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We present an experimental study combining particle tracking, active microrheology, and differential dynamic microscopy (DDM) to investigate the dynamics and rheology of an oil-water interface during biofilm formation by the bacteria Pseudomonas Aeruginosa PA14. The interface transitions from an active fluid dominated by the swimming motion of adsorbed bacteria at early age to an active viscoelastic system at late ages when the biofilm is established. The microrheology measurements using microscale magnetic rods indicate that the biofilm behaves as a viscoelastic solid at late age. The bacteria motility at the interface during the biofilm formation, which is characterized in the DDM measurements, evolves from diffusive motion at early age to constrained, quasi-localized motion at later age. Similarly, the mobility of passively moving colloidal spheres at the interface decreases significantly with increasing interface age and shows a dependence on sphere size after biofilm formation that is orders-of-magnitude larger than that expected in a homogeneous system in equilibrium. We attribute this anomalous size dependence to either length-scale-dependent rheology of the biofilm or widely differing effects of the bacteria activity on the motion of spheres of different sizes.

Lab-on-a-chip devices based on inertial microfluidics have emerged as a promising technique to manipulate particles in a precise way. Inertial microfluidics exploits internal hydrodynamic forces and the mechanical structure of particles to achieve separation and focusing. The article focuses on the hydrodynamic interaction of two particles. This will help to develop an understanding of the dynamics of particle trains in inertial microfluidics, which are typical structures in multi-particle systems. We perform three-dimensional lattice Boltzmann simulations combined with the immersed boundary method to unravel the dynamics of various mono- and bi-dispersed pairs in inertial microfluidics. We study the influence of different starting positions for mono- and bi-dispersed pairs. We also change their deformability from relatively soft to rigid and choose spherical and biconcave particle shapes. The observed two-particle motions in the present work can be categorized into four types: stable pair, stable pair with damped oscillations, stable pair with bounded oscillations, and unstable pair. We show that stable pairs become unstable when increasing the particle stiffness. Furthermore, a pair with both capsules in the same channel half is more prone to become unstable than a pair with capsules in opposite channel halves.

Microswimmers such as E. coli bacteria accumulate and exhibit an intriguing dynamics near walls, governed by hydrodynamic and steric interactions. Insight into the underlying mechanisms and predominant interactions demand a detailed characterization of the entrapment process. We employ a mesoscale hydrodynamics simulation approach to study entrapment of an E. coli-type cell at a no-slip wall. The cell is modeled by a spherocylindrical body with several explicit helical flagella. Three stages of the entrapment process can be distinguished: the approaching regime, where a cell swims toward a wall on a nearly straight trajectory; a scattering regime, where the cell touches the wall and reorients; and a surface-swimming regime. Our simulations show that steric interactions may dominate the entrapment process, yet, hydrodynamic interactions slow down the adsorption dynamics close to the boundary and imply a circular motion on the wall. The locomotion of the cell is characterized by a strong wobbling dynamics, with cells preferentially pointing toward the wall during surface swimming.

The dynamics of passive micro-objects in an active bath has been receiving much attention. However, the influence of the shapes of micro-objects remains unclear. Here, we use 2D simulation to investigate the interaction between active Brownian particles and different-shaped passive micro-objects. We show that active particles accumulate around micro-objects and self-assemble into living aggregations at a high active velocity and high volume fraction. The shapes of micro-objects affect the distributions of the aggregations. In turn, the different distribution of aggregations influences the motion of micro-objects and induces abnormal diffusive behaviors. We further demonstrate that polar distributed aggregations at a high active velocity and the inhibition of the active bath at a low active velocity induce the counterintuitive anisotropic enhanced diffusion of rods, and the steric interaction between active particles induces the reverse translation-rotation coupled diffusion of chevrons.

We study the single-file dynamics of three classes of active particles: run-and-tumble particles, active Brownian particles and active Ornstein-Uhlenbeck particles. At high activity values, the particles, interacting via purely repulsive and short-ranged forces, aggregate into several motile and dynamical clusters of comparable size, and do not display bulk phase-segregation. In this dynamical steady-state, we find that the cluster size distribution of these aggregates is a scaled function of the density and activity parameters across the three models of active particles with the same scaling function. The velocity distribution of these motile clusters is non-Gaussian. We show that the effective dynamics of these clusters can explain the observed emergent scaling of the mean-squared displacement of tagged particles for all the three models with identical scaling exponents and functions. Concomitant with the clustering seen at high activities, we observe that the static density correlation function displays rich structures, including multiple peaks that are reminiscent of particle clustering induced by effective attractive interactions, while the dynamical variant shows non-diffusive scaling. Our study reveals a universal scaling behavior in the single-file dynamics of interacting active particles., Accepted for publication in Soft Matter

Tissues transition between solid-like and fluid-like behavior, which has major implications for morphogenesis and disease. These transitions can occur due to changes in the intrinsic shape of constituent cells and cell motility. We consider an alternative mechanism by studying tissues that explore the energy landscape through stochastic dynamics, driven by turnover of junctional molecular motors. To identify the solid-fluid transition, we start with single-component tissues and show that the mean cell-shape index uniquely describes the effective diffusion coefficient of cell movements, which becomes finite at the transition. We generalize our approach to two-component tissues, and explore cell-sorting dynamics both due to differential adhesion and due to differential degree of junctional fluctuations. We recover some known characteristic scaling relations describing the sorting kinetics, and discover some discrepancies from these relations in the case of differential-fluctuations-driven sorting. Finally, we show that differential fluctuations efficiently sort two solid-like tissues with a fluid intercompartmental boundary.

