From hidden order to antiferromagnetism: Electronic structure changes in Fe-doped URu2Si2

In matter, any spontaneous symmetry breaking induces a phase transition characterized by an order parameter, such as the magnetization vector in ferromagnets, or a macroscopic many-electron wave function in superconductors. Phase transitions with unknown order parameter are rare but extremely appealing, as they may lead to novel physics. An emblematic and still unsolved example is the transition of the heavy fermion compound URu2Si2 (URS) into the so-called hidden-order (HO) phase when the temperature drops below T0=17.5 K. Here, we show that the interaction between the heavy fermion and the conduction band states near the Fermi level has a key role in the emergence of the HO phase. Using angle-resolved photoemission spectroscopy, we find that while the Fermi surfaces of the HO and of a neighboring antiferromagnetic (AFM) phase of well-defined order parameter have the same topography, they differ in the size of some, but not all, of their electron pockets. Such a nonrigid change of the electronic structure indicates that a change in the interaction strength between states near the Fermi level is a crucial ingredient for the HO to AFM phase transition.

The transition of URu2Si2 from a high-temperature paramagnetic (PM) phase to the hidden-order (HO) phase below T0 is accompanied by anomalies in specific heat (1–3), electrical resistivity (1, 3), thermal expansion (4), and magnetic susceptibility (2, 3) that are all typical of magnetic ordering. However, the small associated antiferromagnetic (AFM) moment (5) is insufficient to explain the large entropy loss and was shown to be of extrinsic origin (6). Inelastic neutron scattering (INS) experiments revealed gapped magnetic excitations below T0 at commensurate and incommensurate wave vectors (7–9), while an instability and partial gapping of the Fermi surface was observed by angle-resolved photoemission spectroscopy (ARPES) (10–16) and scanning tunneling microscopy/spectroscopy (17, 18). More recently, high-resolution, low-temperature ARPES experiments imaged the Fermi surface reconstruction across the HO transition, unveiling the nesting vectors between Fermi sheets associated with the gapped magnetic excitations seen in INS experiments (14, 19) and quantitatively explaining, from the changes in Fermi surface size and quasiparticle mass, the large entropy loss in the HO phase (19). Nonetheless, the nature of the HO parameter is still hotly debated (20–23).The HO phase is furthermore unstable above a temperature-dependent critical pressure of about 0.7 GPa at T=0, at which it undergoes a first-order transition into a large moment AFM phase where the value of the magnetic moment per U atom exhibits a sharp increase, by a factor of 10 to 50 (6, 24–30). When the system crosses the HO → AFM phase boundary, the characteristic magnetic excitations of the HO phase are either suppressed or modified (8, 31), while resistivity and specific heat measurements suggest that the partial gapping of the Fermi surface is enhanced (24, 27).As the AFM phase has a well-defined order parameter, studying the evolution of the electronic structure across the HO/AFM transition would help develop an understanding of the HO state. So far, the experimental determination of the Fermi surface by Shubnikov de Haas (SdH) oscillations only showed minor changes across the HO → AFM phase boundary (32). Here, we take advantage of the HO/AFM transition induced by chemical pressure in URu2Si2, through the partial substitution of Ru with Fe (33–37), to directly probe its electronic structure in the AFM phase using ARPES. As we shall see, our results reveal that changes in the Ru 4d–U 5f hybridization across the HO/AFM phase boundary seem essential for a better understanding of the HO state.     

The ferroelectric photo ground state of SrTiO3: Cavity materials engineering

Optical cavities confine light on a small region in space, which can result in a strong coupling of light with materials inside the cavity. This gives rise to new states where quantum fluctuations of light and matter can alter the properties of the material altogether. Here we demonstrate, based on first-principles calculations, that such light–matter coupling induces a change of the collective phase from quantum paraelectric to ferroelectric in the SrTiO3 ground state, which has thus far only been achieved in out-of-equilibrium strongly excited conditions [X. Li et al., Science 364, 1079–1082 (2019) and T. F. Nova, A. S. Disa, M. Fechner, A. Cavalleri, Science 364, 1075–1079 (2019)]. This is a light–matter hybrid ground state which can only exist because of the coupling to the vacuum fluctuations of light, a photo ground state. The phase transition is accompanied by changes in the crystal structure, showing that fundamental ground state properties of materials can be controlled via strong light–matter coupling. Such a control of quantum states enables the tailoring of materials properties or even the design of novel materials purely by exposing them to confined light.

Engineering an out-of-equilibrium state of a material by means of strong light fields can drastically change its properties and even induce new phases altogether. This is considered a new paradigm of material design, especially when the collective behavior of particles in quantum materials can be controlled to provide novel functionalities (1, 2). Alternatively to the intense lasers necessary to reach such out-of-equilibrium states, one can achieve strong light–matter coupling by placing the material inside an optical cavity (3–11). A main advantage of this approach is that strong interaction can be achieved at equilibrium, opening up new possibilities for materials manipulation. Among the proposed effects are novel exciton insulator states (12), control of excitonic energy ordering (13), enhanced electron–phonon coupling (14), photon-mediated electron pairing (15–18), enhanced ferroelectricity (19), and multi-quasi-particles hybridization (20). One enticing possibility is, however, to change the ground state of a material and to create a new phase not through excited quasi-particles but truly as the equilibrium state.Here we show that this can be achieved in the paraelectric SrTiO3 as a photo-correlated ferroelectric ground state. This ground state, which we refer to as photo ground state, is the result of the strong coupling between matter and quantum vacuum fluctuations of light. While similar materials of the perovskite family undergo a para- to ferroelectric phase transition at low temperatures, SrTiO3 remains paraelectric (21), because the nuclear quantum fluctuations prevent the emergence of a collective polarization that is characteristic of the ferroelectric phase (22, 23). Alterations to the material that overcome a relatively small activation energy, however, can induce ferroelectricity: for instance, through isotope substitution (24), strain (25, 26), and, most notably, nonlinear excitation of the lattice by strong and resonant terahertz laser pumping (27, 28). In the latter type of experiments, a transient broken symmetry of the structure as well as macroscopic polarization indicative of a transient ferroelectric phase have been observed.By using atomistic calculations, we show that the off-resonant dressing of the lattice of SrTiO3 with the vacuum fluctuations of the photons in a cavity can suppress the nuclear quantum fluctuations in a process that is analogous to the one of dynamical localization (29): As explained in Results and Discussion, the interaction with cavity photons effectively results in an enhancement of the effective mass of the ions, thus slowing them down and reducing the importance of their quantum fluctuations. We further demonstrate that the effect of cavity-induced localization extends to finite temperatures, even when thermal lattice fluctuations overcome the quantum ones. We thus introduce a revisited paraelectric to ferroelectric phase diagram, with the cavity coupling strength as a new dimension.     

COVID-19 pandemic reveals persistent disparities in nitrogen dioxide pollution

The unequal spatial distribution of ambient nitrogen dioxide (NO2), an air pollutant related to traffic, leads to higher exposure for minority and low socioeconomic status communities. We exploit the unprecedented drop in urban activity during the COVID-19 pandemic and use high-resolution, remotely sensed NO2 observations to investigate disparities in NO2 levels across different demographic subgroups in the United States. We show that, prior to the pandemic, satellite-observed NO2 levels in the least White census tracts of the United States were nearly triple the NO2 levels in the most White tracts. During the pandemic, the largest lockdown-related NO2 reductions occurred in urban neighborhoods that have 2.0 times more non-White residents and 2.1 times more Hispanic residents than neighborhoods with the smallest reductions. NO2 reductions were likely driven by the greater density of highways and interstates in these racially and ethnically diverse areas. Although the largest reductions occurred in marginalized areas, the effect of lockdowns on racial, ethnic, and socioeconomic NO2 disparities was mixed and, for many cities, nonsignificant. For example, the least White tracts still experienced ∼1.5 times higher NO2 levels during the lockdowns than the most White tracts experienced prior to the pandemic. Future policies aimed at eliminating pollution disparities will need to look beyond reducing emissions from only passenger traffic and also consider other collocated sources of emissions such as heavy-duty vehicles.

