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Amorphous packings of frictionless, spherical particles are isostatic at jamming onset, with the number of constraints (contacts) equal to the number of degrees of freedom. Their structural and mechanical properties are controlled by the interparticle contact network. In contrast, amorphous packings of frictional particles are typically hyperstatic at jamming onset. We perform extensive numerical simulations in two dimensions of the geometrical asperity (GA) model for static friction to further investigate the role of isostaticity. In the GA model, interparticle forces are obtained by summing up purely repulsive central forces between periodically spaced circular asperities on contacting grains. We compare the packing fraction, contact number, mobilization distribution, and vibrational density of states (in the harmonic approximation) using the GA model to those generated using the Cundall-Strack approach. We find that static packings of frictional disks obtained from the GA model are mechanically stable and isostatic when we consider interactions between asperities on contacting particles. The crossover in the structural and mechanical properties of static packings from frictionless to frictional behavior as a function of the static friction coefficient coincides with a change in the type of interparticle contacts and the disappearance of a peak in the density of vibrational modes for the GA model. These results emphasize that mesoscale features of the model for static friction play an important role in determining the properties of granular packings. [ABSTRACT FROM AUTHOR]

Typical quasistatic compression algorithms for generating jammed packings of purely repulsive, frictionless particles begin with dilute configurations and then apply successive compressions with the relaxation of the elastic energy allowed between each compression step. It is well known that during isotropic compression these systems undergo a first-order-like jamming transition at packing fraction &phgr;j from an unjammed state with zero pressure and no force-bearing contacts to a jammed, rigid state with nonzero pressure, a percolating network of force-bearing contacts, and contact number z = 2d, where d is the spatial dimension. Using computer simulations of two-dimensional systems with monodisperse and bidisperse particle size distributions, we investigate the second-order-like contact percolation transition, which precedes the jamming transition with &phgr;p < &phgr;J and signals the formation of a system-spanning cluster of non-force-bearing contacts between particles. By measuring the number of nonfloppy modes of the dynamical matrix, the displacement field between successive compression steps, and the overlap between the adjacency matrix, which represents the network of contacting grains, at &phgr; and &phgr;J, we find that the contact percolation transition also signals the onset of a nontrivial mechanical response to applied stress. Our results show that cooperative particle motion occurs in unjammed systems significantly below the jamming transition for &phgr;P < &phgr; < &phgr;J, not only for jammed systems with &phgr; > &phgr;J. [ABSTRACT FROM AUTHOR]

We perform extensive computational studies of two-dimensional static bidisperse disk packings using two distinct packing-generation protocols. The first involves thermally quenching equilibrated liquid configurations to zero temperature over a range of thermal quench rates r and initial packing fractions followed by compression and decompression in small steps to reach packing fractions φJ at jamming onset. For the second, we seed the system with initial configurations that promote micro- and macrophase-separated packings followed by compression and decompression to φJ. Using these protocols, we generate more than 104 static packings over a wide range of packing fraction, contact number, and compositional and positional order. We find that disordered, isostatic packings exist over a finite range of packing fractions in the large-system limit. In agreement with previous calculations, the most dilute mechanically stable packings with φmin≈0.84 are obtained for r>r*, where r* is the rate above which φJ is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, several order parameters, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered (with only small changes in a number of order parameters), whereas bond-orientational and compositional order increase strongly with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies (in the harmonic approximation) of the static packings to understand the extent to which the mechanical properties of disordered, isostatic packings differ from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic. [ABSTRACT FROM AUTHOR]

Many experiments over the past half century have shown that, for a range of protocols, granular materials compact under pressure and repeated small disturbances. A recent experiment on cyclically sheared spherical grains showed significant compaction via homogeneous crystallization (Rietz et al., 2018). Here we present numerical simulations of frictionless, purely repulsive spheres undergoing cyclic simple shear via Newtonian dynamics with linear viscous drag at fixed vertical load. We show that for sufficiently small strain amplitudes, cyclic shear gives rise to homogeneous crystallization at a volume fraction ϕ=0.646±0.001. This result indicates that neither friction nor gravity is essential for homogeneous crystallization in driven granular media. Understanding how crystal formation is initiated within a homogeneous disordered state gives key insights into the old open problem of glass formation in fluids. [ABSTRACT FROM AUTHOR]

We propose a "phase diagram" for particulate systems with purely repulsive contact forces, such as granular media and colloids. We characterize two classes of behavior as a function of the input kinetic energy per degree of freedom T0 and packing fraction deviation from jamming onset ΔΦ = Φ -- ΦJ using simulations of frictionless disks. Isocoordinated solids (ICS) exist above jamming; they possess an average contact number equal to the isostatic value ziso. ICS display "strict" harmonic response, where the density of vibrational modes from the Fourier transform of the velocity autocorrelation function is a set of sharp peaks at eigenfrequencies ωkd of the dynamical matrix. In contrast, hypocoordinated solids (HCS) occur above and below jamming and possess fluctuating networks of interparticle contacts but do not undergo cage-breaking particle rearrangements. The density of vibrational frequencies for the HCS is not a collection of sharp peaks at ωkd, but it does possess a common form over a range of ΔΦ and T0. [ABSTRACT FROM AUTHOR]

