The injection of a long flexible rod into a two-dimensional domain yields a complex pattern commonly studied through elasticity theory, packing analysis, and fractal geometries. "Loop" is a one-vertex entity that is naturally formed in this system. The role of the elastic features of each loop in 2D packing has not yet been discussed. In this work, we point out how the shape of a given loop in the complex structure allows estimating local deformations and forces. First, we build sets of symmetric free loops and performed compression experiments. Then, tight packing configurations are analyzed by using image processing. We found that the dimensions of the loops, confined or not, obey the same dependence on the deformation. The result is consistent with a simple model based on 2D elastic theory for filaments, where the rod adopts the shape of Euler's elasticas between its contact points. The force and the stored energy are obtained from numerical integration of the analytic expressions. In an additional experiment, we obtain that the compression force for deformed loops corroborates the theoretical findings. The importance of the shape of the loop is discussed and we hope that the theoretical curves may allow statistical considerations in future investigations.
We conduct experiments and simulations to study the disordered packing of rods in small containers. Experiments study cylindrical rods with aspect ratio ranging from 4 to 32; simulations use of spherocylinders with similar aspect ratios. In all cases, rods pack randomly in cylindrical containers whose smallest dimension is larger than the rod length. Packings in smaller containers have lower volume fractions than those in larger containers, demonstrating the influence of the boundaries. The volume fraction extrapolated to infinite container size decreases with increasing aspect ratio, in agree…
We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in the geometry of the closest-packed configuration as a function of the aspect ratio $L/D$, where $L$ is the cylinder length and $D$ the diameter of the rods. We find a rich variety of cluster structures. For larger clusters, we find that the best-packed configurations up to around 100 particles are highly dependent on the exact number of particles and aspect r…
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…
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 study the attractive interactions between rod-like charged polymers in solution that appear in the presence of multi-valence counterions. The counterions condensed to the rods exhibit both a strong transversal polarization and a longitudinal crystalline arrangement. At short distances between the rods, the fraction of condensed counterions increases, and the majority of these occupy the region between the rods, where they minimize their repulsive interactions by arranging themselves into packing structures. The attractive interaction is strongest for multivalent counterions. Our model takes…
Using computer simulations, we explore how thermal noise-induced randomness in a self-assembled photonic crystal affects its photonic band gaps (PBGs). We consider a two-dimensional photonic crystal comprised of a self-assembled array of parallel dielectric hard rods of infinite length with circular or square cross section. We find the PBGs can exist over a large range of intermediate packing densities. Counterintuitively, the largest band gap does not always appear at the packing density where the crystal is most ordered, despite the randomness inherent in any self-assembled structure. For ro…
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…
The packing of elastic bodies has emerged as a paradigm for the study of macroscopic disordered systems. However, progress is hampered by the lack of controlled experiments. Here we consider a model experiment for the isotropic two-dimensional confinement of a rod by a central force. We seek to measure how ordered is a folded configuration and we identify two key quantities. A geometrical characterization is given by the number of superposed layers in the configuration. Using temporal modulations of the confining force, we probe the mechanical properties of the configuration and we define and …
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…
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…
Emergent cohesion via self-caging in maximally entangled rod packings
School of Engineering and Applied Sciences, Harvard University（哈佛大学生物工程与应用科学学院）；Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University（哈佛大学物理系、有机体与进化生物学系）
Penetration of Rigid Rods, Flexible Rods, and Granular Jets into Low-Density Granular Media
Instituto de Física, Benemérita Universidad Autónoma de Puebla（普埃布拉自治大学物理研究所）；Gulliver, CNRS, ESPCI Paris, Université PSL（高勒维尔实验室，法国国家科学研究中心，巴黎高等物理化工学院，巴黎文理研究大学）
We compute the entropic interactions between two colloidal spheres immersed in a dilute suspension of semi-flexible rods. Our model treats the semi-flexible rod as a bent rod at fixed angle, set by the rod contour and persistence lengths. The entropic forces arising from this additional rotational degree of freedom are captured quantitatively by the model, and account for observations at short range in a recent experiment. Global fits to the interaction potential data suggest the persistence length of fd-virus is about two to three times smaller than the commonly used value of $2.2 μ{m}$.
