Sho Takatori

All Publications

• Learning continuum-level closures for control of interacting active particles. The Journal of chemical physics Quah, T., Takatori, S. C., Rawlings, J. B. 2026; 164 (4)

  Abstract

  Active matter swarms-collectives of self-propelled particles that can 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 must operate on macroscopic fields like particle density. Yet predicting how density evolves is difficult because of inter-agent interactions. For model-based feedback control methods-such as 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 that express the effects of unresolved microscopic states (e.g., agent positions) on continuum dynamics in terms of the modeled continuum fields (e.g., density)-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 such as 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 by 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, foundational for programmable materials.

  View details for DOI 10.1063/5.0300697

  View details for PubMedID 41614966

• Colloidal hydrodynamic interactions in viscoelastic fluids. Soft matter Kim, D. Y., Nagella, S. G., Malik, S., Park, N., Nam, J., Shaqfeh, E. S., Takatori, S. C. 2025

  Abstract

  The motion of suspended colloidal particles generates fluid disturbances in the surrounding medium that set up 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 exquisite 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 10× 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.

  View details for DOI 10.1039/d5sm00874c

  View details for PubMedID 41059952

• Motility Modulates the Partitioning of Bacteria in Aqueous Two-Phase Systems. Physical review letters Cheon, J., Choi, K. H., Modica, K. J., Mitchell, R. J., Takatori, S. C., Jeong, J. 2025; 135 (12): 128401

  Abstract

  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 nonmotile 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 Bacillus subtilis, the fraction of motile bacteria in the DEX-rich phase increased from 0.58 to 1 as we increased the 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.

  View details for DOI 10.1103/6gm5-cnv1

  View details for PubMedID 41046403

• Motility Modulates the Partitioning of Bacteria in Aqueous Two-Phase Systems PHYSICAL REVIEW LETTERS Cheon, J., Choi, K., Modica, K. J., Mitchell, R. J., Takatori, S. C., Jeong, J. 2025; 135 (12)

  View details for DOI 10.1103/6gm5-cnv1

  View details for Web of Science ID 001575054900008

• Phase field model for viscous inclusions in anisotropic networks. Soft matter Gubbala, A., Jena, A. M., Arnold, D. P., Takatori, S. C. 2025

  Abstract

  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) talpha with alpha < 1/4 for different actin network stiffnesses, in sharp contrast to the t1/3 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.

  View details for DOI 10.1039/d5sm00478k

  View details for PubMedID 40692432

• Direct experimental measurement of many-body hydrodynamic interactions with optical tweezers PHYSICAL REVIEW FLUIDS Kim, D., Nagella, S. G., Choi, K., Takatori, S. C. 2025; 10 (6)

  View details for DOI 10.1103/PhysRevFluids.10.064301

  View details for Web of Science ID 001529022100003

• Feedback Control of Active Matter ANNUAL REVIEW OF CONDENSED MATTER PHYSICS Takatori, S. C., Quah, T., Rawlings, J. B. 2025; 16: 319-341

  View details for DOI 10.1146/annurev-conmatphys-042424-043926

  View details for Web of Science ID 001441665900016

• Lipid Membrane Domains Control Actin Network Viscoelasticity LANGMUIR Arnold, D. P., Takatori, S. C. 2024; 40 (50): 26570-26578

  Abstract

  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 many 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 time scales. 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.

  View details for DOI 10.1021/acs.langmuir.4c03463

  View details for Web of Science ID 001370329500001

  View details for PubMedID 39630960

  View details for PubMedCentralID PMC11656694

• Model predictive control of non-interacting active Brownian particles SOFT MATTER Quah, T., Modica, K. J., Rawlings, J. B., Takatori, S. C. 2024; 20 (43): 8581-8588

  Abstract

  Active matter systems are strongly driven to assume non-equilibrium distributions owing to their self-propulsion, e.g., flocking and clustering. Controlling the active matter systems' spatiotemporal distributions offers exciting applications such as directed assembly, programmable materials, and microfluidic actuation. However, these applications involve environments with coupled dynamics and complex tasks, making intuitive control strategies insufficient. This necessitates the development of an automatic feedback control framework, where an algorithm determines appropriate actions based on the system's current state. In this work, we control the distribution of active Brownian particles by applying model predictive control (MPC), a model-based control algorithm that predicts future states and optimizes the control inputs to drive the system along a user-defined objective. The MPC model is based on the Smoluchowski equation with a self-propulsive convective term and an actuated spatiotemporal-varying external field that aligns particles with the applied direction, similar to a magnetic field. We apply the MPC framework to control a Brownian dynamics simulation of non-interacting active particles and illustrate the controller capabilities with two objectives: splitting and juggling sub-populations, and polar order flocking control.

