Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

Local vs. cooperative: Unraveling glass transition mechanisms with SEER.

Which phenomenon slows down the dynamics in supercooled liquids and turns them into glasses is a long-standing question of condensed matter. Most popular theories posit that as the temperature decreases, many events must occur in a coordinated fashion on a growing length scale for relaxation to occur. Instead, other approaches consider that local barriers associated with the elementary rearrangement of a few particles or "excitations" govern the dynamics. To resolve this conundrum, our central result is to introduce an algorithm, Systematic Excitation ExtRaction, which can systematically extract hundreds of excitations and their energy from any given configuration. We also provide a measurement of the activation energy, characterizing the liquid dynamics, based on fast quenching and reheating. We use these two methods in a popular liquid model of polydisperse particles. Such polydisperse models are known to capture the hallmarks of the glass transition and can be equilibrated efficiently up to millisecond time scales. The analysis reveals that cooperative effects do not control the fragility of such liquids: the change of energy of local barriers determines the change of activation energy. More generally, these methods can now be used to measure the degree of cooperativity of any liquid model.

Solvent constraints for biopolymer folding and evolution in extraterrestrial environments.

We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets.

Liquid-liquid transition and ice crystallization in a machine-learned coarse-grained water model.

Mounting experimental evidence supports the existence of a liquid-liquid transition (LLT) in high-pressure supercooled water. However, fast crystallization of supercooled water has impeded identification of the LLT line TLL(p) in experiments. While the most accurate all-atom (AA) water models display a LLT, their computational cost limits investigations of its interplay with ice formation. Coarse-grained (CG) models provide over 100-fold computational efficiency gain over AA models, enabling the study of water crystallization, but have not yet shown to have a LLT. Here, we demonstrate that the CG machine-learned water model Machine-Learned Bond-Order Potential (ML-BOP) has a LLT that ends in a critical point at pc = 170 ± 10 MPa and Tc = 181 ± 3 K. The TLL(p) of ML-BOP is almost identical to the one of TIP4P/2005, adding to the similarity in the equation of state of liquid water in both models. Cooling simulations reveal that ice crystallization is fastest at the LLT and its supercritical continuation of maximum heat capacity, supporting a mechanistic relationship between the structural transformation of water to a low-density liquid (LDL) and ice formation. We find no signature of liquid-liquid criticality in the ice crystallization temperatures. ML-BOP replicates the competition between formation of LDL and ice observed in ultrafast experiments of decompression of the high-density liquid (HDL) into the region of stability of LDL. The simulations reveal that crystallization occurs prior to the coarsening of the HDL and LDL domains, obscuring the distinction between the highly metastable first-order LLT and pronounced structural fluctuations along its supercritical continuation.

Intrinsic tensile ductility in strain hardening multiprincipal element metallic glass.

Traditional metallic glasses (MGs), based on one or two principal elements, are notoriously known for their lack of tensile ductility at room temperature. Here, we developed a multiprincipal element MG (MPEMG), which exhibits a gigapascal yield strength, significant strain hardening that almost doubles its yield strength, and 2% uniform tensile ductility at room temperature. These remarkable properties stem from the heterogeneous amorphous structure of our MPEMG, which is composed of atoms with significant size mismatch but similar atomic fractions. In sharp contrast to traditional MGs, shear banding in our glass triggers local elemental segregation and subsequent ordering, which transforms shear softening to hardening, hence resulting in shear-band self-halting and extensive plastic flows. Our findings reveal a promising pathway to design stronger, more ductile glasses that can be applied in a wide range of technological fields.

Interpretable algorithmic forensics.

One of the most troubling trends in criminal investigations is the growing use of "black box" technology, in which law enforcement rely on artificial intelligence (AI) models or algorithms that are either too complex for people to understand or they simply conceal how it functions. In criminal cases, black box systems have proliferated in forensic areas such as DNA mixture interpretation, facial recognition, and recidivism risk assessments. The champions and critics of AI argue, mistakenly, that we face a catch 22: While black box AI is not understandable by people, they assume that it produces more accurate forensic evidence. In this Article, we question this assertion, which has so powerfully affected judges, policymakers, and academics. We describe a mature body of computer science research showing how "glass box" AI-designed to be interpretable-can be more accurate than black box alternatives. Indeed, black box AI performs predictably worse in settings like the criminal system. Debunking the black box performance myth has implications for forensic evidence, constitutional criminal procedure rights, and legislative policy. Absent some compelling-or even credible-government interest in keeping AI as a black box, and given the constitutional rights and public safety interests at stake, we argue that a substantial burden rests on the government to justify black box AI in criminal cases. We conclude by calling for judicial rulings and legislation to safeguard a right to interpretable forensic AI.

