Unique cesium-binding sites in proteins, a case study with the sacrificial sulfur transferase LarE
Explore the source record for details and available documents.
Fellner, Matthias↗
SEARCH · Engineering Papers
Results for “Case Study”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
A Coupled Analysis of Atmospheric Mass Loss and Tidal Evolution in XUV Irradiated Exoplanets: The TRAPPIST-1 Case Study
Exoplanets residing close to their stars can experience evolution of both their physical structures and their orbits due to the influence of their host stars. In this work, we present a coupled analysis of dynamical tidal dissipation and atmospheric mass loss for exoplanets in X-ray and ultraviolet (XUV) irradiated environments. As our primary application, we use this model to study the TRAPPIST-1 system and place constraints on the interior structure and orbital evolution of the planets. We start by reporting on an ultraviolet continuum flux measurement (centered around ∼1900 Å) for the star TRAPPIST-1, based on 300 ks of Neil Gehrels Swift Observatory data, and which enables an estimate of the XUV-driven thermal escape arising from XUV photodissociation for each planet. We find that the X-ray flaring luminosity, measured from our X-ray detections, of TRAPPIST-1 is 5.6 × 10{sup −4} L {sub *}, while the full flux including non-flaring periods is 6.1 × 10{sup −5} L {sub *}, when L {sub *} is TRAPPIST-1's bolometric luminosity. We then construct a model that includes both atmospheric mass loss and tidal evolution and requires the planets to attain their present-day orbital elements during this coupled evolution. We use this model to constrain the ratio Q{sup ′}=3Q/2k{sub 2} for each planet. Finally, we use additional numerical models implemented with the Virtual Planet Simulator VPLanet to study ocean retention for these planets using our derived system parameters.
79 ASTRONOMY AND ASTROPHYSICS↗
WASP-107b’s Density Is Even Lower: A Case Study for the Physics of Planetary Gas Envelope Accretion and Orbital Migration
With a mass in the Neptune regime and a radius of Jupiter, WASP-107b presents a challenge to planet formation theories. Meanwhile, the planet’s low surface gravity and the star’s brightness also make it one of the most favorable targets for atmospheric characterization. Here, we present the results of an extensive 4 yr Keck/HIRES radial-velocity (RV) follow-up program of the WASP-107 system and provide a detailed study of the physics governing the accretion of the gas envelope of WASP-107b. We reveal that WASP-107b’s mass is only 1.8 Neptune masses (M {sub b} = 30.5 ± 1.7 M {sub ⊕}). The resulting extraordinarily low density suggests that WASP-107b has a H/He envelope mass fraction of >85% unless it is substantially inflated. The corresponding core mass of <4.6 M {sub ⊕} at 3σ is significantly lower than what is traditionally assumed to be necessary to trigger massive gas envelope accretion. We demonstrate that this large gas-to-core mass ratio most plausibly results from the onset of accretion at ≳1 au onto a low-opacity, dust-free atmosphere and subsequent migration to the present-day a {sub b} = 0.0566 ± 0.0017 au. Beyond WASP-107b, we also detect a second, more massive planet (M{sub c}sin i=0.36±0.04M{sub J}) on a wide eccentric orbit (e {sub c} = 0.28 ± 0.07) that may have influenced the orbital migration and spin–orbit misalignment of WASP-107b. Overall, our new RV observations and envelope accretion modeling provide crucial insights into the intriguing nature of WASP-107b and the system’s formation history. Looking ahead, WASP-107b will be a keystone planet to understand the physics of gas envelope accretion.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
The Utility of Infrasound in Global Monitoring of Extraterrestrial Impacts: A Case Study of the 2008 July 23 Tajikistan Bolide
Abstract Among the various observational techniques used for the detection of large bolides on a global scale is a low-frequency sound known as infrasound. Infrasound, which is also one of the four sensing modalities used by the International Monitoring System, offers continuous global monitoring and can be leveraged for planetary defense. Infrasonic records can provide an additional dimension for event characterization and a distinct perspective that might not be available through any other observational method. This paper describes the infrasonic detection and characterization of the bolide that disintegrated over Tajikistan on 2008 July 23. This event was detected by two infrasound stations at distances of 1530 and 2130 km. Propagation paths to one of the stations were not predicted by the model, despite being clearly detected. The presence of the signal is attributed to the acoustic energy being trapped in a weak but leaky stratospheric AtmoSOFAR channel. The infrasound signal analysis indicates that the shock originated at the point of the main breakup at an altitude of 35 km. The primary mode of the shock production of the signal detected at the two stations was a spherical blast resulting from the main gross fragmentation episode. The energy estimate, based on the signal period, is 0.17–0.51 kt of TNT equivalent, suggesting a mass of 6.6–23.5 tons. The corresponding object radius, assuming the chondritic origin, was 0.78–1.18 m.