  View details for DOI 10.1039/d4sm00902a

  View details for Web of Science ID 001333615500001

  View details for PubMedID 39417392

• Dynamic surfactants drive anisotropic colloidal assembly JOURNAL OF CHEMICAL PHYSICS Xu, Y., Jandhyala, P., Takatori, S. C. 2024; 161 (6)

  Abstract

  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 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.

  View details for DOI 10.1063/5.0220112

  View details for Web of Science ID 001286776400005

  View details for PubMedID 39115172

• Dynamic swarms regulate the morphology and distribution of soft membrane domains PHYSICAL REVIEW E Gubbala, A., Arnold, D. P., Jena, A., Anujarerat, S., Takatori, S. C. 2024; 110 (1): 014410

  Abstract

  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 ≈23× speedup in the relaxation of the intermediate scattering function compared with 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.

  View details for DOI 10.1103/PhysRevE.110.014410

  View details for Web of Science ID 001275918000011

  View details for PubMedID 39160984

• Surface Topography Induces and Orients Nematic Swarms of Active Filaments: Considerations for Lab-On-A-Chip Devices ACS APPLIED NANO MATERIALS Barakat, J. M., Modica, K. J., Lu, L., Anujarerat, S., Choi, K., Takatori, S. C. 2024; 7 (10): 12142-12152

  Abstract

  Surface-bound molecular motors can drive the collective motion of cytoskeletal filaments in the form of nematic bands and polar flocks in reconstituted gliding assays. Although these "swarming transitions" are an emergent property of active filament collisions, they can be controlled and guided by tuning the surface chemistry or topography of the substrate. To date, the impact of surface topography on collective motion in active nematics is only partially understood, with most experimental studies focusing on the escape of a single filament from etched channels. Since the late 1990s, significant progress has been made to utilize the nonequilibrium properties of active filaments and create a range of functional nanodevices relevant to biosensing and parallel computation; however, the complexity of these swarming transitions presents a challenge when attempting to increase filament surface concentrations. In this work, we etch shallow, linear trenches into glass substrates to induce the formation of swarming nematic bands and investigate the mechanisms by which surface topography regulates the two-dimensional (2D) collective motion of driven filamentous actin (F-actin). We demonstrate that nematic swarms only appear at intermediate trench spacings and vanish if the trenches are made too narrow, wide, or tortuous. To rationalize these results, we simulate the F-actin as self-propelled, semiflexible chains subject to a soft, spatially modulated potential that encodes the energetic cost of bending a filament along the edge of a trench. In our model, we hypothesize that an individual filament experiences a penalty when its projected end-to-end distance is smaller than the trench spacing ("bending and turning"). However, chains that span the channel width glide above the trenches in a force- and torque-free manner ("crowd-surfing"). Our simulations demonstrate that collections of filaments form nematic bands only at intermediate trench spacings, consistent with our experimental findings.

  View details for DOI 10.1021/acsanm.4c02020

  View details for Web of Science ID 001225166300001

  View details for PubMedID 38808306

  View details for PubMedCentralID PMC11129142

• Soft confinement of self-propelled rods: simulation and theory SOFT MATTER Modica, K. J., Takatori, S. C. 2024; 20 (10): 2331-2337

  Abstract

  We present an analytical framework for evolving the dynamics of active rods under any periodic external potential, including confining channels and arrays of harmonic traps. As a proof of concept, we analyze the structure and dispersion of self-propelled rods under a soft, periodic one-dimensional (1D) confinement potential and under a two-dimensional (2D) periodic radial harmonic trap. While passive rods and polymers nematically order under 1D confinement, their diffusive transport along the director is limited by thermal diffusion. In contrast, self-propelled rods can generate large convective fluxes when combined with nematic ordering, producing a strong dispersion along the director. Combining theory and simulation, we demonstrate that nematic alignment and self-propulsion generates an exponential enhancement in active diffusivity along the director, in contrast to passive rods that experience at most a 2-fold increase.

