Starting from a minimal physical model of self propelled hard rods on a substrate in two dimensions, we derive a modified Smoluchowski equation for the system. Self -propulsion enhances longitudinal diffusion and modifies the mean field excluded volume interaction. From the Smoluchowski equation we obtain hydrodynamic equations for rod concentration, polarization and nematic order parameter. New results at large scales are a lowering of the density of the isotropic-nematic transition and a strong enhancement of boundary effects in confined self-propelled systems.
We study a robust model of self-propelled rods interacting via volume exclusion and show that its collective dynamics encompasses both that of the corresponding Vicsek-style model (where local alignment is the sole interaction), and motility-induced phase separation (which occurs when repulsion is dominant). These results unify these heretofore largely disconnected bodies of knowledge on dry active matter and clarify the nature of the various phases involved.
Using experiments with anisotropic vibrated rods and quasi-2D numerical simulations, we show that shape plays an important role in the collective dynamics of self-propelled (SP) particles. We demonstrate that SP rods exhibit local ordering, aggregation at the side walls, and clustering absent in round SP particles. Furthermore, we find that at sufficiently strong excitation SP rods engage in a persistent swirling motion in which the velocity is strongly correlated with particle orientation.
Non-equilibrium collective behavior of self-propelled colloidal rods in a confining channel is studied using Brownian dynamics simulations and dynamical density functional theory. We observe an aggregation process in which rods self-organize into transiently jammed clusters at the channel walls. In the early stage of the process, fast-growing hedgehog-like clusters are formed which are largely immobile. At later stages, most of these clusters dissolve and mobilize into nematized aggregates sliding past the walls.
We study the collective dynamics of self-propelled rods in an inhomogeneous motility field. At the interface between two regions of constant but different motility, a smectic rod layer is spontaneously created through aligning interactions between the active rods, reminiscent of an artificial, semi-permeable membrane. This "active membrane" engulfes rods which are locally trapped in low-motility regions and thereby further enhances the trapping efficiency by self-organization, an effect which we call "self-encapsulation". Our results are gained by computer simulations of self-propelled rod mod…
We study, in two space dimensions, the large-scale properties of collections of constant-speed polar point particles interacting locally by nematic alignment in the presence of noise. This minimal approach to self-propelled rods allows one to deal with large numbers of particles, revealing a phenomenology previously unseen in more complicated models, and moreover distinctively different from both that of the purely polar case (e.g. the Vicsek model) and of active nematics.
We derive a set of minimal yet complete nonlinear field equations describing the collective properties of self-propelled rods from a simple microscopic starting point, the Vicsek model with nematic alignment. Analysis of their linear and nonlinear dynamics shows good agreement with the original microscopic model. In particular, we derive an explicit expression for the fronts forming density-segregated, banded solutions, allowing us to develop a more complete analytic picture of the problem at the nonlinear level.
Non-equilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fraction and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state the average internal pressure is high and structural and mechanical relaxation times are long, su…
Motivated by recent simulations and by experiments on aggregation of gliding bacteria, we study a model of the collective dynamics of self-propelled hard rods on a substrate in two dimensions. The rods have finite size, interact via excluded volume and their dynamics is overdamped by the interaction with the substrate. Starting from a microscopic model with non-thermal noise sources, a continuum description of the system is derived. The hydrodynamic equations are then used to characterize the possible steady states of the systems and their stability as a function of the particles packing fract…
Motivated by aggregation phenomena in gliding bacteria, we study collective motion in a twodimensional model of active, self-propelled rods interacting through volume exclusion. In simulations with individual particles, we find that particle clustering is facilitated by a sufficiently large packing fraction (eta) or length-to-width ratio (kappa). The transition to clustering in simulations is well captured by a mean-field model for the cluster size distribution, which predicts that the transition values kappa_c of the aspect ratio for a fixed packing fraction is given by kappa_c = C/eta - 1 wh…
A wide range of experimental systems including gliding, swarming and swimming bacteria, in-vitro motility assays as well as shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a large variety of self-organized, collective phenomena, including formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is …
Using overdamped Brownian dynamics simulations we investigate the isotropic-nematic (IN) transition of self-propelled rods in three spatial dimensions. For two well-known model systems (Gay-Berne potential and hard spherocylinders) we find that turning on activity moves to higher densities the phase boundary separating an isotropic phase from a (nonpolar) nematic phase. This active IN phase boundary is distinct from the boundary between isotropic and polar-cluster states previously reported in two-dimensional simulation studies and, unlike the latter, is not sensitive to the system size. We th…