Experimental and computational model systems composed of frictionless particles in a fixed geometry have a finite number of distinct mechanically stable (MS) packings. The frequency of occurrence for each MS packing is highly variable and depends strongly on preparation protocol. Despite intense work, it is extremely difficult to predict a priori the MS packing probabilities. We describe a novel computational method for calculating the volume and other geometrical properties of the "basin of attraction" for each MS packing. The basin of attraction for an MS packing contains all initial conditions in configuration space that map to that MS packing using a given preparation protocol. We find that the basin is a highly complex structure. For a compressive-quench-from-zero-density protocol, we show the existence of a small core volume of the basin around each MS packing for which all points map to that MS packing. However, in contrast to previous studies for supercooled liquids, glasses, and over-compressed jammed systems, we find that the MS packing probabilities are very weakly correlated with this core volume. Instead, MS packing probabilities obtained from compression protocols that use initially dilute configurations and do not allow particle overlaps (i.e., those relevant to granular media) are determined by complex geometric features of the basin of attraction that are distant from the MS packing. In particular, we find that the shape of the average basin profile function S(l), which gives the probability for a point on a hyperspherical shell a distance / from a given MS packing to map back to that packing, can be described by a T distribution with a peak that increases as the system size increases and as the quench rate decreases. We find a simple model which predicts S(l) for the extreme cases of very slow and fast quench rates. [ABSTRACT FROM AUTHOR]

We analyze the geometric structure and mechanical stability of a complete set of isostatic and hyperstatic sphere packings obtained via exact enumeration. The number of nonisomorphic isostatic packings grows exponentially with the number of spheres N, and their diversity of structure and symmetry increases with increasing N and decreases with increasing hyperstaticity H ≡ Nc -- Miso where Nc is the number of pair contacts and Niso = 3N -- 6. Maximally contacting packings are in general neither the densest nor the most symmetric. Analyses of local structure show that the fraction f of nuclei with order compatible with the bulk (rhcp) crystal decreases sharply with increasing N due to a high propensity for stacking faults, five- and near-fivefold symmetric structures, and other motifs that preclude rhcp order. While f increases with increasing H, a significant fraction of hyperstatic nuclei for N as small as 11 retain non-rhcp structure. Classical theories of nucleation that consider only spherical nuclei, or only nuclei with the same ordering as the bulk crystal, cannot capture such effects. Our results provide an explanation for the failure of classical nucleation theory for hard-sphere systems of N ≲ 10 particles; we argue that in this size regime, it is essential to consider nuclei of unconstrained geometry. Our results are also applicable to understanding kinetic arrest and jamming in systems that interact via hard-core-like repulsive and short-ranged attractive interactions. [ABSTRACT FROM AUTHOR]

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ ≈ 2 x 10-8. From field-dependent scattering data, we estimate that grains of ≈1.2 µm are present during alignment. These results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers. [ABSTRACT FROM AUTHOR]

We performed molecular dynamics simulations of granular beds driven by a model hydrodynamic shear flow to elucidate general grain-scale mechanisms that determine the onset and cessation of sediment transport. By varying the Shields number (the nondimensional shear stress at the top of the bed) and particle Reynolds number (the ratio of particle inertia to viscous damping), we explore how variations of the fluid flow rate, particle inertia, and fluid viscosity affect the onset and cessation of bed motion. For low to moderate particle Reynolds numbers, a critical boundary separates mobile and static states. Transition times between these states diverge as this boundary is approached both from above and below. At high particle Reynolds number, inertial effects become dominant, and particle motion can be sustained well below flow rates at which mobilization of a static bed occurs. We also find that the onset of bed motion (for both low and high particle Reynolds numbers) is described by Weibullian weakest-link statistics and thus is crucially dependent on the packing structure of the granular bed, even deep beneath the surface. [ABSTRACT FROM AUTHOR]

We perform molecular dynamics (MD) simulations of the crystallization process in binary Lennard-Jones systems during heating and cooling to investigate atomic-scale crystallization kinetics in glass-forming materials. For the cooling protocol, we prepared equilibrated liquids above the liquidus temperature Tl and cooled each sample to zero temperature at rate Rc. For the heating protocol, we first cooled equilibrated liquids to zero temperature at rate Rp and then heated the samples to temperature T > Tl at rate Rh. We measured the critical heating and cooling rates Rh* and Rc*, below which the systems begin to form a substantial fraction of crystalline clusters during the heating and cooling protocols. We show that Rh* > Rc* and that the asymmetry ratio Rh*/ Rc*. includes an intrinsic contribution that increases with the glass-forming ability (GFA) of the system and a preparation-rate dependent contribution that increases strongly as Rp → Rc* from above. We also show that the predictions from classical nucleation theory (CNT) can qualitatively describe the dependence of the asymmetry ratio on the GFA and preparation rate Rp from the MD simulations and results for the asymmetry ratio measured in Zr- and Au-based bulk metallic glasses (BMG). This work emphasizes the need for and benefits of an improved understanding of crystallization processes in BMGs and other glass-forming systems. [ABSTRACT FROM AUTHOR]

A bulk metallic glass forming alloy is subjected to shear flow in its supercooled state by compression of a short rod to produce a flat disk. The resulting material exhibits enhanced crystallization kinetics during isothermal annealing as reflected in the decrease of the crystallization time relative to the nondeformed case. The transition from quiescent to shear-accelerated crystallization is linked to strain accumulated during shear flow above a critical shear rate ɣc ≈ 0.3 s-1 which corresponds to Péclet number, Pe ~ O(1). The observation of shear-accelerated crystallization in an atomic system at modest shear rates is uncommon. It is made possible here by the substantial viscosity of the supercooled liquid which increases strongly with temperature in the approach to the glass transition. We may therefore anticipate the encounter of nontrivial shear-related effects during thermoplastic deformation of similar systems. [ABSTRACT FROM AUTHOR]

