Quantitative Constraints Research Articles

A Comparison of Auditory Oddball Responses in Dorsolateral Prefrontal Cortex, Basolateral Amygdala, and Auditory Cortex of Macaque

The mismatch negativity (MMN) is an ERP component seen in response to unexpected "novel" stimuli, such as in an auditory oddball task. The MMN is of wide interest and application, but the neural responses that generate it are poorly understood. This is in part due to differences in design and focus between animal and human oddball paradigms. For example, one of the main explanatory models, the "predictive error hypothesis", posits differences in timing and selectivity between signals carried in auditory and prefrontal cortex (PFC). However, these predictions have not been fully tested because (1) noninvasive techniques used in humans lack the combined spatial and temporal precision necessary for these comparisons and (2) single-neuron studies in animal models, which combine necessary spatial and temporal precision, have not focused on higher order contributions to novelty signals. In addition, accounts of the MMN traditionally do not address contributions from subcortical areas known to be involved in novelty detection, such as the amygdala. To better constrain hypotheses and to address methodological gaps between human and animal studies, we recorded single neuron activity from the auditory cortex, dorsolateral PFC, and basolateral amygdala of two macaque monkeys during an auditory oddball paradigm modeled after that used in humans. Consistent with predictions of the predictive error hypothesis, novelty signals in PFC were generally later than in auditory cortex and were abstracted from stimulus-specific effects seen in auditory cortex. However, we found signals in amygdala that were comparable in magnitude and timing to those in PFC, and both prefrontal and amygdala signals were generally much weaker than those in auditory cortex. These observations place useful quantitative constraints on putative generators of the auditory oddball-based MMN and additionally indicate that there are subcortical areas, such as the amygdala, that may be involved in novelty detection in an auditory oddball paradigm.

The equilibrium size-frequency distribution of small craters reveals the effects of distal ejecta on lunar landscape morphology

Small craters of the lunar maria are observed to be in a state of equilibrium, in which the rate of production of new craters is, on average, equal to the rate of destruction of old craters. Crater counts of multiple lunar terrains over decades consistently show that the equilibrium cumulative size-frequency distribution (SFD) per unit area of small craters of radius >r is proportional r−2, and that the total crater density is a few percent of so-called geometric saturation, which is the maximum theoretical packing density of circular features. While it has long been known that the primary crater destruction mechanism for these small craters is steady diffusive degradation, there are few quantitative constraints on the processes that determine the degradation rate of meter to kilometer scale lunar surface features. Here we combine analytical modeling with a Monte Carlo landscape evolution code known as the Cratered Terrain Evolution Model to place constraints on which processes control the observed equilibrium size-frequency distribution for small craters. We find that the impacts by small distal ejecta fragments, distributed in spatially heterogeneous rays, is the largest contributor to the diffusive degradation which controls the equilibrium SFD of small craters. Other degradation or crater removal mechanisms, such cookie cutting, ejecta burial, seismic shaking, and micrometeoroid bombardment, likely contribute very little to the diffusive topographic degradation of the lunar maria at the meter scale and larger.

Sulphuric acid-mediated weathering on Taiwan buffers geological atmospheric carbon sinks

The chemical composition of the Gaoping River in Taiwan reflects the weathering of both silicate and carbonate rocks found in its metasedimentary catchment. Major dissolved ion chemistry and radiocarbon signatures of dissolved inorganic carbon (DIC) reveal the importance of pyrite-derived sulphuric acid weathering on silicates and carbonates. Two-thirds of the dissolved load of the Gaoping River derives from sulphuric acid-mediated weathering of rocks within its catchment. This is reflected in the lowest reported signatures DI14C for a small mountainous river (43 to 71 percent modern carbon), with rock-derived carbonate constituting a 14C-free DIC source. Using an inverse modelling approach integrating riverine major dissolved ion chemistry and DI14C, we provide quantitative constraints of mineral weathering pathways and calculate atmospheric CO2 fluxes resulting from the erosion of the Taiwan orogeny over geological timescales. The results reveal that weathering on Taiwan releases 0.31 ± 0.12 MtC/yr, which is offset by burial of terrestrial biospheric organic carbon in offshore sediments. The latter tips the balance with respect to the total CO2 budget of Taiwan such that the overall system acts as a net sink, with 0.24 ± 0.13 MtC/yr of atmospheric CO2 consumed over geological timescales.

Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data.

IgA nephropathy (IgAN) is the most prevalent cause of primary glomerular disease worldwide, and the cytokine A PRoliferation-Inducing Ligand (APRIL) is emerging as a key player in IgAN pathogenesis and disease progression. For a panel of anti-human APRIL antibodies with known antagonistic activity, we sought to define their structural mode of engagement to understand molecular mechanisms of action and aid rational antibody engineering. Reliable computational prediction of antibody-antigen complexes remains challenging, and experimental methods such as X-ray co-crystallography and cryoEM have considerable technical, resource, and throughput barriers. To overcome these limitations, we implemented an integrated and accessible experimental-computational workflow to more accurately predict structures of antibody-APRIL complexes. Specifically, a yeast surface display library encoding site-saturation mutagenized surface positions of APRIL was screened against a panel of anti-APRIL antibodies to rapidly obtain a comprehensive biochemical profile of mutational impact on binding for each antibody. The experimentally derived mutational profile data were used as quantitative constraints in a computational docking workflow optimized for antibodies, resulting in robust structural models of antibody-antigen complexes. The model results were confirmed by solving the cocrystal structure of one antibody-APRIL complex, which revealed strong agreement with our model. The models were used to rationally select and engineer one antibody for cross-species APRIL binding, which quite often aids further testing in relevant animal models. Collectively, we demonstrate a rapid, integrated computational-experimental approach to robustly predict antibody-antigen structures information, which can aid rational antibody engineering and provide insights into molecular mechanisms of action.

Retrieving Temperatures and Abundances of Exoplanet Atmospheres with High-resolution Cross-correlation Spectroscopy

Abstract High-resolution spectroscopy (R ≥ 25,000) has recently emerged as one of the leading methods for detecting atomic and molecular species in the atmospheres of exoplanets. However, it has so far been lacking a robust method for extracting quantitative constraints on the temperature structure and molecular/atomic abundances. In this work, we present a novel Bayesian atmospheric retrieval framework applicable to high-resolution cross-correlation spectroscopy (HRCCS) that relies on the cross-correlation between data and models to extract the planetary spectral signal. We successfully test the framework on simulated data and show that it can correctly determine Bayesian credibility intervals on atmospheric temperatures and abundances, allowing for a quantitative exploration of the inherent degeneracies. Furthermore, our new framework permits us to trivially combine and explore the synergies between HRCCS and low-resolution spectroscopy to maximally leverage the information contained within each. This framework also allows us to quantitatively assess the impact of molecular line opacities at high resolution. We apply the framework to VLT CRIRES K-band spectra of HD 209458 b and HD 189733 b and retrieve abundant carbon monoxide but subsolar abundances for water, which are largely invariant under different model assumptions. This confirms previous analysis of these data sets, but is possibly at odds with detections of H2O at different wavelengths and spectral resolutions. The framework presented here is the first step toward a true synergy between space observatories and ground-based high-resolution observations.

Human Stem Cell Structures Measured with Concentration-Calibrated Super-Resolution Microscopy