Collective behavior of self-propelled particles is observed on a microscale for swimmers such as sperm and bacteria as well as for protein filaments in motility assays. The properties of such systems depend both on their dimensionality and the interactions between their particles. We introduce a model for self-propelled rods in two dimensions that interact via a separation-shifted Lennard-Jones potential. Due to the finite potential barrier, the rods are able to cross. This model allows us to efficiently simulate systems of self-propelled rods that effectively move in two dimensions but can oc…
Systems of self-propelled particles are known for their tendency to aggregate and to display swarm behavior. We investigate two model systems, self-propelled rods interacting via volume exclusion, and sinusoidally-beating flagella embedded in a fluid with hydrodynamic interactions. In the flagella system, beating frequencies are Gaussian distributed with a non-zero average. These systems are studied by Brownian-dynamics simulations and by mesoscale hydrodynamics simulations, respectively. The clustering behavior is analyzed as the particle density and the environmental or internal noise are va…
Considering systems of self-propelled polar particles with nematic interactions ("rods"), we compare the continuum equations describing the evolution of polar and nematic order parameters, derived either from Smoluchowski or Boltzmann equations. Our main goal is to understand the discrepancies between the continuum equations obtained so far in both frameworks. We first show that in the simple case of point-like particles with only alignment interactions, the continuum equations obtained have the same structure in both cases. We further study, in the Smoluchowski framework, the case where an in…
We study mixtures of self-propelled and passive rod-like particles in two dimensions using Brownian dynamics simulations. The simulations demonstrate that the two species spontaneously segregate to generate a rich array of dynamical domain structures whose properties depend on the propulsion velocity, density, and composition. In addition to presenting phase diagrams as a function of the system parameters, we investigate the mechanisms driving segregation. We show that the difference in collision frequencies between self-propelled and passive rods provides a driving force for segregation, whic…
Active agents - like phoretic particles, bacteria, sperm, and cytoskeletal filaments in motility assays - show a large variety of motility-induced collective behaviors, such as aggregation, clustering and phase separation. The behavior of dense suspensions of phoretic particles and of bacteria during biofilm formation is determined by two principle physical mechanisms: (i) volume exclusion (short-range steric repulsion) and (ii) quorum sensing (longer-range reduced propulsion due to alteration of the local chemical environment). To systematically characterize such systems, we study semi-penetr…
Orientational ordering driven by mechanical distortion of soft substrates plays a major role in material transformation processes such as elastocapillarity and surface anchoring. We present a theoretical model of the orientational response of anisotropic rods deposited onto a surface of a soft, elastic substrate of finite thickness. We show that anisotropic rods exhibit a continuous isotropic-nematic phase transition, driven by orientational interactions between surface deposited rods. This interaction is mediated by the deformation of the underlying elastic substrate, and is quantified by the…
Dense suspensions of self-propelled rod-like particles exhibit a fascinating variety of non-equilibrium phenomena. By means of computer simulations of a minimal model for rigid self-propelled colloidal rods with variable shape we explore the generic diagram of emerging states over a large range of rod densities and aspect ratios. The dynamics is studied using a simple numerical scheme for the overdamped noiseless frictional dynamics of a many-body system in which steric forces are dominant over hydrodynamic ones. The different emergent states are identified by various characteristic correlatio…
Active screws: Emergent active chiral nematics of spinning self-propelled rods
Institute for Theoretical Physics, Georg-August-Universität Göttingen（哥廷根大学理论物理研究所）；Max Planck Institute for the Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）；Center for Systems Biology Dresden（德累斯顿系统生物学中心）；Cluster of Excellence Physics of Life, TU Dresden（德累斯顿工业大学生命物理卓越集群）；Departament de Física de la Matèria Condensada, Universitat de Barcelona（巴塞罗那大学凝聚态物理系）；Universitat de Barcelona Institute of Complex Systems (UBICS)（巴塞罗那大学复杂系统研究所）；Institució Catalana de Recerca i Estudis Avançats (ICREA)（加泰罗尼亚高级研究学院）
We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy wi…
We use coarse-grained molecular dynamics simulations to study the motility of a 2D vesicle containing self-propelled rods, as a function of the vesicle bending rigidity and the number density, length, and activity of the enclosed rods. Above a threshold value of the rod length, distinct dynamical regimes emerge, including a dramatic enhancement of vesicle motility characterized by a highly persistent random walk. These regimes are determined by clustering of the rods within the vesicle; the maximum motility state arises when there is one long-lived polar cluster. We develop a scaling theory th…
Using the Parsons Lee theory we examined the effect of shape anisotropy and the wall to wall separation on the phase behavior of the hard parallelepiped rods with dimensions L, D, and D (L>D) in such narrow slitlike pores which only one homeotropic layer can form. The phase structures, including biaxiality, planar nematic layering transition as well as planar to homeotropic, were studied for some separations in the range 2.5D<H<10.0D for H-D<L<H.