We demonstrate the emergence of circular collective motion in a system of spherical light-propelled Brownian particles. Light-propulsion occurs as consequence of the coupling between the chirality of polymeric particles - left (L)- or right (R)-type - and the circularly-polarized light that irradiates them. Irradiation with light that has the same helicity as the particle material leads to a circular cooperative vortical motion between the chiral Brownian particles. In contrast, opposite circular-polarization does not induce such coupling among the particles but only affects their Brownian motion. The mean angular momentum of each particle has a value and sign that distinguishes between chiral activity dynamics and typical Brownian motion. These outcomes have relevant implications for chiral separation technologies and provide new strategies for optical torque tunability in mesoscopic optical array systems, micro- and nanofabrication of light-activated engines with selective control and collective motion.

We study the dynamics of a polymer, described as a variant of a Rouse chain, driven by an active terminal monomer (head). The local active force induces a transition from a globule-like to an elongated state, as revealed by the study of the end-to-end distance, the variance of which is analytically predicted under suitable approximations. The change in the relaxation times of the Rouse-modes produced by the local self-propulsion is consistent with the transition from globule to elongated conformations. Moreover, also the bond-bond spatial correlation for the chain head are affected by the self-propulsion and a gradient of over-stretched bonds along the chain is observed. We compare our numerical results both with the phenomenological stiff-polymer theory and several analytical predictions in the Rouse-chain approximation.

The structural relaxation slows down drastically upon approaching the glass transition, accompanied by the significant growth of dynamic heterogeneity. The fundamental question of elusiveness and interest is whether there exists an underlying quantitative relationship between structural relaxation and dynamic heterogeneity. Here, we reveal that which is related to the reduced mean square displacements to overcome the energy barriers of activated jumps, instead of the kinetic fragility m, is the genuine key parameter connecting dynamic heterogeneity with structural relaxation for varying types of glass formers. Furthermore, based on the dependence of dynamic heterogeneity on the Debye–Waller factor we obtained a direct quantitative relation between dynamic heterogeneity and structural relaxation is built for different glass-forming liquids. More importantly, a scaling collapse of structural relaxation and dynamic heterogeneity is achieved by the important parameter . These results are of fundamental and critical importance for developing a unified theory of glassy dynamics.

Actively driven colloids demonstrate complex out-of-equilibrium dynamics often rivaling self-organized patterns and collective behavior observed in living systems. Recent studies revealed the emergence of steady macroscopic states with multiple interacting vortices in an unconfined environment that emerge from the coupling between microscale particle rotation and translation. Yet, insights into the microscopic behavior during the vortex emergence, growth, and formation of a multi-vortical state remain lacking. Here, we investigate in experiments and simulations how the microscale magnetic roller behavior leads to the emergence of seed vortices, their aggregation or annihilation, and the formation of stable large-scale vortical structures. We reveal that the coupling of roller-induced hydrodynamic flows guides the local self-densifications and self-organization of the micro-rollers into seed vortices. The resulting multi-vortical state is sensitive to the external magnetic field amplitude and allows tuning the rollers' number density in a vortex and its characteristic size.

The wetting of soft elastic substrates exhibits many features that have no counterpart on rigid surfaces. Modelling the detailed elastocapillary interactions is challenging, and has so far been limited to single contact lines or single drops. Here we propose a reduced long-wave model that captures the main qualitative features of statics and dynamics of soft wetting, but which can be applied to ensembles of droplets. The model has the form of a gradient dynamics on an underlying free energy that reflects capillarity, wettability and compressional elasticity. With the model we first recover the double transition in the equilibrium contact angles that occurs when increasing substrate softness from ideally rigid towards very soft (i.e., liquid). Second, the spreading of single drops of partially and completely wetting liquids is considered showing that known dependencies of the dynamic contact angle on contact line velocity are well reproduced. Finally, we go beyond the single droplet picture and consider the coarsening for a two-drop system as well as for a large ensemble of drops. It is shown that the dominant coarsening mode changes with substrate softness in a nontrivial way.

Owing to the local/heterogeneous structures in supercooled liquids, after several decades of research, it is now clear that supercooled liquids are structurally different from their conventional liquid counterparts. Accordingly, an approach based on a local probe should provide a better understanding about the local mechanical properties as well as heterogeneous structures. Recently, the superiority of active microrheology over global rheology has been demonstrated [Yu et al., Sci. Adv., 2020, 6, 8766]. Here, we elaborate this new avenue of research and provide more evidence for such superiority. We report on the results of an extensive molecular dynamics simulation of active microrheology of a model glass. We identify several time scales in time series of friction, and detect a transition in dynamical behavior of friction. We discuss the possible relation to structural heterogeneities-a subject of considerable interest in glass physics.