The mission of the Allen Institute for Cell Science is to understand and predict cell behaviors. The current project aims to create a stem cell state space by conjoining genomic, imaging, and phenotypic data from cells. We tagged most major molecular machineries (organelles, membranes and cytoskeleton) of human induced pluripotent stem cells (hiPSCs) with fluorescent proteins, and acquired large, reproducible datasets of each cell line for model input using an automated spinning-disk microscopy pipeline (www.allencell.org). We used the CRISPR/Cas9 system to fuse the fluorescent proteins directly to the protein of interest under the endogenous promoter. Therefore, the measured intensity of fluorescence emission is proportional to the protein distribution, localization, and dynamics of individual cells. To improve the accuracy of the integrated cell models we are building, we collected data with higher spatial resolution and measured absolute protein concentrations. We increased the resolution by about 1.7x using the Zeiss LSM 880 confocal microscope equipped with an Airy fast detector based on pixel reassignment. We created intensity/concentration calibration standards using cytosolic eGFP, cell-lysate, as well as purified eGFP in solution. We calibrated the concentration standards with FCS (Fluorescence Correlation Spectroscopy). The concentration standards allow quantitative comparison of data collected on different systems. We validated these approaches with quantitative Western blots, ELISA, and UV/VIS spectroscopy. We will discuss the advantages and limitations of the different standards, as well as the limitations, corrections, and controls necessary because of mono-allelic expression of eGFP-tagged proteins, inactive eGFP, and environmental changes of eGFP brightness. These results will add additional, quantitative constraints to our integrated models based on concentrations as well as finer structural detail due to the improved resolution.

Geologic Constraints on Early Mars Climate

Early Mars climate research has well-defined goals (MEPAG 2018). Achieving these goals requires geologists and climate modelers to coordinate. Coordination is easier if results are expressed in terms of well-defined parameters. Key parameters include the following quantitative geologic constraints. (1) Cumulative post-3.4 Ga precipitation-sourced water runoff in some places exceeded $1~\mbox{km}$ column. (2) There is no single Early Mars climate problem: the traces of ≥2 river-forming periods are seen. Relative to rivers that formed earlier in Mars history, rivers that formed later in Mars history are found preferentially at lower elevations, and show a stronger dependence on latitude. (3) The duration of the longest individual river-forming climate was ${>}(10^{2}\mbox{--}10^{3})~\mbox{yr}$ , based on paleolake hydrology. (4) Peak runoff production was ${>}0.1~\mbox{mm}/\mbox{hr}$ . However, (5) peak runoff production was intermittent, sustained (in a given catchment) for only <10% of the duration of river-forming climates. (6) The cumulative number of wet years during the valley-network-forming period was ${>}10^{5}~\mbox{yr}$ . (7) Post-Noachian light-toned, layered sedimentary rocks took ${>}10^{7}~\mbox{yr}$ to accumulate. However, (8) an “average” place on Mars saw water for ${<}10^{7}~\mbox{yr}$ after the Noachian, suggesting that the river-forming climates were interspersed with long globally-dry intervals. (9) Geologic proxies for Early Mars atmospheric pressure indicate pressure was not less than 0.012 bar but not much more than 1 bar. A truth table of these geologic constraints versus currently published climate models shows that the late persistence of river-forming climates, combined with the long duration of individual lake-forming climates, is a challenge for most models.

Advances in turbulence measurements using new Correlation ECE and nT-phase diagnostics at ASDEX Upgrade

Guided by predictions from nonlinear gyrokinetic simulations, two new turbulence diagnostics were designed and installed at ASDEX Upgrade (AUG) to probe the fundamentals of ion-scale turbulent electron heat transport. The first, a 30-channel correlation ECE (CECE) radiometer (105-128 GHz, 2nd harmonic X-mode), introduces a novel channel comb arrangement. This allows measurements of high radial resolution profiles (0:5 &lt; r/a &lt; 0:8) of low-k (k⍬⍴s &lt; 0:3) temperature fluctuation amplitudes, frequency spectra and radial correlation length profiles in unprecedented detail. The second diagnostic is formed by the addition of two W-band and one V-band X-mode reflectometers on the same line of sight as the CECE to enable measurements of the phase angle between turbulent density and temperature fluctuations. Historically, the radial alignment between reflectometer and radiometer has been a challenge due to the requirement that alignment is achieved within a radial correlation length (&lt; 5 10 mm). This challenge is significantly alleviated by using the CECE channel comb arrangement and the maximal coherence between reflectometer and radiometer can be unambiguously captured. Measurements of these quantities have been made in an AUG L-mode plasma, at the same radial location and have provided simultaneous quantitative constraints on realistic gyrokinetic simulations [Physics of Plasmas 25, 055903 (2018)] using the gyrokinetic code GENE. Here we present diagnostic detail for this study.