We study collections of self-propelled rods (SPR) moving in two dimensions for packing fractions less than or equal to 0.3. We find that in the thermodynamical limit the SPR undergo a phase transition between a disordered gas and a novel phase-separated system state. Interestingly, (global) orientational order patterns -- contrary to what has been suggested -- vanish in this limit. In the found novel state, the SPR self-organize into a highly dynamical, high-density, compact region - which we call aggregate - which is surrounded by a disordered gas. Active stresses build inside aggregates as r…
We report here a peculiar dynamically ordered state of clustering droplets of a mixture of organic solvent. There droplets are driven by the solutal Marangoni effect on the surface of aqueous surfactant solution. They form temporal ring clusters which start collapsing immediately after its formation. This process is repeated for more than several hours with the period of 5--20 minutes. We propose an inhomogeneous force model to phenomenologically understand the basic mechanism of this dynamics, where the forces acting on each particle are controlled differently. This droplet system offers a si…
We examine the ordering properties of rectangular hard rods with length L and diameter D at a single planar wall and between two parallel hard walls using the second-virial density functional theory. The theory is implemented in the three-state Zwanzig approximation, where only three mutually perpendicular directions are allowed for the orientations of hard rods. The effect of varying shape anisotropy is examined at L/D=10, 15 and 20. In contact with a single hard wall, the density profiles show planar ordering, damped oscillatory behavior, and wall induced surface ordering transition below th…
The effect of strong confinement on the positional and orientational ordering is examined in a system of hard rectangular rods with length L and diameter D (L>D) using the Parsons-Lee modification of the second virial density functional theory. The rods are nonmesogenic (L/D<3)and confined between two parallel hard walls, where the width of the pore (H) is chosen in such a way that both planar (particle's long axis parallel to the walls) and homeotropic (particle's long axis perpendicular to the walls) orderings are possible and a maximum of two layers are allowed to form in the pore. In the e…
Catching fish with a fishing net is typically done either by dragging a fishing net through quiescent water or by placing a stationary basket trap into a stream. We transfer these general concepts to micron-sized self-motile particles moving in a solvent at low Reynolds number and study their collective trapping behaviour by means of computer simulations of a two-dimensional system of self-propelled rods. A chevron-shaped obstacle is dragged through the active suspension with a constant speed $v$ and acts as a trapping "net". Three trapping states can be identified corresponding to no trapping…
The complete orientational ordering tensor of quasi-ideal colloidal rods is obtained as a function of shear rate by performing rheo-SANS (rheology with small angle neutron scattering) measurements on isotropic fd-virus suspensions in the two relevant scattering planes, the flow-gradient (1-2) and the flow-vorticity (1-3) plane. Microscopic ordering can be identified as the origin of the observed shear thinning. A qualitative description of the rheological response by Smoluchowski, as well as Doi--Edwards--Kuzuu theory is possible, as we obtain a master curve for different concentrations, scali…
Based on Monte Carlo (MC) computer simulations we study the structure formation of a system of magnetic nanorods. Our model particles consist of fused spheres with permanent magnetic dipole moments, as inspired by recent experiments. The resulting system behaves significantly different from a system of hard (non-magnetic) rods or magnetic rods with a single longitudinal dipole. In particular, we observe for the magnetic nanorods a significant decrease of the percolation threshold (as compared to non-magnetic rods) at low densities, and a stabilization of the high-density nematic phase. Moreove…
Active matter research focuses on the emergent behavior among interacting self-propelled particles. Unification of seemingly disconnected paradigms -- active phase-separation of repulsive discs and collective motion of self-propelled rods -- is a major challenge in contemporary active matter. Inspired by the quanto-mechanical wave-particle duality, we develop an approach based on the representation of active particles by smoothed continuum fields. On the basis of the collision kinetics, we demonstrate analytically and numerically how nonequilibrium stresses acting among self-driven, anisotropi…