79 ASTRONOMY AND ASTROPHYSICS↗
Bolide Infrasound Signal Morphology and Yield Estimates: A Case Study of Two Events Detected by a Dense Acoustic Sensor Network
Two bolides (2016 June 2 and 2019 April 4) were detected at multiple regional infrasound stations, with many of the locations receiving multiple detections. Analysis of the received signals was used to estimate the yield, location, and trajectory, as well as the type of shock that produced the received signal. The results from the infrasound analysis were compared with ground-truth information that was collected through other sensing modalities. This multimodal framework offers an expanded perspective on the processes governing bolide shock generation and propagation. The majority of signal features showed reasonable agreement between the infrasound-based interpretation and the other observational modalities, though the yield estimate from the 2019 bolide was significantly lower using the infrasound detections. There was also evidence suggesting that one of the detections was from a cylindrical shock that was initially propagating upward, which is unusual though not impossible.
79 ASTRONOMY AND ASTROPHYSICS↗
Exosphere Modeling of Proxima b: A Case Study of Photochemical Escape with a Venus-like Atmosphere
Exoplanets orbiting M dwarfs within habitable zones are exposed to stellar environments more extreme than that terrestrial planets experience in our solar system, which can significantly impact the atmospheres of the exoplanets and affect their habitability and sustainability. This study provides the first prediction of hot oxygen corona structure and the associated photochemical loss from a 1 bar CO 2 -dominated atmosphere of a Venus-like rocky exoplanet, where dissociative recombination of O 2 + ions is assumed to be the major source reaction for the escape of neutral O atoms and formation of the hot O corona (or exospheres) as on Mars and Venus. We employ a 3D Monte Carlo code to simulate the exosphere of Proxima Centauri b (PCb) based on the ionosphere simulated by a 3D magnetohydrodynamic model. Our simulation results show that variability of the stellar wind dynamic pressure over one orbital period of PCb does not affect the overall spatial structure of the hot O corona but contributes to the change in the global hot O escape rate that varies by an order of magnitude. The escape increases dramatically when the planet possesses its intrinsic magnetic fields as the ionosphere becomes more extended with the presence of a global magnetic field. Furthermore, the extended hot O corona may lead to a more extended H exosphere through collisions between thermal H and hot O, which exemplifies the importance of considering nonthermal populations in exospheres to interpret future observations.
79 ASTRONOMY AND ASTROPHYSICS↗
The Thermal and Kinematic Sunyaev–Zeldovich Effect in Galaxy Clusters and Filaments Using Multifrequency Temperature Maps of the Cosmic Microwave Background: A399–A401 Cluster Pair Case Study
We present a multifrequency and multi-instrument methodology to study the physical properties of galaxy clusters and cosmic filaments using cosmic microwave background observations. Our approach enables simultaneous measurement of both the thermal (tSZ) and kinematic Sunyaev–Zeldovich (kSZ) effects, incorporates relativistic corrections, and models astrophysical foregrounds such as thermal dust emission. We do this by jointly fitting a single physical model across multiple maps from multiple instruments at different frequencies, rather than fitting a model to a single Compton-y map. We demonstrate the success of this method by fitting the A399–A401 galaxy cluster pair and filament system using archival data from the Planck satellite and new, targeted deep data from the Atacama Cosmology Telescope, covering 11 different frequencies over 14 maps from 30 GHz to 545 GHz. Our tSZ results are consistent with previous work using Compton-y maps. We measure the line-of-sight peculiar velocities of the cluster–filament system using the kSZ effect and find statistical uncertainties on individual cluster peculiar velocities of ≲600 km s −1 , which are competitive with current state-of-the-art measurements. Additionally, we measure the optical depth of the filament component with a signal-to-noise of 8.5σ and reveal hints of its morphology. This modular approach is well-suited for application to future instruments across a wide range of millimeter and submillimeter wavebands.
