arXiv subjects

Corey S. O'Hern

Publications and source records attributed to Corey S. O'Hern.

At least 91 records · Page 5Linked to original sources

arXiv2013

Isostaticity at Frictional Jamming

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 using the GA model to those generated using the Cundall-Strack (CS) 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.

cond-mat.soft↗

arXiv2013

Computational studies of the glass-forming ability of model bulk metallic glasses

Bulk metallic glasses (BMGs) are produced by rapidly thermally quenching supercooled liquid metal alloys below the glass transition temperature at rates much faster than the critical cooling rate R_c below which crystallization occurs. The glass-forming ability of BMGs increases with decreasing R_c, and thus good glass-formers possess small values of R_c. We perform molecular dynamics simulations of binary Lennard-Jones (LJ) mixtures to quantify how key parameters, such as the stoichiometry, particle size difference, attraction strength, and heat of mixing, influence the glass-formability of model BMGs. For binary LJ mixtures, we find that the best glass-forming mixtures possess atomic size ratios (small to large) less than 0.92 and stoichiometries near 50:50 by number. In addition, weaker attractive interactions between the smaller atoms facilitate glass formation, whereas negative heats of mixing (in the experimentally relevant regime) do not change R_c significantly. These studies represent a first step in the development of computational methods for quantitatively predicting glass-formability.

cond-mat.mtrl-sci↗

arXiv2013

Particle-scale reversibility in athermal particulate media below jamming

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 ϕand maximum strain amplitude per cycle γ_{\rm max}. Point-reversible states, where particles do not collide and exactly retrace their intra-cycle trajectories, occur at low ϕand γ_{\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 ϕfrom contact percolation to jamming onset at ϕ_J. For sufficiently large ϕand γ_{\rm max}, systems display irreversible dynamics with nonzero self-diffusion.

cond-mat.soft↗

arXiv2013

Minimal energy packings of nearly flexible polymers

We extend recent studies of the minimal energy packings of short flexible polymers with hard-core-like repulsions and short-range attractions to include bond-angle interactions with the aim of describing the collapsed conformations of `colloidal' polymers. We find that flexible tangent sticky-hard-sphere (t-SHS) packings provide a useful perturbative basis for analyzing polymer packings with nonzero bending stiffness only for {\it small} ratios of the stiffnesses for the bond-angle ($k_b$) and pair ($k_c$) interactions, i.e. $k_b^{\rm crit}/k_c \lesssim 0.01$ for $N<10$ monomers, and the critical ratio decreases with $N$. Below $k_b^{crit}$, angular interactions give rise to an exponential (in $N$) increase in the number of distinct angular energies arising from the diversity of covalent backbone paths through t-SHS packings. As $k_b$ increases above $k_b^{crit}$, the low-lying energy landscape changes dramatically as finite bending stiffness alters the structure of the polymer packings. This study lays the groundwork for exact-enumeration studies of the collapsed states of t-SHS-like models with larger bending stiffness.

cond-mat.soft↗

arXiv2012

Molecular Simulations of the Fluctuating Conformational Dynamics of Intrinsically Disordered Proteins

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-synuclein 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.

q-bio.BM↗

arXiv2012

Rods are less fragile than spheres: Structural relaxation in dense liquids composed of anisotropic particles

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 scaling function {\cal F}_{\pm}(|ϕ-ϕ_0|,T,α), which is similar to that employed in previous studies of dense liquids composed of purely repulsive spherical particles in 3D. {\cal F_{\pm}} for both the translational and rotational DOF are characterized by the α-dependent scaling exponents μand δand packing fraction ϕ_0(α) that signals the crossover in the scaling form {\cal F}_{\pm} from hard-particle dynamics to super-Arrhenius behavior for each aspect ratio. We find that the fragility at ϕ_0, m(ϕ_0), decreases monotonically with increasing aspect ratio for both ellipses and dimers. Moreover, the results for the slow dynamics of dense liquids composed of dimer- and ellipse-shaped particles are qualitatively the same, despite the fact that zero-temperature static packings of dimers are isostatic, while static packings of ellipses are hypostatic.

cond-mat.soft↗

arXiv2012

Structure of finite sphere packings via exact enumeration: Implications for colloidal crystal nucleation

