extracellular environment. However, the mechanical and thermodynamic interplay between the viscoelastic network and liquid-liquid phase separation of 2-dimensional (2D) lipid condensates remains poorly understood. Here, we engineer materials composed of 2D lipid membrane condensates embedded within a thin viscoelastic actin network. The network generates localized anisotropic stresses that deform lipid condensates into triangular morphologies with sharp edges and corners, shapes unseen in 3D composite gels. Kinetic coarsening of phase-separating lipid condensates accelerates the viscoelastic relaxation of the network, leading to an effectively softer composite material over intermediate timescales. We dynamically manipulate the membrane composition to control the elastic-to-viscous crossover of the network. Such viscoelastic composite membranes may enable the development of coatings, catalytic surfaces, separation membranes, and other interfaces with tunable spatial organization and plasticity mechanisms.

cond-mat.soft↗

arXiv2024

Dynamic swarms regulate the morphology and distribution of soft membrane domains

We study the dynamic structure of lipid domain inclusions embedded within a phase-separated reconstituted lipid bilayer in contact with a swarming flow of gliding filamentous actin. Passive circular domains transition into highly-deformed morphologies that continuously elongate, rotate, and pinch off into smaller fragments, leading to a dynamic steady state with approximately 23x speed up in the relaxation of the intermediate scattering function compared to passive membrane domains driven by purely thermal forces. To corroborate experimental results, we develop a phase-field model of the lipid domains with two-way coupling to the Toner-Tu equations. We report phase domains that become entrained in the chaotic eddy patterns, with oscillating waves of domains that correlate with the dominant wavelengths of the Toner-Tu flow fields.

cond-mat.soft↗

arXiv2024

Dynamic Surfactants Drive Anisotropic Colloidal Assembly

Colloidal building blocks with re-configurable shapes and dynamic interactions can exhibit unusual self-assembly behaviors and pathways. In this work, we consider the phase behavior of colloids coated with surface-mobile polymer brushes that behave as "dynamic surfactants." Unlike traditional polymer-grafted colloids, we show that colloids coated with dynamic surfactants can acquire anisotropic macroscopic assemblies, even for spherical colloids with isotropic attractive interactions. We use Brownian Dynamics simulations and dynamic density functional theory (DDFT) to demonstrate that time-dependent reorganization of the dynamic surfactants leads to phase diagrams with anisotropic assemblies. We observed that the microscopic polymer distributions impose unique geometric constraints between colloids that control their packing into lamellar, string, and vesicle phases. Our work may help discover versatile building blocks and provide extensive design freedom for assembly out of thermodynamic equilibrium.

cond-mat.soft↗

arXiv2023

Active surface flows accelerate the coarsening of lipid membrane domains

Phase separation of multicomponent lipid membranes is characterized by the nucleation and coarsening of circular membrane domains that grow slowly in time as $\sim t^{1/3}$, following classical theories of coalescence and Ostwald ripening. In this work, we study the coarsening kinetics of phase-separating lipid membranes subjected to nonequilibrium forces and flows transmitted by motor-driven gliding actin filaments. We experimentally observe that the activity-induced surface flows trigger rapid coarsening of non-circular membrane domains that grow as $\sim t^{2/3}$, a 2$\times$ acceleration in the growth exponent compared to passive coalescence and Ostwald ripening. We analyze these results by developing analytical theories based on the Smoluchowski coagulation model and the phase field model to predict the domain growth in the presence of active flows. Our work demonstrates that active matter forces may be used to control the growth and morphology of membrane domains driven out of equilibrium.

cond-mat.soft↗

arXiv2023

Dynamic interfaces for contact-time control of colloidal interactions

Understanding multibody interactions between colloidal particles out of equilibrium has a profound impact on dynamical processes such as colloidal self assembly. However, traditional colloidal interactions are effectively quasi-static on colloidal timescales and cannot be modulated out of equilibrium. A mechanism to dynamically tune the interactions during colloidal contacts can provide new avenues for self assembly and material design. In this work, we develop a framework based on polymer-coated colloids and demonstrate that in-plane surface mobility and mechanical relaxation of polymers at colloidal contact interfaces enable an effective, dynamic interaction. Combining analytical theory, simulations, and optical tweezer experiments, we demonstrate precise control of dynamic pair interactions over a range of pico-Newton forces and seconds timescales. Our model may be used to engineer colloids with exquisite control over the kinetics and thermodynamics of colloidal self-assembly dynamics via interface modulation and nonequilibrium processing.

cond-mat.soft↗

arXiv2022

Antibody binding reports spatial heterogeneities in cell membrane organization

The spatial organization of cell membrane glycoproteins and glycolipids is critical for mediating the binding of ligands, receptors, and macromolecules on the plasma membrane. However, we currently do not have the methods to quantify the spatial heterogeneities of macromolecular crowding on live cell surfaces. In this work, we combine experiment and simulation to report crowding heterogeneities on reconstituted membranes and live cell membranes with nanometer spatial resolution. By quantifying the effective binding affinity of IgG monoclonal antibodies to engineered antigen sensors, we discovered sharp gradients in crowding within a few nanometers of the crowded membrane surface. Our measurements on human cancer cells support the hypothesis that raft-like membrane domains exclude bulky membrane proteins and glycoproteins. Our facile and high-throughput method to quantify spatial crowding heterogeneities on live cell membranes may facilitate monoclonal antibody design and provide a mechanistic understanding of plasma membrane biophysical organization.

