The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity.

The physical nature of the bacterial cytoplasm is poorly understood even though it determines cytoplasmic dynamics and hence cellular physiology and behavior. Through single-particle tracking of protein filaments, plasmids, storage granules, and foreign particles of different sizes, we find that the bacterial cytoplasm displays properties that are characteristic of glass-forming liquids and changes from liquid-like to solid-like in a component size-dependent fashion. As a result, the motion of cytoplasmic components becomes disproportionally constrained with increasing size. Remarkably, cellular metabolism fluidizes the cytoplasm, allowing larger components to escape their local environment and explore larger regions of the cytoplasm. Consequently, cytoplasmic fluidity and dynamics dramatically change as cells shift between metabolically active and dormant states in response to fluctuating environments. Our findings provide insight into bacterial dormancy and have broad implications to our understanding of bacterial physiology, as the glassy behavior of the cytoplasm impacts all intracellular processes involving large components.

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

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.

Hopper flows of deformable particles.

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 ∼ (w/σavg - k)ß, where σavg is the average particle diameter, kσavg is an offset where Q ∼ 0, the power-law scaling exponent ß = 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 ß. 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 ß varies continuously with the ratio of the viscous drag to the kinetic friction coefficient, λ = ζ/µ. ß = d - 1/2 in the λ → 0 limit and d - 3/2 in the λ → ∞ limit, with a midpoint λc that depends on the hopper opening angle θw. We also characterize the spatial structure of the flows and associate changes in spatial structure of the hopper flows to changes in the exponent ß. The offset k increases with particle stiffness until k ∼ kmax in the hard-particle limit, where kmax ∼ 3.5 is larger for λ → ∞ compared to that for λ → 0. Finally, we show that the simulations of hopper flows of deformable particles in the λ → ∞ limit recapitulate the experimental results for quasi-2D hopper flows of oil droplets in water.

Using delaunay triangularization to characterize non-affine displacement fields during athermal, quasistatic deformation of amorphous solids.

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 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 〈G〉 scales with pressure P as 〈G〉 ∼ Pß, with ß ≈ 0.75 for jammed packings of deformable particles with zero bending energy. In contrast, ß ≈ 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.

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 side-chain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modeling 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.

Pressure Dependent Shear Response of Jammed Packings of Frictionless 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 ⟨G-G_{0}⟩ scales with p^{α}, where α≈1, but above a characteristic pressure p^{**}, ⟨G-G_{0}⟩∼p^{ß}, where ß≈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 p>p^{**}, geometrical-family and rearrangement contributions to ⟨G⟩ are of opposite signs and remain comparable for all system sizes. ⟨G⟩ can be described by a scaling function that smoothly transitions between two power-law exponents α and ß. We also demonstrate the phenomenon of compression unjamming, where a jammed packing unjams via isotropic compression.

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 via Newtonian dynamics with linear viscous drag at fixed vertical load. We show that for sufficiently small strain amplitudes, cyclic shear gives rise to homogeneous crystallization at a volume fraction ϕ=0.646±0.001. This result indicates that neither friction nor gravity is essential for homogeneous crystallization in driven granular media. Understanding how crystal formation is initiated within a homogeneous disordered state gives key insights into the old open problem of glass formation in fluids.

Contact network changes in ordered and disordered disk packings.

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.

Jammed packings of 3D superellipsoids with tunable packing fraction, coordination 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 superellipsoid packings are hypostatic, with coordination number zJ < ziso, where ziso = 2df and df = 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 depends on at least two particle shape parameters, e.g. the asphericity A and reduced aspect ratio ß of the particles.

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 deformable particle (DP) model that we developed for 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 compare the structural and mechanical properties of jammed packings generated using the SP and DP models as a function of the packing fraction ρ, instead of the reduced number density φ. We show that near jamming onset the excess contact number Δz = z - zJ and shear modulus G scale as Δρ0.5 in the large system limit for both models, where Δρ = ρ - ρJ and zJ ≈ 4 and ρJ ≈ 0.842 are the values at jamming onset. Δz and G for the SP and DP models begin to differ for ρ ⪆ 0.88. In this regime, Δz ∼ G can be described by a sum of two power-laws in Δρ, i.e. Δz ∼ G ∼ C0Δρ0.5 + C1Δρ1.0 to lowest order. We show that the ratio C1/C0 is much larger for the DP model compared to that for the SP model. We also characterize the void space in jammed packings as a function of ρ. We find that the DP model can describe the formation of Plateau borders as ρ → 1. We further show that the results for z and the shape factor A versus ρ for the DP model agree with recent experimental studies of foams and emulsions.

Intrinsic dissipation mechanisms in metallic glass resonators.

Micro- and nanoresonators 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 material class for micro- and nanoscale resonators since they are amorphous and can be fabricated precisely into complex shapes on these length scales. 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 at low temperatures. We calculate the power spectrum of the kinetic energy, redistribution of energy from the fundamental mode of vibration, and Q vs the kinetic energy per atom K of the excitation. In the harmonic and anharmonic response regimes where there are no atomic rearrangements, we find that Q → ∞ over the time periods we consider (since we do not consider coupling to the environment). We identify a characteristic Kr above which atomic rearrangements occur, and there is significant energy leakage from the fundamental mode to higher frequencies, causing finite Q. Thus, Kr is a critical parameter determining resonator performance. We show that Kr decreases as a power-law, Kr ∼ N-k, with increasing system size N, where k ≈ 1.3. We estimate the critical strain ⟨γr⟩∼ 10-8 for micrometer-sized resonators below which atomic rearrangements do not occur in the millikelvin temperature range, and thus, large Q-values can be obtained when they are operated below γr. We also find that Kr for amorphous resonators is comparable to that for resonators with crystalline order.

Jamming of Deformable Polygons.