Adverse air quality is an environmental justice issue, as it disproportionately affects marginalized and disenfranchised populations around the world (1–4). Growing evidence suggests that these populations experience more air pollution than is caused by their consumption (5–7). Within the United States, disparities in exposure are persistent, despite successful regulatory measures that have reduced pollution (8, 9). Nitrogen dioxide (NO2) is a short-lived trace gas formed shortly after fossil fuel combustion and regulated by the National Ambient Air Quality Standards under the Clean Air Act. Exposure to NO2 is associated with a range of respiratory diseases and premature mortality (10–12). NO2 is also a precursor to other pollutants such as ozone and particulate matter (13). Major sources of anthropogenic NO2, such as roadways and industrial facilities, are often located within or nearby marginalized and disenfranchised communities (14, 15), and disparities in NO2 exposure across demographic subgroups have been the focus of several recent studies (4, 8, 16–18).In early 2020, governments around the world imposed lockdowns and shelter-in-place orders in response to the spread of COVID-19. The earliest government-mandated lockdowns in the United States began in California on 19 March 2020, and many states followed suit in the following days. Changes in mobility patterns indicate that self-imposed social distancing practices were underway days to weeks before the formal announcement of lockdowns (19). Lockdowns led to sharp reductions in surface-level NO2 (20–23) and tropospheric column NO2 measured from satellite instruments (21, 24–27) over the United States, China, and Europe. According to government-reported inventories, roughly 60% of anthropogenic emissions of nitrogen oxides (NOx≡ NO + NO2) in the United States in 2010 were emitted by on-road vehicles (28), and up to 80% of ambient NO2 in urban areas can be linked to traffic emissions (29, 30). As such, NO2 is often used as a marker for road traffic in urban areas. Multiple lines of evidence such as seismic quieting and reduced mobility via location-based services point to changes in traffic-related emissions as the main driver of reductions in NO2 pollution during lockdowns, due to the large proportion of the population working from home (21, 23, 31, 32).Here we exploit the unprecedented changes in human activity unique to the COVID-19 lockdowns and remotely sensed NO2 columns with extraordinary spatial resolution and coverage to understand inequalities in the distribution of NO2 pollution for different racial, ethnic, and socioeconomic subgroups in the United States. Specifically, we address the following: Which demographic subgroups received the largest NO2 reductions? Did the lockdowns grow or shrink the perennial disparities in NO2 pollution across different demographic subgroups? Although the lockdowns are economically unsustainable, how can they advance environmental justice and equity by informing long-term policies to reduce NO2 disparities and the associated public health damages?     

Ultrasensitive multispecies spectroscopic breath analysis for real-time health monitoring and diagnostics

Breath analysis enables rapid, noninvasive diagnostics, as well as long-term monitoring of human health, through the identification and quantification of exhaled biomarkers. Here, we demonstrate the remarkable capabilities of mid-infrared (mid-IR) cavity-enhanced direct-frequency comb spectroscopy (CE-DFCS) applied to breath analysis. We simultaneously detect and monitor as a function of time four breath biomarkers—CH3OH, CH4, H2O, and HDO—as well as illustrate the feasibility of detecting at least six more (H2CO, C2H6, OCS, C2H4, CS2, and NH3) without modifications to the experimental apparatus. We achieve ultrahigh detection sensitivity at the parts-per-trillion level. This is made possible by the combination of the broadband spectral coverage of a frequency comb, the high spectral resolution afforded by the individual comb teeth, and the sensitivity enhancement resulting from a high-finesse cavity. Exploiting recent advances in frequency comb, optical coating, and photodetector technologies, we can access a large variety of biomarkers with strong carbon–hydrogen-bond spectral signatures in the mid-IR.

Breath analysis is an exceptionally promising and rapidly developing field of research, which examines the molecular composition of exhaled breath (1–6). The hundreds of different gases that are present in exhaled breath include inorganic compounds, as well as volatile organic compounds (VOCs), and can either result from internal metabolic activity (endogenous emissions) or external factors, such as food consumption or environmental exposure (exogenous emissions). Despite its distinctive advantages of being a rapid, noninvasive technique and its long history dating back to Hippocrates, breath analysis has not yet been as widely deployed for routine diagnostics and monitoring as other methods, such as blood-based analysis. This is partly due to the experimental challenges of dealing with extremely small amounts of gas-phase molecules—in the parts-per-million (ppm) to parts-per-billion (ppb) range for most VOCs—and partly due to the relative scarcity of large-scale clinical studies that can reliably correlate specific diseases with biomarkers present in breath. Nevertheless, through close collaborations between instrument developers, breath-analysis experts, and clinicians, the field of breath analysis is fast approaching its goal of enabling real-time, noninvasive early detection and long-term monitoring of temporary and permanent health conditions (1, 3). Several biomarkers present in breath have been associated with specific conditions—for instance, nitrogen monoxide with asthma, acetone with diabetes, and ammonia with renal failure (5)—and breath is increasingly being used to track diseases and infections, both bacterial and viral (7). Recently, three studies have demonstrated the use of breath analysis to discriminate between SARS-CoV-2–infected patients and patients affected by other conditions (including asthma, chronic obstructive pulmonary disease, bacterial pneumonia, and cardiac conditions) (8, 9) or influenza A-infected patients (10). The possibility of real-time testing for highly infectious diseases in a noninvasive manner, without the need for chemical reagents and complex laboratory facilities, is particularly appealing in view of the current global pandemic.Technologies being explored and adopted for breath analysis include mass spectrometry, nanomaterial-based sensors, and laser spectroscopy. To date, the most widely used analytical technique in breath research is gas chromatography combined with mass spectrometry, which allows for the sensitive detection of hundreds of exhaled molecules, albeit with relatively long analysis times (tens of minutes) limited by the elution time of the various species. On the other hand, selected ion-flow-tube mass spectrometry and proton-transfer reaction mass spectrometry allow for real-time breath analysis at the expense of a reduced number of simultaneously detectable molecules (11). Sensor arrays offer an inexpensive and practical alternative for identifying the presence of a class of compounds based on their functional groups, but they generally do not permit identification of the specific molecules present in the samples (9, 12). Laser spectroscopy is intrinsically fast (≪ second timescale), allowing breath-cycle-resolved (i.e., respiratory-phase-resolved) sampling of breath with high precision and absolute accuracy. Achieving high sensitivity requires both signal enhancement and noise reduction: The former is attained by using multipass cells or high-finesse cavities, while the latter is accomplished through intensity or frequency-modulation techniques. Among others, tunable diode laser absorption spectroscopy, cavity ring-down spectroscopy, cavity-enhanced absorption spectroscopy, and photoacoustic spectroscopy have all successfully been employed in breath analysis, but are typically limited in tunability and therefore in the number of detectable analytes (1). Cavity-enhanced direct-frequency comb spectroscopy (CE-DFCS) offers substantially enhanced capabilities for the simultaneous detection of multiple species due to the combination of high spectral resolution, wide spectral coverage, and high sensitivity (13–18). An early study from 2008 demonstrated this by detecting carbon monoxide, carbon dioxide, methane, ammonia, and water in breath samples by CE-DFCS (19). This previous work measured vibrational (mainly first) overtone transitions in the near-infrared (near-IR) region of the spectrum, from 1.5 μm to 1.7 μm.Here, we report a 2-orders-of-magnitude improvement in the detection sensitivity for multiple species relevant to breath analysis by using CE-DFCS in the mid-infrared (mid-IR) molecular fingerprint region (3.4−3.6 μm). We gain access to fundamental vibrational transitions, as well as employ higher-finesse mid-IR cavity mirrors (15, 20), compared to previous work in this spectral region (21). Exploiting recent advances in frequency comb, high-reflectivity optical coating, and photodetector technologies, we can detect a large variety of biomarkers simultaneously, sensitively, and unambiguously, providing exciting prospects to connect breath to a range of biological functions and diseases.     

Layering transitions and metastable structures of cholesteric liquid crystals in cylindrical confinement

Our study of cholesteric lyotropic chromonic liquid crystals in cylindrical confinement reveals the topological aspects of cholesteric liquid crystals. The double-twist configurations we observe exhibit discontinuous layering transitions, domain formation, metastability, and chiral point defects as the concentration of chiral dopant is varied. We demonstrate that these distinct layer states can be distinguished by chiral topological invariants. We show that changes in the layer structure give rise to a chiral soliton similar to a toron, comprising a metastable pair of chiral point defects. Through the applicability of the invariants we describe to general systems, our work has broad relevance to the study of chiral materials.