Two-step devitrification of ultrastable glasses.

The discovery of ultrastable glasses raises novel challenges about glassy systems. Recent experiments studied the macroscopic devitrification of ultrastable glasses into liquids upon heating but lacked microscopic resolution. We use molecular dynamics simulations to analyze the kinetics of this transformation. In the most stable systems, devitrification occurs after a very large time, but the liquid emerges in two steps. At short times, we observe the rare nucleation and slow growth of isolated droplets containing a liquid maintained under pressure by the rigidity of the surrounding glass. At large times, pressure is released after the droplets coalesce into large domains, which accelerates devitrification. This two-step process produces pronounced deviations from the classical Avrami kinetics and explains the emergence of a giant lengthscale characterizing the devitrification of bulk ultrastable glasses. Our study elucidates the nonequilibrium kinetics of glasses following a large temperature jump, which differs from both equilibrium relaxation and aging dynamics, and will guide future experimental studies.

Dynamic Gardner cross-over in a simple glass.

The criticality of the jamming transition responsible for amorphous solidification has been theoretically linked to the marginal stability of a thermodynamic Gardner phase. While the critical exponents of jamming appear independent of the preparation history, the pertinence of Gardner physics far from equilibrium is an open question. To fill this gap, we numerically study the nonequilibrium dynamics of hard disks compressed toward the jamming transition using a broad variety of protocols. We show that dynamic signatures of Gardner physics can be disentangled from the aging relaxation dynamics. We thus define a generic dynamic Gardner cross-over regardless of the history. Our results show that the jamming transition is always accessed by exploring increasingly complex landscape, resulting in anomalous microscopic relaxation dynamics that remains to be understood theoretically.

Bonded straight and helical flagellar filaments form ultra-low-density glasses.

We study how the three-dimensional shape of rigid filaments determines the microscopic dynamics and macroscopic rheology of entangled semidilute Brownian suspensions. To control the filament shape we use bacterial flagella, which are microns-long helical or straight filaments assembled from flagellin monomers. We compare the dynamics of straight rods, helical filaments, and shape-diblock copolymers composed of seamlessly joined straight and helical segments. Caged by their neighbors, straight rods preferentially diffuse along their long axis, but exhibit significantly suppressed rotational diffusion. Entangled helical filaments escape their confining tube by corkscrewing through the dense obstacles created by other filaments. By comparison, the adjoining segments of the rod-helix shape-diblocks suppress both the translation and the corkscrewing dynamics. Consequently, the shape-diblock filaments become permanently jammed at exceedingly low densities. We also measure the rheological properties of semidilute suspensions and relate their mechanical properties to the microscopic dynamics of constituent filaments. In particular, rheology shows that an entangled suspension of shape rod-helix copolymers forms a low-density glass whose elastic modulus can be estimated by accounting for how shear deformations reduce the entropic degrees of freedom of constrained filaments. Our results demonstrate that the three-dimensional shape of rigid filaments can be used to design rheological properties of semidilute fibrous suspensions.

Chloroplasts in plant cells show active glassy behavior under low-light conditions.

Plants have developed intricate mechanisms to adapt to changing light conditions. Besides phototropism and heliotropism (differential growth toward light and diurnal motion with respect to sunlight, respectively), chloroplast motion acts as a fast mechanism to change the intracellular structure of leaf cells. While chloroplasts move toward the sides of the plant cell to avoid strong light, they accumulate and spread out into a layer on the bottom of the cell at low light to increase the light absorption efficiency. Although the motion of chloroplasts has been studied for over a century, the collective organelle motion leading to light-adapting self-organized structures remains elusive. Here, we study the active motion of chloroplasts under dim-light conditions, leading to an accumulation in a densely packed quasi-2D layer. We observe burst-like rearrangements and show that these dynamics resemble systems close to the glass transition by tracking individual chloroplasts. Furthermore, we provide a minimal mathematical model to uncover relevant system parameters controlling the stability of the dense configuration of chloroplasts. Our study suggests that the meta-stable caging close to the glass transition in the chloroplast monolayer serves a physiological relevance: Chloroplasts remain in a spread-out configuration to increase the light uptake but can easily fluidize when the activity is increased to efficiently rearrange the structure toward an avoidance state. Our research opens questions about the role that dynamical phase transitions could play in self-organized intracellular responses of plant cells toward environmental cues.