  View details for DOI 10.1039/d3sm01340e

  View details for Web of Science ID 001164039800001

  View details for PubMedID 38372150

• Nonequilibrium interactions between multi-scale colloids regulate the suspension microstructure and rheology SOFT MATTER Xu, Y., Takatori, S. C. 2023; 19 (44): 8531-8541

  Abstract

  Understanding nonequilibrium interactions of multi-component colloidal suspensions is critical for many dynamical settings such as self-assembly and material processing. A key question is how the nonequilibrium distributions of individual components influence the effective interparticle interactions and flow behavior. In this work, we develop a first-principle framework to study a bidisperse suspension of colloids and depletants using a Smoluchowski equation and corroborated by Brownian dynamics (BD) simulations. Using nonlinear microrheology as a case study, we demonstrate that effective depletion interactions between driven colloids are sensitive to particle timescales out of equilibrium and cannot be predicted by equilibrium-based pair potentials like Asakura-Oosawa. Furthermore, we show that the interplay between Brownian relaxation timescales of different species plays a critical role in governing the viscosity of multi-component suspensions. Our model highlights the limitations of using equilibrium pair potentials to approximate interparticle interactions in nonequilibrium processes such as hydrodynamic flows and presents a useful framework for studying the transport of driven, interacting suspensions.

  View details for DOI 10.1039/d3sm00947e

  View details for Web of Science ID 001088171300001

  View details for PubMedID 37889475

• Active Surface Flows Accelerate the Coarsening of Lipid Membrane Domains PHYSICAL REVIEW LETTERS Arnold, D. P., Gubbala, A., Takatori, S. C. 2023; 131 (12): 128402

  Abstract

  Phase separation of multicomponent lipid membranes is characterized by the nucleation and coarsening of circular membrane domains that grow slowly in time as ∼t^{1/3}, following classical theories of coalescence and Ostwald ripening. In this Letter, 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 noncircular membrane domains that grow as ∼t^{2/3}, a 2x 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 Letter demonstrates that active matter forces may be used to control the growth and morphology of membrane domains driven out of equilibrium.

  View details for DOI 10.1103/PhysRevLett.131.128402

  View details for Web of Science ID 001102941000002

  View details for PubMedID 37802933

• Colloidal transport phenomena in dynamic, pulsating porous materials AICHE JOURNAL Nagella, S. G., Takatori, S. C. 2023; 69 (12)

  Abstract

  We study the transport phenomena of colloidal particles embedded within a moving array of obstacles that mimics a dynamic, time-varying porous material. While colloidal transport in an array of stationary obstacles ("passive" porous media) has been well studied, we lack the fundamental understanding of colloidal diffusion in a nonequilibrium porous environment. We combine Taylor dispersion theory, Brownian dynamics simulations, and optical tweezer experiments to study the transport of tracer colloidal particles in an oscillating lattice of obstacles. We discover that the dispersion of tracer particles is a non-monotonic function of oscillation frequency and exhibits a maximum that exceeds the Stokes-Einstein-Sutherland diffusivity in the absence of obstacles. By solving the Smoluchowski equation using a generalized dispersion framework, we demonstrate that the enhanced transport of the tracers depends critically on both the direct interparticle interactions with the obstacles and the fluid-mediated, hydrodynamic interactions generated by the moving obstacles.

  View details for DOI 10.1002/aic.18215

  View details for Web of Science ID 001052289300001

  View details for PubMedID 38074409

  View details for PubMedCentralID PMC10706601

• Dynamic interfaces for contact-time control of colloidal interactions SOFT MATTER Xu, Y., Choi, K., Nagella, S. G., Takatori, S. C. 2023; 19 (30): 5692-5700

  Abstract

  Understanding pairwise 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 helps further the general understanding of out-of-equilibrium colloidal assemblies while providing extensive design freedom via interface modulation and nonequilibrium processing.

  View details for DOI 10.1039/d3sm00673e

  View details for Web of Science ID 001022743900001

  View details for PubMedID 37409349

  View details for PubMedCentralID PMC10699160

• Bio-enabled Engineering of Multifunctional "Living" Surfaces ACS NANO Arnold, D. P., Takatori, S. C. 2023; 17 (12): 11077-11086

  Abstract

  Through the magic of "active matter"─matter that converts chemical energy into mechanical work to drive emergent properties─biology solves a myriad of seemingly enormous physical challenges. Using active matter surfaces, for example, our lungs clear an astronomically large number of particulate contaminants that accompany each of the 10,000 L of air we respire per day, thus ensuring that the lungs' gas exchange surfaces remain functional. In this Perspective, we describe our efforts to engineer artificial active surfaces that mimic active matter surfaces in biology. Specifically, we seek to assemble the basic active matter components─mechanical motor, driven constituent, and energy source─to design surfaces that support the continuous operation of molecular sensing, recognition, and exchange. The successful realization of this technology would generate multifunctional, "living" surfaces that combine the dynamic programmability of active matter and the molecular specificity of biological surfaces and apply them to applications in biosensors, chemical diagnostics, and other surface transport and catalytic processes. We describe our recent efforts in bio-enabled engineering of living surfaces through the design of molecular probes to understand and integrate native biological membranes into synthetic materials.

