Using a previously developed experimental method to reduce friction in mechanically stable packings of disks, we find that frictional packings form tree-like structures of geometrical families that lie on reduced dimensional manifolds in configuratio
n space. Each branch of the tree begins at a point in configuration space with an isostatic number of contacts and spreads out to sequentially higher dimensional manifolds as the number of contacts are reduced. We find that gravitational deposition of disks produces an initially under-coordinated packing stabilized by friction on a high-dimensional manifold. Using short vibration bursts to reduce friction, we compact the system through many stable configurations with increasing contact number and decreasing dimensionality until the system reaches an isostatic frictionless state. We find that this progression can be understood as the system moving through the null-space of the rigidity matrix defined by the interparticle contact network in the direction of the gravitational force. We suggest that this formalism can also be used to explain the evolution of frictional packings under other forcing conditions.
We perform molecular dynamics simulations to compress binary hard spheres into jammed packings as a function of the compression rate $R$, size ratio $alpha$, and number fraction $x_S$ of small particles to determine the connection between the glass-f
orming ability (GFA) and packing efficiency in bulk metallic glasses (BMGs). We define the GFA by measuring the critical compression rate $R_c$, below which jammed hard-sphere packings begin to form random crystal structures with defects. We find that for systems with $alpha gtrsim 0.8$ that do not de-mix, $R_c$ decreases strongly with $Delta phi_J$, as $R_c sim exp(-1/Delta phi_J^2)$, where $Delta phi_J$ is the difference between the average packing fraction of the amorphous packings and random crystal structures at $R_c$. Systems with $alpha lesssim 0.8$ partially de-mix, which promotes crystallization, but we still find a strong correlation between $R_c$ and $Delta phi_J$. We show that known metal-metal BMGs occur in the regions of the $alpha$ and $x_S$ parameter space with the lowest values of $R_c$ for binary hard spheres. Our results emphasize that maximizing GFA in binary systems involves two competing effects: minimizing $alpha$ to increase packing efficiency, while maximizing $alpha$ to prevent de-mixing.
Contact breaking and Hertzian interactions between grains can both give rise to nonlinear vibrational response of static granular packings. We perform molecular dynamics simulations at constant energy in 2D of frictionless bidisperse disks that inter
act via Hertzian spring potentials as a function of energy and measure directly the vibrational response from the Fourier transform of the velocity autocorrelation function. We compare the measured vibrational response of static packings near jamming onset to that obtained from the eigenvalues of the dynamical matrix to determine the temperature above which the linear response breaks down. We compare packings that interact via single-sided (purely repulsive) and double-sided Hertzian spring interactions to disentangle the effects of the shape of the potential from contact breaking. Our studies show that while Hertzian interactions lead to weak nonlinearities in the vibrational behavior (e.g. the generation of harmonics of the eigenfrequencies of the dynamical matrix), the vibrational response of static packings with Hertzian contact interactions is dominated by contact breaking as found for systems with repulsive linear spring interactions.
We propose a `phase diagram for particulate systems that interact via purely repulsive contact forces, such as granular media and colloidal suspensions. We identify and characterize two distinct classes of behavior as a function of the input kinetic
energy per degree of freedom $T_0$ and packing fraction deviation above and below jamming onset $Delta phi=phi - phi_J$ using numerical simulations of purely repulsive frictionless disks. Iso-coordinated solids (ICS) only occur above jamming for $Delta phi > Delta phi_c(T_0)$; they possess average coordination number equal to the isostatic value ($< z> = z_{rm iso}$) required for mechanically stable packings. ICS display harmonic vibrational response, where the density of vibrational modes from the Fourier transform of the velocity autocorrelation function is a set of sharp peaks at eigenfrequencies $omega_k^d$ of the dynamical matrix evaluated at $T_0=0$. Hypo-coordinated solids (HCS) occur both above and below jamming onset within the region defined by $Delta phi > Delta phi^*_-(T_0)$, $Delta phi < Delta phi^*_+(T_0)$, and $Delta phi > Delta phi_{cb}(T_0)$. In this region, the network of interparticle contacts fluctuates with $< z> approx z_{rm iso}/2$, but cage-breaking particle rearrangements do not occur. The HCS vibrational response is nonharmonic, {it i.e} the density of vibrational modes $D(omega)$ is not a collection of sharp peaks at $omega_k^d$, and its precise form depends on the measurement method. For $Delta phi > Delta phi_{cb}(T_0)$ and $Delta phi < Delta phi^*_{-}(T_0)$, the system behaves as a hard-particle liquid.