The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and in experiments. A lot of important information which is not immediately accessible from bulk measurements can be accessed via these local measurements. Still, a detailed understanding of how a probe particle dynamics is affected by the surrounding liquid medium is lacking, especially in the supercooled temperature regime. This work shows how the translational dynamics of a rod-like particle immersed in a supercooled liquid can give us information on the growth of the correlation length scales associated with dynamical heterogeneity and the multi-body static correlations in the medium. This work also provides an understanding of the breakdown of Stokes–Einstein and Stokes–Einstein–Debye relations in supercooled liquids along with a unified scaling theory that rationalizes all the observed results. Finally, this work proposes a novel yet simple method accessible in experiments to measure the growth of these important length scales in molecular glass-forming liquids.

Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that cell shape changes are induced by diffusible biomolecules that influence tissue contractility in a concentration-dependent manner – and whose concentration is in turn affected by the macroscopic tissue shape. We perform computational simulations of thin shell elastic dynamics to reveal propagating chemical and three-dimensional deformation patterns arising due to a sequence of buckling instabilities. Depending on the concentration threshold that actuates cell shape change, we find qualitatively different patterns. The mechanochemically coupled patterning dynamics are distinct from those driven by purely mechanical or purely chemical factors, and emerge even without diffusion. Using numerical simulations and theoretical arguments, we analyze the elastic instabilities that result from our model and provide simple scaling laws to identify wrinkling morphologies.

Swimming bacteria can be trapped for prolonged times at the surface of an impenetrable boundary. The subsequent surface confined motility is found to be very sensitive to the physico-chemical properties of the interfaces which determine the boundary conditions for the flow. The quantitative understanding of this complex dynamics requires detailed and systematic experimental data to validate theoretical models for both flagellar propulsion and interfacial dynamics. Using a combination of optical trapping and holographic imaging we study the 3D dynamics of wall entrapment of swimming bacteria that are sequentially released towards a surfactant-covered liquid-air interface. We find that an incompressible surfactant model for the interface quantitatively accounts for the observed normal and tangential speed of bacteria as they approach the boundary. Surprisingly we also find that, although bacteria circulate over the air phase in counterclockwise circular trajectories, typical of free-slip interfaces, the body axis is still tilted "nose down" as found for no-slip interfaces.

The interface between two fluids is roughened by thermally excited capillary waves. By using colloid-polymer systems which exhibit liquid-gas phase separation, the time and length scales of capillary waves become accessible to optical microscopy methods. Here, we study such a system using bright-field optical microscopy combined with a novel extension of differential dynamic microscopy. With differential dynamic microscopy, we analyze images in order to determine the decay time of interfacial fluctuations spanning wavevectors from 0.1 to 1 μm-1. We find capillary velocities on the order of 0.1 μm s-1 that depend on the sample composition in expected ways and that match values from the literature. This work demonstrates the first application of differential dynamic microscopy to the study of interfacial dynamics.

Red blood cells in shear flow show a variety of different shapes due to the complex interplay between hydrodynamics and membrane elasticity. Malaria-infected red blood cells become generally adhesive and less deformable. Adhesion to a substrate leads to a reduction in shape variability and to a flipping motion of the non-spherical shapes during the mid-stage of infection. Here, we present a complete state diagram for wall adhesion of red blood cells in shear flow obtained by simulations, using a particle-based mesoscale hydrodynamics approach, multiparticle collision dynamics. We find that cell flipping at a substrate is replaced by crawling beyond a critical shear rate, which increases with both membrane stiffness and viscosity contrast between the cytosol and suspending medium. This change in cell dynamics resembles the transition between tumbling and tank-treading for red blood cells in free shear flow. In the context of malaria infections, the flipping-crawling transition would strongly increase the adhesive interactions with the vascular endothelium, but might be suppressed by the combined effect of increased elasticity and viscosity contrast.

The mechanosensitivity of cells, which determines how they are able to respond to mechanical signals received from their environment, is crucial for the functioning of all biological systems. In experiments, cells placed on cyclically stretched substrates have been shown to reorient in a direction that depends not only on the type of cell, but also on the mechanical properties of the substrate, and the amplitude and rate of stretching. However, the underlying biochemical and mechanical mechanisms responsible for this realignment are still not completely understood. In this study, we introduce a computational model for fast crawling on cyclically stretched substrates that accounts for the sub-cellular processes responsible for the cell shape and motility, as well as the coupling to the substrate through the focal adhesion sites. In particular, we focus on the role of the focal adhesion dynamics, and show that the reorientation under cyclic stretching is strongly dependent on the frequency, as has been observed experimentally. Furthermore, we show that an asymmetry during the loading and unloading phases of the stretching, whether coming from the response of the cell itself, or from the stretching protocol, can be used to selectively align the cells in either the parallel or perpendicular directions., Comment: 19 pages, 7 figures

We provide a quantitative description of the memory effects existing in the apparently random Markovian dynamics of a pair of optically trapped colloidal microparticles in water. The particles are trapped in very close proximity to each other such that the resultant hydrodynamic interactions lead to non-Markovian signatures manifested by the double exponential auto-correlation function for the Brownian motion of each particle. In connection with the memory effects, we quantify the storage of energy in terms of various system parameters and demonstrate that a pair of Markovian particles - confined in individual optical traps in a viscous fluid - can be described in the framework of a single Brownian particle in a viscoelastic medium. We define and quantify the equivalent storage and loss moduli of the two-particle system, and show experimentally that the memory effects are maximized at a certain trap stiffness ratio, and reduce with increasing particle separation. The technique can be generally used to determine the effective viscoelastic parameters of any such fluid-particle systems, and can thus help understand the interactions between active particles mediated by simple or complex fluids.