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 $H \equiv N_c - N_{ISO}$, where $N_c$ is the number of pair contacts and $N_{ISO} = 3N-6$. 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, 5- and near-5-fold 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 $N\lesssim 10$ 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.

cond-mat.soft↗

arXiv2012

Constraints and vibrations in static packings of ellipsoidal particles

We numerically investigate the mechanical properties of static packings of ellipsoidal particles in 2D and 3D over a range of aspect ratio and compression $Δϕ$. While amorphous packings of spherical particles at jamming onset ($Δϕ=0$) are 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 $Δϕ$, 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 $δ^4$ for perturbations by amplitude $δ$ along these `quartic' modes, ${\hat e}_0$. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles.

cond-mat.soft↗

arXiv2011

Glassy dynamics of crystallite formation: The role of covalent bonds

We examine nonequilibrium features of collapse behavior in model polymers with competing crystallization and glass transitions using extensive molecular dynamics simulations. By comparing to "colloidal" systems with no covalent bonds but the same non-bonded interactions, we find three principal results: (i) Tangent-sphere polymers and colloids, in the equilibrium-crystallite phase, have nearly identical static properties when the temperature T is scaled by the crystallization temperature T_{cryst}; (ii) Qualitative features of nonequilibrium relaxation below T_{cryst}, measured by the evolution of local structural properties (such as the number of contacts) toward equilibrium crystallites, are the same for polymers and colloids; and (iii) Significant quantitative differences in rearrangements in polymeric and colloidal crystallites, in both far-from equilibrium and near-equilibrium systems, can be understood in terms of chain connectivity. These results have important implications for understanding slow relaxation processes in collapsed polymers, partially folded, misfolded, and intrinsically disordered proteins.

cond-mat.soft↗

arXiv2011

The contact percolation transition

Typical quasistatic compression algorithms for generating jammed packings of athermal, purely repulsive particles begin with dilute configurations and then apply successive compressions with relaxation of the elastic energy allowed between each compression step. It is well-known that during isotropic compression athermal systems with purely repulsive interactions undergo a jamming transition at packing fraction $ϕ_J$ from an unjammed state with zero pressure to a jammed, rigid state with nonzero pressure. Using extensive computer simulations, we show that a novel second-order-like transition, the contact percolation transition, which signals the formation of a system-spanning cluster of mutually contacting particles, occurs at $ϕ_P < ϕ_J$, preceding the jamming transition. By measuring the number of non-floppy modes of the dynamical matrix, and the displacement field and time-dependent pressure following compression, we find that the contact percolation transition also heralds the onset of complex spatiotemporal response to applied stress. Thus, highly heterogeneous, cooperative, and non-affine particle motion occurs in unjammed systems significantly below the jamming transition for $ϕ_P < ϕ< ϕ_J$, not only for jammed systems with $ϕ> ϕ_J$.

cond-mat.soft↗

arXiv2011

Photonic Band Gaps in 3D Network Structures with Short-range Order

We present a systematic study of photonic band gaps (PBGs) in three-dimensional (3D) photonic amorphous structures (PAS) with short-range order. From calculations of the density of optical states (DOS) for PAS with different topologies, we find that tetrahedrally connected dielectric networks produce the largest isotropic PBGs. Local uniformity and tetrahedral order are essential to the formation of PBGs in PAS, in addition to short-range geometric order. This work demonstrates that it is possible to create broad, isotropic PBGs for vector light fields in 3D PAS without long-range order.

physics.optics↗

arXiv2010

Jammed particulate systems are inherently nonharmonic

Jammed particulate systems, such as granular media, colloids, and foams, interact via one-sided forces that are nonzero only when particles overlap. We find that systems with one-sided repulsive interactions possess no linear response regime in the large system limit ($N\rightarrow \infty$) for all pressures $p$ (or compressions $Δϕ$), and for all $N$ near jamming onset $p\rightarrow 0$. We perform simulations on 2D frictionless bidisperse mechanically stable disk packings over a range of packing fractions $Δϕ= ϕ-ϕ_J$ above jamming onset $ϕ_J$. We apply perturbations with amplitude $δ$ to the packings along each eigen-direction from the dynamical matrix and determine whether the response of the system evolving at constant energy remains in the original eigenmode of the perturbation. For $δ> δ_c$, which we calculate analytically, a single contact breaks and fluctuations abruptly spread to all harmonic modes. As $δ$ increases further all discrete harmonic modes disappear into a continuous frequency band. We find that $<δ_c >\sim Δϕ/N^λ$, where $1 > λ> 0.5$, and thus jammed particulate systems are inherently nonharmonic with no linear vibrational response regime as $N\rightarrow \infty$ over the full range of $Δϕ$, and as $Δϕ\rightarrow 0$ at any $N$.