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs of residues in five IDPs: α-, β-, and γ-synuclein, the microtubule-associated protein τ, and prothymosin α. We find that our CG model is able to recapitulate the average interresidue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein. [ABSTRACT FROM AUTHOR]

We perform molecular dynamics simulations to compress binary hard spheres into jammed packings as a function of the compression rate R, size ratio ɑ, and number fraction xS of small particles to determine the connection between the glass-forming ability (GFA) and packing efficiency in bulk metallic glasses (BMGs). We define the GFA by measuring the critical compression rate Rc, below which jammed hard-sphere packings begin to form "random crystal" structures with defects. We find that for systems with ɑ0.8 that do not demix, Rc decreases strongly with ΔϕJ, as Rc~exp(-1/ΔϕJ²), where ΔϕJ is the difference between the average packing fraction of the amorphous packings and random crystal structures at Rc. Systems with ɑ0.8 partially demix, which promotes crystallization, but we still find a strong correlation between Rc and ΔϕJ. We show that known metal-metal BMGs occur in the regions of the ɑ and xS parameter space with the lowest values of Rc for binary hard spheres. Our results emphasize that maximizing GFA in binary systems involves two competing effects: minimizing ɑ to increase packing efficiency, while maximizing ɑ to prevent demixing. [ABSTRACT FROM AUTHOR]

We perform numerical simulations of repulsive, frictionless athermal disks in two and three spatial dimensions undergoing cyclic quasistatic simple shear to investigate particle-scale reversible motion. We identify three classes of steady-state dynamics as a function of packing fraction ɸ and maximum strain amplitude per cycle ymax- Point-reversible states, where particles do not collide and exactly retrace their intracycle trajectories, occur at low ɸ and ymax. Particles in loop-reversible states undergo numerous collisions and execute complex trajectories but return to their initial positions at the end of each cycle. For sufficiently large

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 a-synuclein that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent single-molecule fluorescence energy transfer (smFRET) experiments. We find that a-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 a-synuclein proteins that may precede amyloid formation. [ABSTRACT FROM AUTHOR]

We perform extensive molecular dynamics simulations of dense liquids composed of bidisperse dimer- and ellipse-shaped particles in two dimensions that interact via purely repulsive contact forces. We measure the structural relaxation times obtained from the long-time a 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 ø, temperature T, and aspect ratio ɑ. We are able to collapse the packing-fraction and temperature-dependent structural relaxation times for disks, and dimers and ellipses over a wide range of a, onto a universal scaling function f±(|&b.phish;-&b.phish;0|,T,ɑ>, which is similar to that employed in previous studies of dense liquids composed of purely repulsive spherical particles in three dimensions. T± for both the translational and rotational DOF are characterized by the a-dependent scaling exponents p. and S and packing fraction 0, m(4>0), decreases monotonically with increasing aspect ratio for both ellipses and dimers. For a > ap, where ap is the location of the peak in the packing fraction

We numerically investigate the mechanical properties of static packings of frictionless ellipsoidal particles in two and three dimensions over a range of aspect ratio and compression A0. While amorphous packings of spherical particles at jamming onset (A<¡> = 0) are isostatic and possess the minimum contact number ziso required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming (z < z¡s0) 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 5 matrices. We find that the stiffness matrix possesses 2Ar(z¡S0 -- z) eigenmodes êo with zero eigenvalues even at finite compression, where N is the number of particles. In addition, these modes êo are nearly eigenvectors of the dynamical matrix with eigenvalues that scale as A0, 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 á4 for perturbations by amplitude S along these "quartic" modes, ê0. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles. [ABSTRACT FROM AUTHOR]

The mechanical response of packings of purely repulsive, spherical particles to athermal, quasistatic simple shear near jamming onset is highly nonlinear. Previous studies have shown that, at small pressure p, the ensemble-averaged static shear modulus ⟨G-G0⟩ scales with pα, where α≈1, but above a characteristic pressure p**, ⟨G-G0⟩∼pβ, where β≈0.5. However, we find that the shear modulus Gi for an individual packing typically decreases linearly with p along a geometrical family where the contact network does not change. We resolve this discrepancy by showing that, while the shear modulus does decrease linearly within geometrical families, ⟨G⟩ also depends on a contribution from discontinuous jumps in ⟨G⟩ that occur at the transitions between geometrical families. For p>p**, geometrical-family and rearrangement contributions to ⟨G⟩ are of opposite signs and remain comparable for all system sizes. ⟨G⟩ can be described by a scaling function that smoothly transitions between two power-law exponents α and β. We also demonstrate the phenomenon of compression unjamming, where a jammed packing unjams via isotropic compression. [ABSTRACT FROM AUTHOR]

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations. [ABSTRACT FROM AUTHOR]

We introduce the deformable particle (DP) model for cells, foams, emulsions, and other soft particulate materials, which adds to the benefits and eliminates deficiencies of existing models. The DP model combines the ability to model individual soft particles with the shape-energy function of the vertex model, and adds arbitrary particle deformations. We focus on 2D deformable polygons with a shape-energy function that is minimized for area a0 and perimeter p0 and repulsive interparticle forces. We study the onset of jamming versus particle asphericity, A=p²0/4πa0, and find that the packing fraction grows with A until reaching A*=1.16 of the underlying Voronoi cells at confluence. We find that DP packings above and below A* are solidlike, which helps explain the solid-to-fluid transition at A* in the vertex model as a transition from tension- to compression-dominated regimes. [ABSTRACT FROM AUTHOR]

