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The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll must develop from an initially confluent tissue into a tortuous network of cells with a large proportion of intercellular airspace. How the airspace in the spongy mesophyll develops while the tissue remains mechanically stable is unknown. Here, we use computer simulations of deformable polygons to develop a purely mechanical model for the development of the spongy mesophyll tissue. By stipulating that cell wall growth and remodelling occurs only near void space, our computational model is able to recapitulate spongy mesophyll development observed in Arabidopsis thaliana leaves. We find that robust generation of pore space in the spongy mesophyll requires a balance of cell growth, adhesion, stiffness and tissue pressure to ensure cell networks become porous yet maintain mechanical stability. The success of this mechanical model of morphogenesis suggests that simple physical principles can coordinate and drive the development of complex plant tissues like the spongy mesophyll.

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 $\langle G\rangle = (1-{\cal F}_-) \langle G_+ \rangle + {\cal F}_- \langle G_-\rangle$, where ${\cal F}_-$ is the fraction of jammed packings with negative shear moduli and $\langle G_+\rangle$ and $\langle G_-\rangle$ are the average values from packings with positive and negative moduli, respectively. We show that $\langle G_+\rangle$ and $\langle|G_-|\rangle$ obey different power-law scaling relations above and below $pN^2 \sim 1$. We then calculate analytically that ${\cal P}(G)$ is a Gamma distribution in the $pN^2 \ll 1$ limit. As $pN^2$ increases, the skewness of ${\cal P}(G)$ decreases and ${\cal P}(G)$ becomes a skew-normal distribution with negative skewness in the $pN^2 \gg 1$ limit. We also partition jammed disk packings into subsystems using Delanunay 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 $C({\vec r})$ displays weak correlations for $pn_{\rm sub}^2 < 10^{-2}$, where $n_{\rm sub}$ is the number of particles within each subsystem. However, $C({\vec r})$ begins to develop long-ranged spatial correlations with four-fold angular symmetry for $pn_{\rm sub}^2 \gtrsim 10^{-2}$., 17 pages, 21 figures

Numerous experimental and computational studies show that continuous hopper flows of granular materials obey the Beverloo equation that relates the volume flow rate $Q$ and the orifice width $w$: $Q \sim (w/\sigma_{\rm avg}-k)^{\beta}$, where $\sigma_{\rm avg}$ is the average particle diameter, $k\sigma_{\rm avg}$ is an offset where $Q\sim 0$, the power-law scaling exponent $\beta=d-1/2$, and $d$ is the spatial dimension. Recent studies of hopper flows of deformable particles in different background fluids suggest that the particle stiffness and dissipation mechanism can also strongly affect the power-law scaling exponent $\beta$. We carry out computational studies of hopper flows of deformable particles with both kinetic friction and background fluid dissipation in two and three dimensions. We show that the exponent $\beta$ varies continuously with the ratio of the viscous drag to the kinetic friction coefficient, $\lambda=\zeta/\mu$. $\beta = d-1/2$ in the $\lambda \rightarrow 0$ limit and $d-3/2$ in the $\lambda \rightarrow \infty$ limit, with a midpoint $\lambda_c$ that depends on the hopper opening angle $\theta_w$. We also characterize the spatial structure of the flows and associate changes in spatial structure of the hopper flows to changes in the exponent $\beta$. The offset $k$ increases with particle stiffness until $k \sim k_{\rm max}$ in the hard-particle limit, where $k_{\rm max} \sim 3.5$ is larger for $\lambda \rightarrow \infty$ compared to that for $\lambda \rightarrow 0$. Finally, we show that the simulations of hopper flows of deformable particles in the $\lambda \rightarrow \infty$ limit recapitulate the experimental results for quasi-2D hopper flows of oil droplets in water., Comment: 15 pages, 12 figures

Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by X-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared with those of high-resolution X-ray crystal structures. Our current work investigates this result in more detail and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and sidechain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by X-ray crystallography at high resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and X-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments.

We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D). Each 3D deformable particle is modeled as a surface-triangulated polyhedron, with spherical vertices whose positions are determined by a shape-energy function with terms that constrain the particle surface area, volume, and curvature, and prevent interparticle overlap. We show that jammed packings of deformable particles without bending energy possess low-frequency, quartic vibrational modes, whose number decreases with increasing asphericity and matches the number of missing contacts relative to the isostatic value. In contrast, jammed packings of deformable particles with non-zero bending energy are isostatic in 3D, with no quartic modes. We find that the contributions to the eigenmodes of the dynamical matrix from the shape degrees of freedom are significant over the full range of frequency and shape parameters for particles with zero bending energy. We further show that the ensemble-averaged shear modulus $\langle G \rangle$ scales with pressure $P$ as $\langle G \rangle \sim P^{\beta}$, with $\beta \approx 0.75$ for jammed packings of deformable particles with zero bending energy. In contrast, $\beta \approx 0.5$ for packings of deformable particles with non-zero bending energy, which matches the value for jammed packings of soft, spherical particles with fixed shape. These studies underscore the importance of incorporating particle deformability and shape change when modeling the properties of jammed soft materials.