Chiral liquid crystals (LCs) are ubiquitous, useful, and rich systems (1–4). From the first discovery of the liquid crystalline phase to the variety of chiral structures formed by biomolecules (5–9), the twisted structure, breaking both mirror and continuous spatial symmetries, is omnipresent. The unique structure also makes the chiral nematic (cholesteric) LC, an essential material for applications utilizing the tunable, responsive, and periodic modulation of anisotropic properties.The cholesteric is also a popular model system to study the geometry and topology of partially ordered matter. The twisted ground state of the cholesteric is often incompatible with confinement and external fields, exhibiting a large variety of frustrated and metastable director configurations accompanying topological defects. Besides the classic example of cholesterics in a Grandjean−Cano wedge (10, 11), examples include cholesteric droplets (12–16), colloids (17–19), shells (20–22), tori (23, 24), cylinders (25–29), microfabricated structures (30, 31), and films between parallel plates with external fields (32–40). These structures are typically understood using a combination of nematic (achiral) topology (41, 42) and energetic arguments, for example, the highly successful Landau−de Gennes approach (43). However, traditional extensions of the nematic topological approach to cholesterics are known to be conceptually incomplete and difficult to apply in regimes where the system size is comparable to the cholesteric pitch (41, 44).An alternative perspective, chiral topology, can give a deeper understanding of these structures (45–47). In this approach, the key role is played by the twist density, given in terms of the director field n by n⋅∇×n. This choice is not arbitrary; the Frank free energy prefers n⋅∇×n≈−q0=2π/p0 with a helical pitch p0, and, from a geometric perspective, n⋅∇×n≠0 defines a contact structure (48). This allows a number of new integer-valued invariants of chiral textures to be defined (45). A configuration with a single sign of twist is chiral, and two configurations which cannot be connected by a path of chiral configurations are chirally distinct, and hence separated by a chiral energy barrier. Within each chiral class of configuration, additional topological invariants may be defined using methods of contact topology (45–48), such as layer numbers. Changing these chiral topological invariants requires passing through a nonchiral configuration. Cholesterics serve as model systems for the exploration of chirality in ordered media, and the phenomena we describe here—metastability in chiral systems controlled by chiral topological invariants—has applicability to chiral order generally. This, in particular, includes chiral ferromagnets, where, for example, our results on chiral topological invariants apply to highly twisted nontopological Skyrmions (49, 50) (“Skyrmionium”).Our experimental model to explore the chiral topological invariants is the cholesteric phase of lyotropic chromonic LCs (LCLCs). The majority of experimental systems hitherto studied are based on thermotropic LCs with typical elastic and surface-anchoring properties. The aqueous LCLCs exhibiting unusual elastic properties, that is, very small twist modulus K2 and large saddle-splay modulus K24 (51–56), often leading to chiral symmetry breaking of confined achiral LCLCs (53, 54, 56–61), may enable us to access uncharted configurations and defects of topological interests. For instance, in the layer configuration by cholesteric LCLCs doped with chiral molecules, their small K2 provides energetic flexibility to the thickness of the cholesteric layer, that is, the repeating structure where the director n twists by π. The large K24 affords curvature-induced surface interactions in combination with a weak anchoring strength of the lyotropic LCs (62–64).We present a systematic investigation of the director configuration of cholesteric LCLCs confined in cylinders with degenerate planar anchoring, depending on the chiral dopant concentration. We show that the structure of cholesteric configurations is controlled by higher-order chiral topological invariants. We focus on two intriguing phenomena observed in cylindrically confined cholesterics. First, the cylindrical symmetry renders multiple local minima to the energy landscape and induces discontinuous increase of twist angles, that is, a layering transition, upon the dopant concentration increase. Additionally, the director configurations of local minima coexist as metastable domains with point-like defects between them. We demonstrate that a chiral layer number invariant distinguishes these configurations, protects the distinct layer configurations (45), and explains the existence of the topological defect where the invariant changes.     

Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

Seep sediments are dominated by intensive microbial sulfate reduction coupled to the anaerobic oxidation of methane (AOM). Through geochemical measurements of incubation experiments with methane seep sediments collected from Hydrate Ridge, we provide insight into the role of iron oxides in sulfate-driven AOM. Seep sediments incubated with ¹³C-labeled methane showed co-occurring sulfate reduction, AOM, and methanogenesis. The isotope fractionation factors for sulfur and oxygen isotopes in sulfate were about 40‰ and 22‰, respectively, reinforcing the difference between microbial sulfate reduction in methane seeps versus other sedimentary environments (for example, sulfur isotope fractionation above 60‰ in sulfate reduction coupled to organic carbon oxidation or in diffusive sedimentary sulfate–methane transition zone). The addition of hematite to these microcosm experiments resulted in significant microbial iron reduction as well as enhancing sulfate-driven AOM. The magnitude of the isotope fractionation of sulfur and oxygen isotopes in sulfate from these incubations was lowered by about 50%, indicating the involvement of iron oxides during sulfate reduction in methane seeps. The similar relative change between the oxygen versus sulfur isotopes of sulfate in all experiments (with and without hematite addition) suggests that oxidized forms of iron, naturally present in the sediment incubations, were involved in sulfate reduction, with hematite addition increasing the sulfate recycling or the activity of sulfur-cycling microorganisms by about 40%. These results highlight a role for natural iron oxides during bacterial sulfate reduction in methane seeps not only as nutrient but also as stimulator of sulfur recycling.Microbial dissimilatory processes generate energy through the decomposition of substrates, whereas assimilatory processes use substrates for intracellular biosynthesis of macromolecules. The most known and energetically favorable dissimilatory process is the oxidation of organic carbon coupled to oxygen as terminal electron acceptor (Eq. 1). In sediments with a high supply of organic carbon, oxygen can be depleted within the upper few millimeters, leading to anoxic conditions deeper in the sediment column. Under these conditions, microbial dissimilatory processes are coupled to the reduction of a series of other terminal electron acceptors besides oxygen (1). The largest free-energy yields are associated with nitrate reduction (denitrification), followed by manganese and iron oxide reduction, and then sulfate reduction. Due to the high concentration of sulfate in the ocean, dissimilatory bacterial sulfate reduction (Eq. 2) is responsible for the majority of organic matter oxidation in marine sediments (2). Below the depth of sulfate depletion, traditionally the only presumed process is methanogenesis (methane production), where its main pathways are fermentation of organic matter, mainly acetate (Eq. 3), or the reduction of carbon dioxide with hydrogen as substrate (Eq. 4) (3):O₂ + CH₂O → H₂O + CO₂[1]SO42−+2CH2O→H2S+2HCO3−[2]CH₃COOH→CH₄ + CO₂[3]CO₂ + 4H₂→CH₄ + 2H₂O[4]When methane that has been produced deep in sediments diffuses into contact with an available electron acceptor, it can be oxidized (methanotrophy). Methanotrophy is the main process that prevents the escape of methane produced within marine and fresh water sediments into the atmosphere. In fresh water systems, methanotrophic bacteria are responsible for oxidizing methane to dissolved inorganic carbon (DIC) typically using oxygen as an electron acceptor (4, 5). In marine sediments, however, where oxygen diffusion is limited, anaerobic oxidation of methane (AOM) coupled to sulfate reduction [e.g., refs. 6 and 7 (Eq. 5)] has been shown to consume up to 90% of the methane produced within the subseafloor environment (8). Often, when methane is present, the majority of sulfate available in marine pore fluids is reduced through sulfate-driven AOM (9–13):CH4+SO42−→HS−+HCO3−+H2O.[5]Other electron acceptors such as nitrate and oxides of iron and manganese, could also oxidize methane anaerobically and provide a greater free-energy yield than sulfate-coupled methane oxidation (14). Indeed, Beal et al. (15) showed the potential for iron- and manganese-driven AOM in microcosm experiments with methane seep sediments from Eel River Basin and Hydrate Ridge, and iron-driven AOM has been interpreted from modeling geochemical profiles in deep-sea sediments (13, 16). AOM has been shown to occur in nonmarine sediments via denitrification (17–21) and iron reduction (22, 23). However, all geochemical and microbiological studies point to sulfate-driven AOM as the dominant sink for methane in marine sediments.Sulfate-driven AOM is understood to involve microbial consortia of archaea and bacteria affiliated with archaeal methanotrophs (“methane oxidizers”) and sulfate-reducing bacteria (11, 24). A common view is that anaerobic methanotrophic archaea (ANME) oxidize methane, while the sulfate-reducing syntrophic partner scavenges the resulting reducing equivalents to reduce sulfate to sulfide (7, 25, 26). Recently, however, cultured AOM enrichments from seeps were reported to be capable of direct coupling of methane oxidation and sulfate reduction by the ANME-2 archaea, with the passage of zero valent sulfur to a disproportionating bacterial partner, capable of simultaneously oxidizing and reducing this substrate to sulfate and sulfide in a ratio of 1:7, respectively (27). Whether this “single organism mechanism” for sulfate-driven AOM is widespread in the natural environment, or whether there is a diversity of mechanisms for sulfate-driven AOM, remains enigmatic.Carbon isotopes provide a good constraint on the depth distribution and location of methanogenesis and methanotrophy because of the carbon isotope fractionation associated with these processes (e.g., refs. 28 and 29). During methanogenesis, ¹²C is strongly partitioned into methane; the δ¹³C of the methane produced can be between −50‰ to −110‰. In parallel, the residual DIC pool in methanogenic zones becomes highly enriched in ¹³C, occasionally by as much as 50‰ to 70‰ (e.g., ref. 28). Oxidizing this methane on the other hand, results in ¹³C-depleted DIC and slightly heavier δ¹³C values of the residual methane, caused by a fractionation of 0‰ to 10‰ during methane oxidation and the initial negative δ¹³C value of the methane itself (30, 31).The sulfur and oxygen isotopes in dissolved sulfate (δ³⁴S_SO4 and δ¹⁸O_SO4) may also be a diagnostic tool for tracking the pathways of sulfate reduction by methane or other organic compounds. Sulfur isotope fractionation during dissimilatory bacterial sulfate reduction, which partitions ³²S into the sulfide, leaving ³⁴S behind in the residual sulfate, can be as high as 72‰ (32–35). As sulfate is reduced to sulfide via intracellular intermediates (34, 36–40), the magnitude of this sulfur isotope fractionation depends upon the isotope partitioning at each of the intercellular steps and on the ratio between the backward and forward sulfur fluxes within the bacterial cells (34, 36).Oxygen isotopes in sulfate, however, have been shown to be strongly influenced by the oxygen isotope composition of water in which the bacteria are grown (41–45). The consensus is that, within the cell, sulfur compounds, such as sulfite, and water exchange oxygen atoms; some of these isotopically equilibrated molecules return to the extracellular sulfate pool. As all of the intercellular steps are considered to be reversible (e.g., refs. 34, 36, 46, and 47), water–oxygen is also incorporated during the oxidation of these sulfur intermediates back to sulfate (41–43, 48–51).Therefore, both oxygen and sulfur isotopes in the residual sulfate during dissimilatory sulfate reduction are affected by the changes in the intracellular fluxes of sulfur species. However, these isotopes in the residual sulfate are affected in different ways, and thus the change of one isotope vs. the other helps uniquely solve for the relative change in the flux of each intracellular step as sulfate is being reduced (42, 43, 50). The sulfur and oxygen isotope composition of residual sulfate has been used to explore the mechanism of traditional (organoclastic) sulfate reduction both in pure culture (e.g., refs. 44, 45, and 52) and in the natural environment (e.g., refs. 12, 49, 50, and 53–55). The coupled isotope approach has been used specifically to study sulfate-driven AOM recently in estuaries (56). In the work of Antler et al. (56), it was shown that the oxygen and sulfur isotopes in the residual sulfate in the pore fluids are linearly correlated during sulfate-driven AOM, whereas during organoclastic bacterial sulfate reduction, the isotopes exhibit a concaved curve relationship.Although iron and manganese oxides should be reduced before the onset of dissimilatory bacterial sulfate reduction in the natural environment from thermodynamic considerations, due to their low solubility, they may not be completely reduced through dissimilatory respiration when sulfate reduction starts (e.g., ref. 22). These lower reactivity manganese and iron oxides therefore may still be present during the lower-energy yielding anaerobic processes such as sulfate reduction, methanotrophy, and methanogenesis. Indeed, iron oxides have been shown to serve as electron acceptors for methane oxidation even in the sulfate “zone” (15, 16, 22, 57), although the mechanism of this coupling remains enigmatic. In the context of deep-sea methane seep ecosystems, earlier work by Beal et al. (15) demonstrated stimulation of AOM by the addition of iron and manganese oxides in sediment incubation experiments. In that work, however, the nature of the coupling between methane oxidation and metal oxides was not ascertained, and the multiple links between the sediment sulfur, iron, and methane cycles are equivocal.Here, we conducted microcosm experiments with sediments collected from Hydrate Ridge South (Fig. S1) and used synergistic combinations of isotope analyses (δ³⁴S_SO4, δ¹⁸O_SO4, and δ¹³C_DIC) to aid in assessing whether methane oxidation is directly coupled to the respiration of iron oxides or whether stimulation in methanotrophy is a result of the coupling between iron and sulfate. We provide compelling evidence for the stimulation of AOM in seep sediments through the coupling between iron and sulfate, and propose a mechanism for iron involvement in sulfate-driven AOM. Using microcosm experiments with seep sediments dominated by sulfate-driven AOM and amended with hematite and ¹³C-labeled methane and glucose, we are able to demonstrate the role of iron in sulfate-driven AOM. Hematite is a less reactive form of iron oxide than, for example, amorphous iron (58), and it was used to prevent the microbial populations from “switching” completely to the more energetically favorable process of iron reduction.     