The orientational order in vertically agitated granular rod monolayers is investigated experimentally and compared quantitatively with equilibrium Monte Carlo simulations and density functional theory. At sufficiently high number density, short rods form a tetratic state and long rods form a uniaxial nematic state. The length-to-width ratio at which the order changes from tetratic to uniaxial is around $7.3$ in both experiments and simulations. This agreement illustrates the universal aspects of the ordering of rod-shaped particles across equilibrium and nonequilibrium systems. Moreover, the a…
We suggest a geometrical mechanism for the ordering of slender filaments inside non-isotropic containers, using cortical microtubules in plant cells and packing of viral genetic material inside capsids as concrete examples. We show analytically how the shape of the cell affects the ordering of phantom, non-self-avoiding, stiff rods. We find that for oblate cells the preferred orientation is along the equator, while for prolate spheroids with an aspect ratio close to one, the orientation is along the principal (long axis). Surprisingly, at high enough aspect ratio, a configurational phase trans…
The study of active matter consisting of many self-propelled (active) swimmers in an imposed flow is important for many applications. Self-propelled swimmers may represent both living and artificial ones such as bacteria and chemically driven bi-metallic nano-particles. In this work we focus on a kinetic description of active matter represented by self-propelled rods swimming in a viscous fluid confined by a wall. It is well-known that walls may significantly affect the trajectories of active rods in contrast to unbounded or periodic containers. Among such effects are accumulation at walls and…
The isotropic-to-nematic transition in an athermal solution of long rigid rods subject to a gravitational (or centrifugal) field is theoretically considered in the Onsager approximation. The new feature emerging in the presence of gravity is a concentration gradient which coupled with the nematic ordering. For rodlike molecules this effect becomes noticeable at centrifugal acceleration g ~ 10^3--10^4 m/s^2, while for biological rodlike objects, such as tobacco mosaic virus, TMV, the effect is important even for normal gravitational acceleration conditions. Rods are concentrated near the bottom…
We report on experiments to measure the temporal and spatial evolution of packing arrangements of anisotropic, cylindrical granular material, using high-resolution capacitive monitoring. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical vibrations evolve to a dense, highly ordered, nematic state in which the long particle axes align with the vertical tube walls. We find that the orientational ordering process is reflected in a characteristic, steep rise in the local packing fraction. At any given height inside th…
We investigate the ordering properties of vertically-vibrated monolayers of granular cylinders in a circular container at high packing fraction. In line with previous works by other groups, we identify liquid-crystalline ordering behaviour similar to that of two-dimensional hard rectangular particles subject to thermal equilibrium fluctuations. However, due to dissipation, there is a much stronger tendency for particles to cluster into parallel arrangements in the granular system. These clusters behave as a polydisperse mixture of long life-time `superparticles', and some aspects of the system…
For many applications, it is important to catch collections of autonomously navigating microbes and man-made microswimmers in a controlled way. Here we propose an efficient trap to collectively capture self-propelled colloidal rods. By means of computer simulation in two dimensions, we show that a static chevron-shaped wall represents an optimal boundary for a trapping device. Its catching efficiency can be tuned by varying the opening angle of the trap. For increasing angles, there is a sequence of three emergent states corresponding to partial, complete, and no trapping. A trapping `phase di…
We theoretically study the nematic ordering transition of rods that are able to elastically adjust their mutually excluded volumes. The model rods, which consist of a hard core surrounded by a deformable shell, mimic the structure of polymer-coated, rod-like fd virus particles that have recently been the object of experimental study [K.~Purdy et al., Phys. Rev. Lett. \textbf{94}, 057801 (2005)]. We find that fluids of such soft rods exhibit an isotropic-nematic phase transition at a density higher than that of the corresponding hard-rod system of identical diameter, and that at coexistence the…
Spatially ordered systems confined to surfaces such as spheres exhibit interesting topological structures because of curvature induced frustration in orientational as well as translational order. The study of these structures is important for investigating the interplay between geometry, topology, and elasticity, and for their potential applications in materials science. In this work we numerically simulate a spherical monolayer of soft repulsive spherocylinders (SRS) and study the packing of rods and their ordering transition as a function of the packing fraction. In the model that we study, …