The glass-forming ability (GFA) of alloys, colloidal dispersions, and other particulate materials, as measured by the critical cooling rate $R_c$, can span more than ten orders of magnitude. Even after numerous previous studies, the physical features that control the GFA are still not well understood. For example, it is well-known that mixtures are better glass-formers than monodisperse systems and that particle size and cohesive energy differences among constituents improve the GFA, but it is not currently known how particle size differences couple to cohesive energy differences to determine the GFA. We perform molecular dynamics simulations to determine the GFA of equimolar, binary Lennard-Jones (LJ) mixtures versus the normalized cohesive energy difference $\epsilon_\_$ and mixing energy $\bar \epsilon_{AB}$ between particles A and B. We find several important results. First, the $\log_{10} R_c$ contours in the $\bar \epsilon_{AB}$-$\epsilon_\_$ plane are ellipsoidal for all diameter ratios, and thus $R_c$ is determined by the Mahalanobis distance $d_M$ from a given point in the $\bar \epsilon_{AB}$-$\epsilon_\_$ plane to the center of the ellipsoidal contours. Second, LJ systems for which the larger particles have larger cohesive energy are generally better glass formers than those for which the larger particles have smaller cohesive energy. Third, $d_M(\epsilon_\_,\bar \epsilon_{AB})$ is determined by the relative Voronoi volume difference between particles and local chemical order $S_{AB}$, which gives the average fraction of nearest-neighbor B particles surrounding an A particle and vice-versa. In particular, the shifted Mahalanobis distance $d_M - d^0_M$ versus the shifted chemical order $S_{AB}-S_{AB}^0$ collapses onto a hyperbolic master curve for all diameter ratios.

We investigate the mechanical response of packings of purely repulsive, frictionless disks to quasistatic deformations. The deformations include simple shear strain at constant packing fraction and at constant pressure, "polydispersity" strain (in which we change the particle size distribution) at constant packing fraction and at constant pressure, and isotropic compression. For each deformation, we show that there are two classes of changes in the interparticle contact networks: jump changes and point changes. Jump changes occur when a contact network becomes mechanically unstable, particles "rearrange", and the potential energy (when the strain is applied at constant packing fraction) or enthalpy (when the strain is applied at constant pressure) and all derivatives are discontinuous. During point changes, a single contact is either added to or removed from the contact network. For repulsive linear spring interactions, second- and higher-order derivatives of the potential energy/enthalpy are discontinuous at a point change, while for Hertzian interactions, third- and higher-order derivatives of the potential energy/enthalpy are discontinuous. We illustrate the importance of point changes by studying the transition from a hexagonal crystal to a disordered crystal induced by applying polydispersity strain. During this transition, the system only undergoes point changes, with no jump changes. We emphasize that one must understand point changes, as well as jump changes, to predict the mechanical properties of jammed packings., Comment: 14 pages, 4 figures

We investigate the non-affine displacement fields that occur in two-dimensional Lennard-Jones models of metallic glasses subjected to athermal, quasistatic simple shear (AQS). During AQS, the shear stress versus strain displays continuous quasi-elastic segments punctuated by rapid drops in shear stress, which correspond to atomic rearrangement events. We capture all information concerning the atomic motion during the quasi-elastic segments and shear stress drops by performing Delaunay triangularizations and tracking the deformation gradient tensor Fα associated with each triangle α. To understand the spatio-temporal evolution of the displacement fields during shear stress drops, we calculate Fα along minimal energy paths from the mechanically stable configuration immediately before to that after the stress drop. We find that quadrupolar displacement fields form and dissipate both during the quasi-elastic segments and shear stress drops. We then perform local perturbations (rotation, dilation, simple and pure shear) to single triangles and measure the resulting displacement fields. We find that local pure shear deformations of single triangles give rise to mostly quadrupolar displacement fields, and thus pure shear strain is the primary type of local strain that is activated by bulk, athermal quasistatic simple shear. Other local perturbations, e.g. rotations, dilations, and simple shear of single triangles, give rise to vortex-like and dipolar displacement fields that are not frequently activated by bulk AQS. These results provide fundamental insights into the non-affine atomic motion that occurs in driven, glassy materials.

