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Direct mechanical coupling is known to be critical for establishing synchronization among cilia. However, the actual role of the connections is still elusive - partly because controlled experiments in live samples are challenging. Here, we employ an artificial ciliary system to address this issue. Two cilia are formed by chains of self-propelling robots and anchored to a shared base so that they are purely mechanically-coupled. The system mimics biological ciliary beating but allows fine control over the beating dynamics. We find that the artificial cilia exhibit rich motion behaviors, depending on the mechanical coupling scheme. Particularly, their synchronous beating display two distinct modes - analogous to those observed in C. reinhardtii, the biciliated model organism for studying synchronization. Close examination suggests that the system evolves towards the most dissipative mode. Using this guideline in both simulations and experiments, we are able to direct the system into a desired state by altering the modes' respective dissipation. Our results have significant implications in understanding the synchronization of cilia.

A fluid in contact with a flat structureless wall constitutes the simplest interface system, but the fluid-wall interfacial tension cannot be trivially and even unequivocally determined due to the ambiguity in identifying the precise location of fluid-wall dividing surface. To resolve this long-standing problem, we here derive the interfacial tension from two independent routes without needing the identification of dividing surface. The first one exploits a natural idea that the interfacial profiles of intensive quantities should remain perfectly invariant when deforming the fluid-wall system just to change its interface area. The second one considers the fluid-wall system as the limit of a fluid under a finite external potential field. By calculating the work required to create a differential interface area, the two methods yield exactly the same interfacial tension. Thus, our work provides strong evidence that the fluid-wall interfacial tension can be unambiguously quantified., Comment: 6 pages, 3 figures

The confliction between the stable interface in phase-separated active Brownian particles and its negative surface tension, obtained mechanically via the active pressure, has sparked considerable debate about the formula of active surface tension. Based on the intrinsic pressure of active system, we here derive a proper mechanical expression of active surface tension by calculating the work required to create a differential interface area, while remaining interfacial profile invariant (not considered previously). Our expression yields a significantly positive surface tension that increases with the particle actvity, which is supported by mechanical analysis on the interface. Our results thus fundamentally resolve the contradiction related to active surface tension., Comment: 6 pages, 4 figures

Prior studies have revealed that nonzero odd viscosity is an essential property for chiral active fluids. Here we report that such an odd viscosity also exists in suspensions of non-active or non-externally-driven but chirally-shaped particles. Computational simulations are carried out for monolayers of dense ratchets in simple shear and planar extensional flows. The contact between two ratchets can be either frictionless or infinitely-frictional, depending on their teeth and sliding directions at the contact point. Our results show that the ratchet suspension has the intermediate shear/extensional viscosity as compared with the suspensions of smooth and gear-like particles. Meanwhile, the ratchet suspensions show nonzero even and odd components of the first normal stress coefficient, which indicates the mixed feature of conventional complex fluids and chiral viscous fluids., Comment: 8 pages, 5 figures

An active system consisting of many self-spinning dimers is simulated, and a distinct local rotational jamming transition is observed as the density increases. In the low density regime, the system stays in an absorbing state, in which each dimer rotates independently subject to the applied torque. While in the high density regime, a fraction of the dimers become rotationally jammed into local clusters, and the system exhibits spinodal-decomposition like two-phase morphologies. For high enough densities, the system becomes completely jammed in both rotational and translational degrees of freedom. Such a simple system is found to exhibit rich and multiscale disordered hyperuniformities among the above phases: the absorbing state shows a critical hyperuniformity of the strongest class and subcritically preserves the vanishing density-fluctuation scaling up to some length scale; the locally-jammed state shows a two-phase hyperuniformity conversely beyond some length scale with respect to the phase cluster sizes; the totally jammed state appears to be a monomer crystal, but intrinsically loses large-scale hyperuniformity. These results are inspiring for designing novel phase-separation and disordered hyperuniform systems through dynamical organization.