We perform computational studies of repulsive, frictionless disks to investigate the development of stress anisotropy in mechanically stable (MS) packings at jamming onset. We focus on two protocols for generating MS packings at jamming onset: (1) isotropic compression and (2) applied simple or pure shear strain γ at fixed packing fraction ϕ. MS packings of frictionless disks occur as geometric families (i.e., quasiparabolic segments with positive curvature) in the ϕ-γ plane. MS packings from protocol 1 populate parabolic segments with both signs of the slope, dϕ/dγ>0 and dϕ/dγ<0. In contrast, MS packings from protocol 2 populate segments with dϕ/dγ<0 only. For both simple and pure shear, we derive a relationship between the stress anisotropy and local dilatancy dϕ/dγ obeyed by MS packings along geometrical families. We show that for MS packings prepared using isotropic compression, the stress anisotropy distribution is Gaussian centered at zero with a standard deviation that decreases with increasing system size. For shear jammed MS packings, the stress anisotropy distribution is a convolution of Weibull distributions that depend on strain, which has a nonzero average and standard deviation in the large-system limit. We also develop a framework to calculate the stress anisotropy distribution for packings generated via protocol 2 in terms of the stress anisotropy distribution for packings generated via protocol 1. [ABSTRACT FROM AUTHOR]

We show that the yielding transition in granular media displays second-order critical-point scaling behavior. We carry out discrete element simulations in the low-inertial-number limit for frictionless, purely repulsive spherical grains undergoing simple shear at fixed nondimensional shear stress Σ in two and three spatial dimensions. To find a mechanically stable (MS) packing that can support the applied Σ, isotropically prepared states with size L must undergo a total strain γms (Σ,L). The number density of MS packings (∝ γ-1ms) vanishes for Σ > Σc ≈ 0.11 according to a critical scaling form with a length scale ξ ∝ | Σ - Σc|-ν, where ν ≈ 1.7 - 1.8. Above the yield stress (Σ > Σc), no MS packings that can support Σ exist in the large-system limit L/ξ ≫ 1. MS packings generated via shear possess anisotropic force and contact networks, suggesting that Σc is associated with an upper limit in the degree to which these networks can be deformed away from those for isotropic packings. [ABSTRACT FROM AUTHOR]

We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naive constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and cir-polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a masterlike form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of "quartic" modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable. [ABSTRACT FROM AUTHOR]

We focus on the response of mechanically stable (MS) packings of frictionless, bidisperse disks to thermal fluctuations, with the aim of quantifying how nonlinearities affect system properties at finite temperature. In contrast, numerous prior studies characterized the structural and mechanical properties of MS packings of frictionless spherical particles at zero temperature. Packings of disks with purely repulsive contact interactions possess two main types of nonlinearities, one from the form of the interaction potential (e.g., either linear or Hertzian spring interactions) and one from the breaking (or forming) of interparticle contacts. To identify the temperature regime at which the contact-breaking nonlinearities begin to contribute, we first calculated the minimum temperatures Tcb required to break a single contact in the MS packing for both single- and multiple-eigenmode perturbations of the T=0 MS packing. We find that the temperature required to break a single contact for equal velocity-amplitude perturbations involving all eigenmodes approaches the minimum value obtained for a perturbation in the direction connecting disk pairs with the smallest overlap. We then studied deviations in the constant volume specific heat CV and deviations of the average disk positions Δr from their T=0 values in the temperature regime TCV100 for linear spring interactions is independent of system size. This result emphasizes that contact-breaking nonlinearities are dominant over form nonlinearities in the low-temperature range Tcb

We present the experimental and numerical studies of a two-dimensional sheared amorphous material composed of bidisperse photoelastic disks. We analyze the statistics of avalanches during shear including the local and global fluctuations in energy and changes in particle positions and orientations. We find scale-free distributions for these global and local avalanches denoted by power laws whose cutoffs vary with interparticle friction and packing fraction. Different exponents are found for these power laws depending on the quantity from which variations are extracted. An asymmetry in time of the avalanche shapes is evidenced along with the fact that avalanches are mainly triggered by the shear bands. A simple relation independent of the intensity is found between the number of local avalanches and the global avalanches they form. We also compare these experimental and numerical results for both local and global fluctuations to predictions from mean-field and depinning theories. [ABSTRACT FROM AUTHOR]

Amorphous materials such as metallic, polymeric, and colloidal glasses exhibit complex preparation-dependent mechanical response to applied shear. In particular, glassy solids yield, with a mechanical response that transitions from elastic to plastic, with increasing shear strain. We perform numerical simulations to investigate the mechanical response of binary Lennard-Jones glasses undergoing athermal, quasistatic pure shear as a function of the cooling rate R used to prepare them. The ensemble-averaged stress versus strain curve 〈σ(γ)〉 resembles the spatial average in the large size limit, which appears smooth and displays a putative elastic regime at small strains, a yielding-related peak in stress at intermediate strain, and a plastic flow regime at large strains. In contrast, for each glass configuration in the ensemble, the stress-strain curve σ(γ) consists of many short nearly linear segments that are punctuated by particle-rearrangement-induced rapid stress drops. To explain the nonlinearity of 〈σ(γ)〉, we quantify the shape of the small stress-strain segments and the frequency and size of the stress drops in each glass configuration. We decompose the stress loss [i.e., the deviation in the slope of 〈σ(γ)〉 from that at 〈σ(0)〉] into the loss from particle rearrangements and the loss from softening [i.e., the reduction of the slopes of the linear segments in σ(γ)], and then compare the two contributions as a function of R and γ. For the current studies, the rearrangement-induced stress loss is larger than the softening-induced stress loss, however, softening stress losses increase with decreasing cooling rate. We also characterize the structure of the potential energy landscape along the strain direction for glasses prepared with different R, and observe a dramatic change of the properties of the landscape near the yielding transition. We then show that the rearrangement-induced energy loss per strain can serve as an order parameter for the yielding transition, which sharpens for slow cooling rates and in large systems. [ABSTRACT FROM AUTHOR]