The effect of grain size on the critical shear stress required to initiate sediment transport in erodible granular beds is typically described by the Shields number which compares the hydrodynamic stress to the particle weight. Although this framework works well for beds composed of grains of the same size, we find that it does not capture the behavior of polydisperse beds. In particular, we find that larger grains are mobilized by nominally subcritical stresses when small grains are present. Our results highlight the importance of granular contact and force networks in controlling the onset of sediment transport.

Functional particles that respond to external stimuli are spurring technological evolution across various disciplines. While large-scale production of functional particles is needed for their use in real-life applications, precise control over particle shapes and directional properties has remained elusive for high-throughput processes. We developed a high-throughput emulsion-based process that exploits rapid vitrification of a thixotropic medium to manufacture diverse functional particles in large quantities. The vitrified medium renders stationary emulsion droplets that preserve their shape and size during solidification, and energetic fields can be applied to build programmed anisotropy into the particles. We showcase mass-production of several functional particles, including low-melting point metallic particles, self-propelling Janus particles, and unidirectionally-magnetized robotic particles, via this static-state particle fabrication process., Upscale fabrication of functionalized microparticles is a pending challenge. Here, Kim et al. exploit the rheology of a thixotropic medium to grind sizeable amounts of raw material into well-defined colloidal dispersions, physically stabilized for further production steps.

Green cooling towers, or thermal green-walls, recirculate hot water flowing through a living plant and porous material. Through convective and evaporative heat and mass transfer they can actively cool a building or an industrial heat waste. Thus they can provide an alternative cooling technology. Thermal green-walls use wetland plant species in highly constructed wetlands selected for their heat tolerance. In addition, they offer such co-benefits as carbon capture and control of local microclimates. Optimal heat rejection (HR) requires the plant rhizosphere to be completely inundated at temperatures much higher than the ambient air temperature, potentially inducing thermal physiological stress. To study the viability of specific plants within a HR system, we exposed three macrophytes, Iris versicolor, Scirpus cyperinus and Carex lurida, to hydroponic recirculating water at three different temperatures (25 °C, 35 °C, and 40 °C). We assessed the plant responses over a period of eight weeks by measuring photochemical efficiency, leaf temperature, stomatal conductance, G s and biomass output. Plant biomass was highest at 35 °C (particularly in I. versicolor), even higher than ambient water temperature at 25 °C. We observed a general homeothermic-like response in G s over a 5-week time period, but the response was species-specific with respect to temperature. Results suggests a possible leaf-level physiological acclimation mechanism as well as high maintenance of tissue moisture that allows macrophytes to tolerate hydro-thermal stress, and support their suitability to perform in HR systems at input temperature, T win = 35 °C.

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, $\ensuremath{\langle}G(P)\ensuremath{\rangle}\ensuremath{\sim}{P}^{\ensuremath{\beta}}$, with $\ensuremath{\beta}\ensuremath{\sim}0.5$, over a wide range of pressure. For packings of circulo-lines, we also find robust power-law scaling of $\ensuremath{\langle}G(P)\ensuremath{\rangle}$ over the same range of pressure for aspect ratios $\mathcal{R}\ensuremath{\gtrsim}1.2$. However, the power-law scaling exponent $\ensuremath{\beta}\ensuremath{\sim}0.8$--0.9 is much larger than that for jammed disk packings. To understand the origin of this behavior, we decompose $\ensuremath{\langle}G\ensuremath{\rangle}$ into separate contributions from geometrical families, ${G}_{f}$, and from changes in the interparticle contact network, ${G}_{r}$, such that $\ensuremath{\langle}G\ensuremath{\rangle}=\ensuremath{\langle}{G}_{f}\ensuremath{\rangle}+\ensuremath{\langle}{G}_{r}\ensuremath{\rangle}$. 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 $\ensuremath{\langle}{G}_{f}\ensuremath{\rangle}$ 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 $\ensuremath{\langle}G(P)\ensuremath{\rangle}$.

