arXiv subjects

Corey S. O'Hern

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

At least 37 records · Page 2Linked to original sources

arXiv2023

Mechanical Plasticity of Cell Membranes Enhances Epithelial Wound Closure

During epithelial wound healing, cell morphology near the healed wound and the healing rate vary strongly among different developmental stages even for a single species like \textit{Drosophila}. We develop deformable particle (DP) model simulations to understand how variations in cell mechanics give rise to distinct wound closure phenotypes in the \textit{Drosophila} embryonic ectoderm and larval wing disc epithelium. We find that plastic deformation of the cell membrane can generate large changes in cell shape consistent with wound closure in the embryonic ectoderm. Our results show that the embryonic ectoderm is best described by cell membranes with an elasto-plastic response, whereas the larval wing disc is best described by cell membranes with an exclusively elastic response. By varying the mechanical response of cell membranes in DP simulations, we recapitulate the wound closure behavior of both the embryonic ectoderm and the larval wing disc.

physics.bio-ph↗

arXiv2023

Modeling the effects of varying Ti concentration on the mechanical properties of Cu-Ti alloys

The mechanical properties of Cu-Ti alloys have been characterized extensively through experimental studies. However, a detailed understanding of why the strength of Cu increases after a small fraction of Ti atoms is added to the alloy is still missing. In this work, we address this question using density functional theory (DFT) and molecular dynamics (MD) simulations with modified embedded atom method (MEAM) interatomic potentials. First, we performed calculations of uniaxial tension deformations of small bicrystalline Cu cells using DFT static simulations. We then carried out uniaxial tension deformations on much larger bicrystalline and polycrystalline Cu cells using MEAM MD simulations. In bicrystalline Cu, the inclusion of Ti increases the grain boundary separation energy and maximum tensile stress. The DFT calculations demonstrate that the increase in tensile stress can be attributed to an increase in the local charge density arising from Ti. MEAM simulations in larger bicrystalline systems have shown that increasing the Ti concentration decreases the density of stacking faults. This observation is enhanced in polycrystalline Cu, where the addition of Ti atoms, even at concentrations as low as 1.5 at.%, increases the yield strength and elastic modulus of the material compared to pure Cu. Under uniaxial tensile loading, the addition of small amounts of Ti hinders the formation of partial Shockley dislocations in the grain boundaries of Cu, leading to reduced local deformation. These results shed light on the role of Ti in determining the mechanical properties of polycrystalline Cu and will enable the engineering of grain boundaries and the inclusion of Ti to improve degradation resistance.

cond-mat.mtrl-sci↗

arXiv2023

The connection between polymer collapse and the onset of jamming

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 attractive systems quenched to temperatures below the glass transition $T \ll T_g$ 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 contacts $N_c$ matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymers are hypostatic at jamming onset, but effectively isostatic when including quartic modes. While attractive disk and polymer packings are hyperstatic, 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 ${\it isostatic}$ 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.

cond-mat.soft↗

arXiv2023

Designing the pressure-dependent shear modulus using tessellated granular metamaterials

Jammed packings of granular materials display complex mechanical response. For example, the ensemble-averaged shear modulus $\left\langle G \right\rangle$ 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 {\it or} decrease with pressure without particle rearrangements even in the large-system limit. To do this, we construct {\it 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, $λ_c < 0$ for all packings in single cells with PBC where the number of particles per cell $N \ge 6$. In contrast, single cells with FXW and FLW can possess $λ_c > 0$, as well as $λ_c < 0$, for $N \le 16$. We show that we can force the mechanical properties of multi-cell granular metamaterials to possess those of single cells by constraining the endpoints of the outer walls and enforcing an affine shear response. These studies demonstrate that tessellated granular metamaterials provide a novel platform for the design of soft materials with specified mechanical properties.

cond-mat.soft↗

arXiv2023

Universal Mechanical Polycomputation in Granular Matter

Unconventional computing devices are increasingly of interest as they can operate in environments hostile to silicon-based electronics, or compute in ways that traditional electronics cannot. Mechanical computers, wherein information processing is a material property emerging from the interaction of components with the environment, are one such class of devices. This information processing can be manifested in various physical substrates, one of which is granular matter. In a granular assembly, vibration can be treated as the information-bearing mode. This can be exploited to realize "polycomputing": materials can be evolved such that a single grain within them can report the result of multiple logical operations simultaneously at different frequencies, without recourse to quantum effects. Here, we demonstrate the evolution of a material in which one grain acts simultaneously as two different NAND gates at two different frequencies. NAND gates are of interest as any logical operations can be built from them. Moreover, they are nonlinear thus demonstrating a step toward general-purpose, computationally dense mechanical computers. Polycomputation was found to be distributed across each evolved material, suggesting the material's robustness. With recent advances in material sciences, hardware realization of these materials may eventually provide devices that challenge the computational density of traditional computers.