cond-mat.soft↗

arXiv2010

Photonic Band Gap Effects in Two-dimensional Polycrystalline and Amorphous Structures

We study numerically the density of optical states (DOS) in two-dimensional photonic structures with short-range positional order, and observe a clear transition from polycrystalline to amorphous photonic systems. In polycrystals, photonic band gaps (PBGs) are formed within individual do- mains, which leads to a depletion of the DOS similar to that in periodic structures. In amorphous photonic media, the domain sizes are too small to form PBGs, thus the depletion of the DOS is weakened significantly. The critical domain size that separates the polycrystalline and amorphous regimes is determined by the attenuation length of Bragg scattering, which depends not only on the degree of positional order but also the refractive index contrast of the photonic material. Even with relatively low refractive index contrast, we find that modest short-range positional order in photonic structures enhances light confinement via collective scattering and interference.

cond-mat.dis-nn↗

arXiv2010

Minimal energy packings and collapse of sticky tangent hard-sphere polymers

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 over high and low symmetries. 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 quench rate increases, the core size decreases and the exterior becomes more disordered. By examining the contact number, we connect suppression of crystallization to the onset of isostaticity in disordered packings. These studies represent a significant step forward in our ability to predict how the structural and mechanical properties of compact polymers depend on collapse dynamics.

cond-mat.soft↗

arXiv2010

Viscoplasticity and large-scale chain relaxation in glassy-polymeric strain hardening

A simple theory for glassy polymeric mechanical response which accounts for large scale chain relaxation is presented. It captures the crossover from perfect-plastic response to strong 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 $N$ dependence of the characteristic relaxation time by a factor $\sim \dotεN$ during active deformation at strain rate $\dotε$. This prediction is consistent with results from recent experiments and simulations, and we suggest how it may be further tested experimentally.

cond-mat.soft↗

arXiv2010

Tuning Jammed Frictionless Disk Packings from Isostatic to Hyperstatic

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 $ϕ_J$ 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 $ϕ_J$. We find that amorphous, isostatic packings exist over a finite range of packing fractions from $ϕ_{\rm min} \le ϕ_J \le ϕ_{\rm max}$ in the large-system limit, with $ϕ_{\rm max} \approx 0.853$. In agreement with previous calculations, we obtain $ϕ_{\rm min} \approx 0.84$ for $r > r^*$, where $r^*$ is the rate above which $ϕ_J$ is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, bond orientational order, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered, whereas bond-orientational and compositional order increase with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies of the static packings to understand the extent to which the mechanical properties of amorphous, isostatic packings are different from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic.

cond-mat.soft↗

arXiv2010

Biomimetic isotropic nanostructures for structural coloration

We describe the self-assembly of biomimetic isotropic films which display structural color amenable to potential applications in coatings. Isotropic structures can produce color if there is a pronounced characteristic length-scale comparable to the wavelength of visible light and wavelength-independent scattering is suppressed.

cond-mat.soft↗

arXiv2010

A comparison of jamming behavior in systems composed of dimer- and ellipse-shaped particles

We compare the structural and mechanical properties of static packings composed of frictionless convex (ellipses) and concave (rigid dimers) particles in two dimensions. We employ numerical simulations to generate static packings and measure the shear stress in response to applied simple shear strain as a function of the aspect ratio and amount of compression. We find that the behavior near jamming is significantly different for ellipses and dimers even though both shapes are roughly characterized by the aspect ratio and possess the same number of translational and rotational degrees of freedom per particle. For example, we find that ellipse packings are hypostatic (not isostatic as found for dimers), display novel power-law scaling of the static linear shear modulus and contact number with the amount of compression, and possess stress-strain relations that are qualitatively different from that for dimers. Thus, we observe that important macroscopic properties of static packings of anisotropic particles can depend on the microscale geometrical features of individual particles.

cond-mat.soft↗