We study suspensions of semi-flexible colloidal rods and biopolymers using an Onsager-type second-virial functional for a segmented-chain model. For suspensions of thin and thick fd virus particles we calculate phase diagrams in quantitative agreement with experimental observations, and we find their effective state-point dependent shape to be much shorter and thicker than the actual shape. We also calculate the stretching of worm-like micelles in a host fd virus solution, again finding agreement with experiments. For both systems, our results show that the fd virus stiffness can play a key ro…
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…
This paper examines the mechanical response of flexible fiber packings subject to triaxial compression. Short fibers yield in a manner similar to typical granular materials in which the deviatoric stress remains nearly constant with increasing strain after reaching a peak value. Interestingly, long fibers exhibit a hardening behavior, where the stress increases rapidly with increasing strain at large strains and the packing density continuously increases. Phase diagrams for classifying the bulk mechanical response as yielding, hardening, or a transition regime are generated as a function of th…
We perform extensive molecular dynamics simulations of dense liquids composed of bidisperse dimer- and ellipse-shaped particles in 2D that interact via repulsive contact forces. We measure the structural relaxation times obtained from the long-time decay of the self-part of the intermediate scattering function for the translational and rotational degrees of freedom (DOF) as a function of packing fraction ϕ, temperature T, and aspect ratio α. We are able to collapse the ϕand T-dependent structural relaxation times for disks, and dimers and ellipses over a wide range of α, onto a universal scali…
The present work deals with the injection and packing of a flexible polymeric rod of length $L$ into a simply connected rectangular domain of area $XY$. As the injection proceeds, the rod bends over itself and it stores elastic energy in closed loops. In a typical experiment $N$ of these loops can be identified inside the cavity in the jammed state. We have performed an extensive experimental analysis of the total length $L(N, X, Y)$ in the tight packing limit, and have obtained robust power laws relating these variables. Additionally, we have examined a version of this packing problem when th…
We develop a novel biased Monte-Carlo simulation technique to measure the force-extension curves and the distribution function of the extension of fluctuating filaments stretched by external force. The method is applicable for arbitrary ratio of the persistence length to the contour length and for arbitrary forces. The simulation results agree with analytic expressions for the force-extension curves and for the renormalized length-scale-dependent elastic moduli, derived in the rigid rod and in the strong force limits. We find that orientational fluctuations and wall effects produce non-Gaussia…
We report numerical results of effective attractive forces on the packing properties of two-dimensional elongated grains. In deposits of non-cohesive rods in 2D, the topology of the packing is mainly dominated by the formation of ordered structures of aligned rods. Elongated particles tend to align horizontally and the stress is mainly transmitted from top to bottom, revealing an asymmetric distribution of local stress. However, for deposits of cohesive particles, the preferred horizontal orientation disappears. Very elongated particles with strong attractive forces form extremely loose struct…
Using a combination of theory and experiments we study the interface between two immiscible domains in a colloidal membrane composed of rigid rods of different lengths. Geometric considerations of rigid rod packing imply that a domain of sufficiently short rods in a background membrane of long rods is more susceptible to twist than the inverse structure, a long-rod domain in a short-rod membrane background. The tilt at the inter-domain edge forces splay, which in turn manifests as a spontaneous edge curvature whose energetics are controlled by the length asymmetry of constituent rods. A thermo…
We investigated the effects of particle shape on shear thickening in densely packed suspensions. Rods of different aspect ratios and non-convex hooked rods were fabricated. Viscosity curves and normal stresses were measured using a rheometer for a wide range of packing fractions for each shape. Suspensions of each shape exhibit qualitatively similar Discontinuous Shear Thickening. The logarithmic slope of the stress/shear-rate relation increases dramatically with packing fraction and diverges at a critical packing fraction phi_c which depends on particle shape. The packing fraction dependence …
