arXiv subjects

Corey S. O'Hern

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

At least 55 records · Page 3Linked to original sources

arXiv2020

Glass formation in binary alloys with different atomic symmetries

Prediction of the glass forming ability (GFA) of alloys remains a major challenge. We are not able to predict the composition dependence of the GFA of even binary alloys. To investigate the effect of each element's propensity to form particular crystal structures on glass formation, we focus on binary alloys composed of elements with the same size, but different atomic symmetries using the patchy-particle model. For mixtures with atomic symmetries that promote different crystal structures, the minimum critical cooling rate $R_c$ is only a factor of $5$ lower than that for the pure substances. For mixtures with different atomic symmetries that promote local crystalline and icosahedral order, the minimum $R_c$ is more than $3$ orders of magnitude lower than that for pure substances. Results for $R_c$ for the patchy-particle model are in agreement with those from embedded atom method simulations and sputtering experiments of NiCu, TiAl, and high entropy alloys.

cond-mat.mtrl-sci↗

arXiv2020

Using physical features of protein core packing to distinguish real proteins from decoys

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute significantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (specifically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features.

q-bio.BM↗

arXiv2019

Jammed packings of 3D superellipsoids with tunable packing fraction, contact number, and ordering

We carry out numerical studies of static packings of frictionless superellipsoidal particles in three spatial dimensions. We consider more than $200$ different particle shapes by varying the three shape parameters that define superellipsoids. We characterize the structural and mechanical properties of both disordered and ordered packings using two packing-generation protocols. We perform athermal quasi-static compression simulations starting from either random, dilute configurations (Protocol 1) or thermalized, dense configurations (protocol $2$), which allows us to tune the orientational order of the packings. In general, we find that the contact numbers at jamming onset for superellipsoid packings are hypostatic, with $z_J < z_{\rm iso}$, where $z_{\rm iso} = 2d_f$ and $d_f = 5$ or $6$ depending on whether the particles are axi-symmetric or not. Over the full range of orientational order, we find that the number of quartic modes of the dynamical matrix for the packings always matches the number of missing contacts relative to the isostatic value. This result suggests that there are no mechanically redundant contacts for ordered, yet hypostatic packings of superellipsoidal particles. Additionally, we find that the packing fraction at jamming onset for disordered packings of superellipsoidal particles can be collapsed using two particle shape parameters, e.g. the asphericity $\mathcal{A}$ and reduced aspect ratio $β$ of the particles.

cond-mat.soft↗

arXiv2019

Pressure-dependent shear response of jammed packings of spherical particles

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 $\langle G-G_0 \rangle$ scales with $p^α$, where $α\approx 1$, but above a characteristic pressure $p^{**}$, $\langle G-G_0 \rangle \sim p^β$, where $β\approx 0.5$. However, we find that the shear modulus $G^i$ 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, $\langle G \rangle$ also depends on a contribution from discontinuous jumps in $\langle G \rangle$ that occur at the transitions between geometrical families. For $p > p^{**}$, geometrical-family and rearrangement contributions to $\langle G \rangle$ are of opposite signs and remain comparable for all system sizes. $\langle G \rangle$ can be described by a scaling function that smoothly transitions between the two power-law exponents $α$ and $β$. We also demonstrate the phenomenon of {\it compression unjamming}, where a jammed packing can unjam via isotropic compression.

cond-mat.soft↗

arXiv2019

The role of deformability in determining the structural and mechanical properties of bubbles and emulsions