Gill, Ajay S. [National Research Council of Canada↗
Neutrino and Electromagnetic Signatures from Superluminous Supernovae: A Case Study for SN 2017egm
Superluminous supernovae (SLSNe) are rare transients that are ∼10–100 times more luminous than ordinary stellar explosions, reaching peak optical luminosities ∼10 44 –10 45 erg s −1 . The energy source powering SLSNe remains uncertain. In this work, we explore the multiwavelength and multimessenger signatures of the scenario in which SLSNe are powered by a newly born millisecond magnetar. We model the dynamical evolution and emission from the coupled system comprised of the magnetar, wind, nebula, and supernova ejecta, consistently evaluating the pair multiplicity of the wind and nebula regions, and the bulk wind Lorentz factor governing the e + − e − injection spectra in the nebula. We compute the thermal and nonthermal electromagnetic signatures, neutrino signatures, and investigate their detection prospects. For SN 2017egm, the nearest observed SLSNe, our prediction for high-energy gamma rays matches the recent detection by the Fermi Large Area Telescope. For neutrinos, using SN 2017egm a canonical SLSNe, we find that in the era of the Vera C. Rubin Observatory, a stacking analysis with upcoming neutrino observatories can lead to 3σ detection significance of neutrino events from a population of SLSNe within a decade of operation.
Mukhopadhyay, Mainak [Fermi National Accelerator L↗
Wave Data Assimilation In Support Of Wave Energy Converter Power Prediction: Yakutat Alaska Case Study.
Abstract not provided.
Dallman, Ann Renee↗
Subgrid-scale horizontal and vertical variation of cloud water in stratocumulus clouds: a case study based on LES and comparisons with in situ observations
Abstract. Stratocumulus clouds in the marine boundary layer cover a large fraction of ocean surface and play an important role in the radiative energy balance of the Earth system. Simulating these clouds in Earth system models (ESMs) has proven to be extremely challenging, in part because cloud microphysical processes such as the autoconversion of cloud water into precipitation occur at scales much smaller than typical ESM grid sizes. An accurate autoconversion parameterization needs to account for not only the local microphysical process (e.g., the dependence on cloud water content qc and cloud droplet number concentration Nc) but also the subgrid-scale variability of the cloud properties that determine the process rate. Accounting for subgrid-scale variability is often achieved by the introduction of a so-called enhancement factor E. Previous studies of E for autoconversion have focused more on its dependence on cloud regime and ESM grid size, but they have largely overlooked the vertical dependence of E within the cloud. In this study, we use a large-eddy simulation (LES) model, initialized and constrained with in situ and surface-based measurements from a recent airborne field campaign, to characterize the vertical dependence of the horizontal variation of qc in stratocumulus clouds and the implications for E. Similar to our recent observational study (Zhang et al., 2021), we found that the inverse relative variance of qc, an index of horizontal homogeneity, generally increases from cloud base upward through the lower two-thirds of the cloud and then decreases in the uppermost one-third of the cloud. As a result, E decreases from cloud base upward and then increases towards the cloud top. We apply a decomposition analysis to the LES cloud water field to understand the relative roles of the mean and variances of qc in determining the vertical dependence of E. Our analysis reveals that the vertical dependence of the horizontal qc variability and enhancement factor E is a combined result of condensational growth throughout the lower portion of the cloud and entrainment mixing at cloud top. The findings of this study indicate that a vertically dependent E should be used in ESM autoconversion parameterizations.
54 ENVIRONMENTAL SCIENCES↗
Tools for uranium characterization in carbonate samples: case studies of natural U–Pb geochronology reference materials
Laser ablation U–Pb analyses of carbonate (LAcarb) samples has greatly expanded the potential for U–Pb dating to a variety of carbonate-producing settings. Carbonates that were previously considered impossible to date using isotope dilution methods may preserve radiogenic domains that can be dated using spatially resolved laser ablation geochronology techniques. Work is ongoing to identify reference materials and to consider best practices for LAcarb. In this study we apply standard and emerging characterization tool sets on three natural samples with the dual goal of enhancing the study of carbonates and establishing a new set of well-characterized natural reference materials for LAcarb studies. We start with the existing carbonate reference material WC-1 from the Permian Reef Complex of Texas, building on the published description to offer a deeper look at U and associated trace elements. We consider a tufa sample from the Miocene Barstow Formation of the Mojave Block, California, as a possible secondary calcite reference material due to its well-behaved U–Pb systematics. There are currently no natural dolomite standards. We present an unusual dolomite sample with very well-behaved U–Pb systematics from the Miocene of the Turkana Basin of Kenya as a possible dolomite reference material for LAcarb dating. In addition to using X-ray fluorescence (XRF) mapping and spectroscopy to better understand U in these natural samples, we have analyzed multiple aliquots of each of them for 87 Sr/ 86 Sr by thermal ionization mass spectrometry (TIMS). The Sr isotope compositions are analytically homogeneous within petrographically homogeneous regions of all three samples, and thus these materials could be used as Sr isotope standards as well. While not part of the current contribution, this combination could streamline simultaneous LA analyses of 87 Sr/ 86 Sr and U–Pb geochronology.