Amorphous solids, such as metallic, polymeric, and colloidal glasses, display complex spatiotemporal response to applied deformations. In contrast to crystalline solids, during loading, amorphous solids exhibit a smooth crossover from elastic response to plastic flow. In this study, we investigate the mechanical response of binary Lennard-Jones glasses to athermal, quasistatic pure shear as a function of the cooling rate used to prepare them. We find several key results concerning the connection between strain-induced particle rearrangements and mechanical response. We show that the energy loss per strain dUloss/dγ caused by particle rearrangements for more rapidly cooled glasses is larger than that for slowly cooled glasses. We also find that the cumulative energy loss Uloss can be used to predict the ductility of glasses even in the putative linear regime of stress versus strain. Uloss increases (and the ratio of shear to bulk moduli decreases) with increasing cooling rate, indicating enhanced ductility. In addition, we characterized the degree of reversibility of particle motion during a single shear cycle. We find that irreversible particle motion occurs even in the linear regime of stress versus strain. However, slowly cooled glasses, which undergo smaller rearrangements, are more reversible during a single shear cycle than rapidly cooled glasses. Thus, we show that more ductile glasses are also less reversible. [ABSTRACT FROM AUTHOR]

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ≈0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ≈0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure. [ABSTRACT FROM AUTHOR]

We propose a theoretical framework for predicting the protocol dependence of the jamming transition for frictionless spherical particles that interact via repulsive contact forces. We study isostatic jammed disk packings obtained via two protocols: isotropic compression and simple shear. We show that for frictionless systems, all jammed packings can be obtained via either protocol. However, the probability to obtain a particular jammed packing depends on the packing-generation protocol. We predict the average shear strain required to jam initially unjammed isotropically compressed packings from the density of jammed packings, shape of their basins of attraction, and path traversed in configuration space. We compare our predictions to simulations of shear strain-induced jamming and find quantitative agreement. We also show that the packing fraction range, over which shear strain-induced jamming occurs, tends to zero in the large system limit for frictionless packings with overdamped dynamics. [ABSTRACT FROM AUTHOR]

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪T&#95;{g} and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts N&#95;{c} matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static packings generated via attractive collapse or compression of repulsive particles possess similar structural and mechanical properties.

Jammed packings of granular materials display complex mechanical response. For example, the ensemble-averaged shear modulus 〈G〉 increases as a power law in pressure p for static packings of soft spherical particles that can rearrange during compression. We seek to design granular materials with shear moduli that can either increase or decrease with pressure without particle rearrangements even in the large-system limit. To do this, we construct tessellated granular metamaterials by joining multiple particle-filled cells together. We focus on cells that contain a small number of bidisperse disks in two dimensions. We first study the mechanical properties of individual disk-filled cells with three types of boundaries: periodic boundary conditions (PBC), fixed-length walls (FXW), and flexible walls (FLW). Hypostatic jammed packings are found for cells with FLW, but not in cells with PBC and FXW, and they are stabilized by quartic modes of the dynamical matrix. The shear modulus of a single cell depends linearly on p. We find that the slope of the shear modulus with pressure λ&#95;{c}<0 for all packings in single cells with PBC where the number of particles per cell N≥6. In contrast, single cells with FXW and FLW can possess λ&#95;{c}>0, as well as λ&#95;{c}<0, for N≤16. We show that we can force the mechanical properties of multicell granular metamaterials to possess those of single cells by constraining the end points of the outer walls and enforcing an affine shear response. These studies demonstrate that tessellated granular metamaterials provide a platform for the design of soft materials with specified mechanical properties.

Strain-controlled isotropic compression gives rise to jammed packings of repulsive, frictionless disks with either positive or negative global shear moduli. We carry out computational studies to understand the contributions of the negative shear moduli to the mechanical response of jammed disk packings. We first decompose the ensemble-averaged, global shear modulus as 〈G〉=(1-F&#95;{-})〈G&#95;{+}〉+F&#95;{-}〈G&#95;{-}〉, where F&#95;{-} is the fraction of jammed packings with negative shear moduli and 〈G&#95;{+}〉 and 〈G&#95;{-}〉 are the average values from packings with positive and negative moduli, respectively. We show that 〈G&#95;{+}〉 and 〈|G&#95;{-}|〉 obey different power-law scaling relations above and below pN^{2}∼1. For pN^{2}>1, both 〈G&#95;{+}〉N and 〈|G&#95;{-}|〉N∼(pN^{2})^{β}, where β∼0.5 for repulsive linear spring interactions. Despite this, 〈G〉N∼(pN^{2})^{β^{'}} with β^{'}≳0.5 due to the contributions from packings with negative shear moduli. We show further that the probability distribution of global shear moduli P(G) collapses at fixed pN^{2} and different values of p and N. We calculate analytically that P(G) is a Γ distribution in the pN^{2}≪1 limit. As pN^{2} increases, the skewness of P(G) decreases and P(G) becomes a skew-normal distribution with negative skewness in the pN^{2}≫1 limit. We also partition jammed disk packings into subsystems using Delaunay triangulation of the disk centers to calculate local shear moduli. We show that the local shear moduli defined from groups of adjacent triangles can be negative even when G>0. The spatial correlation function of local shear moduli C(r[over ⃗]) displays weak correlations for pn&#95;{sub}^{2}<10^{-2}, where n&#95;{sub} is the number of particles within each subsystem. However, C(r[over ⃗]) begins to develop long-ranged spatial correlations with fourfold angular symmetry for pn&#95;{sub}^{2}≳10^{-2}.