We characterize the mechanical recovery of compliant silicone gels following adhesive contact failure. We establish broad, stable adhesive contacts between rigid microspheres and soft gels, then stretch the gels to large deformations by pulling quasi-statically on the contact. Eventually, the adhesive contact begins to fail, and ultimately slides to a final contact point on the bottom of the sphere. Immediately after detachment, the gel recoils quickly with a self-similar surface profile that evolves as a power law in time, suggesting that the adhesive detachment point is singular. The singular dynamics we observe are consistent with a relaxation process driven by surface stress and slowed by viscous flow through the porous, elastic network of the gel. Our results emphasize the importance of accounting for both the liquid and solid phases of gels in understanding their mechanics, especially under extreme deformation.

The site-specific migration dynamics of small particles at the air-nematic liquid crystal (LC) interface is investigated, using a LC film with a unique gradient of LC distortions. This gradient has been identified as the direct origin of the site-specific migration, while the elastic multipole interaction between the pre-existing distortion and that induced around particles is negligible. The results reveal a basic behavior of small particles with weak anchoring strength in LC distortions, which is often hidden in prominent elastic multipole interactions typically found with larger particles. Moreover, the present mechanism of the site-specific attraction of particles is specifically relevant to directed patterning and manipulations of nano-particles in nematic LCs with distortions.

A possible application of self-propelling particles is the transport of microscopic cargo. Maximizing the collection and transport efficiency of particulate matter requires the area swept by the moving particle to be as large as possible. One such particle geometry are rods propelled perpendicular to their long axis, that act as “sweepers” for collecting particles. Here we report on the required Janus coating to achieve such motion, and on the dynamics of the collection and transport of microscopic cargo by sideways propelled Janus rods. ispartof: Soft Matter vol:17 issue:9 ispartof: location:England status: Published online

Foams have unique properties that distinguish them from ordinary liquids and gases, and are ubiquitously observed in nature, both in biological systems and industrial products. Foams are known to eventually collapse over time; given their wide-range industrial application, understanding how bubbles in a foam collapse is an important aspect for product longevity and tailoring physical properties. Previously, it was shown that droplets are emitted during the collective bubble collapse, however the mechanism of the droplet emission in a foam is not yet clearly understood. It is directly related to the stability of the foam, thus we quantitatively investigate collapse dynamics in liquid films in a foam, and identify some unique features. When one film breaks, we see that the oscillation of the vertical Plateau border to which it is connected induces anomalous liquid transport from the edge of the border to the center. Once a crack appears near the border and a collapse front is formed, we find that the curvature of the front reverses as it migrates, followed by the emergence and emission of droplets. We elucidate the origins of this behavior and discuss the stability of foams, establishing how the characteristic time scales of the process relate to each other.

Avalanche dynamics in an ensemble of self-propelled camphor boats are studied. The self-propelled agents are camphor infused circular paper disks moving on the surface of water. The ensemble exhibits bursts of activity in the autonomous state triggered by stochastic fluctuations. This type of dynamics has been previously reported in a slightly different system (J. Phys. Soc. Jpn., 2015, 84, 034802). Fourier analysis of the autonomous ensemble's average speed reveals a unimodal spectrum, indicating the presence of a preferred time scale in the dynamics. We therefor, entrain such an ensemble by external forcing by using periodic air perturbations on the surface of the water. This forcing is able to replace the stochastic fluctuations which trigger a burst in the autonomous ensemble, thus entraining the system. Upon varying the periodic forcing frequency, an optimal frequency is revealed at which the quality of entrainment of the ensemble by the forcing is augmented. This optimal frequency is found to be in the vicinity of the Fourier spectrum peak of the autonomous ensemble's average speed. This indicates the existence of an underlying deterministic component in the apparent aperiodic bursts of motion of the autonomous ensemble of active particles. A qualitative reasoning for the observed phenomenon is presented.

Onsager's variational principle (OVP) was originally proposed by Lars Onsager in 1931 [L. Onsager, $Phys. Rev.$, 1931, $37$, 405]. This fundamental principle provides a very powerful tool for formulating thermodynamically consistent models. It can also be employed to find approximate solutions, especially in the study of soft matter dynamics. In this work, OVP is extended and applied to the dynamic modeling of active soft matter such as suspensions of bacteria and aggregates of animal cells. We first extend the general formulation of OVP to active matter dynamics where active forces are included as external non-conservative forces. We then use OVP to analyze the directional motion of individual active units: a molecular motor walking on a stiff biofilament and a toy two-sphere microswimmer. Next, we use OVP to formulate a diffuse-interface model for an active polar droplet on a solid substrate. In addition to the generalized hydrodynamic equations for active polar fluids in the bulk region, we have also derived thermodynamically consistent boundary conditions. Finally, we consider the dynamics of a thin active polar droplet under the lubrication approximation. We use OVP to derive a generalized thin film equation and then employ OVP as an approximation tool to find the spreading laws for the thin active polar droplet. By incorporating the activity of biological systems into OVP, we develop a general approach to construct thermodynamically consistent models for better understanding the emergent behaviors of individual animal cells and cell aggregates or tissues.