We perform computational studies of jammed particle packings in two dimensions undergoing isotropic compression using the well-characterized soft particle (SP) model and the deformable particle (DP) model that we developed for compressed bubbles and emulsions. In the SP model, circular particles are allowed to overlap, generating purely repulsive forces. In the DP model, particles minimize their perimeter, while deforming at fixed area to avoid overlap during compression. We directly compare the structural and mechanical properties of jammed particle packings generated using the SP and DP models as a function of the true packing fraction $ρ$, instead of the reduced number density $ϕ$. We show that near jamming onset the excess contact number $Δz=z-z_J$ and shear modulus ${\cal G}$ scale as $Δρ^{0.5}$ in the large system limit for both the SP and DP models, where $Δρ= ρ-ρ_J$ and $z_J \approx 4$ and $ρ_J \approx 0.842$ are the values at jamming onset. $Δz$ and ${\cal G}$ for the SP and DP models begin to differ for $ρ\gtrsim 0.88$. In this regime, $Δz \sim {\cal G}$ can be described by a sum of two power-laws in $Δρ$, i.e. $Δz \sim {\cal G} \sim C_0Δρ^{0.5} +C_1Δρ^{1.0}$ to lowest order. We show that the ratio $C_1/C_0$ is much larger for the DP model compared to to that for the SP model. We also characterize the void space in jammed packings as a function of $ρ$. We find that, unlike the SP model, the DP model is able to describe the formation of Plateau borders as the system approaches $ρ= 1$. We further show that the results for $z$ and the shape factor ${\cal A}$ versus $ρ$ for the DP model agree with recent experimental studies of compressed foams and emulsions.

physics.app-ph↗

arXiv2019

Analyses of protein cores reveal fundamental differences between solution and crystal structures

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures---in the root-mean-square deviations of the C$_α$ atomic positions, identities of core amino acids, backbone and sidechain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modelling protein cores as jammed packings of amino-acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to generate the packings. For an athermal protocol, we find that the average jammed packing fraction is identical to that observed in the cores of protein structures solved by x-ray crystallography. In contrast, highly thermalized packing-generation protocols yield jammed packing fractions that are even higher than those observed in NMR structures. These results indicate that thermalized systems can pack more densely than athermal systems, which suggests a physical basis for the structural differences between protein structures solved by NMR and x-ray crystallography.

q-bio.BM↗

arXiv2019

Intrinsic dissipation mechanisms in metallic glass resonators

Micro- and nano-resonators have important applications including sensing, navigation, and biochemical detection. Their performance is quantified using the quality factor $Q$, which gives the ratio of the energy stored to the energy dissipated per cycle. Metallic glasses are a promising materials class for micro- and nano-scale resonators since they are amorphous and can be fabricated precisely into complex shapes on these lengthscales. To understand the intrinsic dissipation mechanisms that ultimately limit large $Q$-values in metallic glasses, we perform molecular dynamics simulations to model metallic glass resonators subjected to bending vibrations. We calculate the vibrational density of states, redistribution of energy from the fundamental mode of vibration, and $Q$ versus the kinetic energy per atom $K$ of the excitation. In the linear and nonlinear response regimes where there are no atomic rearrangements, we find that $Q \rightarrow \infty$ (since we do not consider coupling to the environment). We identify a characteristic $K_r$ above which atomic rearrangements occur, and there is significant energy leakage from the fundamental mode to higher frequencies, causing finite $Q$. Thus, $K_r$ is a critical parameter determining resonator performance. We show that $K_r$ decreases as a power-law, $K_r\sim N^{-k},$ with increasing system size $N$, where $k \approx 1.3$. We estimate the critical strain $\langle γ_r \rangle \sim 10^{-8}$ for micron-sized resonators below which atomic rearrangements do not occur, and thus large $Q$-values can be obtained when they are operated below $γ_r$. We find that $K_r$ for amorphous resonators is comparable to that for resonators with crystalline order.

cond-mat.mtrl-sci↗

arXiv2019

Tuning the glass-forming ability of metallic glasses through energetic frustration