Moving Dirac nodes by chemical substitution

Dirac fermions play a central role in the study of topological phases, for they can generate a variety of exotic states, such as Weyl semimetals and topological insulators. The control and manipulation of Dirac fermions constitute a fundamental step toward the realization of novel concepts of electronic devices and quantum computation. By means of Angle-Resolved Photo-Emission Spectroscopy (ARPES) experiments and ab initio simulations, here, we show that Dirac states can be effectively tuned by doping a transition metal sulfide, BaNiS2, through Co/Ni substitution. The symmetry and chemical characteristics of this material, combined with the modification of the charge-transfer gap of BaCo1−xNixS2 across its phase diagram, lead to the formation of Dirac lines, whose position in k-space can be displaced along the Γ−M symmetry direction and their form reshaped. Not only does the doping x tailor the location and shape of the Dirac bands, but it also controls the metal-insulator transition in the same compound, making BaCo1−xNixS2 a model system to functionalize Dirac materials by varying the strength of electron correlations.

In the vast domain of topological Dirac and Weyl materials (1–9), the study of various underlying mechanisms (10–15) leading to the formation of nontrivial band structures is key to discovering new topological electronic states (16–23). A highly desirable feature of these materials is the tunability of the topological properties by an external parameter, which will make them suitable in view of technological applications, such as topological field-effect transistors (24). While a thorough control of band topology can be achieved, in principle, in optical lattices (25) and photonic crystals (26) through the wandering, merging, and reshaping of nodal points and lines in k-space (27, 28), in solid-state systems, such a control is much harder to achieve. Proposals have been made by using optical cavities (29), twisted van der Waals heterostructures (30), intercalation (31), chemical deposition (32, 33), impurities (34), and magnetic and electric applied fields (35), both static (36) and time-periodic (17, 37). Here, we prove that it is possible to move and reshape Dirac nodal lines in reciprocal space by chemical substitution. Namely, by means of Angle-Resolved Photo-Emission Spectroscopy (ARPES) experiments and ab initio simulations, we observe a sizable shift of robust massive Dirac nodes toward Γ in BaCo1−xNixS2 as a function of doping x, obtained by replacing Ni with Co. At variance with previous attempts of controlling Dirac states by doping (19, 38), in our work, we report both a reshape and a significant k-displacement of the Dirac nodes.BaCo1−xNixS2 is a prototypical transition metal system with a simple square lattice (39). In BaCo1−xNixS2 , the same doping parameter x that tunes the position of the Dirac nodes also controls the electronic phase diagram, which features a first-order metal-insulator transition (MIT) at a critical substitution level, xcr∼ 0.22 (40, 41), as shown in Fig. 1A. The Co rich side (x=0) is an insulator with columnar antiferromagnetic (AF) order and with local moments in a high-spin (S = 3/2) configuration (42). This phase can be seen as a spin density wave (SDW) made of antiferromagnetically coupled collinear spin chains. Both electron-correlation strength and charge-transfer gap ΔCT increase with decreasing x, as typically found in the late-transition metal series. The MIT at x=0.22 is of interest because it is driven by electron correlations (43) and is associated with a competition between an insulating antiferromagnetic phase and an unconventional paramagnetic semimetal (44), where the Dirac nodes are found at the Fermi level. We show that a distinctive feature of these Dirac states is their dominant d-orbital character and that the underlying band-inversion mechanism is driven by a large d−p hybridization combined with the nonsymmorphic symmetry (NSS) of the crystal (Fig. 1B). It follows that an essential role in controlling the properties of Dirac states is played by electron correlations and by the charge-transfer gap (Fig. 1C), as they have a direct impact on the hybridization strength. This results into an effective tunability of shape, energy, and wave vector of the Dirac lines in the proximity of the Fermi level. Specifically, the present ARPES study unveils Dirac bands moving from M to Γ with decreasing x. The bands are well explained quantitatively by ab initio calculations, in a hybrid density functional approximation suitable for including nonlocal correlations of screened-exchange type, which affect the hybridization between the d and p states. The same functional is able to describe the insulating SDW phase at x=0, driven by local correlations, upon increase of the optimal screened-exchange fraction. These calculations confirm that the Dirac nodes mobility in k-space stems directly from the evolution of the charge-transfer gap, i.e., the relative position between d and p on-site energies. These results clearly suggest that BaCo1−xNixS2 is a model system to tailor Dirac states and, more generally, that two archetypal features of correlated systems, such as the hybrid d−p bands and the charge-transfer gap, constitute a promising playground to engineer Dirac and topological materials using chemical substitution and other macroscopic control parameters.Open in a separate windowFig. 1.Experimental observation of Dirac states in the phase diagram of BaCo1−xNixS2. (A) Phase diagram of BaCo1−xNixS2. The transition lines between the PM, the paramagnetic insulator (PI), and the antiferromagnetic insulator (AFI) are reported. Colored circles indicate the different doping levels x studied in this work. This doping alters the d−p charge-transfer gap (ΔCT). (B) Crystal structure of BaNiS2. Blue, red, and yellow spheres represent the Ni, S, and Ba atoms, respectively. The tetragonal unit cell is indicated by black solid lines. Lattice parameters are a = 4.44 Å and c = 8.93 Å (45). (B, Upper) Projection of the unit cell in the xy plane, containing two Ni atoms. (C) Schematics of the energy levels. The hybridization of d− and p− orbitals creates the Dirac states, and the d−p charge-transfer gap fixes the position of these states in the E−k space. (D) A three-dimensional ARPES map of BaNiS2 (x=1) taken at 70-eV photon energy. The top surface shows the Fermi surface, and the sides of the cube present the band dispersion along high-symmetry directions. The linearly dispersing bands along Γ−M cross each other at the Fermi level, EF, thus creating four Dirac nodes. (E) We observe the oval-shaped section of the linearly dispersing bands on the kx−ky plane for E−EF=−100 meV. The linearly dispersing bands along the major and minor axis of the oval are also shown.     