Toward a Proteome-Complete Computational Model of the Human Red Blood Cell

The human red blood cell has served as a starting point for the application and development of systems biology approaches due to its simplicity, intrinsic experimental accessibility, and importance in human health applications. Here, we present a multi-scale computational model of the human red blood cell that accounts for metabolism and macromolecules. Proteomics data are used to place quantitative constraints on individual protein complexes that catalyze metabolic reactions, as well as a total proteome capacity constraint. We explicitly describe molecular mechanisms-such as hemoglobin binding and the formation and detoxification of reactive oxygen species-and account for sequence variations between individuals, allowing for personalized physiological predictions. This model allows for direct computation of the oxyhemoglobin curve as a function of model species and a more accurate computation of the flux state of the metabolic network. More broadly, this work represents another step toward building increasingly more complete systems biology whole-cell models. DisclosuresNo relevant conflicts of interest to declare.

Unprecedented rains decimate surface microbial communities in the hyperarid core of the Atacama Desert

The hyperarid core of the Atacama Desert, the driest and oldest desert on Earth, has experienced a number of highly unusual rain events over the past three years, resulting in the formation of previously unrecorded hypersaline lagoons, which have lasted several months. We have systematically analyzed the evolution of the lagoons to provide quantitative field constraints of large-scale impacts of the rains on the local microbial communities. Here we show that the sudden and massive input of water in regions that have remained hyperarid for millions of years is harmful for most of the surface soil microbial species, which are exquisitely adapted to survive with meager amounts of liquid water, and quickly perish from osmotic shock when water becomes suddenly abundant. We found that only a handful of bacteria, remarkably a newly identified species of Halomonas, remain metabolically active and are still able to reproduce in the lagoons, while no archaea or eukaryotes were identified. Our results show that the already low microbial biodiversity of extreme arid regions greatly diminishes when water is supplied quickly and in great volumes. We conclude placing our findings in the context of the astrobiological exploration of Mars, a hyperarid planet that experienced catastrophic floodings in ancient times.

Quantitative constraints on autoxidation and dimer formation from direct probing of monoterpene-derived peroxy radical chemistry

Organic peroxy radicals (RO2) are key intermediates in the atmospheric degradation of organic matter and fuel combustion, but to date, few direct studies of specific RO2 in complex reaction systems exist, leading to large gaps in our understanding of their fate. We show, using direct, speciated measurements of a suite of RO2 and gas-phase dimers from O3-initiated oxidation of α-pinene, that ∼150 gaseous dimers (C16-20H24-34O4-13) are primarily formed through RO2 cross-reactions, with a typical rate constant of 0.75-2 × 10-12 cm3 molecule-1 s-1 and a lower-limit dimer formation branching ratio of 4%. These findings imply a gaseous dimer yield that varies strongly with nitric oxide (NO) concentrations, of at least 0.2-2.5% by mole (0.5-6.6% by mass) for conditions typical of forested regions with low to moderate anthropogenic influence (i.e., ≤50-parts per trillion NO). Given their very low volatility, the gaseous C16-20 dimers provide a potentially important organic medium for initial particle formation, and alone can explain 5-60% of α-pinene secondary organic aerosol mass yields measured at atmospherically relevant particle mass loadings. The responses of RO2, dimers, and highly oxygenated multifunctional compounds (HOM) to reacted α-pinene concentration and NO imply that an average ∼20% of primary α-pinene RO2 from OH reaction and 10% from ozonolysis autoxidize at 3-10 s-1 and ≥1 s-1, respectively, confirming both oxidation pathways produce HOM efficiently, even at higher NO concentrations typical of urban areas. Thus, gas-phase dimer formation and RO2 autoxidation are ubiquitous sources of low-volatility organic compounds capable of driving atmospheric particle formation and growth.