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 with dissipative Newtonian dynamics at fixed vertical load. We show that for sufficiently small strain amplitudes, cyclic shear gives rise to homogeneous crystallization at a volume fraction $\phi = 0.646 \pm 0.001$. This result indicates that neither friction nor gravity is essential for homogeneous crystallization in driven granular media., Comment: 5 pages, 4 figures

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., Comment: 6 pages, 5 figures

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 $\alpha$, have found that the ensemble-averaged shear modulus $\langle G \rangle$ increases with pressure $P$ as $\sim P^{(\alpha-3/2)/(\alpha-1)}$ at large pressures. However, a deep theoretical understanding of this scaling behavior is lacking. We show that the shear modulus of jammed packings of frictionless, spherical particles 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. We show that the shear modulus of the first geometrical family for jammed packings can be collapsed onto a master curve: $G^{(1)}/G_0 = (P/P_0)^{(\alpha-2)/(\alpha-1)} - P/P_0$, where $P_0 \sim N^{-2(\alpha-1)}$ is a characteristic pressure that separates the two power-law scaling regions and $G_0 \sim N^{-2(\alpha-3/2)}$. Deviations from this form can occur when there is significant non-affine particle motion near changes in the contact network. We further show that $\langle G (P)\rangle$ is not simply a sum of two power-laws, but $\langle G \rangle \sim (P/P_c)^a$, where $a \approx (\alpha -2)/(\alpha-1)$ in the $P \rightarrow 0$ limit and $\langle G \rangle \sim (P/P_c)^b$, where $b \gtrsim (\alpha -3/2)/(\alpha-1)$ above a characteristic pressure $P_c$. In addition, the magnitudes of both contributions to $\langle G\rangle$ from geometrical families and changes in the contact network remain comparable in the large-system limit for $P >P_c$., Comment: 15 pages, 19 figures

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$_{\alpha}$ 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., Comment: 9 pages, 4 figures

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 $⟨G\ensuremath{-}{G}_{0}⟩$ scales with ${p}^{\ensuremath{\alpha}}$, where $\ensuremath{\alpha}\ensuremath{\approx}1$, but above a characteristic pressure ${p}^{**}$, $⟨G\ensuremath{-}{G}_{0}⟩\ensuremath{\sim}{p}^{\ensuremath{\beta}}$, where $\ensuremath{\beta}\ensuremath{\approx}0.5$. 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, $⟨G⟩$ also depends on a contribution from discontinuous jumps in $⟨G⟩$ that occur at the transitions between geometrical families. For $pg{p}^{**}$, 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 $\ensuremath{\alpha}$ and $\ensuremath{\beta}$. We also demonstrate the phenomenon of compression unjamming, where a jammed packing unjams via isotropic compression.

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., Comment: 7 pages, 5 figures

Soft, amorphous solids such as tissues, foams, and emulsions are composed of deformable particles. However, the effect of single-particle deformability on the collective behavior of soft solids is still poorly understood. We perform numerical simulations of two-dimensional jammed packings of explicitly deformable particles to study the mechanical response of model soft solids. We find that jammed packings of deformable particles with excess shape degrees of freedom possess low-frequency quartic vibrational modes that stabilize the packings even though they possess fewer interparticle contacts than the nominal isostatic value. Adding intra-particle constraints can rigidify the particles, but these particles undergo a buckling transition and gain an effective shape degree of freedom when their preferred perimeter is above a threshold value. We find that the mechanical response of jammed packings of deformable particles with shape degrees of freedom differs significantly from that of jammed packings of rigid-shape particles, which emphasizes the importance of particle deformability in modelling soft solids., Comment: 12 pages total, 6 main figures, 4 appendices, 5 appendix figures

Correction for ‘The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions’ by Dong Wang et al., Soft Matter, 2021, 17, 9901–9915, DOI: 10.1039/D1SM01228B.

We present the structure of an engineered protein–protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close‐packing of the Thr residues, with only one intermonomer hydrogen bond (H‐bond) between two of the Thr residues. This Thr‐rich interface provides a unique opportunity to study the behavior of Thr in the context of many other Thr residues. In previous work, we have shown that the side chain (χ (1)) dihedral angles of interface and core Thr residues can be predicted with high accuracy using a hard sphere plus stereochemical constraint (HS) model. Here, we demonstrate that in the Thr‐rich local environment of the Thr zipper structure, we are able to predict the χ (1) dihedral angles of most of the Thr residues. Some, however, are not well predicted by the HS model. We therefore employed explicitly solvated molecular dynamics (MD) simulations to further investigate the side chain conformations of these residues. The MD simulations illustrate the role that transient H‐bonding to water, in combination with steric constraints, plays in determining the behavior of these Thr side chains. Broader Audience Statement: Protein–protein interactions are critical to life and the search for ways to disrupt adverse protein–protein interactions involved in disease is an ongoing area of drug discovery. We must better understand protein–protein interfaces, both to be able to disrupt existing ones and to engineer new ones for a variety of biotechnological applications. We have discovered and characterized an artificial Thr‐rich protein–protein interface. This novel interface demonstrates a heretofore unknown property of Thr‐rich surfaces: mediating protein–protein interactions.