The shear-induced self-organization of active rotors into stripy aggregates is studied by carrying out computational simulations. The rotors, modeled by monolayers of frictional spheres, develop to stripy microstructures only when they counterrotate with respect to the vorticity of the imposed shear flow. The average width of the stripes is demonstrated to be linearly dependent on the relative intensity of active torque to the shear rate. By giving insight into three collective particle behaviors, i.e., shear-induced diffusion, rotation-induced rearrangement, and edge flows, we explain the mechanisms of formation of the particle stripes. Additionally, the rheological result shows the dependence of shear and rotational viscosities on the active torque direction and the oddness of the normal stress response. By exhibiting a collective phenomenon of active rotors, our study paves the way to understanding chiral active matter., Comment: 13 pages, 16 figures

Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they offer a new platform for studying non-equilibrium physics, in which computer simulation and analytical theory have played an important role. Here we review the recent progress in understanding the dynamic assembly of active colloids by using numerical and analytical tools. We review the progress in understanding the motility induced phase separation in the past decade, followed by the discussion on the effect of shape anisotropy and hydrodynamics on the dynamic assembly of active colloids., Comment: Invited Review in Advanced Theory and Simulations

Fluid flow along microchannels can be induced by keeping opposite walls at different temperatures, and placing elongated tilted pillars inside the channel. The driving force for this fluid motion arises from the anisotropic thermophoretic effect of the elongated pillars that generates a force parallel to the walls, and perpendicular to the temperature gradient. The force is not determined by the thermophilic or thermophobic character of the obstacle surface, but by the geometry and the thermophoretic anisotropy of the obstacle. Via mesoscale hydrodynamic simulations, we investigate the pumping properties of the device as a function of the channel geometry, and pillar surface properties. Applications as fluidic mixers, and fluid alternators are also outlined, together with the potential use of all these devices to harvest waste heat energy. Furthermore, similar devices can be also built employing diffusiophoresis or electrophoresis., Comment: 12 pages, 14 figures

Colloidal migration in temperature gradient is referred to as thermophoresis. In contrast to particles with spherical shape, we show that elongated colloids may have a thermophoretic response that varies with the colloid orientation. Remarkably, this can translate into a non-vanishing thermophoretic force in the direction perpendicular to the temperature gradient. Oppositely to the friction force, the thermophoretic force of a rod oriented with the temperature gradient can be larger or smaller than when oriented perpendicular to it. The precise anisotropic thermophoretic behavior clearly depends on the colloidal rod aspect ratio, and also on its surface details, which provides an interesting tunability to the devices constructed based on this principle. By means of mesoscale hydrodynamic simulations, we characterize this effect for different types of rod-like colloids., Comment: 8 pages, 10 figures

Using an event-driven molecular dynamics simulation, we show that simple monodisperse granular beads confined in coupled columns may oscillate as a new type of granular clock. To trigger this oscillation, the system needs to be driven against gravity into a density-inverted state, with a high-density clustering phase supported from below by a gas-like low-density phase (Leidenfrost effect) in each column. Our analysis reveals that the density-inverted structure and the relaxation dynamics between the phases can amplify any small asymmetry between the columns, and lead to a giant oscillation. The oscillation occurs only for an intermediate range of the coupling strength, and the corresponding phase diagram can be universally described with a characteristic height of the density-inverted structure. A minimal two-phase model is proposed and linear stability analysis shows that the triggering mechanism of the oscillation can be explained as a switchable two-parameter Hopf bifurcation. Numerical solutions of the model also reproduce similar oscillatory dynamics to the simulation results., Comment: 5 figures

We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy $S_{2}$ positively correlates with observed rearrangements in colloidal glasses. The high $S_{2}$ values of the rearranging clusters in glasses indicate that fragile regions in glasses are structurally less correlated, similar to structural defects in crystalline solids. Slow-evolving high $S_{2}$ spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high $S_{2}$ spots best correlate with local deformations right before the rearrangement events. Local free volumes are also found to correlate with particle rearrangements at extreme values, although the ability to identify relaxation sites is substantially lower than $S_{2}$. Our experiments provide an efficient structural identifier for the fragile regions in glasses, and highlight the important role of structural correlations in the physics of glasses.