Active matter deals with systems whose particles consume energy at the individual level in order to move. To unravel features such as the emergence of collective structures, several models have been suggested, such as the on-lattice model of run-and-tumble particles implemented via the persistent exclusion process (PEP). In our work, we study a one-dimensional system of run-and-tumble repulsive or attractive particles, both on-lattice and off-lattice. Additionally, we implement cluster motility dynamics in the on-lattice case (since in the off-lattice case, cluster motility arises from the individual particle dynamics). While we observe important differences between discrete and continuous dynamics, few common features are of particular importance. Increasing particle density drives aggregation across all different systems explored. For non-attractive particles, the effects of particle activity on aggregation are largely independent of the details of the dynamics. In contrast, once attractive interactions are introduced, the steady-state, which is completely determined by the interplay between these and the particles' activity, becomes highly dependent on the details of the dynamics.

The rhythmic beating motion of autonomously motile filaments has many practical applications. Here, we present an experimental study on a filament made of camphor infused paper disks, stitched together adjacent to each other using nylon thread. The filament displays spontaneous translatory motion when it is placed on the surface of water due to the surface tension gradients created by camphor molecules on the water surface. When this filament is clamped on one end, we obtain regular oscillatory motion instead of translation. The filament shows qualitatively different dynamics at different activity levels, which is controlled by the amount of camphor infused into the paper disks. For a better physical understanding of the filament dynamics, we develop a minimal numerical model involving a semi-flexible filament made of active polar disks, where the polarity is coupled to the instantaneous velocity of the particle. This model qualitatively reproduces different oscillatory modes of the filament. Moreover, our model reveals a rich dynamical state diagram of the system, as a function of filament activity and the coupling strength.

Hydrodynamic interactions are fundamental for the dynamics of swimming self-propelled particles. Specifically, bonds between microswimmers enforce permanent spatial proximity and, thus, enhance emergent correlations by microswimmer-specific flow fields. We employ the squirmer model to study the swimming behavior of microswimmer dumbbells by mesoscale hydrodynamic simulations, where the squirmers’ rotational motion is geometrically unrestricted. An important aspect of the applied particle-based simulation approach—the multiparticle collision dynamics method—is the intrinsic account for thermal fluctuations. We find a strong effect of active stress on the motility of dumbbells. In particular, pairs of strong pullers exhibit orders of magnitude smaller swimming efficiency than pairs of pushers. This is a consequence of the inherent thermal fluctuations in combination with the strong coupling of the squirmers’ rotational motion, which implies non-exponentially decaying auto- and cross-correlation functions of the propulsion directions, and active stress-dependent characteristic decay times. As a consequence, specific stationary-state relative alignments of the squirmer propulsion directions emerge, where pullers are preferentially aligned in an antiparallel manner along the bond vector, whereas pushers are preferentially aligned normal to the bond vector with a relative angle of approximately 60° at weak active stress, and one of the propulsion directions is aligned with the bond at strong active stress. The distinct differences between dumbbells comprised of pusher or pullers suggest means to control microswimmer assemblies for future microbot applications.

The role of gravity on the dynamics of granular particles is examined via their velocity distributions. Acceleration due to gravity, particle number and the coefficient of restitution have all been varied. Various quantitative relationships governing the relationship between parameters involved in the vertical and horizontal velocity component distributions are derived and applied to the data, and for the horizontal velocity components' distribution in particular remarkably good agreement is obtained.

We employ a dynamic micro light scattering technique to probe the thermal concentration fluctuations in surface-attached poly-N-isopropylacrylamide (PNIPAAm) gel layers swollen in ethanol as a good solvent. At the equilibrium swelling state, the relaxation function exhibits two decays in the time range between microseconds and seconds and the characteristic rates display a pure diffusive behavior. The fast cooperative diffusion increases with crosslinking density as a result of the decrease in the dynamic network mesh size. This increase is significantly stronger than the concentration dependence of the cooperative diffusion in uncrosslinked linear PNIPPAm solutions. Uniaxial swelling due to the surface attachment and structural inhomogeneities intrinsic to photo-crosslinked gels alter the dynamics of the surface anchored networks compared to the solutions. In contrast to the frozen inhomogeneities in conventional gels, the slow diffusion in the present anchored layers was found to be ergodic. It might relate to structural inhomogeneities but its nature is not clarified yet.