We introduce the deformable particle (DP) model for cells, foams, emulsions, and other soft particulate materials, which adds to the benefits and eliminates deficiencies of existing models. The DP model combines the ability to model individual soft particles with the shape-energy function of the vertex model, and adds arbitrary particle deformations. We focus on 2D deformable polygons with a shape-energy function that is minimized for area a_{0} and perimeter p_{0} and repulsive interparticle forces. We study the onset of jamming versus particle asphericity, A=p_{0}^{2}/4πa_{0}, and find that the packing fraction grows with A until reaching A^{*}=1.16 of the underlying Voronoi cells at confluence. We find that DP packings above and below A^{*} are solidlike, which helps explain the solid-to-fluid transition at A^{*} in the vertex model as a transition from tension- to compression-dominated regimes.

Understanding the physical basis for the side-chain conformational preferences of methionine.

Methionine (Met) is a structurally versatile amino acid most commonly found in protein cores and at protein-protein interfaces. Thus, a complete description of the structure of Met is important for a fundamental understanding of protein structure and design. In previous work, we showed that the hard-sphere dipeptide model is able to recapitulate the side-chain dihedral angle distributions observed in high-resolution protein crystal structures for the nine amino acids we have studied to date: Val, Thr, Ser, Leu, Ile, Cys, Tyr, Trp, and Phe. Using the same approach, we are also able to predict the observed χ1 and χ2 side-chain dihedral angle distributions for Met. However, the form of the side-chain dihedral angle distribution P(χ3 ) predicted by the hard-sphere model does not match the observed distribution. We investigate the possible origins of the discrepancy and find that specific bond lengths and angles in Met side chains strongly influence P(χ3 ). We then identify minimal additions to the hard-sphere dipeptide model necessary to quantitatively predict P(χ3 ) of Met, and its near isosteres norleucine (Nle) and selenomethionine (Mse). We find that adding weak attractive interactions between hydrogen atoms to the model is sufficient to achieve predictions for P(χ3 ) that closely match the observed P(χ3 ) distributions for Met, Nle, and Mse. We explicitly show that weak attractive interactions between hydrogens do not negatively affect the agreement between the predicted and observed side-chain dihedral angle distribution for Val, Leu, Ile, and Phe, as we expect for other amino acids. Proteins 2016; 84:900-911. © 2016 Wiley Periodicals, Inc.

Equilibrium transitions between side-chain conformations in leucine and isoleucine.

Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different χ(1) and χ(2) dihedral angle combinations as a function of the backbone dihedral angles ϕ and ψ. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of χ(2), the Leu side-chain bond angles κ(1) and κ(2) must increase, whereas to transition in χ(1), the Ile bond angles λ(1) and λ(2) must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design.

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

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

Protein design: Past, present, and future.

Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental features of protein structure and stability. We are now in the era that the early work presaged - the design of new proteins with practical applications and uses. Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations.

The glass-forming ability of model metal-metalloid alloys.

Bulk metallic glasses (BMGs) are amorphous alloys with desirable mechanical properties and processing capabilities. To date, the design of new BMGs has largely employed empirical rules and trial-and-error experimental approaches. Ab initio computational methods are currently prohibitively slow to be practically used in searching the vast space of possible atomic combinations for bulk glass formers. Here, we perform molecular dynamics simulations of a coarse-grained, anisotropic potential, which mimics interatomic covalent bonding, to measure the critical cooling rates for metal-metalloid alloys as a function of the atomic size ratio σS/σL and number fraction xS of the metalloid species. We show that the regime in the space of σS/σL and xS where well-mixed, optimal glass formers occur for patchy and LJ particle mixtures, coincides with that for experimentally observed metal-metalloid glass formers. Thus, our simple computational model provides the capability to perform combinatorial searches to identify novel glass-forming alloys.

On the origin of multi-component bulk metallic glasses: Atomic size mismatches and de-mixing.

The likelihood that an undercooled liquid vitrifies or crystallizes depends on the cooling rate R. The critical cooling rate R(c), below which the liquid crystallizes upon cooling, characterizes the glass-forming ability (GFA) of the system. While pure metals are typically poor glass formers with R(c)>10(12)K/s, specific multi-component alloys can form bulk metallic glasses (BMGs) even at cooling rates below R∼1 K/s. Conventional wisdom asserts that metal alloys with three or more components are better glass formers (with smaller R(c)) than binary alloys. However, there is currently no theoretical framework that provides quantitative predictions for R(c) for multi-component alloys. In this manuscript, we perform simulations of ternary hard-sphere systems, which have been shown to be accurate models for the glass-forming ability of BMGs, to understand the roles of geometric frustration and demixing in determining R(c). Specifically, we compress ternary hard sphere mixtures into jammed packings and measure the critical compression rate, below which the system crystallizes, as a function of the diameter ratios σ(B)/σ(A) and σ(C)/σ(A) and number fractions x(A), x(B), and x(C). We find two distinct regimes for the GFA in parameter space for ternary hard spheres. When the diameter ratios are close to 1, such that the largest (A) and smallest (C) species are well-mixed, the GFA of ternary systems is no better than that of the optimal binary glass former. However, when σ(C)/σ(A) ≲ 0.8 is below the demixing threshold for binary systems, adding a third component B with σ(C) < σ(B) < σ(A) increases the GFA of the system by preventing demixing of A and C. Analysis of the available data from experimental studies indicates that most ternary BMGs are below the binary demixing threshold with σ(C)/σ(A) < 0.8.

Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses.

When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate Rc, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. Rc (or the corresponding critical casting thickness dc) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small Rc < 10(-2) K/s, pure metals and most alloys are typically poor glass-formers with large Rc > 10(10) K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with Rc approaching that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for designing BMGs with cm or greater casting thickness.