physics.bio-ph↗

arXiv2022

Enhanced dispersion in an oscillating array of harmonic traps

Experiment, theory, and simulation are employed to understand the dispersion of colloidal particles in a periodic array of oscillating harmonic traps generated by optical tweezers. In the presence of trap oscillation, a non-monotonic and anisotropic dispersion is observed. Surprisingly, the stiffest traps produce the largest dispersion at a critical frequency, and the particles diffuse significantly faster in the direction of oscillation than those undergoing passive Stokes-Einstein-Sutherland diffusion. Theoretical predictions for the effective diffusivity of the particles as a function of trap stiffness and oscillation frequency are developed using generalized Taylor dispersion theory and Brownian dynamics simulations. Both theory and simulation demonstrate excellent agreement with the experiments, and reveal a new ``slingshot'' mechanism that predicts a significant enhancement of colloidal diffusion in dynamic external fields.

cond-mat.soft↗

arXiv2020

Active Contact Forces Drive Non-Equilibrium Fluctuations in Membrane Vesicles

We analyze the non-equilibrium shape fluctuations of giant unilamellar vesicles encapsulating motile bacteria. Owing to bacteria--membrane collisions, we experimentally observe a significant increase in the magnitude of membrane fluctuations at low wave numbers, compared to the well-known thermal fluctuation spectrum. We interrogate these results by numerically simulating membrane height fluctuations via a modified Langevin equation, which includes bacteria--membrane contact forces. Taking advantage of the length and time scale separation of these contact forces and thermal noise, we further corroborate our results with an approximate theoretical solution to the dynamical membrane equations. Our theory and simulations demonstrate excellent agreement with non-equilibrium fluctuations observed in experiments. Moreover, our theory reveals that the fluctuation--dissipation theorem is not broken by the bacteria; rather, membrane fluctuations can be decomposed into thermal and active components.

cond-mat.soft↗

arXiv2020

Motility-induced buckling and glassy dynamics regulate three-dimensional transitions of bacterial monolayers

Many mature bacterial colonies and biofilms are complex three-dimensional (3D) structures. One key step in their developmental program is a transition from a two-dimensional (2D) monolayer into a 3D architecture. Despite the importance of controlling the growth of microbial colonies and biofilms in a variety of medical and industrial settings, the underlying physical mechanisms behind single-cell dynamics, collective behaviors of densely-packed cells, and 3D complex colony expansion remain largely unknown. In this work, we explore the mechanisms behind the 2D-to-3D transition of motile Pseudomonas aeruginosa colonies; we provide a new motility-induced, rate-dependent buckling mechanism for their out-of-plane growth. We find that swarming of motile bacterial colonies generate sustained in-plane flows. We show that the viscous shear stresses and dynamic pressures arising from these flows allow cells to overcome cell-substrate adhesion, leading to buckling of bacterial monolayers and growth into the third dimension. Modeling bacterial monolayers as 2D fluid films, we identify universal relationships that elucidate the competition between in-plane viscous stresses, pressure and cell-substrate adhesion. Furthermore, we show that bacterial monolayers can exhibit crossover from swarming to kinetically-arrested, glassy-like states above an onset density, resulting in distinct 2D-to-3D transition mechanisms. Combining experimental observations of P. aeruginosa colonies at single-cell resolution, molecular dynamics simulations of active systems, and theories of glassy dynamics and 2D fluid films, we develop a dynamical state diagram that predicts the state of the colony, and the mechanisms governing their 2D-to-3D transitions.

cond-mat.soft↗

arXiv2017

Inertial Effects on the Stress Generation of Active Fluids

Suspensions of self-propelled bodies generate a unique mechanical stress owing to their motility that impacts their large-scale collective behavior. For microswimmers suspended in a fluid with negligible particle inertia, we have shown that the virial `swim stress' is a useful quantity to understand the rheology and nonequilibrium behaviors of active soft matter systems. For larger self-propelled organisms like fish, it is unclear how particle inertia impacts their stress generation and collective movement. Here, we analyze the effects of finite particle inertia on the mechanical pressure (or stress) generated by a suspension of self-propelled bodies. We find that swimmers of all scales generate a unique `swim stress' and `Reynolds stress' that impacts their collective motion. We discover that particle inertia plays a similar role as confinement in overdamped active Brownian systems, where the reduced run length of the swimmers decreases the swim stress and affects the phase behavior. Although the swim and Reynolds stresses vary individually with the magnitude of particle inertia, the sum of the two contributions is independent of particle inertia. This points to an important concept when computing stresses in computer simulations of nonequilibrium systems---the Reynolds and the virial stresses must both be calculated to obtain the overall stress generated by a system.

cond-mat.soft↗

arXiv2014

Towards a 'Thermodynamics' of Active Matter

Self-propulsion allows living systems to display unusual collective behavior. Unlike passive systems in thermal equilibrium, active matter systems are not constrained by conventional thermodynamic laws. A question arises however as to what extent, if any, can concepts from classical thermodynamics be applied to nonequilibrium systems like active matter. Here we use the new swim pressure perspective to develop a simple theory for predicting phase separation in active matter. Using purely mechanical arguments we generate a phase diagram with a spinodal and critical point, and define a nonequilibrium chemical potential to interpret the "binodal." We provide a generalization of thermodynamic concepts like the free energy and temperature for nonequilibrium active systems. Our theory agrees with existing simulation data both qualitatively and quantitatively and may provide a framework for understanding and predicting the behavior of nonequilibrium active systems.

cond-mat.soft↗