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 agreement with previous work. X-ray tomography experiments show that the boundary effects depend on the orientation of the boundary, indicating a strong influence of gravity, whereas the simulation finds boundary effects that are purely geometric. In all cases, the boundary influence extends approximately half a particle length into the interior of the container.
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…
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 …
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…
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）
What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution. Arbitrary particle shape is represented by a set of overlapping spheres of varying diameter, enabling us to approximate smooth surfaces with a resolution proportional to the number of spheres included. We discover a family of planar triangular particles, whose packing fraction of $ϕ\sim$ 0.73 outpaces almost all reported experimental results for random packi…
If a collection of identical particles is poured into a container, different shapes will fill to different densities. But what is the shape that fills a container as close as possible to a pre-specified, desired density? We demonstrate a solution to this inverse-packing problem by framing it in the context of artificial evolution. By representing shapes as bonded spheres, we show how shapes may be mutated, simulated, and selected to produce particularly dense or loose packing aggregates, both with and without friction. Moreover, we show how motifs emerge linking these shapes together. The resu…
Stiff, elongated biomolecules such as filamentous viruses, DNA or cellulose nanocrystals are known to form liquid crystals often exhibiting a helical supramolecular organization. Little is known about the microscopic origin, size and handedness of the helical pitch in these, so-called cholesteric phases. Experimental observations in chiral lyotropics suggest that long-ranged chiral forces of electrostatic origin acting between the mesogens are responsible for such organization. Using large-scale computer simulation we study the sensitivity of the pitch imparted by soft microscopic helices and …
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…
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…
Using grand canonical Monte Carlo (GCMC) simulations, we investigate the isotropic-nematic phase transition for hard rods of size Lx1x1 on a 3D cubic lattice. We observe such a transition for L >= 6. For L = 6, the nematic state has a negative order parameter, reflecting the co--occurrence of two dominating orientations. For L >= 7, the nematic state has a positive order parameter, corresponding to the dominance of one orientation. We investigate rod lengths up to L = 25 and find evidence for a very weakly first-order isotropic-nematic transition, while we cannot completely rule out a second o…
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,…
This paper presents the experiments and simulations on the resonance-induced acceleration of the reverse Brazil nut effect (RBNE)-Brazil nut effect (BNE) segregation inversion of binary mixtures in flat-bottom and circular-bottom containers. Both experimental and simulation results indicate that the starting location of the sinkage of heavier grains at the top layer is triggered with certain randomness in the flat-bottom container, whereas it first occurs at either of the lateral edges of the bottom in the circular-bottom container. The quantified segregation factors in simulations show that t…
Using sedimentation to obtain precisely controlled packings of noncohesive spheres, we find that the volume fraction $ϕ_{\rm RLP}$ of the loosest mechanically stable packing is in an operational sense well defined by a limit process. This random loose packing volume fraction decreases with decreasing pressure $p$ and increasing interparticle friction coefficient $μ$. Using X-ray tomography to correct for a container boundary effect that depends on particle size, we find for rough particles in the limit $p \to 0$ a new lower bound, $ϕ_{\rm RLP} = 0.550 \pm 0.001$.
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 use of glass for pharmaceutical new applications such as high-technology drugs, requires the strictest container inertness. A common theme of paramount importance in glass container integrity preservation is the detailed mechanism driving the sudden failure due the crack propagation. Using a combination of Discrete Element Method (DEM) and Finite Element Method (FEM), a stress map for glass cartridges packed into an accumulation table and transported by a conveyor belt at a fixed velocity is obtained under realistic conditions. The DEM calculation provides a full description of the dynamic…
Randomly packing spheres of equal size into a container consistently results in a static configuration with a density of ~64%. The ubiquity of random close packing (RCP) rather than the optimal crystalline array at 74% begs the question of the physical law behind this empirically deduced state. Indeed, there is no signature of any macroscopic quantity with a discontinuity associated with the observed packing limit. Here we show that RCP can be interpreted as a manifestation of a thermodynamic singularity, which defines it as the "freezing point" in a first-order phase transition between ordere…
We have found that the ability of long thin rods to jam into a solid-like state in response to a local perturbation depends upon both the particle aspect ratio and the container size. The dynamic phase diagram in this parameter space reveals a broad transition region separating granular stick-slip and solid-like behavior. In this transition region the pile displays both solid and stick-slip behavior. We measure the force on a small object pulled through the pile, and find the fluctuation spectra to have power law tails with an exponent characteristic of the region. The exponent varies from $β=…
We measure experimentally the rearrangements due to a small localized cyclic displacement applied to a packing of rigid grains under gravity in a 2D geometry. We analyze the evolution of the response to this perturbation by considering the individual particle displacement and the coarse grained displacement field, as well as the mean packing fraction and coordination number. We find that the displacement response is rather long ranged, and evolves considerably with the number of cycles. We show that a small difference in the preparation method (induced by tapping the container) leads to a sign…