Hybrid metabolic network completion

AbstractMetabolic networks play a crucial role in biology since they capture all chemical reactions in an organism. While there are networks of high quality for many model organisms, networks for less studied organisms are often of poor quality and suffer from incompleteness. To this end, we introduced in previous work an answer set programming (ASP)-based approach to metabolic network completion. Although this qualitative approach allows for restoring moderately degraded networks, it fails to restore highly degraded ones. This is because it ignores quantitative constraints capturing reaction rates. To address this problem, we propose a hybrid approach to metabolic network completion that integrates our qualitative ASP approach with quantitative means for capturing reaction rates. We begin by formally reconciling existing stoichiometric and topological approaches to network completion in a unified formalism. With it, we develop a hybrid ASP encoding and rely upon the theory reasoning capacities of the ASP system clingo for solving the resulting logic program with linear constraints over reals. We empirically evaluate our approach by means of the metabolic network of Escherichia coli. Our analysis shows that our novel approach yields greatly superior results than obtainable from purely qualitative or quantitative approaches.

Dual‐Isotope Constraints on Seasonally Resolved Source Fingerprinting of Black Carbon Aerosols in Sites of the Four Emission Hot Spot Regions of China

AbstractDespite much recent efforts, the emission sources of black carbon (BC) aerosols―central input to understanding and predicting environmental and climate impact―remain highly uncertain. Here we present observational δ13C/Δ14C‐based constraints on the sources of BC aerosols over the four seasons in each of the four key hot spot emission regions of China: Beijing‐Tianjin‐Hebei (BTH‐Wuqing; where Wuqing is the sampling location), Yangtze River Delta (YRD‐Haining), Pearl River Delta (PRD‐Zhongshan), and Sichuan Basin (SC‐Deyang). Overall, BC loadings were highest in winter, yet elevated loadings were also observed in other seasons, for example, spring at SC‐Deyang and fall at PRD‐Zhongshan. Annually, the dominant BC sources were coal (50 ± 20%) for BTH‐Wuqing, liquid fossil for YRD‐Haining (46 ± 8%) and PRD‐Zhongshan (48 ± 18%), whereas liquid fossil (42 ± 17%) and biomass burning (41 ± 14%) equally affected SC‐Deyang. There is also different but distinct seasonalities in BC sources for the different sites. As an example, for BTH‐Wuqing coal burning increased from summer to winter, while summer and spring BTH‐Wuqing were more influenced by liquid fossil. In contrast, for YRD‐Haining, the relative importance of emission sources was more constant over the year. These quantitative observational constraints on source‐seasonality of BC aerosols in receptor sites located in China's four key economic zones highlight that regulatory control on BC aerosol emissions from different fuels should consider both seasonal and regional variations. Our results also suggest that models on estimates of BC‐induced climate and air quality should consider variations over both regional and seasonal scales.

Adjoint inversion of Chinese non-methane volatile organic compound emissions using space-based observations of formaldehyde and glyoxal