We investigate the mechanical response of jammed packings of circulo-lines in two spatial dimensions, interacting via purely repulsive, linear spring forces, as a function of pressure P during athermal, quasistatic isotropic compression. The surface of a circulo-line is defined as the collection of points that is equidistant to a line; circulo-lines are composed of a rectangular central shaft with two semicircular end caps. Prior work has shown that the ensemble-averaged shear modulus for jammed disk packings scales as a power law, 〈G(P)〉∼P^{β}, with β∼0.5, over a wide range of pressure. For packings of circulo-lines, we also find robust power-law scaling of 〈G(P)〉 over the same range of pressure for aspect ratios R≳1.2. However, the power-law scaling exponent β∼0.8-0.9 is much larger than that for jammed disk packings. To understand the origin of this behavior, we decompose 〈G〉 into separate contributions from geometrical families, G&#95;{f}, and from changes in the interparticle contact network, G&#95;{r}, such that 〈G〉=〈G&#95;{f}〉+〈G&#95;{r}〉. We show that the shear modulus for low-pressure geometrical families for jammed packings of circulo-lines can both increase and decrease with pressure, whereas the shear modulus for low-pressure geometrical families for jammed disk packings only decreases with pressure. For this reason, the geometrical family contribution 〈G&#95;{f}〉 is much larger for jammed packings of circulo-lines than for jammed disk packings at finite pressure, causing the increase in the power-law scaling exponent for 〈G(P)〉.

We investigate the mechanical response of jammed packings of repulsive, frictionless spherical particles undergoing isotropic compression. Prior simulations of the soft-particle model, where the repulsive interactions scale as a power law in the interparticle overlap with exponent α, have found that the ensemble-averaged shear modulus 〈G(P)〉 increases with pressure P as ∼P^{(α-3/2)/(α-1)} at large pressures. 〈G〉 has two key contributions: (1) continuous variations as a function of pressure along geometrical families, for which the interparticle contact network does not change, and (2) discontinuous jumps during compression that arise from changes in the contact network. Using numerical simulations, we show that the form of the shear modulus G^{f} for jammed packings within near-isostatic geometrical families is largely determined by the affine response G^{f}∼G&#95;{a}^{f}, where G&#95;{a}^{f}/G&#95;{a0}=(P/P&#95;{0})^{(α-2)/(α-1)}-P/P&#95;{0}, P&#95;{0}∼N^{-2(α-1)} is the characteristic pressure at which G&#95;{a}^{f}=0, G&#95;{a0} is a constant that sets the scale of the shear modulus, and N is the number of particles. For near-isostatic geometrical families that persist to large pressures, deviations from this form are caused by significant nonaffine particle motion. We further show that the ensemble-averaged shear modulus 〈G(P)〉 is not simply a sum of two power laws, but 〈G(P)〉∼(P/P&#95;{c})^{a}, where a≈(α-2)/(α-1) in the P→0 limit and 〈G(P)〉∼(P/P&#95;{c})^{b}, where b≳(α-3/2)/(α-1), above a characteristic pressure that scales as P&#95;{c}∼N^{-2(α-1)}.

Many experiments over the past half century have shown that, for a range of protocols, granular materials compact under pressure and repeated small disturbances. A recent experiment on cyclically sheared spherical grains showed significant compaction via homogeneous crystallization (Rietz et al., 2018). Here we present numerical simulations of frictionless, purely repulsive spheres undergoing cyclic simple shear via Newtonian dynamics with linear viscous drag at fixed vertical load. We show that for sufficiently small strain amplitudes, cyclic shear gives rise to homogeneous crystallization at a volume fraction ϕ=0.646±0.001. This result indicates that neither friction nor gravity is essential for homogeneous crystallization in driven granular media. Understanding how crystal formation is initiated within a homogeneous disordered state gives key insights into the old open problem of glass formation in fluids.

We employ numerical simulations to study active transistor-like switches made from two-dimensional (2D) granular crystals containing two types of grains with the same size but different masses. We tune the mass contrast and arrangement of the grains to maximize the width of the frequency band gap in the device. The input signal is applied to a single grain on one side of the device, and the output signal is measured from another grain on the other side of the device. Changing the size of one or many grains tunes the pressure, which controls the vibrational response of the device. Switching between the on and off states is achieved using two mechanisms: (1) pressure-induced switching where the interparticle contact network is the same in the on and off states and (2) switching through contact breaking. In general, the performance of the acoustic switch, as captured by the gain ratio and switching time between the on and off states, is better for pressure-induced switching. We show that in these acoustic switches the gain ratio between the on and off states can be larger than 10^{4} and the switching time (multiplied by the driving frequency) is comparable to that obtained recently for sonic crystals and less than that for photonic transistor-like switches. Since the self-assembly of grains with different masses into 2D granular crystals is challenging, we describe simulations of circular grains with small circular knobs placed symmetrically around the perimeter mixed with circular grains without knobs. Using umbrella sampling techniques, we show that grains with six knobs most efficiently form the hexagonal crystals that yield the largest frequency band gap. Using the simulation results, we estimate the time required for vibration experiments to generate granular crystals of millimeter-sized steel beads with maximal band gaps.