We computationally investigate the dynamics of a self-propelled Janus probe in crowded environments. The crowding is caused by the presence of viscoelastic polymers or non-viscoelastic disconnected monomers. Our simulations show that the translational, as well as rotational mean square displacements, have a distinctive three-step growth for fixed values of self-propulsion force, and steadily increase with self-propulsion, irrespective of the nature of the crowder. On the other hand, in the absence of crowders, the rotational dynamics of the Janus probe is independent of self-propulsion force. On replacing the repulsive polymers with sticky ones, translational and rotational mean square displacements of the Janus probe show a sharp drop. Since different faces of a Janus particle interact differently with the environment, we show that the direction of self-propulsion also affects its dynamics. The ratio of long-time translational and rotational diffusivities of the self-propelled probe with a fixed self-propulsion, when plotted against the area fraction of the crowders, passes through a minima and at higher area fraction merges to its value in the absence of the crowder. This points towards the decoupling of translational and rotational dynamics of the self-propelled probe at intermediate area fraction of the crowders. However, such translational-rotational decoupling is absent for passive probes., Comment: Simulation videos are available on request

Soft matter systems show a rich non-equilibrium behaviour that sensitively depends on external perturbations. This opinion discusses why significant progress in the understanding of their non-equilibrium behaviour is to be expected within the next few years.

We experimentally study the stochastic transport of a self-propelled camphor boat, driven by Marangoni forces, through a crowd of passive paper discs floating on water. We analyze the statistics of the first passage times of the active particle to travel from the center of a circular container to its boundary. While the mean times rise monotonically as a function of the covered area fraction φ of the passive paper discs, their fluctuations show a non-monotonic behavior - being higher at low and high value of φ compared to intermediate values. The reason is traced to an interplay of two distinct sources of fluctuations - one intrinsic to the dynamics, while the other due to the crowding.

We study the dynamics of a self-propelled particle advected by a steady laminar flow. The persistent motion of the self-propelled particle is described by an active Ornstein-Uhlenbeck process. We focus on the diffusivity properties of the particle as a function of persistence time and free-diffusion coefficient, revealing non-monotonic behaviors, with the occurrence of a minimum and a steep growth in the regime of large persistence time. In the latter limit, we obtain an analytical prediction for the scaling of the diffusion coefficient with the parameters of the active force. Our study sheds light on the effect of a flow-field on the diffusion of active particles, such as living microorganisms and motile phytoplankton in fluids. This journal is

Geometrical features play a very important role in neuronal growth and the formation of functional connections between neuronal cells. Here, we analyze the dynamics of axonal growth for neuronal cells cultured on micro-patterned polydimethylsiloxane surfaces. We utilize fluorescence microscopy to image axons, quantify their dynamics, and demonstrate that periodic geometrical patterns impart strong directional bias to neuronal growth. We quantify axonal alignment and present a general stochastic approach that quantitatively describes the dynamics of the growth cones. Neuronal growth is described by a general phenomenological model, based on a simple automatic controller with a closed-loop feedback system. We demonstrate that axonal alignment on these substrates is determined by the surface geometry, and it is quantified by the deterministic part of the stochastic (Langevin and Fokker-Planck) equations. We also show that the axonal alignment with the surface patterns is greatly suppressed by the neuron treatment with Blebbistatin, a chemical compound that inhibits the activity of myosin II. These results give new insight into the role played by the molecular motors and external geometrical cues in guiding axonal growth, and could lead to novel approaches for bioengineering neuronal regeneration platforms.

Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.

We present systematic numerical simulations to understand the behavior of colloidal swimmers near a wall. We extend previous theoretical calculations based on lubrication theory to include walls with arbitrary curvature, and show how to extract from simulations a set of parameters crucial to accurately estimate the leading hydrodynamic contributions associated with the curvature of a wall. Our results show explicitly how introducing curvature to the wall not only affects the average incident angle the swimmer acquires when swimming near it, but it also leads to much broader angular distributions. This suggests an increasingly leading role of thermal fluctuations with curvature, which in turn results in significantly different motility of the swimmers. We also show how the backwards motion previously reported for pushers also extends to puller-like swimmers under the appropriate conditions. Finally, aiming at understanding the behavior of colloidal swimmers near a colloidal crystal, we also considered the case of a wall built from colloidal particles that are either free to rotate, representing a crystal held together by isotropic forces, or have their rotational degrees of freedom locked-in, representing a crystal held together by directional interactions. In both cases, we find that puller-like swimmers follow a stochastic run-and-tumble-like dynamics.

We formulate the dynamics of overdamped Brownian active particles (swimmers) moving on any Riemannian 2-manifold. To characterize such dynamics at short times, an analytical expression for the variance of swimmers diffusing on any Riemmanian 2-manifold is derived. To show the generality of the present work, we apply the latter dynamics to swimmers moving on the surface of a spheroid and a torus, and offer analytical expressions for both their long-time variances and steady angular marginal probability density functions. Finally, Brownian dynamics simulations are used to validate our theoretical findings.

Air bubbles rising through an aqueous medium have been studied extensively and are routinely used for the separation of particulates via froth flotation, a key step in many industrial processes. Oil-coated bubbles can be more effective for separating hydrophilic particles with low affinity for the air-water interface, but the rise dynamics of oil-coated bubbles has not yet been explored. In the present work, we report the first systematic study of the shape and rise trajectory of bubbles engulfed in a layer of oil. Results from direct observation of the coated bubbles with a high-speed camera are compared to computer simulations and confirm a pronounced effect of the oil coat on the bubble dynamics. We consistently find that the oil-coated bubbles display a more spherical shape and straighter trajectory, yet slower rise than uncoated bubbles of comparable size. These characteristics may provide practical benefits for flotation separations with oil-coated bubbles.