36 MATERIALS SCIENCE↗
Improving climate model coupling through a complete mesh representation: a case study with E3SM (v1) and MOAB (v5.x)
One of the fundamental factors contributing to the spatiotemporal inaccuracy in climate modeling is the mapping of solution field data between different discretizations and numerical grids used in the coupled component models. The typical climate computational workflow involves evaluation and serialization of the remapping weights during the preprocessing step, which is then consumed by the coupled driver infrastructure during simulation to compute field projections. Tools like Earth System Modeling Framework (ESMF) and TempestRemap offer capability to generate conservative remapping weights, while the Model Coupling Toolkit (MCT) that is utilized in many production climate models exposes functionality to make use of the operators to solve the coupled problem. However, such multistep processes present several hurdles in terms of the scientific workflow and impede research productivity. In order to overcome these limitations, we present a fully integrated infrastructure based on the Mesh Oriented datABase (MOAB) library, which allows for a complete description of the numerical grids and solution data used in each submodel. Through a scalable advancing-front intersection algorithm, the supermesh of the source and target grids are computed, which is then used to assemble the high-order, conservative, and monotonicity-preserving remapping weights between discretization specifications. The Fortran-compatible interfaces in MOAB are utilized to directly link the submodels in the Energy Exascale Earth System Model (E3SM) to enable online remapping strategies in order to simplify the coupled workflow process. We demonstrate the superior computational efficiency of the remapping algorithms in comparison with other state-of-the-science tools and present strong scaling results on large-scale machines for computing remapping weights between the spectral element atmosphere and finite volume discretizations on the polygonal ocean grids.
58 GEOSCIENCES↗
Novel estimation of aerosol processes with particle size distribution measurements: a case study with the TOMAS algorithm v1.0.0
Atmospheric aerosol microphysical processes are a significant source of uncertainty in predicting climate change. Specifically, aerosol nucleation, emissions, and growth rates, which are simulated in chemical transport models to predict the particle size distribution, are not understood well. However, long-term size distribution measurements made at several ground-based sites across Europe implicitly contain information about the processes that created those size distributions. This work aims to extract that information by developing and applying an inverse technique to constrain aerosol emissions as well as nucleation and growth rates based on hourly size distribution measurements. We developed an inverse method based upon process control theory into an online estimation technique to scale aerosol nucleation, emissions, and growth so that the model–measurement bias in three measured aerosol properties exponentially decays. The properties, which are calculated from the measured and predicted size distributions, used to constrain aerosol nucleation, emission, and growth rates are the number of particles with a diameter between 3 and 6 nm, the number with a diameter greater than 10 nm, and the total dry volume of aerosol ( N 3–6 , N 10 , V dry ), respectively. In this paper, we focus on developing and applying the estimation methodology in a zero-dimensional “box” model as a proof of concept before applying it to a three-dimensional simulation in subsequent work. The methodology is first tested on a dataset of synthetic and perfect measurements that span diverse environments in which the true particle emissions, growth, and nucleation rates are known. The inverse technique accurately estimates the aerosol microphysical process rates with an average and maximum error of 2 % and 13 %, respectively. Next, we investigate the effect that measurement noise has on the estimated rates. The method is robust to typical instrument noise in the aerosol properties as there is a negligible increase in the bias of the estimated process rates. Finally, the methodology is applied to long-term datasets of in situ size distribution measurements in western Europe from May 2006 through June 2007. At Melpitz, Germany, and Hyytiälä, Finland, the average diurnal profiles of estimated 3 nm particle formation rates are reasonable, having peaks near noon local time with average peak values of 1 and 0.15 cm –3 s –1 , respectively. The normalized absolute error in estimated N 3–6 , N 10 , and V dry at three European measurement sites is less than 15 %, showing that the estimation framework developed here has potential to decrease model–measurement bias while constraining uncertain aerosol microphysical processes.