  View details for DOI 10.1021/acsnano.3c03138

  View details for Web of Science ID 001069895900001

  View details for PubMedID 37294942

  View details for PubMedCentralID PMC10311588

• Antibody binding reports spatial heterogeneities in cell membrane organization NATURE COMMUNICATIONS Arnold, D. P., Xu, Y., Takatori, S. C. 2023; 14 (1): 2884

  Abstract

  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 discover 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.

  View details for DOI 10.1038/s41467-023-38525-2

  View details for Web of Science ID 001001312500001

  View details for PubMedID 37208326

  View details for PubMedCentralID PMC10199101

• Engineered molecular sensors for quantifying cell surface crowding PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Takatori, S. C., Son, S., Lee, D. S. W., Fletcher, D. A. 2023; 120 (21): e2219778120

  Abstract

  Cells mediate interactions with the extracellular environment through a crowded assembly of transmembrane proteins, glycoproteins and glycolipids on their plasma membrane. The extent to which surface crowding modulates the biophysical interactions of ligands, receptors, and other macromolecules is poorly understood due to the lack of methods to quantify surface crowding on native cell membranes. In this work, we demonstrate that physical crowding on reconstituted membranes and live cell surfaces attenuates the effective binding affinity of macromolecules such as IgG antibodies in a surface crowding-dependent manner. We combine experiment and simulation to design a crowding sensor based on this principle that provides a quantitative readout of cell surface crowding. Our measurements reveal that surface crowding decreases IgG antibody binding by 2 to 20 fold in live cells compared to a bare membrane surface. Our sensors show that sialic acid, a negatively charged monosaccharide, contributes disproportionately to red blood cell surface crowding via electrostatic repulsion, despite occupying only ~1% of the total cell membrane by mass. We also observe significant differences in surface crowding for different cell types and find that expression of single oncogenes can both increase and decrease crowding, suggesting that surface crowding may be an indicator of both cell type and state. Our high-throughput, single-cell measurement of cell surface crowding may be combined with functional assays to enable further biophysical dissection of the cell surfaceome.

  View details for DOI 10.1073/pnas.2219778120

  View details for Web of Science ID 001039552600008

  View details for PubMedID 37186825

  View details for PubMedCentralID PMC10214205

• Boundary design regulates the diffusion of active matter in heterogeneous environments SOFT MATTER Modica, K. J. J., Omar, A. K. K., Takatori, S. C. C. 2023; 19 (10): 1890-1899

  Abstract

  Physical boundaries play a key role in governing the overall transport properties of nearby self-propelled particles. In this work, we develop dispersion theories and conduct Brownian dynamics simulations to predict the coupling between surface accumulation and effective diffusivity of active particles in boundary-rich media. We focus on three models that are well-understood for passive systems: particle transport in (i) an array of fixed volume-excluding obstacles; (ii) a pore with spatially heterogeneous width; and (iii) a tortuous path with kinks and corners. While the impact of these entropic barriers on passive particle transport is well established, we find that these classical models of porous media flows break down due to the unique interplay between activity and the microstructure of the internal geometry. We study the activity-induced slowdown of effective diffusivity by formulating a Smoluchowski description of long-time self diffusivity which contains contributions from the density and fluctuation fields of the active particles. Particle-based and finite element simulations corroborate this perspective and reveal important nonequilibrium considerations of active transport.

  View details for DOI 10.1039/d2sm01421a

  View details for Web of Science ID 000933346700001

  View details for PubMedID 36790413

• Enhanced dispersion in an oscillating array of harmonic traps PHYSICAL REVIEW E Barakat, J. M., Takatori, S. C. 2023; 107 (1): 014601

  Abstract

  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 nonmonotonic 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 "slingshot" mechanism that predicts a significant enhancement of colloidal diffusion in dynamic external fields.