We use a combination of computer simulations and iso-flux tension propagation (IFTP) theory to investigate translocation dynamics of a flexible linear polymer through a nanopore into an environment composed of repulsive active rods in 2D. We demonstrate that the rod activity induces a crowding effect on the polymer, leading to a time-dependent net force that facilitates translocation into the active environment. Incorporating this force into the IFTP theory for pore-driven translocation allows us to characterise translocation dynamics in detail and derive a scaling form for the average translo…
Superellipse sector particles (SeSPs) are segments of superelliptical curves that form a tunable set of hard-particle shapes for granular and colloidal systems. SeSPs allow for continuous parameterization of corner sharpness, aspect ratio, and particle curvature; rods, circles, rectangles, and staples are examples of shapes SeSPs can model. We compare three computational processes: pair-wise Monte Carlo simulations that look only at particle-particle geometric constraints, Monte Carlo simulations that look at how these geometric constraints play out over extended dispersions of many particles,…
In the first part of this paper, an approximate theory is developed for the leading order concentration dependence of the sedimentation coefficient for rod-like colloids/polymers/macromolecules. To first order in volume fraction $ϕ$ of rods, the sedimentation coefficient is written as $1+αϕ$. For large aspect ratio L/D (L is the rod length, D it's thickness) $α$ is found to very like $\propto (\frac{L}{D})^2/\log (\frac{L}{D})$. This theoretical prediction is compared to experimental results. In the second part, experiments on {\it fd}-virus are described, both in the isotropic and nematic pha…
We extend recent studies of the minimal energy packings of short flexible polymers with hard-core-like repulsions and short-range attractions to include bond-angle interactions with the aim of describing the collapsed conformations of `colloidal' polymers. We find that flexible tangent sticky-hard-sphere (t-SHS) packings provide a useful perturbative basis for analyzing polymer packings with nonzero bending stiffness only for {\it small} ratios of the stiffnesses for the bond-angle ($k_b$) and pair ($k_c$) interactions, i.e. $k_b^{\rm crit}/k_c \lesssim 0.01$ for $N<10$ monomers, and the criti…
A liquid meniscus, a bending rod (also called elastica) and a simple pendulum are all described by the same non-dimensional equation. The oscillatory regime of the pendulum corresponds to buckling rods and pendant drops, and the high-velocity regime corresponds to spherical drops, puddles and multiple rod loopings. We study this analogy in a didactic way and discuss how, despite this common governing equation, the three systems are not completely equivalent. We also consider the cylindrical deformations of an inextensible, flexible membrane containing a liquid, which in some sense interpolates…
We study experimentally the nonequilibrium phase behaviour of a horizontal monolayer of macroscopic rods. The motion of the rods in two dimensions is driven by vibrations in the vertical direction. Aside from the control variables of packing fraction and aspect ratio that are typically explored in molecular liquid crystalline systems, due to the macroscopic size of the particles we are also able to investigate the effect of the precise shape of the particle on the steady states of this driven system. We find that the shape plays an important role in determining the nature of the orientational …
The continuous packing of a flexible rod in two-dimensional cavities yields a countable set of interacting domains that resembles non-equilibrium cellular systems and belongs to a new class of light-weight material. However, the link between the length of the rod and the number of domains requires investigation especially in the case of non-simply connected cavities, where the number of avoided regions emulates an effective topological temperature. In the present article we report the results of an experiment of injection of a single flexible rod into annular cavities in order to find the tota…
We construct colloidal ``sticky'' rods from the semi-flexible filamentous fd virus and temperature-sensitive polymers poly(N-isopropylacrylamide) (PNIPAM). The phase diagram of fd-PNIPAM system becomes independent of ionic strength at high salt concentration and low temperature, i.e. the rods are sterically stabilized by the polymer. However, the network of sticky rods undergoes a sol-gel transition as the temperature is raised. The viscoelastic moduli of fd and fd-PNIPAM suspensions are compared as a function of temperature, and the effect of ionic strength on the gelling behavior of fd-PNIPA…
Motivated by recent experiments showing nonlinear elasticity of in vitro networks of the biopolymer actin cross-linked with filamin, we present an effective medium theory of flexibly cross-linked stiff polymer networks. We model such networks by randomly oriented elastic rods connected by flexible connectors to a surrounding elastic continuum, which self-consistently represents the behavior of the rest of the network. This model yields a crossover from a linear elastic regime to a highly nonlinear elastic regime that stiffens in a way quantitatively consistent with experiment.