The local segmental and secondary dynamics of tetramethylene oxide oligomer grafted to silica nanoparticles (NPs) were investigated as a function of grafting density and molecular weight. Grafting slows the segmental (α) dynamics, but gives rise to faster secondary (β) motions. Interestingly, the magnitude of these effects decreases with the extent of grafting (i.e., surface coverage), as well as with oligomer molecular weight. The disparity in dynamical effects reflects the decoupling of the segmental and more local β dynamics, the former is associated with stronger dynamic correlations that extend over a greater spatial range. This results in greater sensitivity to interactions, including tethering of the chains to the NP surface.

We model a polymer-grafted stealth nanoparticle (SNP) as a composite system consisting of a spherical core coated with a porous polymeric brush with end-ligands. Adjacent to target cells, the near-wall hydrodynamics, thermal fluctuations, and thermodynamic adhesive interactions simultaneously impact the transient motion of the SNP. Employing both the Langevin framework for the effective hard sphere dynamics and the coupled generalized Langevin framework for the nanoparticle-polymer dynamics, we comprehensively investigate the velocity and position temporal relaxations of the SNP in the absence and presence of end-to-end distance fluctuations for the tethered polymer. We demonstrate that polymer structural relaxations substantially impact the SNP adhesive dynamics, especially when the grafted polymer is more flexible. Moreover, a long-time tail with t-3/2 scaling due to polymer chain-length fluctuations is observed in the velocity autocorrelation for a bound SNP. Finally, the thermodynamic effects of membrane morphology on SNP adhesion are explored by modifying the membrane-mediated binding potential of mean force.

We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over the fast DNA dynamics leads to an evolution equation for the particle in isolation, which contains both friction and diffusion. The DNA-induced friction coefficient depends on the physical properties of the DNA, and substituting parameter values typical of a 1$\mu$m colloid coated densely with weakly interacting DNA gives a coefficient about 100 times larger than the corresponding coefficient of hydrodynamic friction. We use a mean-field extension of the model to higher dimensions to estimate the friction tensor for a disc rotating and translating horizontally along a line. When the DNA strands are very stiff and short, the friction coefficient for the disc rolling approaches zero while the friction for the disc sliding remains large. Together, these results could have significant implications for the dynamics of DNA-coated colloids or other ligand-receptor systems, implying that DNA-induced friction between colloids can be stronger than hydrodynamic friction and should be incorporated into simulations, and that it depends nontrivially on the type of relative motion, possibly causing the particles to assemble into out-of-equilibrium metastable states governed by the pathways with the least friction., Comment: 13 pages text, and 6 pages appendices

The term single file (SF) dynamics refers to the motion of an assembly of particles through a channel with cross-sections comparable to the particles' diameter. Single file diffusion (SFD) is then the diffusion of a tagged particle in a single file, i.e., under the condition that particle passing is not allowed. SFD accounts for a large variety of processes in nature, including diffusion of colloids in synthetic and natural channels, biological motors along molecular chains, electrons in proteins and liquid helium, ions through membranes, just to mention a few examples. Albeit introduced in 1965s, over the last decade the classical notion of SF dynamics has been generalised to account for a more realistic modelling of the particle properties, file geometry, particle-particle and channel-particle interactions, which paves the way to remarkable applications of the SF model, for instance, in the technology of bio-integrated nanodevices. We provide here a comprehensive review of the recent advances in the theory of SF dynamics with the purpose of spurring further experimental work.

Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought out of equilibrium by the action of active fluctuations caused by molecular motors. We show that within such a model, the motion of a free particle crosses over from superdiffusive to subdiffusive as observed for tracer particles in an in vitro cytoskeleton or in a cell. We investigate the dynamics of a particle confined by a harmonic potential as a simple model for the motion of the tethered head of kinesin-1. We find that the probability that the head is close to its binding site on the microtubule can be enhanced by a factor of two due to active forces. Finally, we study the dynamics of a particle in a double well potential as a model for the dynamics of DNA-hairpins. We show that the active forces effectively lower the potential barrier between the two minima and study the impact of this phenomenon on the zipping/unzipping rate. crosscheck: This document is CrossCheck deposited related_data: Supplementary Information identifier: Carlo Vanderzande (ORCID) copyright_licence: The Royal Society of Chemistry has an exclusive publication licence for this journal history: Received 14 November 2016; Accepted 20 February 2017; Accepted Manuscript published 21 February 2017; Advance Article published 27 February 2017; Version of Record published 15 March 2017 ispartof: Soft Matter vol:13 issue:11 pages:2181-2191 ispartof: location:England status: published

We study the 3D dynamics of an elastic dimer consisting of an active swimmer bound to a passive cargo, both suspended in a Couette flow. Using numerical simulations, we determine the diffusivity of such an active dimer in the presence of long-range hydrodynamic interactions for different values of its self-propulsion speed and the Couette flow. We observe that the effect of hydrodynamic interactions is greatly enhanced under the condition that self-propulsion is strong enough to contrast the shear flow. The magnitude of the effect grows with the size of the dimer's constituents relative to their distance, which makes it appreciable under experimental conditions.