Abstract. We used the GEOS-Chem model and its adjoint to quantify Chinese non-methane volatile organic compound (NMVOC) emissions for the year 2007, using the tropospheric column concentrations of formaldehyde and glyoxal observed by the Global Ozone Monitoring Experiment 2A (GOME-2A) instrument and the Ozone Monitoring Instrument (OMI) as quantitative constraints. We conducted a series of inversion experiments using different combinations of satellite observations to explore their impacts on the top-down emission estimates. Our top-down estimates for Chinese annual total NMVOC emissions were 30.7 to 49.5 (average 41.9) Tg yr−1, including 16.4 to 23.6 (average 20.2) Tg yr−1 from anthropogenic sources, 12.2 to 22.8 (average 19.2) Tg yr−1 from biogenic sources, and 2.08 to 3.13 (average 2.48) Tg yr−1 from biomass burning. In comparison, the a priori estimate for Chinese annual total NMVOC emissions was 38.3 Tg yr−1, including 18.8 Tg yr−1 from anthropogenic sources, 17.3 Tg yr−1 from biogenic sources, and 2.27 Tg yr−1 from biomass burning. The simultaneous use of glyoxal and formaldehyde observations helped distinguish the NMVOC species from different sources and was essential in constraining anthropogenic emissions. Our four inversion experiments consistently showed that the Chinese anthropogenic emissions of NMVOC precursors of glyoxal were larger than the a priori estimates. Our top-down estimates for Chinese annual emission of anthropogenic aromatics (benzene, toluene, and xylene) ranged from 5.5 to 7.9 Tg yr−1, 2 % to 46 % larger than the estimate of the a priori emission inventory (5.4 Tg yr−1). Three out of our four inversion experiments indicated that the seasonal variation in Chinese NMVOC emissions was significantly stronger than indicated in the a priori inventory. Model simulations driven by the average of our top-down NMVOC emission estimates (which had a stronger seasonal variation than the a priori) showed that surface afternoon ozone concentrations over eastern China increased by 1–8 ppb in June and decreased by 1–10 ppb in December relative to the simulations using the a priori emissions and were in better agreement with measurements. We concluded that the satellite observations of formaldehyde and glyoxal together provided quantitative constraints on the emissions and source types of NMVOCs over China and improved our understanding on regional chemistry.

Long-term evolution of the West African transform margin: estimates of denudation from Benin using apatite thermochronology

The Benin continental margin was formed during the breakup of Gondwana through oblique rifting along transform faults. The evolution of topography following breakup directly affects the evolution of sedimentary basins, which has major implications for hydrocarbon exploration in the region. Quantitative constraints on erosion across Benin are limited to the Cenozoic, based on analysis of dissected lateritic palaeolandscapes. To resolve the Mesozoic erosion history, we have obtained apatite fission-track and single-grain (U–Th–Sm)/He data from 18 samples collected across a 600 km long transect through Benin. We invert these data, including available geological and geomorphological constraints, to obtain time–temperature paths, which are used to estimate magnitudes of denudation over the last 200 myr. Our study suggests that denudation was focused over a c. 300 km long seaward sloping limb of the marginal upwarp and at the southern margin of the interior Iullemmeden Basin from 140 to 100 Ma with lower magnitudes of denudation characterizing the continental interior and post-Cretaceous evolution of the margin. Models are consistent with modest burial ( c. 1 km) of the Iullemmeden Basin between 120 and 85 Ma, and of the continental margin between 85 and 45 Ma. By the Eocene the first-order relief of Benin had developed, with regional erosion rates &lt;20 m Ma −1 since then. Supplementary information: Full details of the analytical data and modelling results, including the various constraints, and further data on denudation and burial magnitudes and rates are available at https://doi.org/10.6084/m9.figshare.c.4220804

A treasure chest full of nanogranitoids: an archive to investigate crustal melting in the Bohemian Massif

Abstract The central European Bohemian Massif has undergone over two centuries of scientific investigation which has made it a pivotal area for the development and testing of modern geological theories. The discovery of melt inclusions in high-grade rocks, either crystallized as nanogranitoids or as glassy inclusions, prompted the re-evaluation of the area with an ‘inclusionist’ eye. Melt inclusions have been identified in a wide range of rocks, including felsic/perpotassic granulites, migmatites, eclogites and garnet clinopyroxenites, all the result of melting events albeit over a wide range of pressure/temperature conditions (800–1000°C/0.5–5 GPa). This contribution provides an overview of such inclusions and discusses the qualitative and quantitative constraints they provide for melting processes, and the nature of melts and fluids involved in these processes. In particular, data on trace-element signatures of melt inclusions trapped at mantle depths are presented and discussed. Moreover, experimental re-homogenization of nanogranitoids provided microstructural criteria allowing assessment of the conditions at which melt and host are mutually stable during melting. Overall this work aims to provide guidelines and suggestions for petrologists wishing to explore the fascinating field of melt inclusions in metamorphic terranes worldwide, based on the newest discoveries from the still-enigmatic Bohemian Massif.