The properties of the processes of deformation of a packing of rigid grains are analysed when the exact distribution of the normal forces at contacts is known. Importance of grain rotation and of counter-rotation of adjacent grains is stressed. It is shown that all deformation modes form an incomplete vectorial space D. This allows the statistics of fluctuation to be determined. Parallel with anti-ferromagnetism is then drawn and frustration of rotation is shown to be the leading dissipating mechanism. However this does not allow making the parallel with spinglass due to the structure of the s…
The packing problem of long thin filaments that are injected into confined spaces is of fundamental interest for physicists and biologists alike. How linear threads pack and coil is well known only for the ideal case of rigid containers, though. Here, we force long elastic rods into flexible spatial confinement borne by an elastic shell to examine under which conditions recently acquired knowledge on wire packing in rigid spheres breaks down. We find that unlike in rigid cavities, friction plays a key role by giving rise to the emergence of two distinct packing patterns. At low friction, the w…
The classical Oseen-Frank theory of liquid crystal elasticity is based on the experimentally verified fact that there are three independent modes of distortion, each with its associated elastic constant. On the other hand, the arguably more first-principles order parameter-based Landau-de Gennes theory only involves two independent elastic modes. The resulting 'elastic constants problem' has led to a considerable amount of vexation among theorists. In a series of papers at the turn of the century, Fukuda and Yokoyama suggested that the resolution of this problem could be found in the proper tr…
We report on a comprehensive computer simulation study of the liquid-crystal phase behaviour of purely repulsive, semi-flexible rod-like particles. For the four aspect ratios we consider, the particles form five distinct phases depending on their packing fraction and bending flexibility: the isotropic, nematic, smectic A, smectic B and crystal phase. Upon increasing the particle bending flexibility, the various phase transitions shift to larger packing fractions. Increasing the aspect ratio achieves the opposite effect. We find two different ways how the layer spacing of the particles in the s…
This paper presents a numerical method for the simulation of fluid-structure interaction specifically tailored to interactions between Newtonian fluids and a large number of slender viscoelastic Cosserat rods. Because of their high flexibility and low weight the rods considered here exhibit large deflections, even under moderate fluid loads. Their motion, in turn, modifies the flow so that fluid and structures are strongly coupled to each other which is numerically very challenging. The paper proposes a new coupling approach based on an immersed boundary method which improves upon existing met…
We present a generalized van der Waals theory for a lyotropic cholesteric system of chiral spherocylinders based on the classical Onsager theory for hard anisometric bodies. The rods consist of a hard spherocylindrical backbone surrounded with a square-well potential to account for attractive (or soft repulsive) interactions. Long-ranged chiral interactions are described by means of a simple pseudo-scalar potential which is appropriate for weak chiral forces of a predominant electrostatic origin. Based on the formalism proposed by Straley [Phys. Rev. A {\bf 14}, 1835 (1976)] we derive explicit…
Recent experiments have demonstrated that the nonlinear elasticity of in vitro networks of the biopolymer actin is dramatically altered in the presence of a flexible cross-linker such as the abundant cytoskeletal protein filamin. The basic principles of such networks remain poorly understood. Here we describe an effective medium theory of flexibly cross-linked stiff polymer networks. We argue that the response of the cross-links can be fully attributed to entropic stiffening, while softening due to domain unfolding can be ignored. The network is modeled as a collection of randomly oriented rod…
Using field theoretic approach, we study equilibrium shape deformation of a vesicle induced by the presence of enclosed flexible polymers, which is a simple model of drug delivery system or endocytosis. To evaluate the total free energy of this system, it is necessary to calculate the bending elastic energy of the membrane, the conformation entropy of the polymers and their interactions. For this purpose, we combine phase field theory for the membrane and self-consistent field theory for the polymers. Simulations on this coupled model system for axiosymmetric shapes show a shape deformation of…
Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals has been demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. Here, we show quantitatively that shape drives the…
The deformation of thin rods in a viscous liquid is central to the mechanics of motility in cells ranging from \textit{Escherichia coli} to sperm. Here we use experiments and theory to study the shape transition of a flexible rod rotating in a viscous fluid driven either by constant torque or at constant speed. The rod is tilted relative to the rotation axis. At low applied torque, the rod bends gently and generates small propulsive force. At a critical torque, the rotation speed increases abruptly and the rod forms a helical shape with much greater propulsive force. We find good agreement bet…
Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect-ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze this results in terms of the interplay between the effective stiffn…
The fluid-structure interactions between flexible fibers and viscous flows play an essential role in various biological phenomena, medical problems, and industrial processes. Of particular interest is the case of particles freely transported in time-dependent flows. This work elucidates the dynamics and morphologies of actin filaments under oscillatory shear flows by combining microfluidic experiments, numerical simulations, and theoretical modeling. Our work reveals that, in contrast to steady shear flows, in which small orientational fluctuations from a flow-aligned state initiate tumbling a…