Structural relaxation during isothermal annealing, quantified by enthalpy recovery of Zr 44 Ti 11 Cu 10 Ni 10 Be 25 towards its metastable equilibrium and correlation to embrittlement, quantified through fracture toughness, K Q , is studied. Enthalpy relaxation over time obeys the Kohlrausch-William-Watts (KWW) stretch exponent with β = 0.74 and τ = 11,000 s. Such β and τ are used to fit experimental K Q ( t ) with KWW, resulting in R 2 = 0.79. This finding combined with a controlled characterization of the glasses' K Q versus temperature, fictive temperature, and their combination, revealed that embrittlement in metallic glasses is predominantly controlled by structural rearrangements, whereas volume changes from thermal expansion have negligible influence.

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these three protein classes. We show that the solvent-inaccessible cores of the three classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (> 90%) as core residues in soluble proteins. We also find that for all three classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA ≲ 0.3, for all three protein classes. Our results show that ≈ 40% of the interface regions in protein complexes are ‘core’, i.e. densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.

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 superellipsoid packings are hypostatic, with coordination number z(J) < z(iso), where z(iso) = 2d(f) and d(f) = 5 or 6 depending on whether the particles are axisymmetric 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 depends on at least two particle shape parameters, e.g. the asphericity [Formula: see text] and reduced aspect ratio β of the particles.

We compare the structural and mechanical properties of mechanically stable (MS) packings of frictional disks in two spatial dimensions (2D) generated with isotropic compression and simple shear protocols from discrete element modeling (DEM) simulations. We find that the average contact number and packing fraction at jamming onset are similar (with relative deviations $$ 0$$ for MS packings generated via simple shear. To investigate the difference in the stress state of MS packings, we develop packing-generation protocols to first unjam the MS packings, remove the frictional contacts, and then rejam them. Using these protocols, we are able to obtain rejammed packings with nearly identical particle positions and stress anisotropy distributions compared to the original jammed packings. However, we find that when we directly compare the original jammed packings and rejammed ones, there are finite stress anisotropy deviations $$\varDelta {{\hat{\varSigma }}}_{xy}$$. The deviations are smaller than the stress anisotropy fluctuations obtained by enumerating the force solutions within the null space of the contact networks generated via the DEM simulations. These results emphasize that even though the compression and shear jamming protocols generate packings with the same contact networks, there can be residual differences in the normal and tangential forces at each contact, and thus differences in the stress anisotropy.

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 $\rho$, instead of the reduced number density $\phi$. We show that near jamming onset the excess contact number $\Delta z=z-z_J$ and shear modulus ${\cal G}$ scale as $\Delta \rho^{0.5}$ in the large system limit for both the SP and DP models, where $\Delta \rho = \rho-\rho_J$ and $z_J \approx 4$ and $\rho_J \approx 0.842$ are the values at jamming onset. $\Delta z$ and ${\cal G}$ for the SP and DP models begin to differ for $\rho \gtrsim 0.88$. In this regime, $\Delta z \sim {\cal G}$ can be described by a sum of two power-laws in $\Delta \rho$, i.e. $\Delta z \sim {\cal G} \sim C_0\Delta \rho^{0.5} +C_1\Delta \rho^{1.0}$ 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 $\rho$. We find that, unlike the SP model, the DP model is able to describe the formation of Plateau borders as the system approaches $\rho = 1$. We further show that the results for $z$ and the shape factor ${\cal A}$ versus $\rho$ for the DP model agree with recent experimental studies of compressed foams and emulsions., Comment: 12 pages, 11 figures, 9 main figures, and 2 supplemental figures

Summary Embryonic organizers establish gradients of diffusible signaling molecules to pattern the surrounding cells. Here, we elucidate an additional mechanism of embryonic organizers that is a secondary consequence of morphogen signaling. Using pharmacological and localized transgenic perturbations, 4D imaging of the zebrafish embryo, systematic analysis of cell motion, and computational modeling, we find that the vertebrate tail organizer orchestrates morphogenesis over distances beyond the range of morphogen signaling. The organizer regulates the rate and coherence of cell motion in the elongating embryo using mechanical information that is transmitted via relay between neighboring cells. This mechanism is similar to a pressure front in granular media and other jammed systems, but in the embryo the mechanical information emerges from self-propelled cell movement and not force transfer between cells. The propagation likely relies upon local biochemical signaling that affects cell contractility, cell adhesion, and/or cell polarity but is independent of transcription and translation.

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.