The swimming properties of an E. coli-type model bacterium are investigated by mesoscale hy- drodynamic simulations, combining molecular dynamics simulations of the bacterium with the multiparticle particle collision dynamics method for the embedding fluid. The bacterium is com- posed of a spherocylindrical body with attached helical flagella, built up from discrete particles for an efficient coupling with the fluid. We measure the hydrodynamic friction coefficients of the bacterium and find quantitative agreement with experimental results of swimming E. coli. The flow field of the bacterium shows a force-dipole-like pattern in the swimming plane and two vor- tices perpendicular to its swimming direction arising from counterrotation of the cell body and the flagella. By comparison with the flow field of a force dipole and rotlet dipole, we extract the force- dipole and rotlet-dipole strengths for the bacterium and find that counterrotation of the cell body and the flagella is essential for describing the near-field hydrodynamics of the bacterium.

Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counter-clockwise direction; they continuously evolve, merge with others and split into smaller ones. Measurements indicate that long-ranged hydrodynamic interactions have strong influences on cluster properties. Bacterial clusters change material and fluid transport near the interface and hence may have environmental and biological consequences., Comment: 4 figures

A mesoscopic hydrodynamic model to simulate synthetic self-propelled Janus particles which is thermophoretically or diffusiophoretically driven is here developed. We first propose a model for a passive colloidal sphere which reproduces the correct rotational dynamics together with strong phoretic effect. This colloid solution model employs a multiparticle collision dynamics description of the solvent, and combines potential interactions with the solvent, with stick boundary conditions. Asymmetric and specific colloidal surface is introduced to produce the properties of self-phoretic Janus particles. A comparative study of Janus and microdimer phoretic swimmers is performed in terms of their swimming velocities and induced flow behavior. Self-phoretic microdimers display long range hydrodynamic interactions and can be characterized as pullers or pushers. In contrast, Janus particles are characterized by short range hydrodynamic interactions and behave as neutral swimmers. Our model nicely mimics those recent experimental realization of the self-phoretic Janus particles., Comment: 11pages, 12figures, 2tables

The solid-solid coexistence of a polydisperse hard sphere system is studied by using the Monte Carlo simulation. The results show that for large enough polydispersity the solid-solid coexistence state is more stable than the single-phase solid. The two coexisting solids have different composition distributions but the same crystal structure. Moreover, there is evidence that the solid-solid transition terminates in a critical point as in the case of the fluid-fluid transition., Comment: 9 pages, 4 figures

A new Monte Carlo approach is proposed to investigate the fluid-solid phase transition of the polydisperse system. By using the extended ensemble, a reversible path was constructed to link the monodisperse and corresponding polydisperse system. Once the fluid-solid coexistence point of the monodisperse system is known, the fluid-solid coexistence point of the polydisperse system can be obtained from the simulation. The validity of the method is checked by the simulation of the fluid-solid phase transition of a size-polydisperse hard sphere colloid. The results are in agreement with the previous studies., Comment: 11 pages, 4 figures

By extending the nonequilibrium potential refinement algorithm and lattice switch method to the semigrand ensemble, the semigrand potentials of the fcc and hcp structures of polydisperse hard-sphere crystals are calculated with the bias sampling scheme. The result shows that the fcc structure is more stable than the hcp structure for polydisperse hard-sphere crystals below the terminal polydispersity., Comment: 17 pages, 5 figures

We propose a simple Monte Carlo method to calculate the interfacial free energy between the substrate and the material. Using this method we investigate the interfacial free energys of the hard sphere fluid and solid phases near a smooth hard wall. According to the obtained interfacial free energys of the coexisting fluid and solid phases and the Young equation we are able to determine the contact angle with high accuracy, cos$\theta$ = 1:010(31), which indicates that a smooth hard wall can be wetted completely by the hard sphere crystal at the interface between the wall and the hard sphere fluid., Comment: 13 pages, 5 figures

A general Monte Carlo simulation method of calculating the elastic constants of polydisperse hard-sphere colloidal crystal was developed. The elastic constants of a size polydisperse hard sphere fcc crystal is calculated. The pressure and three elastic constants(C11, C12 and C44) increase significantly with the polydispersity. It was also found from extrapolation that there is a mechanical terminal polydispersity above which a fcc crystal will be mechanically unstable., Comment: 17 pages, 3 figures