The design of multi-functional BMGs is limited by the lack of a quantitative understanding of the variables that control the glass-forming ability (GFA) of alloys. Both geometric frustration (e.g. differences in atomic radii) and energetic frustration (e.g. differences in the cohesive energies of the atomic species) contribute to the GFA. We perform molecular dynamics simulations of binary Lennard-Jones mixtures with only energetic frustration. We show that there is little correlation between the heat of mixing and critical cooling rate $R_c$, below which the system crystallizes, except that $ΔH_{\rm mix} < 0$. By removing the effects of geometric frustration, we show strong correlations between $R_c$ and the variables $ε_- = (ε_{BB}-ε_{AA})/(ε_{AA}+ε_{BB})$ and ${\overline ε}_{AB} = 2ε_{AB}/(ε_{AA}+ε_{BB})$, where $ε_{AA}$ and $ε_{BB}$ are the cohesive energies of atoms $A$ and $B$ and $ε_{AB}$ is the pair interaction between $A$ and $B$ atoms. We identify a particular $f_B$-dependent combination of $ε_-$ and ${\overline ε}_{AB}$ that collapses the data for $R_c$ over nearly $4$ orders of magnitude in cooling rate.

cond-mat.mtrl-sci↗

arXiv2019

Active acoustic switches using 2D granular crystals

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 devices with grains with $3$ knobs most efficiently form the hexagonal crystals that yield the largest band gap.

cond-mat.soft↗

arXiv2018

Void distributions reveal structural link between jammed packings and protein cores

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $ϕ\approx 0.56$, 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. By measuring the critical exponent $τ$ that characterizes the size distribution of connected void clusters at the onset of percolation, we show that void percolation in packings of amino acid-shaped particles and protein cores belong to the same universality class, which is different from that for void percolation in jammed sphere packings. We propose that the connected void regions of proteins are a defining 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.

q-bio.BM↗

arXiv2018

Stress anisotropy in shear-jammed packings of frictionless disks

We perform computational studies of repulsive, frictionless disks to investigate the development of stress anisotropy in mechanically stable (MS) packings. We focus on two protocols for generating MS packings: 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. parabolic 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 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. These results emphasize that for repulsive frictionless disks, different packing-generation protocols give rise to different MS packing probabilities, which lead to differences in macroscopic properties of MS packings.

cond-mat.soft↗

arXiv2018

Critical scaling near the yielding transition in granular media

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 $γ_{\rm ms}(Σ,L)$. The number density of MS packings ($\propto γ_{\rm ms}^{-1}$) vanishes for $Σ> Σ_c \approx 0.11$ according to a critical scaling form with a length scale $ξ\propto |Σ- Σ_c|^{-ν}$, where $ν\approx 1.7-1.8$. Above the yield stress ($Σ>Σ_c$), no MS packings that can support $Σ$ exist in the large system limit, $L/ξ\gg 1$. MS packings generated via shear possess anisotropic force and contact networks, suggesting that $Σ_c$ is associated with an upper limit in the degree to which these networks can be deformed away from those for isotropic packings.

cond-mat.soft↗

arXiv2018

Jamming of Deformable Polygons

There are two main classes of physics-based models for two-dimensional cellular materials: packings of repulsive disks and the vertex model. These models have several disadvantages. For example, disk interactions are typically a function of particle overlap, yet the model assumes that the disks remain circular during overlap. The shapes of the cells can vary in the vertex model, however, the packing fraction is fixed at $ϕ=1$. Here, we describe the deformable particle model (DPM), where each particle is a polygon composed of a large number of vertices. The total energy includes three terms: two quadratic terms to penalize deviations from the preferred particle area $a_0$ and perimeter $p_0$ and a repulsive interaction between DPM polygons that penalizes overlaps. We performed simulations to study the onset of jamming in packings of DPM polygons as a function of asphericity, ${\cal A} = p_0^2/4πa_0$. We show that the packing fraction at jamming onset $ϕ_J({\cal A})$ grows with increasing ${\cal A}$, reaching confluence at ${\cal A} \approx 1.16$. ${\cal A}^*$ corresponds to the value at which DPM polygons completely fill the cells obtained from a surface-Voronoi tessellation. Further, we show that DPM polygons develop invaginations for ${\cal A} > {\cal A}^*$ with excess perimeter that grows linearly with ${\cal A}-{\cal A}^*$. We confirm that packings of DPM polygons are solid-like over the full range of ${\cal A}$ by showing that the shear modulus is nonzero.

cond-mat.soft↗

arXiv2017

Hypostatic jammed packings of frictionless nonspherical particles

We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, and dumbbells to determine which shapes form hypostatic versus isostatic packings and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naïve constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and -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 master-like form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity ${\cal A}$, 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 ${\cal A}$. 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. 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.