This is a response to the comment on our manuscript Repulsive contact interactions make jammed particulate systems inherently nonharmonic (Physical Review Letters 107 (2011) 078301) by C. P. Goodrich, A. J. Liu, and S. R. Nagel.
We perform numerical simulations of athermal repulsive frictionless disks and spheres in two and three spatial dimensions undergoing cyclic quasi-static simple shear to investigate particle-scale reversible motion. We identify three classes of steady
-state dynamics as a function of packing fraction phi and maximum strain amplitude per cycle gamma_{rm max}. Point-reversible states, where particles do not collide and exactly retrace their intra-cycle trajectories, occur at low phi and gamma_{rm max}. Particles in loop-reversible states undergo numerous collisions and execute complex trajectories, but return to their initial positions at the end of each cycle. Loop-reversible dynamics represents a novel form of self-organization that enables reliable preparation of configurations with specified structural and mechanical properties over a broad range of phi from contact percolation to jamming onset at phi_J. For sufficiently large phi and gamma_{rm max}, systems display irreversible dynamics with nonzero self-diffusion.
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP alpha-synucle
in that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent smFRET experiments. We find that alpha-synuclein is disordered with conformational statistics that are intermediate between random walk and collapsed globule behavior. An advantage of calibrated molecular simulations over constraint methods is that physical forces act on all residues, not only on residue pairs that are monitored experimentally, and these simulations can be used to study oligomerization and aggregation of multiple alpha-synuclein proteins that may precede amyloid formation.
We numerically investigate the mechanical properties of static packings of ellipsoidal particles in 2D and 3D over a range of aspect ratio and compression $Delta phi$. While amorphous packings of spherical particles at jamming onset ($Delta phi=0$) a
re isostatic and possess the minimum contact number $z_{rm iso}$ required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming ($z < z_{rm iso}$) from naive counting arguments, which assume that all contacts give rise to linearly independent constraints on interparticle separations. To understand this behavior, we decompose the dynamical matrix $M=H-S$ for static packings of ellipsoidal particles into two important components: the stiffness $H$ and stress $S$ matrices. We find that the stiffness matrix possesses $N(z_{rm iso} - z)$ eigenmodes ${hat e}_0$ with zero eigenvalues even at finite compression, where $N$ is the number of particles. In addition, these modes ${hat e}_0$ are nearly eigenvectors of the dynamical matrix with eigenvalues that scale as $Delta phi$, and thus finite compression stabilizes packings of ellipsoidal particles. At jamming onset, the harmonic response of static packings of ellipsoidal particles vanishes, and the total potential energy scales as $delta^4$ for perturbations by amplitude $delta$ along these `quartic modes, ${hat e}_0$. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles.
There are a finite number of distinct mechanically stable (MS) packings in model granular systems composed of frictionless spherical grains. For typical packing-generation protocols employed in experimental and numerical studies, the probabilities wi
th which the MS packings occur are highly nonuniform and depend strongly on parameters in the protocol. Despite intense work, it is extremely difficult to predict {it a priori} the MS packing probabilities, or even which MS packings will be the most versus the least probable. We describe a novel computational method for calculating the MS packing probabilities by directly measuring the volume of the MS packing `basin of attraction, which we define as the collection of initial points in configuration space at {it zero packing fraction} that map to a given MS packing by following a particular dynamics in the density landscape. We show that there is a small core region with volume $V^c_n$ surrounding each MS packing $n$ in configuration space in which all initial conditions map to a given MS packing. However, we find that the MS packing probabilities are very weakly correlated with core volumes. Instead, MS packing probabilities obtained using initially dilute configurations are determined by complex geometric features of the basin of attraction that are distant from the MS packing.