cs.ET↗

arXiv2023

Tessellated granular metamaterials with tunable elastic moduli

Most granular packings possess shear moduli ($G$) that increase with the applied external pressure, and bulk moduli ($B$) that increase or remain constant with pressure. This paper presents "tessellated" granular metamaterials for which both $G$ and the ratio $G/B$ decrease with increasing pressure. The granular metamaterials are made from flexible tessellations forming a ring of closed cells, each containing a small number of solid particles. For under-constrained tessellations, the dominant contributions to $G$ and $B$ are the particle-particle and particle-cell interactions. With specific particle configurations in the cells, we limit the number of possible particle rearrangements to achieve decreasing $G$ as we increase the pressure difference between the inside and outside of the tessellation, leading to $G/B \ll 1$ at large pressures. We further study tessellated granular metamaterials with cells containing a single particle and many particles to determine the variables that control the mechanical response of particle-filled tessellations as a function of pressure.

cond-mat.soft↗

arXiv2023

Characterizing the mechanical response of metallic glasses to uniaxial tension using a spring network model

Metallic glasses are frequently used as structural materials. Therefore, it is important to develop methods to predict their mechanical response as a function of the microstructure prior to loading. We develop a coarse-grained spring network model, which describes the mechanical response of metallic glasses using an equivalent series network of springs, which can break and re-form to mimic atomic rearrangements during deformation. To validate the model, we perform simulations of quasistatic, uniaxial tension of Lennard-Jones and embedded atom method (EAM) potentials for Cu$_{50}$Zr$_{50}$ metallic glasses. We consider samples prepared using a wide range of cooling rates and with different amounts of crystalline order. We show that both the Lennard-Jones and EAM models possess qualitatively similar stress $σ$ versus strain $γ$ curves. By specifying five parameters in the spring network model (ultimate strength, strain at ultimate strength, slopes of $σ(γ)$ at $γ=0$ and at large strain, and strain at fracture where $σ=0$), we can accurately describe the form of the stress-strain curves during uniaxial tension for the computational studies of Cu$_{50}$Zr$_{50}$, as well as recent experimental studies of several Zr-based metallic glasses. For the computational studies of Cu$_{50}$Zr$_{50}$, we find that the yield strain distribution is shifted to larger strains for slowly cooled glasses compared to rapidly cooled glasses. In addition, the average number of new springs and their rate of formation decreases with decreasing cooling rate. These effects offset each other at large strains, causing the stress-strain curve to become independent of the sample preparation protocol in this regime. In future studies, we will extract the parameters that define the spring network model directly from atomic rearrangements that occur during uniaxial deformation.

cond-mat.mtrl-sci↗

arXiv2022

The Jamming Transition and the Marginally Stable Solid

We review the physics of jamming from the theoretical, experimental and numerical perspectives. We summarize the mean-field theory of jamming and the marginally stable solid phase, with particular emphasis on the connection with the Replica Symmetry Breaking theory of glasses. We report validations of the mean-field theory of jamming from experimental and numerical studies of critical behaviors near the transition. In particular, we describe the physics of jamming of frictionless, spherical particles, as well as more recent work on jamming of frictionless, non-spherical particles and frictional, nearly spherical particles. We also present current efforts in expanding the mean-field theory to systems that more closely resemble externally driven granular media, cell aggregates, and active colloidal suspensions.

cond-mat.soft↗

arXiv2022

Localized growth drives spongy mesophyll morphogenesis

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 cells remain mechanically stable remains unknown. Here, we used computer simulations of deformable particles to develop a purely mechanical model for the development of the spongy mesophyll tissue. By stipulating that (1) cell perimeter grows only near voids, (2) cells both form and break adhesive bonds, and (3) the tissue pressure remains constant, the computational model was able to recapitulate the developmental trajectory of the microstructure of the spongy mesophyll observed in Arabidopsis thaliana leaves. Robust generation of pore space in the spongy mesophyll requires a balance of cell growth, adhesion, stiffness and tissue pressure to ensure cell networks remain both porous yet mechanically robust. The success of this mechanical model of tissue growth and porosity evolution suggests that simple physical principles can coordinate and drive the development of complex plant tissues like the spongy mesophyll.

physics.bio-ph↗

arXiv2022

Evolving Programmable Computational Metamaterials

Granular metamaterials are a promising choice for the realization of mechanical computing devices. As preliminary evidence of this, we demonstrate here how to embed Boolean logic gates (AND and XOR) into a granular metamaterial by evolving where particular grains are placed in the material. Our results confirm the existence of gradients of increasing "AND-ness" and "XOR-ness" within the space of possible materials that can be followed by evolutionary search. We measure the computational functionality of a material by probing how it transforms bits encoded as vibrations with zero or non-zero amplitude. We compared the evolution of materials built from mass-contrasting particles and materials built from stiffness-contrasting particles, and found that the latter were more evolvable. We believe this work may pave the way toward evolutionary design of increasingly sophisticated, programmable, and computationally dense metamaterials with certain advantages over more traditional computational substrates.

