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.