  View details for DOI 10.1103/PhysRevE.107.014601

  View details for Web of Science ID 000951821200004

  View details for PubMedID 36797955

• Porous Media Microstructure Determines the Diffusion of Active Matter: Experiments and Simulations FRONTIERS IN PHYSICS Modica, K. J., Xi, Y., Takatori, S. C. 2022; 10

  View details for DOI 10.3389/fphy.2022.869175

  View details for Web of Science ID 000808053600001

• Molecular height measurement by cell surface optical profilometry (CSOP) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Son, S., Takatori, S. C., Belardi, B., Podolski, M., Bakalar, M. H., Fletcher, D. A. 2020; 117 (25): 14209-14219

  Abstract

  The physical dimensions of proteins and glycans on cell surfaces can critically affect cell function, for example, by preventing close contact between cells and limiting receptor accessibility. However, high-resolution measurements of molecular heights on native cell membranes have been difficult to obtain. Here we present a simple and rapid method that achieves nanometer height resolution by localizing fluorophores at the tip and base of cell surface molecules and determining their separation by radially averaging across many molecules. We use this method, which we call cell surface optical profilometry (CSOP), to quantify the height of key multidomain proteins on a model cell, as well as to capture average protein and glycan heights on native cell membranes. We show that average height of a protein is significantly smaller than its contour length, due to thermally driven bending and rotation on the membrane, and that height strongly depends on local surface and solution conditions. We find that average height increases with cell surface molecular crowding but decreases with solution crowding by solutes, both of which we confirm with molecular dynamics simulations. We also use experiments and simulations to determine the height of an epitope, based on the location of an antibody, which allows CSOP to profile various proteins and glycans on a native cell surface using antibodies and lectins. This versatile method for profiling cell surfaces has the potential to advance understanding of the molecular landscape of cells and the role of the molecular landscape in cell function.

  View details for DOI 10.1073/pnas.1922626117

  View details for Web of Science ID 000546772500024

  View details for PubMedID 32513731

  View details for PubMedCentralID PMC7322024

• Active Contact Forces Drive Nonequilibrium Fluctuations in Membrane Vesicles PHYSICAL REVIEW LETTERS Takatori, S. C., Sahu, A. 2020; 124 (15): 158102

  Abstract

  We analyze the nonequilibrium 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 lengthscale and timescale 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 nonequilibrium 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.

  View details for DOI 10.1103/PhysRevLett.124.158102

  View details for Web of Science ID 000526038600019

  View details for PubMedID 32357050

• Inertial effects on the stress generation of active fluids Takatori, S. C., Brady, J. F. AMER PHYSICAL SOC. 2017

  View details for DOI 10.1103/PhysRevFluids.2.094305

  View details for Web of Science ID 000412064400015

• Superfluid Behavior of Active Suspensions from Diffusive Stretching PHYSICAL REVIEW LETTERS Takatori, S. C., Brady, J. F. 2017; 118 (1): 018003

  Abstract

  The current understanding is that the non-Newtonian rheology of active matter suspensions is governed by fluid-mediated hydrodynamic interactions associated with active self-propulsion. Here we discover an additional contribution to the suspension shear stress that predicts both thickening and thinning behavior, even when there is no nematic ordering of the microswimmers with the imposed flow. A simple micromechanical model of active Brownian particles in homogeneous shear flow reveals the existence of off-diagonal shear components in the swim stress tensor, which are independent of hydrodynamic interactions and fluid disturbances. Theoretical predictions from our model are consistent with existing experimental measurements of the shear viscosity of active suspensions, but also suggest new behavior not predicted by conventional models.

  View details for DOI 10.1103/PhysRevLett.118.018003

  View details for Web of Science ID 000391474900015

  View details for PubMedID 28106451

• Acoustic trapping of active matter NATURE COMMUNICATIONS Takatori, S. C., De Dier, R., Vermant, J., Brady, J. F. 2016; 7: 10694

  Abstract

  Confinement of living microorganisms and self-propelled particles by an external trap provides a means of analysing the motion and behaviour of active systems. Developing a tweezer with a trapping radius large compared with the swimmers' size and run length has been an experimental challenge, as standard optical traps are too weak. Here we report the novel use of an acoustic tweezer to confine self-propelled particles in two dimensions over distances large compared with the swimmers' run length. We develop a near-harmonic trap to demonstrate the crossover from weak confinement, where the probability density is Boltzmann-like, to strong confinement, where the density is peaked along the perimeter. At high concentrations the swimmers crystallize into a close-packed structure, which subsequently 'explodes' as a travelling wave when the tweezer is turned off. The swimmers' confined motion provides a measurement of the swim pressure, a unique mechanical pressure exerted by self-propelled bodies.

  View details for DOI 10.1038/ncomms10694

  View details for Web of Science ID 000371735300001

  View details for PubMedID 26961816

  View details for PubMedCentralID PMC4792924

• Forces, stresses and the (thermo?) dynamics of active matter CURRENT OPINION IN COLLOID & INTERFACE SCIENCE Takatori, S. C., Brady, J. F. 2016; 21: 24-33

  View details for DOI 10.1016/j.cocis.2015.12.003

  View details for Web of Science ID 000374357900004