Photonic crystals built by time in ancient Roman glass.

Ancient glass objects typically show distinctive effects of deterioration as a result of environmentally induced physicochemical transformations of their surface over time. Iridescence is one of the distinctive signatures of aging that is most commonly found on excavated glass. In this work, we present an ancient glass fragment that exhibits structural color through surface weathering resulting in iridescent patinas caused by silica reprecipitation in nanoscale lamellae. This archaeological artifact reveals an unusual hierarchically assembled photonic crystal with extremely ordered nanoscale domains, high spectral selectivity, and reflectivity (~90%), that collectively behaves like a gold mirror. Optical characterization paired with nanoscale elemental analysis further underscores the high quality of this structure providing a window into this sophisticated natural photonic crystal assembled by time.

Investigation of the yielding transition in concentrated colloidal systems via rheo-XPCS.

We probe the microstructural yielding dynamics of a concentrated colloidal system by performing creep/recovery tests with simultaneous collection of coherent scattering data via X-ray Photon Correlation Spectroscopy (XPCS). This combination of rheology and scattering allows for time-resolved observations of the microstructural dynamics as yielding occurs, which can be linked back to the applied rheological deformation to form structure-property relations. Under sufficiently small applied creep stresses, examination of the correlation in the flow direction reveals that the scattering response recorrelates with its predeformed state, indicating nearly complete microstructural recovery, and the dynamics of the system under these conditions slows considerably. Conversely, larger creep stresses increase the speed of the dynamics under both applied creep and recovery. The data show a strong connection between the microstructural dynamics and the acquisition of unrecoverable strain. By comparing this relationship to that predicted from homogeneous, affine shearing, we find that the yielding transition in concentrated colloidal systems is highly heterogeneous on the microstructural level.

Pressure-induced nonmonotonic cross-over of steady relaxation dynamics in a metallic glass.

Relaxation dynamics, as a key to understand glass formation and glassy properties, remains an elusive and challenging issue in condensed matter physics. In this work, in situ high-pressure synchrotron high-energy X-ray photon correlation spectroscopy has been developed to probe the atomic-scale relaxation dynamics of a cerium-based metallic glass during compression. Although the sample density continuously increases, the collective atomic motion initially slows down as generally expected and then counterintuitively accelerates with further compression (density increase), showing an unusual nonmonotonic pressure-induced steady relaxation dynamics cross-over at ~3 GPa. Furthermore, by combining in situ high-pressure synchrotron X-ray diffraction, the relaxation dynamics anomaly is evidenced to closely correlate with the dramatic changes in local atomic structures during compression, rather than monotonically scaling with either sample density or overall stress level. These findings could provide insight into relaxation dynamics and their relationship with local atomic structures of glasses.

HEG1 Protects Against Atherosclerosis by Regulating Stable Flow-Induced KLF2/4 Expression in Endothelial Cells.

BACKGROUND: Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow, and stable flow (s-flow) protects against atherosclerosis by incompletely understood mechanisms. METHODS: Our single-cell RNA-sequencing data using the mouse partial carotid ligation model was reanalyzed, which identified Heart-of-glass 1 (HEG1) as an s-flow-induced gene. HEG1 expression was studied by immunostaining, quantitive polymerase chain reaction, hybridization chain reaction, and Western blot in mouse arteries, human aortic endothelial cells (HAECs), and human coronary arteries. A small interfering RNA-mediated knockdown of HEG1 was used to study its function and signaling mechanisms in HAECs under various flow conditions using a cone-and-plate shear device. We generated endothelial-targeted, tamoxifen-inducible HEG1 knockout (HEG1iECKO) mice. To determine the role of HEG1 in atherosclerosis, HEG1iECKO and littermate-control mice were injected with an adeno-associated virus-PCSK9 [proprotein convertase subtilisin/kexin type 9] and fed a Western diet to induce hypercholesterolemia either for 2 weeks with partial carotid ligation or 2 months without the surgery. RESULTS: S-flow induced HEG1 expression at the mRNA and protein levels in vivo and in vitro. S-flow stimulated HEG1 protein translocation to the downstream side of HAECs and release into the media, followed by increased messenger RNA and protein expression. HEG1 knockdown prevented s-flow-induced endothelial responses, including monocyte adhesion, permeability, and migration. Mechanistically, HEG1 knockdown prevented s-flow-induced KLF2/4 (Kruppel-like factor 2/4) expression by regulating its intracellular binding partner KRIT1 (Krev interaction trapped protein 1) and the MEKK3-MEK5-ERK5-MEF2 pathway in HAECs. Compared with littermate controls, HEG1iECKO mice exposed to hypercholesterolemia for 2 weeks and partial carotid ligation developed advanced atherosclerotic plaques, featuring increased necrotic core area, thin-capped fibroatheroma, inflammation, and intraplaque hemorrhage. In a conventional Western diet model for 2 months, HEG1iECKO mice also showed an exacerbated atherosclerosis development in the arterial tree in both sexes and the aortic sinus in males but not in females. Moreover, endothelial HEG1 expression was reduced in human coronary arteries with advanced atherosclerotic plaques. CONCLUSIONS: Our findings indicate that HEG1 is a novel mediator of atheroprotective endothelial responses to flow and a potential therapeutic target.