Glasses denser than the supercooled liquid

When aged below the glass transition temperature, Tg, the density of a glass cannot exceed that of the metastable supercooled liquid (SCL) state, unless crystals are nucleated. The only exception is when another polyamorphic SCL state exists, with a density higher than that of the ordinary SCL. Experimentally, such polyamorphic states and their corresponding liquid–liquid phase transitions have only been observed in network-forming systems or those with polymorphic crystalline states. In otherwise simple liquids, such phase transitions have not been observed, either in aged or vapor-deposited stable glasses, even near the Kauzmann temperature. Here, we report that the density of thin vapor-deposited films of N,N′-bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD) can exceed their corresponding SCL density by as much as 3.5% and can even exceed the crystal density under certain deposition conditions. We identify a previously unidentified high-density supercooled liquid (HD-SCL) phase with a liquid–liquid phase transition temperature (TLL) ∼35 K below the nominal glass transition temperature of the ordinary SCL. The HD-SCL state is observed in glasses deposited in the thickness range of 25 to 55 nm, where thin films of the ordinary SCL have exceptionally enhanced surface mobility with large mobility gradients. The enhanced mobility enables vapor-deposited thin films to overcome kinetic barriers for relaxation and access the HD-SCL state. The HD-SCL state is only thermodynamically favored in thin films and transforms rapidly to the ordinary SCL when the vapor deposition is continued to form films with thicknesses more than 60 nm.

Glasses are formed when the structural relaxations in supercooled liquids (SCLs) become too slow, causing the system to fall out of equilibrium at the glass transition temperature (Tg). The resulting out-of-equilibrium glass state has a thermodynamic driving force to evolve toward the SCL state through physical aging (1). At temperatures just below Tg, the extent of equilibration is limited by the corresponding SCL state, while at much lower temperatures, equilibration is limited by the kinetic barriers for relaxation. As such, the degree of thermodynamic stability achieved through physical aging is limited (2).Physical vapor deposition (PVD) is an effective technique to overcome kinetic barriers for relaxation to produce thermodynamically stable glasses (3–10). The accelerated equilibration in these systems is due to their enhanced surface mobility (11–14). During PVD, when the substrate temperature is held below Tg, molecules or atoms can undergo rearrangements and adopt more stable configurations at the free surface and proximate layers underneath (13). After the molecules are buried deeper into the film, their relaxation dynamics significantly slow down, which prevents further equilibration. Through this surface-mediated equilibration process, stable glasses can achieve low-energy states on the potential energy landscape that would otherwise require thousands or millions of years of physical aging (2, 3, 15, 16).As such, the degree of enhanced surface mobility and mobility gradients are critical factors in the formation of stable glasses (3, 11, 17, 18). While the effect of film thickness on the surface mobility and gradients of liquid-quenched (LQ) glasses has been studied in the past (19, 20), there are limited data on the role of film thickness in the stability of vapor-deposited glasses. In vapor-deposited toluene, it has been shown that decreasing the film thickness from 70 to 5 nm can increase the thermodynamic stability but decrease the apparent kinetic stability (5, 6). In contrast, thin films covered with a top layer of another material do not show a significant evidence of reduced kinetic stability (21), indicating the nontrivial role of mobility gradients in thermal and kinetic stability.Stable glasses of most organic molecules, with short-range intramolecular interactions, have properties that are indicative of the same corresponding metastable SCL state as LQ and aged glasses, without any evidence of the existence of generic liquid–liquid phase transitions that can potentially provide a resolution for the Kauzmann entropy crisis (22). The Kauzmann crisis occurs at the Kauzmann temperature (TK), where the extrapolated SCL has the same structural entropy as the crystal, producing thermodynamically impossible states just below this temperature. Recently, Beasley et al. (16) showed that near-equilibrium states of ethylbenzene can be produced using PVD down to 2 K above TK and hypothesized that any phase transition to an “ideal glass” state to avoid the Kauzmann crisis must occur at TK.In some glasses of elemental substances (23, 24) and hydrogen-bonding compounds (25, 26), liquid–liquid phase transitions can occur between polyamorphic states with distinct local packing structures that correspond to polymorphic crystalline phases. For example, at high pressures, high- and low-density supercooled water phases are interconvertible through a first-order phase transition (27, 28). Recent studies have demonstrated that such polyamorphic states can also be accessed through PVD in hydrogen-bonding systems with polymorphic crystal states at depositions above the nominal Tg (29, 30). However, these structure-specific transitions do not provide a general resolution for the Kauzmann crisis.Here, we report the observation of a liquid–liquid phase transition in vapor-deposited thin films of N,N′-bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD). TPD is a molecular glass former with only short-range intermolecular interactions. When thin films of TPD are vapor deposited onto substrates held at deposition temperatures (Tdep) below the nominal glass transition temperature of bulk TPD, Tg (bulk), films in the thickness range of 25 nm<h<55 nm achieve a high-density supercooled liquid (HD-SCL) state, which has not been previously observed. The liquid–liquid phase transition temperature (TLL) between the ordinary SCL and HD-SCL states is measured to be TLL≃Tg(bulk)−35 K. The density of thin films deposited below TLL tangentially follows the HD-SCL line, which has a stronger temperature dependence than the ordinary SCL. When vapor deposition is continued to produce thicker films (h>60 nm), the HD-SCL state transforms into the ordinary SCL state, indicating that the HD-SCL is only thermodynamically favored in the thin-film geometry. This transition is qualitatively different from the previously reported liquid–liquid phase transitions, as it is not related to a specific structural motif in TPD crystals, and it can only be observed in thin films, indicating that the energy landscape of thin films is favoring this high-density state.We observe an apparent correlation between enhanced mobility gradients in LQ thin films of TPD and the thickness range where HD-SCL states are produced during PVD. We hypothesize that enhanced mobility gradients are essential in providing access to regions of the energy landscape corresponding to the HD-SCL state, which are otherwise kinetically inaccessible. This hypothesis should be further investigated to better understand the origin of this phenomenon.     

Unusual magnetotransport in twisted bilayer graphene

We present transport measurements of bilayer graphene with a 1.38^∘ interlayer twist. As with other devices with twist angles substantially larger than the magic angle of 1.1^∘, we do not observe correlated insulating states or band reorganization. However, we do observe several highly unusual behaviors in magnetotransport. For a large range of densities around half filling of the moiré bands, magnetoresistance is large and quadratic. Over these same densities, the magnetoresistance minima corresponding to gaps between Landau levels split and bend as a function of density and field. We reproduce the same splitting and bending behavior in a simple tight-binding model of Hofstadter’s butterfly on a triangular lattice with anisotropic hopping terms. These features appear to be a generic class of experimental manifestations of Hofstadter’s butterfly and may provide insight into the emergent states of twisted bilayer graphene.

The mesmerizing Hofstadter butterfly spectrum arises when electrons in a two-dimensional periodic potential are immersed in an out-of-plane magnetic field. When the magnetic flux Φ through a unit cell is a rational multiple p / q of the magnetic flux quantum Φ0=h/e, each Bloch band splits into q subbands (1). The carrier densities corresponding to gaps between these subbands follow straight lines when plotted as a function of normalized density n/ns and magnetic field (2). Here, n_s is the density of carriers required to fill the (possibly degenerate) Bloch band. These lines can be described by the Diophantine equation (n/ns)=t(Φ/Φ0)+s for integers s and t. In experiments, they appear as minima or zeros in longitudinal resistivity coinciding with Hall conductivity quantized at σxy=te2/h (3, 4). Hofstadter originally studied magnetosubbands emerging from a single Bloch band on a square lattice. In the following decades, other authors considered different lattices (5–7), the effect of anisotropy (6, 8–10), next-nearest-neighbor hopping (11–15), interactions (16, 17), density wave states (9), and graphene moirés (18, 19).It took considerable ingenuity to realize clean systems with unit cells large enough to allow conventional superconducting magnets to reach Φ/Φ0∼1. The first successful observation of the butterfly in electrical transport measurements was in GaAs/AlGaAs heterostructures with lithographically defined periodic potentials (20–22). These experiments demonstrated the expected quantized Hall conductance in a few of the largest magnetosubband gaps. In 2013, three groups mapped out the full butterfly spectrum in both density and field in heterostructures based on monolayer (23, 24) and bilayer (25) graphene. In all three cases, the authors made use of the 2% lattice mismatch between their graphene and its encapsulating hexagonal boron nitride (hBN) dielectric. With these layers rotationally aligned, the resulting moiré pattern was large enough in area that gated structures studied in available high-field magnets could simultaneously approach normalized carrier densities and magnetic flux ratios of 1. Later work on hBN-aligned bilayer graphene showed that, likely because of electron–electron interactions, the gaps could also follow lines described by fractional s and t (26).In twisted bilayer graphene (TBG), a slight interlayer rotation creates a similar-scale moiré pattern. Unlike with graphene–hBN moirés, in TBG there is a gap between lowest and neighboring moiré subbands (27). As the twist angle approaches the magic angle of 1.1^∘ the isolated moiré bands become flat (28, 29), and strong correlations lead to fascinating insulating (30–37), superconducting (31–33, 35–37), and magnetic (34, 35, 38) states. The strong correlations tend to cause moiré subbands within a fourfold degenerate manifold to move relative to each other as one tunes the density, leading to Landau levels that project only toward higher magnitude of density from charge neutrality and integer filling factors (37, 39). This correlated behavior obscures the single-particle Hofstadter physics that would otherwise be present.In this work, we present measurements from a TBG device twisted to 1.38^∘. When we apply a perpendicular magnetic field, a complicated and beautiful fan diagram emerges. In a broad range of densities on either side of charge neutrality, the device displays large, quadratic magnetoresistance. Within the magnetoresistance regions, each Landau level associated with ν=±8,±12,±16,… appears to split into a pair, and these pairs follow complicated paths in field and density, very different from those predicted by the usual Diophantine equation. Phenomenology similar in all qualitative respects appears in measurements on several regions of this same device with similar twist angles and in two separate devices, one at 1.59^∘ and the other at 1.70^∘ (see SI Appendix for details).We reproduce the unusual features of the Landau levels (LLs) in a simple tight-binding model on a triangular lattice with anisotropy and a small energetic splitting between two species of fermions. At first glance, this is surprising, because that model does not represent the symmetries of the experimental moiré structure. We speculate that the unusual LL features we experimentally observe can generically emerge from spectra of Hofstadter models that include the same ingredients we added to the triangular lattice model. With further theoretical work it may be possible to use our measurements to gain insight into the underlying Hamiltonian of TBG near the magic angle.     