cond-mat.soft↗

arXiv2017

Local and global avalanches in a 2D sheared granular medium

We present the experimental and numerical studies of a 2D sheared amorphous material constituted of bidisperse photo-elastic 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 cut-offs vary with inter-particle 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 from the shear bands. A simple relation independent from 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 meanfield and depinning theories.

cond-mat.soft↗

arXiv2017

Determining the Onset of Hydrodynamic Erosion in Turbulent Flow

We revisit the longstanding question of the onset of sediment transport driven by a turbulent fluid flow via laboratory measurements. We use particle tracking velocimetry to quantify the fluid flow as well as the motion of individual grains. As we increase the flow speed above the transition to sediment transport, we observe that an increasing fraction of grains are transported downstream, although the average downstream velocity of the transported grains remains roughly constant. However, we find that the fraction of mobilized grains does not vanish sharply at a critical flow rate. Additionally, the distribution of the fluctuating velocities of non-transported grains becomes broader with heavier tails, meaning that unambiguously separating mobile and static grains is not possible. As an alternative approach, we quantify the statistics of grain velocities by using a mixture model consisting of two forms for the grain velocities: a decaying-exponential tail, which represents grains transported downstream, and a peaked distribution centered at zero velocity, which represents grains that fluctuate due to the turbulent flow but remain in place. Our results suggest that more sophisticated statistical measures may be required to quantify grain motion near the onset of sediment transport, particularly in the presence of turbulence.

physics.flu-dyn↗

arXiv2017

Particle rearrangement and softening contributions to the nonlinear mechanical response of glasses

Amorphous materials such as metallic, polymeric, and colloidal glasses, exhibit complex preparation-dependent mechanical response to applied shear. 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 $\langleσ(γ)\rangle$ 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 at intermediate strain, and a plastic flow regime at large strains. In contrast, for each glass configuration in the ensemble, the stress-strain curve consists of many short nearly linear segments that are punctuated by particle-rearrangement-induced rapid stress drops. We quantify the shape of the small stress-strain segments, as well as the frequency and size of the stress drops in each glass configuration. We decompose the stress loss into the loss from particle rearrangements and 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 the large system-size limit.

cond-mat.stat-mech↗

arXiv2017

The role of grain dynamics in determining the onset of sediment transport

Sediment transport occurs when the nondimensional fluid shear stress $Θ$ at the bed surface exceeds a minimum value $Θ_c$. A large collection of data, known as the Shields curve, shows that $Θ_c$ is primarily a function of the shear Reynolds number ${\rm{Re}}_*$. It is commonly assumed that $Θ>Θ_c({\rm{Re}}_*)$ occurs when the ${\rm Re}_*$-dependent fluid forces are too large to maintain static equilibrium for a typical surface grain. A complimentary approach, which remains relatively unexplored, is to identify $Θ_c({\rm{Re}}_*)$ as the applied shear stress at which grains cannot stop moving. With respect to grain dynamics, ${\rm{Re}}_*$ can be viewed as the viscous time scale for a grain to equilibrate to the fluid flow divided by the typical time for the fluid force to accelerate a grain over the characteristic bed roughness. We performed simulations of granular beds sheared by a model fluid, varying only these two time scales. We find that the critical Shields number $Θ_c({\rm Re}_*)$ obtained from the model mimics the Shields curve and is insensitive to the grain properties, the model fluid flow, and the form of the drag law. Quantitative discrepancies between the model results and the Shields curve are consistent with previous calculations of lift forces at varying ${\rm Re}_*$. Grains at low ${\rm Re}_*$ find more stable configurations than those at high ${\rm{Re}}_*$ due to differences in the grain reorganization dynamics. Thus, instead of focusing on mechanical equilibrium of a typical grain at the bed surface, $Θ_c({\rm{Re}}_*)$ may be better described by the stress at which mobile grains cannot find a stable configuration and stop moving.

cond-mat.soft↗