Association of Ground Glass Opacities with Systemic Inflammation and Progression of Emphysema.

RATIONAL: Ground glass opacities (GGO) in the absence of interstitial lung disease are understudied. OBJECTIVE: To assess the association of GGO with white blood cells (WBCs) and progression of quantified chest CT emphysema. METHODS: We analyzed data of participants in the Subpopulations and Intermediate Outcome Measures In COPD Study (SPIROMICS). Chest radiologists and pulmonologists labeled regions of the lung as GGO and adaptive multiple feature method (AMFM) trained the computer to assign those labels to image voxels and quantify the volume of the lung with GGO (%GGOAMFM). We used multivariable linear regression, zero-inflated negative binomial, and proportional hazards regression models to assess the association of %GGOAMFM with WBC, changes in %emphysema, and clinical outcomes. MEASUREMENTS AND MAIN RESULTS: Among 2,714 participants, 1,680 had COPD and 1,034 had normal spirometry. Among COPD participants, based on the multivariable analysis, current smoking and chronic productive cough was associated with higher %GGOAMFM. Higher %GGOAMFM was cross-sectionally associated with higher WBCs and neutrophils levels. Higher %GGOAMFM per interquartile range at visit 1 (baseline) was associated with an increase in emphysema at one-year follow visit by 11.7% (Relative increase; 95%CI 7.5-16.1%;P<0.001). We found no association between %GGOAMFM and one-year FEV1 decline but %GGOAMFM was associated with exacerbations and all-cause mortality during a median follow-up time of 1,544 days (Interquartile Interval=1,118-2,059). Among normal spirometry participants, we found similar results except that %GGOAMFM was associated with progression to COPD at one-year follow-up. CONCLUSIONS: Our findings suggest that GGOAMFM is associated with increased systemic inflammation and emphysema progression.

Experimental observations of marginal criticality in granular materials.

SignificanceAmorphous materials, such as grains, foams, colloids, and glasses, are ubiquitous in nature and our daily life. They can undergo glass transitions or jamming transitions to obtain rigidity either by fast quench or compression, but show subtle changes in the structures compared to the liquid states or liquid-like states. Recent progress on the first-principle replica theory unifies the glass transition and the jamming transition and points out the marginal phase with fractal free-energy landscape within the stable glass phase. Independently, marginal stability analysis predicts the relations between the exponents of the marginal phase. Here, we perform experiments with photoelastic disks and provide direct evidence of these theories in real-world amorphous materials.

Prince Rupert's Drops: An analysis of fragmentation by thermal stresses and quench granulation of glass and bubbly glass.