Synthesis of the structure for the optimal system of flow treatment of raw materials

This paper demonstrates that contemporary studies into optimization of technological processes do not take into consideration in the models of systems and in the applied criteria the requirements to the overall efficiency of the process and compliance with the objectives of the owner of a privately-held industrial enterprise. This necessitates the reduction of cost and time of a technological operation, as well as maximization of the added value of the primary product. The effectiveness of the system of a flow treatment of raw materials is estimated using a specialized model, which was synthesized in the course of this work. The proposed model is different in that it includes units to calculate the unit cost of a product depending on the quality indicator and the degree of correspondence to the proposed quantitative and qualitative constraints. There are calculation units for the dynamics of change in a qualitative indicator of the finished product depending on a flow of raw materials and the energy supplied to treatment. The units are also required to calculate the consumption of resource and energy for the transporting and treatingg parts of the system in the interval, defined as the time taken for a conditional batch to pass through the installation. Using the developed model makes it possible to determine the value for the performance indicator for any permissible technological mode and to perform a global optimization of the process. Thus, there is a transition from the requirements to efficiency in general terms to setting the technological process parameters. Here we propose the analytical form for a performance indicator, suitable as an optimization criterion for modes of the technological installation with a continuous supply of raw-material and energy products. We have experimentally studied a model of the flow-through electric heater with units that calculate time and cost parameters, which has demonstrated its adequacy. The developed optimality criterion was verified and the possibility of its application was proven for determining the optimal permissible operating modes of the technological equipment with a continuous supply of raw materials and energy.

Quantitative Constraints on the Reionization History from the IGM Damping Wing Signature in Two Quasars at z &gt; 7

Abstract During reionization, neutral hydrogen in the intergalactic medium (IGM) imprints a damping wing absorption feature on the spectrum of high-redshift quasars. A detection of this signature provides compelling evidence for a significantly neutral universe, and enables measurements of the hydrogen neutral fraction x H i (z) at that epoch. Obtaining reliable quantitative constraints from this technique, however, is challenging due to stochasticity induced by the patchy inside-out topology of reionization, degeneracies with quasar lifetime, and the unknown unabsorbed quasar spectrum close to rest-frame Lyα. We combine a large-volume semi-numerical simulation of reionization topology with 1D radiative transfer through high-resolution hydrodynamical simulations of the high-redshift universe to construct models of quasar transmission spectra during reionization. Our state-of-the-art approach captures the distribution of damping wing strengths in biased quasar halos that should have reionized earlier, as well as the erosion of neutral gas in the quasar environment caused by its own ionizing radiation. Combining this detailed model with our new technique for predicting the quasar continuum and its associated uncertainty, we introduce a Bayesian statistical method to jointly constrain the neutral fraction of the universe and the quasar lifetime from individual quasar spectra. We apply this methodology to the spectra of the two quasars with the highest redshifts known, ULAS J1120+0641 and ULAS J1342+0928, and measure volume-averaged neutral fractions and (posterior medians and 68% credible intervals) when marginalized over quasar lifetimes of 103 ≤ t q ≤ 108 yr.

Seconds after impact: Insights into the thermal history of impact ejecta from diffusion between lechatelierite and host glass in tektites and experiments