Thermodynamic controls on rates of iron oxide reduction by extracellular electron shuttles

Anaerobic microbial respiration in suboxic and anoxic environments often involves particulate ferric iron (oxyhydr-)oxides as terminal electron acceptors. To ensure efficient respiration, a widespread strategy among iron-reducing microorganisms is the use of extracellular electron shuttles (EES) that transfer two electrons from the microbial cell to the iron oxide surface. Yet, a fundamental understanding of how EES–oxide redox thermodynamics affect rates of iron oxide reduction remains elusive. Attempts to rationalize these rates for different EES, solution pH, and iron oxides on the basis of the underlying reaction free energy of the two-electron transfer were unsuccessful. Here, we demonstrate that broadly varying reduction rates determined in this work for different iron oxides and EES at varying solution chemistry as well as previously published data can be reconciled when these rates are instead related to the free energy of the less exergonic (or even endergonic) first of the two electron transfers from the fully, two-electron reduced EES to ferric iron oxide. We show how free energy relationships aid in identifying controls on microbial iron oxide reduction by EES, thereby advancing a more fundamental understanding of anaerobic respiration using iron oxides.

The use of iron oxides as terminal electron acceptors in anaerobic microbial respiration is central to biogeochemical element cycling and pollutant transformations in many suboxic and anoxic environments (1–6). To ensure efficient electron transfer to solid-phase ferric iron, Fe(III), at circumneutral pH, metal-reducing microorganisms from diverse phylae use dissolved extracellular electron shuttle (EES), including quinones (7–9), flavins (10–16), and phenazines (17–19), to transfer two electrons per EES molecule from the respiratory chain proteins in the outer membrane of the microbial cell to the iron oxide (17, 20, 21). The oxidized EES can diffuse back to the cell surface for rereduction, thereby completing the catalytic redox cycle involving the EES.The electron transfer from the reduced EES to Fe(III) is considered a key step in overall microbial Fe(III) respiration. Several lines of evidence suggest that the free energy of the electron transfer reaction, ΔrG, controls Fe(III) reduction rates (15, 17, 22, 23). For instance, microbial Fe(III) oxide reduction by dissolved model quinones as EES was accelerated only for quinones with standard two-electron reduction potentials, EH,1,20, that fell into a relatively narrow range of −180±80 mV at pH 7 (24). Furthermore, in abiotic experiments, Fe(III) reduction rates by EES decreased with increasing ΔrG that resulted from increasing either EH,1,20 of the EES (25, 26), the concentration of Fe(II) in the system (27), or solution pH (25, 26, 28). However, substantial efforts to relate Fe(III) reduction rates for different EES species, iron oxides, and pH to the EH,1,20 averaged over both electrons transferred from the EES to the iron oxides were only partially successful (25, 28). Reaction free energies of complex redox processes involving the transfer of multiple electrons can readily be calculated using differences in the reduction potentials averaged over all electrons transferred, and this approach is well established in biogeochemistry and microbial ecology. For kinetic considerations, however, the use of averaged reduction potentials is inappropriate.Herein, we posit that rates of Fe(III) reduction by EES instead relate to the ΔrG of the less exergonic first one-electron transfer from the two-electron reduced EES species to the iron oxide, following the general notion that reaction rates scale with reaction free energies (29). Our hypothesis is based on the fact that, at circumneutral to acidic pH and for many EES, the reduction potential of the first electron transferred to the fully oxidized EES to form the one-electron reduced intermediate semiquinone species, EH,1, is lower than the reduction potential of the second electron transferred to the semiquinone to form the fully two-electron reduced EES species, EH,2 [i.e., EH,1<EH,2 (30–33)]. This difference in one-electron reduction potentials implies that the two-electron reduced EES (i.e., the hydroquinone) is the weaker one-electron reductant for Fe(III) as compared to the semiquinone species. We therefore expect that rates of iron oxide reduction relate to the ΔrG of the first electron transferred from the hydroquinone to Fe(III). The ΔrG of this first electron transfer may even be endergonic provided that the two-electron transfer is exergonic.We verified our hypothesis in abiotic model systems by demonstrating that reduction rates of two geochemically important crystalline iron oxides, goethite and hematite, by two-electron reduced quinone- and flavin-based EES over a wide pH range, and therefore thermodynamic driving force for Fe(III) reduction, correlate with the ΔrG of the first electron transferred from the fully reduced EES to Fe(III). We further show that rates of goethite and hematite reduction by EES reported in the literature are in excellent agreement with our rate data when comparing rates on the basis of the thermodynamics of the less exergonic first of the two electron transfers.     

Oxygen hole content,charge-transfer gap,covalency, and cuprate superconductivity

Experiments have shown that the families of cuprate superconductors that have the largest transition temperature at optimal doping also have the largest oxygen hole content at that doping [D. Rybicki et al., Nat. Commun. 7, 1–6 (2016)]. They have also shown that a large charge-transfer gap [W. Ruan et al., Sci. Bull. (Beijing) 61, 1826–1832 (2016)], a quantity accessible in the normal state, is detrimental to superconductivity. We solve the three-band Hubbard model with cellular dynamical mean-field theory and show that both of these observations follow from the model. Cuprates play a special role among doped charge-transfer insulators of transition metal oxides because copper has the largest covalent bonding with oxygen. Experiments [L. Wang et al., arXiv [Preprint] (2020). https://arxiv.org/abs/2011.05029 (Accessed 10 November 2020)] also suggest that superexchange is at the origin of superconductivity in cuprates. Our results reveal the consistency of these experiments with the above two experimental findings. Indeed, we show that covalency and a charge-transfer gap lead to an effective short-range superexchange interaction between copper spins that ultimately explains pairing and superconductivity in the three-band Hubbard model of cuprates.

Although several classes of high-temperature superconductors have been discovered, including pnictides, sulfur hydrides, and rare earth hydrides, cuprate high-temperature superconductors are still particularly interesting from a fundamental point of view because of the strong quantum effects expected from their doped charge-transfer insulator nature and single-band spin-one-half Fermi surface (1, 2).Among the most enduring mysteries of cuprate superconductivity is the experimental discovery, early on, that the hole content on oxygen plays a crucial role (2–5). Oxygen hole content (2np) is particularly relevant since NMR (5, 6) suggests a correlation between optimal Tc and 2np on the CuO2 planes: A higher oxygen hole content at the optimal doping of a given family of cuprates leads to a higher critical temperature. This is summarized in figure 2 of ref. 6. The charge-transfer gap also seems to play a central role for the value of Tc, as suggested by scanning tunneling spectroscopy (7) and by theory (8). Many studies have shown that doped holes primarily occupy oxygen orbitals (3, 9–11). This long unexplained role of oxygen hole content and charge-transfer gap on the strength of superconductivity in cuprates is addressed in this paper.The vast theoretical literature on the one-band Hubbard model in the strong-correlation limit shows that many of the qualitative experimental features of cuprate superconductors (12, 13) can be understood (14), but obviously not the above experimental facts regarding oxygen hole content. Furthermore, variational calculations (15) and various Monte Carlo approaches (16, 17) suggest that d-wave superconductivity in the one-band Hubbard model may not be the ground state, at least in certain parameter ranges (18, 19).It is thus important to investigate more realistic models, such as the three-band Emery-VSA (Varma–Schmitt-Rink–Abrahams) model that accounts for copper–oxygen hybridization of the single band that crosses the Fermi surface (20, 21). A variety of theoretical methods (8, 22–27) revealed many similarities with the one-band Hubbard model, but also differences related to the role of oxygen (28, 29).Investigating the causes for the variation of the transition temperature Tc for various cuprates is a key scientific goal of the quantum materials roadmap (30).^* We find and explain the above correlations found in NMR and in scanning tunnelling spectroscopy; highlight the importance of the difference between electron affinity of oxygen and ionization energy of copper (21, 31); and, finally, document how oxygen hole content, charge-transfer gap, and covalency conspire to create an effective superexchange interaction between copper spins that is ultimately responsible for superconductivity.We do not address questions related to intraunit-cell order (32, 33).     