We focus on the response of mechanically stable (MS) packings of frictionless, bidisperse disks to thermal fluctuations, with the aim of quantifying how nonlinearities affect system properties at finite temperature. In contrast, numerous prior studies characterized the structural and mechanical properties of MS packings of frictionless spherical particles at zero temperature. Packings of disks with purely repulsive contact interactions possess two main types of nonlinearities, one from the form of the interaction potential (e.g., either linear or Hertzian spring interactions) and one from the breaking (or forming) of interparticle contacts. To identify the temperature regime at which the contact-breaking nonlinearities begin to contribute, we first calculated the minimum temperatures T&#95;{cb} required to break a single contact in the MS packing for both single- and multiple-eigenmode perturbations of the T=0 MS packing. We find that the temperature required to break a single contact for equal velocity-amplitude perturbations involving all eigenmodes approaches the minimum value obtained for a perturbation in the direction connecting disk pairs with the smallest overlap. We then studied deviations in the constant volume specific heat C[over ¯]&#95;{V} and deviations of the average disk positions Δr from their T=0 values in the temperature regime T&#95;{C[over ¯]&#95;{V}}100 for linear spring interactions is independent of system size. This result emphasizes that contact-breaking nonlinearities are dominant over form nonlinearities in the low-temperature range T&#95;{cb}

Amorphous materials such as metallic, polymeric, and colloidal glasses exhibit complex preparation-dependent mechanical response to applied shear. In particular, glassy solids yield, with a mechanical response that transitions from elastic to plastic, with increasing shear strain. We perform numerical simulations to investigate the mechanical response of binary Lennard-Jones glasses undergoing athermal, quasistatic pure shear as a function of the cooling rate R used to prepare them. The ensemble-averaged stress versus strain curve 〈σ(γ)〉 resembles the spatial average in the large size limit, which appears smooth and displays a putative elastic regime at small strains, a yielding-related peak in stress at intermediate strain, and a plastic flow regime at large strains. In contrast, for each glass configuration in the ensemble, the stress-strain curve σ(γ) consists of many short nearly linear segments that are punctuated by particle-rearrangement-induced rapid stress drops. To explain the nonlinearity of 〈σ(γ)〉, we quantify the shape of the small stress-strain segments and the frequency and size of the stress drops in each glass configuration. We decompose the stress loss [i.e., the deviation in the slope of 〈σ(γ)〉 from that at 〈σ(0)〉] into the loss from particle rearrangements and the loss from softening [i.e., the reduction of the slopes of the linear segments in σ(γ)], and then compare the two contributions as a function of R and γ. For the current studies, the rearrangement-induced stress loss is larger than the softening-induced stress loss, however, softening stress losses increase with decreasing cooling rate. We also characterize the structure of the potential energy landscape along the strain direction for glasses prepared with different R, and observe a dramatic change of the properties of the landscape near the yielding transition. We then show that the rearrangement-induced energy loss per strain can serve as an order parameter for the yielding transition, which sharpens for slow cooling rates and in large systems.

Amorphous solids, such as metallic, polymeric, and colloidal glasses, display complex spatiotemporal response to applied deformations. In contrast to crystalline solids, during loading, amorphous solids exhibit a smooth crossover from elastic response to plastic flow. In this study, we investigate the mechanical response of binary Lennard-Jones glasses to athermal, quasistatic pure shear as a function of the cooling rate used to prepare them. We find several key results concerning the connection between strain-induced particle rearrangements and mechanical response. We show that the energy loss per strain dU&#95;{loss}/dγ caused by particle rearrangements for more rapidly cooled glasses is larger than that for slowly cooled glasses. We also find that the cumulative energy loss U&#95;{loss} can be used to predict the ductility of glasses even in the putative linear regime of stress versus strain. U&#95;{loss} increases (and the ratio of shear to bulk moduli decreases) with increasing cooling rate, indicating enhanced ductility. In addition, we characterized the degree of reversibility of particle motion during a single shear cycle. We find that irreversible particle motion occurs even in the linear regime of stress versus strain. However, slowly cooled glasses, which undergo smaller rearrangements, are more reversible during a single shear cycle than rapidly cooled glasses. Thus, we show that more ductile glasses are also less reversible.

We perform molecular dynamics (MD) simulations of the crystallization process in binary Lennard-Jones systems during heating and cooling to investigate atomic-scale crystallization kinetics in glass-forming materials. For the cooling protocol, we prepared equilibrated liquids above the liquidus temperature Tl and cooled each sample to zero temperature at rate Rc. For the heating protocol, we first cooled equilibrated liquids to zero temperature at rate Rp and then heated the samples to temperature T>Tl at rate Rh. We measured the critical heating and cooling rates Rh* and Rc*, below which the systems begin to form a substantial fraction of crystalline clusters during the heating and cooling protocols. We show that Rh*>Rc* and that the asymmetry ratio Rh*/Rc* includes an intrinsic contribution that increases with the glass-forming ability (GFA) of the system and a preparation-rate dependent contribution that increases strongly as Rp→Rc* from above. We also show that the predictions from classical nucleation theory (CNT) can qualitatively describe the dependence of the asymmetry ratio on the GFA and preparation rate Rp from the MD simulations and results for the asymmetry ratio measured in Zr- and Au-based bulk metallic glasses (BMG). This work emphasizes the need for and benefits of an improved understanding of crystallization processes in BMGs and other glass-forming systems.

A bulk metallic glass forming alloy is subjected to shear flow in its supercooled state by compression of a short rod to produce a flat disk. The resulting material exhibits enhanced crystallization kinetics during isothermal annealing as reflected in the decrease of the crystallization time relative to the nondeformed case. The transition from quiescent to shear-accelerated crystallization is linked to strain accumulated during shear flow above a critical shear rate γ̇(c)≈0.3 s(-1) which corresponds to Péclet number, Pe∼O(1). The observation of shear-accelerated crystallization in an atomic system at modest shear rates is uncommon. It is made possible here by the substantial viscosity of the supercooled liquid which increases strongly with temperature in the approach to the glass transition. We may therefore anticipate the encounter of nontrivial shear-related effects during thermoplastic deformation of similar systems.