We report on the dynamics in colloidal suspensions of stiff viral rods, called fd-Y21M. This mutant filamentous virus exhibits a persistence length 3.5 times larger than the wild-type fd-wt. Such a virus system can be used as a model system of rodlike particles for studying their self-diffusion. In this paper, the physical features, such as rod contour length and polydispersity have been determined for both viruses. The effect of viral rod flexibility on the location of the nematic-smectic phase transition has been investigated, with a focus on the underlying dynamics studied more specifically…
Ordering dynamics of self-propelled particles in an inhomogeneous medium in two-dimensions is studied. We write coarse-grained hydrodynamic equations of motion for coarse-grained density and velocity fields in the presence of an external random disorder field, which is quenched in time. The strength of inhomogeneity is tuned from zero disorder (clean system) to large disorder. In the clean system, the velocity field grows algebraically as $L_{\rm V} \sim t^{0.5}$. The density field does not show clean power-law growth; however, it follows $L_{\rm ρ} \sim t^{0.8}$ approximately. In the inhomoge…
Understanding the relaxation dynamics of colloidal suspensions is crucial to identify the elements that influence the mobility of their constituents, assess their macroscopic response across the relevant time and length scales, and thus disclose the fundamentals underpinning their exploitation in formulation engineering. In this work, we specifically assess the impact of long-ranged ordering on the relaxation dynamics of suspensions of soft-repulsive rod-like particles, which are able to self-organise into nematic and smectic liquid-crystalline phases. By performing Dynamic Monte Carlo simulat…
Using Brownian Dynamics simulations, we study effective interactions mediated between two identical and impermeable disks (inclusions) immersed in a bath of identical, active (self-propelled), Brownian rods in two spatial dimensions, by assuming that the self-propulsion axis of the rods may generally deviate from their longitudinal axis. When the self-propulsion is transverse (perpendicular to the rod axis), the accumulation of active rods around the inclusions is significantly enhanced, causing a more expansive steric layering (ring formation) of the rods around the inclusions, as compared wi…
Active (i.e., self-propelled or swimming) particles moving through an isotropic fluid exhibit conventional diffusive behavior. We report anomalous diffusion of an active particle moving in an anisotropic, nematic background. Whilst the translational motion parallel to the nematic director shows ballistic behavior, the long-time transverse motion is super-diffusive, with an anomalous scaling $\propto t \ln t$ of the mean squared displacement with time $t$. This behavior is predicted by an analytical theory that we present here, and is corroborated by numerical simulation of active particle diff…
We study dynamical ordering of rods. In this process, rod alignment via pairwise interactions competes with diffusive wiggling. Under strong diffusion, the system is disordered, but at weak diffusion, the system is ordered. We present an exact steady-state solution for the nonlinear and nonlocal kinetic theory of this process. We find the Fourier transform as a function of the order parameter, and show that Fourier modes decay exponentially with the wave number. We also obtain the order parameter in terms of the diffusion constant. This solution is obtained using iterated partitions of the int…
We report phase separation and liquid-crystal ordering induced by scalar activity in a system of Soft Repulsive Spherocylinders (SRS) of aspect ratio $L/D = 5 $. Activity was introduced by increasing the temperature of half of the SRS (labeled \textit{`hot'}) while maintaining the temperature of the other half constant at a lower value (labeled \textit{`cold'}). The difference between the two temperatures scaled by the lower temperature provides a measure of the activity. Starting from different equilibrium initial phases, we find that activity leads to segregation of the hot and cold particle…
Evidence of a special chiral nematic phase is provided using numerical simulation and Onsager theory for systems of hard helical particles. This phase appears at the high density end of the nematic phase, when helices are well aligned, and is characterized by the C$_2$ symmetry axes of the helices spiraling around the nematic director with periodicity equal to the particle pitch. This coupling between translational and rotational degrees of freedom allows a more efficient packing and hence an increase of translational entropy. Suitable order parameters and correlation functions are introduced …
We present the exact solution of a Brownian inchworm model of a self-propelled elastic dimer which has recently been proposed in [K. V. Kumar \textit{et al}, Phys. Rev. E \textbf{77}, 020102(R) (2008)] as a unifying model for the propulsion mechanisms of DNA helicase, polar rods on a vibrated surface, crawling keratocytes, and Myosin VI.