Submesoscale dispersion in the vicinity of the Deepwater Horizon spill

Reliable forecasts for the dispersion of oceanic contamination are important for coastal ecosystems, society, and the economy as evidenced by the Deepwater Horizon oil spill in the Gulf of Mexico in 2010 and the Fukushima nuclear plant incident in the Pacific Ocean in 2011. Accurate prediction of pollutant pathways and concentrations at the ocean surface requires understanding ocean dynamics over a broad range of spatial scales. Fundamental questions concerning the structure of the velocity field at the submesoscales (100 m to tens of kilometers, hours to days) remain unresolved due to a lack of synoptic measurements at these scales. Using high-frequency position data provided by the near-simultaneous release of hundreds of accurately tracked surface drifters, we study the structure of submesoscale surface velocity fluctuations in the Northern Gulf of Mexico. Observed two-point statistics confirm the accuracy of classic turbulence scaling laws at 200-m to 50-km scales and clearly indicate that dispersion at the submesoscales is local, driven predominantly by energetic submesoscale fluctuations. The results demonstrate the feasibility and utility of deploying large clusters of drifting instruments to provide synoptic observations of spatial variability of the ocean surface velocity field. Our findings allow quantification of the submesoscale-driven dispersion missing in current operational circulation models and satellite altimeter-derived velocity fields.The Deepwater Horizon (DwH) incident was the largest accidental oil spill into marine waters in history with some 4.4 million barrels released into the DeSoto Canyon of the northern Gulf of Mexico (GoM) from a subsurface pipe over ∼84 d in the spring and summer of 2010 (1). Primary scientific questions, with immediate practical implications, arising from such catastrophic pollutant injection events are the path, speed, and spreading rate of the pollutant patch. Accurate prediction requires knowledge of the ocean flow field at all relevant temporal and spatial scales. Whereas ocean general circulation models were widely used during and after the DwH incident (2–6), such models only capture the main mesoscale processes (spatial scale larger than 10 km) in the GoM. The main factors controlling surface dispersion in the DeSoto Canyon region remain unclear. The region lies between the mesoscale eddy-driven deep water GoM (7) and the wind-driven shelf (8) while also being subject to the buoyancy input of the Mississippi River plume during the spring and summer months (9). Images provided by the large amounts of surface oil produced in the DwH incident revealed a rich array of flow patterns (10) showing organization of surface oil not only by mesoscale straining into the loop current “Eddy Franklin,” but also by submesoscale processes. Such processes operate at spatial scales and involve physics not currently captured in operational circulation models. Submesoscale motions, where they exist, can directly influence the local transport of biogeochemical tracers (11, 12) and provide pathways for energy transfer from the wind-forced mesoscales to the dissipative microscales (13–15). Dynamics at the submesoscales have been the subject of recent research (16–20). However, the investigation of their effect on ocean transport has been predominantly modeling based (13, 21–23) and synoptic observations, at adequate spatial and temporal resolutions, are rare (24, 25). The mechanisms responsible for the establishment, maintenance, and energetics of such features in the Gulf of Mexico remain unclear.Instantaneous measurement of all representative spatiotemporal scales of the ocean state is notoriously difficult (26). As previously reviewed (27), traditional observing systems are not ideal for synoptic sampling of near-surface flows at the submesoscale. Owing to the large spacing between ground tracks (28) and along-track signal contamination from high-frequency motions (29), gridded altimeter-derived sea level anomalies only resolve the largest submesoscale motions. Long time-series ship-track current measurements attain similar, larger than 2 km, spatial resolutions, and require averaging the observations over evolving ocean states (30). Simultaneous, two-point accoustic Doppler current profiler measurements from pairs of ships (25) provide sufficient resolution to show the existence of energetic submesoscale fluctuations in the mixed layer, but do not explicitly quantify the scale-dependent transport induced by such motions at the surface. Lagrangian experiments, centered on tracking large numbers of water-following instruments, provide the most feasible means of obtaining spatially distributed, simultaneous measurements of the structure of the ocean’s surface velocity field on 100-m to 10-km length scales.Denoting a trajectory by x(a, t), where x(a, t₀) = a, the relative separation of a particle pair is given by D(t,D0)=x(a1,t)−x(a2,t)=D0+∫t0tΔv(t′,D0)dt′, where the Lagrangian velocity difference is defined by Δv(t, D₀) = v(a₁, t) − v(a₂, t). The statistical quantities of interest, both practically and theoretically, are the scale-dependent relative dispersion D²(t) = 〈D ⋅ D〉 (averaged over particle pairs) and the average longitudinal or separation velocity, Δv(r), at a given separation, r. The velocity scale is defined by the second order structure function Δv(r)=〈δv2〉, where δv(r) = (v(x + r) − v(x)) ⋅ r/∥r∥ (31, 32) where the averaging is now conditioned on the pair separation r.The applicability of classical dispersion theories (32–34) developed in the context of homogeneous, isotropic turbulence with localized spectral forcing, to ocean flows subject to the effects of rotation, stratification, and complex forcing at disparate length and time scales remains unresolved. Turbulence theories broadly predict two distinct dispersion regimes depending upon the shape of the spatial kinetic energy spectrum, E(k) ∼ k^−β, of the velocity field (35). For sufficiently steep spectra (β ≥ 3) the dispersion is expected to grow exponentially, D ∼ e^λt with a scale-independent rate. At the submesoscales (∼ 100 m–10 km), this nonlocal growth rate will then be determined by the mesoscale motions currently resolved by predictive models. For shallower spectra (1 < β < 3), however, the dispersion is local, D ∼ t^2/(3−β), and the growth rate of a pollutant patch is dominated by advective processes at the scale of the patch. Accurate prediction of dispersion in this regime requires resolution of the advecting field at smaller scales than the mesoscale.Whereas compilations of data from dye measurements broadly support local dispersion in natural flows (36), the range of scales in any particular dye experiment is limited. A number of Lagrangian observational studies have attempted to fill this gap. LaCasce and Ohlmann (37) considered 140 pairs of surface drifters on the GoM shelf over a 5-y period and found evidence of a nonlocal regime for temporally smoothed data at 1-km scales. Koszalka et al. (38) using ??(100) drifter pairs with D₀ < 2 km launched over 18 mo in the Norwegian Sea, found an exponential fit for D²(t) for a limited time (t = 0.5 − 2 d), although the observed longitudinal velocity structure function is less clearly fit by a corresponding quadratic. They concluded that a nonlocal dispersion regime could not be identified. In contrast, Lumpkin and Elipot (39) found evidence of local dispersion at 1-km scales using 15-m drogued drifters launched in the winter-time North Atlantic. It is not clear how the accuracy of the Argos positioning system (150–1,000 m) used in these studies affects the submesoscale dispersion estimates. Schroeder et al. (40), specifically targeting a coastal front using a multiscale sampling pattern, obtained results consistent with local dispersion, but the statistical significance (maximum 64 pairs) remained too low to be definitive.     