Tektites contain inclusions of lechatelierite, nearly pure SiO2 glass formed by quenching of quartz grains melted during hypervelocity impacts. We report the discovery in a tektite of chemically zoned boundary layers (ca 20 μm) between lechatelierite and host felsic glass. These boundary layers in tektites formed by chemical diffusion between molten silica inclusions (quenched to lechatelierite on cooling) and surrounding felsic melt. We reproduced the details of these boundary layers via experiments on mixtures of powdered natural tektite plus quartz grains heated to 1800–2400 °C for 1–120 s using an aerodynamic levitation laser heating furnace. The results of these experiments were used to provide quantitative constraints on possible thermal histories of the natural sample.The experiments successfully reproduced all major aspects of the concentration profiles from the natural sample including diffusion length scale, strong asymmetry of the concentration profiles with respect to the Matano plane (due to the strong concentration dependence of the diffusivities of all oxides on SiO2 content), similarities in lengths of the diffusive profiles (due to control by the diffusion of SiO2 on the diffusivity of the other oxides), and differences in the shapes of the profiles among the oxides (including a maximum in the diffusion profile of K2O due to uphill diffusion). The characteristic lengths of all non-alkali oxide profiles are proportional to t from which diffusivities and activation energies can be derived; these results are consistent with measurements in melts with lower SiO2 contents and at lower temperatures reported in the literature. We also fit the experimental profiles of SiO2 and Al2O3 using simple formulations of the dependence of their diffusivities on SiO2 content and temperature, yielding results similar to those obtained from the t dependence of the characteristic profile lengths.The quantitative characterization of diffusion in boundary layers based on our experiments allow us to set limits on the thermal history of the natural tektite in which the boundary layers were discovered. If the interdiffusion between the silica and felsic melts occurred at constant temperature, the duration of heating experienced by the natural tektite we studied depends on temperature; possible solutions include heating at ∼2000 °C for ∼70 s, −2400 °C for ∼3 s. We also explored non-isothermal, asymptotic cooling histories; for a maximum temperature of 2400 °C, a characteristic cooling time scale of ∼50 s is implied, whereas, for 2000 °C, the time scale is ∼1400 s. Further, a maximum temperature of ∼2360 °C yields an effective diffusive time scale of ∼5 s, a cooling time scale of ∼90 s, and a cooling rate at the glass transition temperature of ∼5 °C/s; results that are consistent with independent estimates of cooling time scales for ∼1 cm clasts (Xu and Zhang, 2002), as well as cooling rates at the glass transition temperature (Wilding et al., 1996) – thus satisfying all currently available relevant data. More complex T-t paths are possible and can also be modeled using our experimental results and compared with and used as tests of the accuracy of physical models of tektite-forming impact events.

Proton auroras during the transitional stage of substorm onset

Optical auroral measurements repeatedly reveal the existence of a transitional stage between a quiescent preexisting arc and its significant auroral expansion in a substorm onset. Such a transitional stage of substorm onset (TSSO) is characterized by a gradual intensification and the emergence of auroral beads, along the preexisting arc. However, existing studies on TSSO are limited to electron auroras which are dominant in optical luminosity. In this study, we collect 12 substorm events to investigate the proton auroral features during the late growth phase and the TSSO. Our major results include: (1) we confirm the previous notion that the onset electron auroral arc is usually located at the poleward “shoulder” of the main proton auroral band. (2) While the electron auroral arc typically intensifies by a few times or even an order of magnitude during the TSSO, the concurrent proton aurora at the same location as the electron auroral arc shows much less noticeable variations. The proton auroral variations averaged over the arc band, as well as that integrated over the entire latitudinal range, are mostly within 10% of their mean late-growth-phase levels during the TSSO. Substantial intensifications of proton auroras occur after the poleward expansion of electron auroras. Even considering the spatial spreading of proton auroras, we estimate that the variation of ion precipitation fluxes on top of the ionosphere would be typically < 30% during the TSSO. The above observations impose implications and quantitative constraints on the possible mechanisms of TSSO and substorm onset. We assert that there is no significant ion energization or large-scale magnetic field reconfiguration during the TSSO. Instead, it is likely that the underlying mechanism of the TSSO might be certain kind of ky-dominated instability wave mode. The instability wavelength is comparable to the ion gyroradius, so that the ions are demagnetized, suppressing ion flux variations with the instability. Enhancing upward electric fields in the auroral acceleration region during the TSSO may also play a partial role in weakening the ion precipitation flux variation.