In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose stability and dynamics under the influence of MPs has been studied extensively. Although passive cross linkers (PCL) were known to provide structural stability to filamentous network, consequences of the interplay between ATP dependent active forces of MPs and passive entropic forces of PCLs on MT overlap remains largely unexplored. Here, we formulate and characterize a model to study this, using linear stability analysis and numerical integration. In presence of PCLs, we find dynamic phase transitions with changing activity exhibiting regimes of stable partial overlap with or without oscillations, instability towards complete overlap, and stable limit cycle oscillations that emerge via a supercritical Hopf bifurcation characterized by an oscillation frequency determined by the MP and PCL parameters. We show that the overlap dynamics and stability depend crucially on whether both the MTs of overlapping pair are movable or one is immobilized, having potential implications for in vivo and in vitro studies., 13 pages, 9 figures

The enhanced motion of dispersed particles driven by a concentration gradient is the basis for diffusiophoresis. Here we present the dynamics of colloids in a phase separating medium probed by X-Ray Photon Correlation Spectroscopy (XPCS) in the ultra-small angle scattering range. Charge stabilized silica colloids suspended in a binary mixture of 3-methylpyridine and water/heavy water are preferentially wetted by 3-methylpyridine and consequently display a phoretic motion towards that phase upon demixing. This activity lasts for hundreds of seconds before the phase separation is complete and the enhanced motion is arrested as the colloids return to normal diffusive dynamics.

Collective behavior of active matter is observed for self-propelled particles, such as vibrated disks and active Brownian particles, as well as for cytoskeletal filaments in motile cells. Here, a system of quasi two-dimensional penetrable self-propelled rods inside rigid rings is used to construct a complex self-propelled particle. The rods interact sterically with each other and with a stationary or mobile ring via a separation-shifted Lennard-Jones potential. They either have a sliding attachment to the inside of the ring at one of their ends, or can move freely within the ring confinement. We study the inner structure and dynamics of the mobile self-propelled rings. We find that these complex particles cannot only be characterized as active Brownian particles, but can also exhibit cell-like motility: random walks, persistent motion, circling, and run-and-circle motion.

The dynamics of nucleate cells in shear flow is of great relevance in cancer cells and circulatory tumor cells where they determine the flow properties of blood. Buoyed by the success of giant unilamellar vesicles in explaining the dynamics of anucleate cells such as red blood cells, compound vesicles have been suggested as a simple model for nucleate cells. A compound vesicle consists of two concentric unilamellar vesicles with the inner, annular and outer regions filled with aqueous Newtonian solvents. In this work, a theoretical model is presented to study the deformation and dynamics of a compound vesicle in linear shear flow using small deformation theory and spherical harmonics with higher order approximation to the membrane forces. A coupling of viscous and membrane stresses at the membrane interface of the two vesicles results in highly nonlinear shape evolution equations for the inner and the outer vesicles which are solved numerically. The results indicate that the size of the inner vesicle (χ) does not affect the tank-treading dynamics of the outer vesicle. The inner vesicle admits a greater inclination angle than the outer vesicle. However, the transition to trembling/swinging and tumbling is significantly affected. The inner and outer vesicles exhibit identical dynamics in the parameter space defined by the nondimensional rotational (Λan) and extensional (S) strength of the general shear flow. At moderate χ, a swinging mode is observed for the inner vesicle while the outer vesicle exhibits tumbling. The inner vesicle also exhibits modification of the TU mode to IUS (intermediate tumbling swinging) mode. Moreover, synchronization of the two vesicles at higher χ and a Capillary number sensitive motion at lower χ is observed in the tumbling regime. These results are in accordance with the few experimental observations reported by Levant and Steinberg. A reduction in the inclination angle is observed with an increase in χ when the inner vesicle is replaced by a solid inclusion. Additionally, a very elaborate phase diagram is presented in the Λan–S parameter space, which could be tested in future experiments or numerical simulations.

Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains unclear. In this work, the motion of single microtubules was characterized by means of 2D gliding assays and compared with the flows of 3D active fluids. While the scales of the two systems differ by ∼1000×, both were driven by processive, non-processive or an equal mixture of both molecular motor proteins. To search for the dynamic correlation between both systems, the motor activities were tuned by varying temperature and ATP concentration, and the changes in both systems were compared. Motor processivity played an important role in active fluid flows but only when the fluids were nearly motionless; otherwise, flows were dominated by hydrodynamic resistance controlled by sample size. Furthermore, while the motors’ thermal reaction led active fluids to flow faster with increasing temperature, such temperature dependence could be reversed by introducing temperature-varying depletants, emphasizing the potential role of the depletant in designing an active fluid's temperature response. The temperature response of active fluids was nearly immediate (≲10 s). Such a characteristic enables active fluids to be controlled with a temperature switch. Overall, this work not only clarifies the role of temperature in active fluid activity, but also sheds light on the underlying principles of the relationship between the collective dynamics of active fluids and the dynamics of their constituent single microtubules.