When volcanic eruptions involve interaction with external water (hydrovolcanism), the result is an ash-rich and energetic volcanic plume, as illustrated dramatically by the January 2022 Tonga eruption. The origin of the high explosive energy of these events remains an important question. We investigate this question by studying Prince Rupert's Drops (PRDs)-tadpole-shaped glass beads formed by dripping molten glass into water-which have long fascinated materials scientists because the great strength of the head contrasts with the explosivity of the metastable interior when the tail is broken. We show that the fragment size distribution (FSD) produced by explosive fragmentation changes systematically with PRD fragmentation in air, water, and syrup. Most FSDs are fractal over much of the size range, scaling that can be explained by the repeated fracture bifurcation observed in three-dimensional images from microcomputed tomography. The shapes of constituent fragments are determined by their position within the original PRD, with platey fragments formed from the outer (compressive) shell and blocky fragments formed by fractures perpendicular to interior voids. When molten drops fail to form PRDs, the glass disintegrates by quench granulation, a process that produces fractal FSDs but with a larger median size than explosively generated fragments. Critically, adding bubbles to the molten glass prevents PRD formation and promotes quench granulation, suggesting that granulation is modulated by heterogeneous stress fields formed around the bubbles during sudden cooling and contraction. Together, these observations provide insight into glass fragmentation and potentially, processes operating during hydrovolcanism.

Self-assembled nanocomposites of high water content and load-bearing capacity.

Biological tissues, such as cartilage, tendon, ligament, skin, and plant cell wall, simultaneously achieve high water content and high load-bearing capacity. The high water content enables the transport of nutrients and wastes, and the high load-bearing capacity provides structural support for the organisms. These functions are achieved through nanostructures. This biological fact has inspired synthetic mimics, but simultaneously achieving both functions has been challenging. The main difficulty is to construct nanostructures of high load-bearing capacity, characterized by multiple properties, including elastic modulus, strength, toughness, and fatigue threshold. Here we develop a process that self-assembles a nanocomposite using a hydrogel-forming polymer and a glass-forming polymer. The process separates the polymers into a hydrogel phase and a glass phase. The two phases arrest at the nanoscale and are bicontinuous. Submerged in water, the nanocomposite maintains the structure and resists further swelling. We demonstrate the process using commercial polymers, achieving high water content, as well as load-bearing capacity comparable to that of polyethylene. During the process, a rubbery stage exists, enabling us to fabricate objects of complex shapes and fine features. We conduct further experiments to discuss likely molecular origins of arrested phase separation, swell resistance, and ductility. Potential applications of the nanocomposites include artificial tissues, high-pressure filters, low-friction coatings, and solid electrolytes.

Shear transformations in metallic glasses without excessive and predefinable defects.

Plastic flow in metallic glasses (MGs) is known to be mediated by shear transformations (STs), which have been hypothesized to preferentially initiate from identifiable local "defect" regions with loose atomic packing. Here we show that the above idea is incorrect, i.e., STs do not arise from signature structural defects that can be recognized a priori. This conclusion is reached via a realistic MG model obtained by combining molecular dynamics (MD) and Monte Carlo simulations, achieving liquid solidification at an effective cooling rate as slow as 500 K/s to approach that typical in experiments for producing bulk MGs. At shear stresses before global yielding, only about 2% of the total atoms participate in STs, each event involving typically ~10 atoms. These observations rectify the excessive content of "liquid-like regions" retained from unrealistically fast quench in MD-produced glass models. Our findings also shed light on the indeterministic aspect of the ST sites/zones, which emerge with varying spatial locations and distribution depending on specific mechanical loading conditions.

Anomalous magnetic noise in an imperfectly flat landscape in the topological magnet Dy2Ti2O7.

Noise generated by motion of charge and spin provides a unique window into materials at the atomic scale. From temperature of resistors to electrons breaking into fractional quasiparticles, "listening" to the noise spectrum is a powerful way to decode underlying dynamics. Here, we use ultrasensitive superconducting quantum interference device (SQUIDs) to probe the puzzling noise in a frustrated magnet, the spin-ice compound Dy2Ti2O7 (DTO), revealing cooperative and memory effects. DTO is a topological magnet in three dimensions-characterized by emergent magnetostatics and telltale fractionalized magnetic monopole quasiparticles-whose real-time dynamical properties have been an enigma from the very beginning. We show that DTO exhibits highly anomalous noise spectra, differing significantly from the expected Brownian noise of monopole random walks, in three qualitatively different regimes: equilibrium spin ice, a "frozen" regime extending to ultralow temperatures, and a high-temperature "anomalous" paramagnet. We present several distinct mechanisms that give rise to varied colored noise spectra. In addition, we identify the structure of the local spin-flip dynamics as a crucial ingredient for any modeling. Thus, the dynamics of spin ice reflects the interplay of local dynamics with emergent topological degrees of freedom and a frustration-generated imperfectly flat energy landscape, and as such, it points to intriguing cooperative and memory effects for a broad class of magnetic materials.