We develop a theoretical description for mechanically stable frictional packings in terms of the difference between the total number of contacts required for isostatic packings of frictionless disks and the number of contacts in frictional packings, m=Nc0 - Nc. The saddle order m represents the number of unconstrained degrees of freedom that a static packing would possess if friction were removed. Using a novel numerical method that allows us to enumerate disk packings for each m, we show that the probability to obtain a packing with saddle order m at a given static friction coefficient μ, Pm(μ), can be expressed as a power series in μ. Using this form for Pm(μ), we quantitatively describe the dependence of the average contact number on the friction coefficient for static disk packings obtained from direct simulations of the Cundall-Strack model for all μ and N.

We perform molecular dynamics simulations to compress binary hard spheres into jammed packings as a function of the compression rate R, size ratio α, and number fraction x(S) of small particles to determine the connection between the glass-forming 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 α≳0.8 that do not demix, R(c) decreases strongly with Δϕ(J), as R(c)∼exp(-1/Δϕ(J)(2)), where Δϕ(J) is the difference between the average packing fraction of the amorphous packings and random crystal structures at R(c). Systems with α≲0.8 partially demix, which promotes crystallization, but we still find a strong correlation between R(c) and Δϕ(J). We show that known metal-metal BMGs occur in the regions of the α 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 α to increase packing efficiency, while maximizing α to prevent demixing.

Many jammed particulate systems, such as granular and colloidal materials, interact via repulsive contact forces. We find that these systems possess no harmonic regime in the large system limit (N→∞) for all compressions Δϕ studied, and at jamming onset Δϕ→0 for all N. We perform fixed energy simulations following perturbations with amplitude δ along eigendirections of the dynamical matrix. The fluctuations abruptly spread to all modes for δ≈δ(c) (where a single contact breaks) in contrast to linear and weakly nonlinear behavior. For δ > δ(c), all discrete modes disappear into a continuous frequency band. <δ(c)> scales with 1/N and Δϕ, which limits harmonic behavior to only overcompressed systems. The density of vibrational modes deviates strongly from that predicted from the dynamical matrix when the system enters the nonharmonic regime, which significantly affects its mechanical and transport properties.

A simple theory for glassy-polymeric mechanical response that accounts for large-scale chain relaxation is presented. It captures the crossover from perfect-plastic response to Gaussian strain hardening as the degree of polymerization N increases, without invoking entanglements. By relating hardening to interactions on the scale of monomers and chain segments, we correctly predict its magnitude. Strain-activated relaxation arising from the need to maintain constant chain contour length reduces the characteristic relaxation time by a factor ~εN during active deformation at strain rate ε. This prediction is consistent with results from recent experiments and simulations, and we suggest how it may be further tested experimentally.

We enumerate all minimal energy packings (MEPs) for small single linear and ring polymers composed of spherical monomers with contact attractions and hard-core repulsions and compare them to corresponding results for monomer packings. We define and identify "dividing surfaces" in polymer packings, which reduce the number of arrangements that satisfy hard-sphere and covalent-bond constraints. Compared to monomer MEPs, polymer MEPs favor intermediate structural symmetry. We also examine the packing-preparation dependence for longer single chains using molecular dynamics simulations. For slow temperature quenches, chains form crystallites with close-packed cores. As the quench rate increases, the core size decreases and the exterior becomes more disordered. By examining the contact number, we connect the suppression of crystallization to the onset of isostaticity in disordered packings.

We perform simulations of model proteins to study folding on rugged energy landscapes. We construct "first-passage" networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to basins and transitions between them in the energy landscape. We find power-law relations between the folding time and the number of nodes and bonds. We show that these scalings are determined by the fractal properties of first-passage networks. Thus, we have identified a possible mechanism--the small fractal dimension of first passage networks--which can give rise to reliable folding in proteins with rugged energy landscapes.

We enumerate and classify nearly all of the possible mechanically stable (MS) packings of bidipserse mixtures of frictionless disks in small sheared systems. We find that MS packings form continuous geometrical families, where each family is defined by its particular network of particle contacts. We also monitor the dynamics of MS packings along geometrical families by applying quasistatic simple shear strain at zero pressure. For small numbers of particles (N<16), we find that the dynamics is deterministic and highly contracting. That is, if the system is initialized in a MS packing at a given shear strain, it will quickly lock into a periodic orbit at subsequent shear strain, and therefore sample only a very small fraction of the possible MS packings in steady state. In studies with N>16, we observe an increase in the period and random splittings of the trajectories caused by bifurcations in configuration space. We argue that the ratio of the splitting and contraction rates in large systems will determine the distribution of MS-packing geometrical families visited in steady state. This work is part of our long-term research program to develop a master-equation formalism to describe macroscopic slowly driven granular systems in terms of collections of small subsystems.

We developed an experimental method to generate mechanically stable (MS) packings of frictionless disks and performed coordinated experiments and simulations to characterize MS packings in small systems. For a given system geometry, MS packings occur as discrete, well-separated points in configuration space with probabilities that vary by many orders of magnitude and are robust with respect to the packing preparation. Over a continuous range of system geometries, MS packings occur as distinct geometrical families and only a small fraction of families are sampled via quasistatic dynamics. These results suggest that the most frequent MS packings may dominate the structural and mechanical properties of dense granular media.