cs.ET↗

arXiv2022

Universal mechanical response of metallic glasses during strain-rate-dependent uniaxial compression

Experimental data on the compressive strength $σ_{\rm max}$ versus strain rate ${\dot \varepsilon}_{\rm eng}$ for metallic glasses undergoing uniaxial compression shows significantly different behavior for different alloys. For some metallic glasses, $σ_{\rm max}$ decreases with increasing ${\dot \varepsilon}_{\rm eng}$, for others, $σ_{\rm max}$ increases with increasing ${\dot \varepsilon}_{\rm eng}$, and for others $σ_{\rm max}$ versus ${\dot \varepsilon}_{\rm eng}$ is nonmonotonic. Using numerical simulations of metallic glasses undergoing uniaxial compression at nonzero strain rate and temperature, we show that they obey a universal relation for the compressive strength versus temperature, which determines their mechanical response. At low ${\dot \varepsilon}_{\rm eng}$, increasing strain rate leads to increases in temperature and decreases in $σ^*_{\rm max}$, whereas at high ${\dot \varepsilon}_{\rm eng}$, increasing strain rate leads to decreases in temperature and increases in $σ^*_{\rm max}$. This non-monotonic behavior of $σ^*_{\rm max}$ versus temperature causes the nonmonotonic behavior of $σ^*_{\rm max}$ versus ${\dot \varepsilon}_{\rm eng}$. Variations in the internal dissipation change the characteristic strain rate at which the nonmonotonic behavior occurs. These results are general for a wide range of metallic glasses with different atomic interactions, damping coefficients, and chemical compositions.

cond-mat.soft↗

arXiv2022

The glass-forming ability of binary Lennard-Jones systems

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 $ε_\_$ and mixing energy $\bar ε_{AB}$ between particles A and B. We find several important results. First, the $\log_{10} R_c$ contours in the $\bar ε_{AB}$-$ε_\_$ 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 $\bar ε_{AB}$-$ε_\_$ 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, $d_M(ε_\_,\bar ε_{AB})$ 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.

cond-mat.mtrl-sci↗

arXiv2022

Core packing of well-defined x-ray and NMR structures is the same

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 to 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 side chain 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.

q-bio.BM↗

arXiv2021

The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions

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 $\langle G \rangle \sim P^β$, with $β\approx 0.75$ for jammed packings of deformable particles with zero bending energy. In contrast, $β\approx 0.5$ 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.

cond-mat.soft↗

arXiv2021

Bridging particle deformability and collective response in soft solids

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.

cond-mat.soft↗

arXiv2020

Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies, it is unclear whether molecular dynamics (MD) simulations can accurately recapitulate protein conformations. We therefore perform extensive MD simulations across multiple force fields and sampling techniques to investigate the degree to which computer simulations can capture the ensemble of conformations observed in experiments. By analyzing fluctuations in the atomic coordinates and core packing, we show that conformations sampled in MD simulations both move away from and sample a larger conformational space than the ensemble of structures observed in NMR experiments. However, we find that adding inter-residue distance restraints that match those obtained via Nuclear Overhauser Effect measurements enables the MD simulations to sample more NMR-like conformations, though significant differences between the core packing features in restrained MD and the NMR ensemble remain. Given that the protein structures obtained from the MD simulations possess smaller and less dense protein cores compared to those solved by NMR, we suggest that future improvements to MD forcefields should aim to increase the packing of hydrophobic residues in protein cores.

physics.bio-ph↗

arXiv2020

Shear response of granular packings compressed above jamming onset

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 $\langle G \rangle$ increases with pressure $P$ as $\sim P^{(α-3/2)/(α-1)}$ 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: $G^{(1)}/G_0 = (P/P_0)^{(α-2)/(α-1)} - P/P_0$, where $P_0 \sim N^{-2(α-1)}$ is a characteristic pressure that separates the two power-law scaling regions and $G_0 \sim N^{-2(α-3/2)}$. 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 $a \approx (α-2)/(α-1)$ in the $P \rightarrow 0$ limit and $\langle G \rangle \sim (P/P_c)^b$, where $b \gtrsim (α-3/2)/(α-1)$ 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 $P >P_c$.

cond-mat.soft↗

arXiv2020

Homogeneous crystallization in cyclically sheared frictionless grains

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 $ϕ= 0.646 \pm 0.001$. This result indicates that neither friction nor gravity is essential for homogeneous crystallization in driven granular media.

cond-mat.soft↗