Residue level quantification of protein stability in living cells

The intracellular milieu differs from the dilute conditions in which most biophysical and biochemical studies are performed. This difference has led both experimentalists and theoreticians to tackle the challenging task of understanding how the intracellular environment affects the properties of biopolymers. Despite a growing number of in-cell studies, there is a lack of quantitative, residue-level information about equilibrium thermodynamic protein stability under nonperturbing conditions. We report the use of NMR-detected hydrogen–deuterium exchange of quenched cell lysates to measure individual opening free energies of the 56-aa B1 domain of protein G (GB1) in living Escherichia coli cells without adding destabilizing cosolutes or heat. Comparisons to dilute solution data (pH 7.6 and 37 °C) show that opening free energies increase by as much as 1.14 ± 0.05 kcal/mol in cells. Importantly, we also show that homogeneous protein crowders destabilize GB1, highlighting the challenge of recreating the cellular interior. We discuss our findings in terms of hard-core excluded volume effects, charge–charge GB1-crowder interactions, and other factors. The quenched lysate method identifies the residues most important for folding GB1 in cells, and should prove useful for quantifying the stability of other globular proteins in cells to gain a more complete understanding of the effects of the intracellular environment on protein chemistry.Proteins function in a heterogeneous and crowded intracellular environment. Macromolecules comprise 20–30% of the volume of an Escherichia coli cell and reach concentrations of 300–400 g/L (1, 2). Theory predicts that the properties of proteins and nucleic acids can be significantly altered in cells compared with buffer alone (3, 4). Nevertheless, most biochemical and biophysical studies are conducted under dilute (<10 g/L macromolecules) conditions. Here, we augment the small but growing list of reports probing the equilibrium thermodynamic stability of proteins in living cells (5–9), and provide, to our knowledge, the first measurement of residue-level stability under nonperturbing conditions.Until recently, the effects of macromolecular crowding on protein stability were thought to be caused solely by hard-core, steric repulsions arising from the impenetrability of matter (4, 10, 11). The expectation was that crowding enhances stability by favoring the compact native state over the ensemble of denatured states. Increased attention to transient, nonspecific protein-protein interactions (12–15) has led both experimentalists (16–19) and theoreticians (20–22) to recognize the effects of chemical interactions between crowder and test protein when assessing the net effect of macromolecular crowding. These weak, nonspecific interactions can reinforce or oppose the effect of hard-core repulsions, resulting in increased or decreased stability depending on the chemical nature of the test protein and crowder (23–26).We chose the B1 domain of streptococcal protein G (GB1) (27) as our test protein because its structure, stability and folding kinetics have been extensively studied in dilute solution (28–38). Its small size (56 aa; 6.2 kDa) and high thermal stability make GB1 well suited for studies by NMR spectroscopy.Quantifying the equilibrium thermodynamic stability of proteins relies on determining the relative populations of native and denatured states. Because the denatured state ensemble of a stable protein is sparsely populated under native conditions, stability is usually probed by adding heat or a cosolute to promote unfolding so that the concentration ratio of the two states can be determined (39). However, stability can be measured without these perturbations by exploiting the phenomenon of backbone amide H/D exchange (40) detected by NMR spectroscopy (41). The observed rate of amide proton (N–H) exchange, k_obs, is related to equilibrium stability by considering a protein in which each N–H exists in an open (exposed, exchange-competent) state, or a closed (protected, exchange-incompetent) state (40, 42):closed(N−H)⇌kclkopopen(N−H)→kintopen(N−D)⇌kopkclclosed(N−D).[1]Each position opens and closes with rate constants, k_op and k_cl (where K_op = k_op/k_cl), and exchange from the open state occurs with intrinsic rate constant, k_int. Values for k_int are based on exchange data from unstructured peptides (43, 44). If the test protein is stable (i.e., k_cl >> k_op), the observed rate becomes:kobs=kopkintkcl+kint.[2]Exchange occurs within two limits (42). At the EX1 limit, closing is rate determining, and k_obs = k_op. This limit is usually observed for less stable proteins and at basic pH (45). Most globular proteins undergo EX2 kinetics, where exchange from the open state is rate limiting (i.e., k_cl >> k_int), and k_obs values can be converted to equilibrium opening free energies, ΔGop°′ (46):kobs=kopkclkint=Kopkint[3]ΔGop°′=−RT⁡lnkobskint,[4]where RT is the molar gas constant multiplied by the absolute temperature.The backbone amides most strongly involved in H-bonded regions of secondary structure exchange only from the fully unfolded state, yielding a maximum value of ΔGop°′ (47–49). For these residues ΔGop°′ approximates the free energy of denaturation, ΔGden°′, providing information on global stability. Lower amplitude fluctuations of the native state can give rise to partially unfolded forms (50), resulting in residues with ΔGop°′ values less than those of the global unfolders.In summary, NMR-detected H/D exchange can measure equilibrium thermodynamic stability of a protein at the level of individual amino acid residues under nonperturbing conditions. Inomata et al. (51) used this technique to measure k_obs values in human cells for four residues in ubiquitin, but experiments confirming the exchange mechanism were not reported and opening free energies were not quantified. Our results fill this void and provide quantitative residue-level protein stability measurements in living cells under nonperturbing conditions.     

Label-free probe of HIV-1 TAT peptide binding to mimetic membranes

The transacting activator of transduction (TAT) protein plays a key role in the progression of AIDS. Studies have shown that a +8 charged sequence of amino acids in the protein, called the TAT peptide, enables the TAT protein to penetrate cell membranes. To probe mechanisms of binding and translocation of the TAT peptide into the cell, investigators have used phospholipid liposomes as cell membrane mimics. We have used the method of surface potential sensitive second harmonic generation (SHG), which is a label-free and interface-selective method, to study the binding of TAT to anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-1′-rac-glycerol (POPG) and neutral 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) liposomes. It is the SHG sensitivity to the electrostatic field generated by a charged interface that enabled us to obtain the interfacial electrostatic potential. SHG together with the Poisson–Boltzmann equation yielded the dependence of the surface potential on the density of adsorbed TAT. We obtained the dissociation constants K_d for TAT binding to POPC and POPG liposomes and the maximum number of TATs that can bind to a given liposome surface. For POPC K_d was found to be 7.5 ± 2 μM, and for POPG K_d was 29.0 ± 4.0 μM. As TAT was added to the liposome solution the POPC surface potential changed from 0 mV to +37 mV, and for POPG it changed from −57 mV to −37 mV. A numerical calculation of K_d, which included all terms obtained from application of the Poisson–Boltzmann equation to the TAT liposome SHG data, was shown to be in good agreement with an approximated solution.The HIV type 1 (HIV-1) transacting activator of transduction (TAT) is an important regulatory protein for viral gene expression (1–3). It has been established that the TAT protein has a key role in the progression of AIDS and is a potential target for anti-HIV vaccines (4). For the TAT protein to carry out its biological functions, it needs to be readily imported into the cell. Studies on the cellular internalization of TAT have led to the discovery of the TAT peptide, a highly cationic 11-aa region (protein transduction domain) of the 86-aa full-length protein that is responsible for the TAT protein translocating across phospholipid membranes (5–8). The TAT peptide is a member of a class of peptides called cell-penetrating peptides (CPPs) that have generated great interest for drug delivery applications (ref. 9 and references therein). The exact mechanism by which the TAT peptide enters cells is not fully understood, but it is likely to involve a combination of energy-independent penetration and endocytosis pathways (8, 10). The first step in the process is high-affinity binding of the peptide to phospholipids and other components on the cell surface such as proteins and glycosaminoglycans (1, 9).The binding of the TAT peptide to liposomes has been investigated using a variety of techniques, each of which has its own advantages and limitations. Among the techniques are isothermal titration calorimetry (9, 11), fluorescence spectroscopy (12, 13), FRET (12, 14), single-molecule fluorescence microscopy (15, 16), and solid-state NMR (17). Second harmonic generation (SHG), as an interface-selective technique (18–24), does not require a label, and because SHG is sensitive to the interface potential, it is an attractive method to selectively probe the binding of the highly charged (+8) TAT peptide to liposome surfaces. Although coherent SHG is forbidden in centrosymmetric and isotropic bulk media for reasons of symmetry, it can be generated by a centrosymmetric structure, e.g., a sphere, provided that the object is centrosymmetric over roughly the length scale of the optical coherence, which is a function of the particle size, the wavelength of the incident light, and the refractive indexes at ω and 2ω (25–30). As a second-order nonlinear optical technique SHG has symmetry restrictions such that coherent SHG is not generated by the randomly oriented molecules in the bulk liquid, but can be generated coherently by the much smaller population of oriented interfacial species bound to a particle or planar surfaces. As a consequence the SHG signal from the interface is not overwhelmed by SHG from the much larger populations in the bulk media (25–28).The total second harmonic electric field, E_2ω, originating from a charged interface in contact with water can be expressed as (31–33)E2ω∝∑iχc,i(2)EωEω+∑jχinc,j(2)EωEω+χH2O(3)EωEωΦ,[1]where χc,i(2) represents the second-order susceptibility of the species i present at the interface; χinc,j(2) represents the incoherent contribution of the second-order susceptibility, arising from density and orientational fluctuations of the species j present in solution, often referred to as hyper-Rayleigh scattering; χH2O(3) is the third-order susceptibility originating chiefly from the polarization of the bulk water molecules polarized by the charged interface; Φ is the potential at the interface that is created by the surface charge; and E_ω is the electric field of the incident light at the fundamental frequency ω. The second-order susceptibility, χc,i(2), can be written as the product of the number of molecules, N, at the surface and the orientational ensemble average of the hyperpolarizability α_i⁽²⁾ of surface species i, yielding χc,i(2)=N〈αi(2)〉 (18). The bracket ?? indicates an orientational average over the interfacial molecules. The third term in Eq. 1 depicts a third-order process by which a second harmonic field is generated by a charged interface. This term is the focus of our work. The SHG signal is dependent on the surface potential created by the electrostatic field of the surface charges, often called the χ⁽³⁾ contribution to the SHG signal. The χ⁽³⁾ method has been used to extract the surface charge density of charged planar surfaces and microparticle surfaces, e.g., liposomes, polymer beads, and oil droplets in water (21, 25, 34–39).In this work, the χ⁽³⁾ SHG method is used to explore a biomedically relevant process. The binding of the highly cationic HIV-1 TAT peptide to liposome membranes changes the surface potential, thereby enabling the use of the χ⁽³⁾ method to study the binding process in a label-free manner. Two kinds of liposomes, neutral 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-1′-rac-glycerol (POPG), were investigated. The chemical structures of TAT, POPC, and POPG lipids are shown in Scheme 1.Open in a separate windowScheme 1.Chemical structures of HIV-1 TAT (47–57) peptide and the POPC and POPG lipids.