54 ENVIRONMENTAL SCIENCES↗
Towards physics-inspired data-driven weather forecasting: integrating data assimilation with a deep spatial-transformer-based U-NET in a case study with ERA5
Abstract. There is growing interest in data-driven weather prediction (DDWP), e.g., using convolutional neural networks such as U-NET that are trained on data from models or reanalysis. Here, we propose three components, inspired by physics, to integrate with commonly used DDWP models in order to improve their forecast accuracy. These components are (1) a deep spatial transformer added to the latent space of U-NET to capture rotation and scaling transformation in the latent space for spatiotemporal data, (2) a data-assimilation (DA) algorithm to ingest noisy observations and improve the initial conditions for next forecasts, and (3) a multi-time-step algorithm, which combines forecasts from DDWP models with different time steps through DA, improving the accuracy of forecasts at short intervals. To show the benefit and feasibility of each component, we use geopotential height at 500 hPa (Z500) from ERA5 reanalysis and examine the short-term forecast accuracy of specific setups of the DDWP framework. Results show that the spatial-transformer-based U-NET (U-STN) clearly outperforms the U-NET, e.g., improving the forecast skill by 45 %. Using a sigma-point ensemble Kalman (SPEnKF) algorithm for DA and U-STN as the forward model, we show that stable, accurate DA cycles are achieved even with high observation noise. This DDWP+DA framework substantially benefits from large (O(1000)) ensembles that are inexpensively generated with the data-driven forward model in each DA cycle. The multi-time-step DDWP+DA framework also shows promise; for example, it reduces the average error by factors of 2–3. These results show the benefits and feasibility of these three components, which are flexible and can be used in a variety of DDWP setups. Furthermore, while here we focus on weather forecasting, the three components can be readily adopted for other parts of the Earth system, such as ocean and land, for which there is a rapid growth of data and need for forecast and assimilation.
54 ENVIRONMENTAL SCIENCES↗
KGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N<sub>2</sub>O emission using data from mesocosm experiments
Abstract. Agricultural nitrous oxide (N2O) emission accounts for a non-trivial fraction of global greenhouse gas (GHG) budget. To date, estimating N2O fluxes from cropland remains a challenging task because the related microbial processes (e.g., nitrification and denitrification) are controlled by complex interactions among climate, soil, plant and human activities. Existing approaches such as process-based (PB) models have well-known limitations due to insufficient representations of the processes or uncertainties of model parameters, and due to leverage recent advances in machine learning (ML) a new method is needed to unlock the “black box” to overcome its limitations such as low interpretability, out-of-sample failure and massive data demand. In this study, we developed a first-of-its-kind knowledge-guided machine learning model for agroecosystems (KGML-ag) by incorporating biogeophysical and chemical domain knowledge from an advanced PB model, ecosys, and tested it by comparing simulating daily N2O fluxes with real observed data from mesocosm experiments. The gated recurrent unit (GRU) was used as the basis to build the model structure. To optimize the model performance, we have investigated a range of ideas, including (1) using initial values of intermediate variables (IMVs) instead of time series as model input to reduce data demand; (2) building hierarchical structures to explicitly estimate IMVs for further N2O prediction; (3) using multi-task learning to balance the simultaneous training on multiple variables; and (4) pre-training with millions of synthetic data generated from ecosys and fine-tuning with mesocosm observations. Six other pure ML models were developed using the same mesocosm data to serve as the benchmark for the KGML-ag model. Results show that KGML-ag did an excellent job in reproducing the mesocosm N2O fluxes (overall r2=0.81, and RMSE=3.6 mgNm-2d-1 from cross validation). Importantly, KGML-ag always outperforms the PB model and ML models in predicting N2O fluxes, especially for complex temporal dynamics and emission peaks. Besides, KGML-ag goes beyond the pure ML models by providing more interpretable predictions as well as pinpointing desired new knowledge and data to further empower the current KGML-ag. We believe the KGML-ag development in this study will stimulate a new body of research on interpretable ML for biogeochemistry and other related geoscience processes.
54 ENVIRONMENTAL SCIENCES↗
Lossy checkpoint compression in full waveform inversion: a case study with ZFPv0.5.5 and the overthrust model
This paper proposes a new method that combines checkpointing methods with error-controlled lossy compression for large-scale high-performance full-waveform inversion (FWI), an inverse problem commonly used in geophysical exploration. This combination can significantly reduce data movement, allowing a reduction in run time as well as peak memory. In the exascale computing era, frequent data transfer (e.g., memory bandwidth, PCIe bandwidth for GPUs, or network) is the performance bottleneck rather than the peak FLOPS of the processing unit. Like many other adjoint-based optimization problems, FWI is costly in terms of the number of floating-point operations, large memory footprint during backpropagation, and data transfer overheads. Past work for adjoint methods has developed checkpointing methods that reduce the peak memory requirements during backpropagation at the cost of additional floating-point computations. Combining this traditional checkpointing with error-controlled lossy compression, we explore the three-way tradeoff between memory, precision, and time to solution. We investigate how approximation errors introduced by lossy compression of the forward solution impact the objective function gradient and final inverted solution. Empirical results from these numerical experiments indicate that high lossy-compression rates (compression factors ranging up to 100) have a relatively minor impact on convergence rates and the quality of the final solution.
58 GEOSCIENCES↗
Nudging allows direct evaluation of coupled climate models with in situ observations: a case study from the MOSAiC expedition
Comparing the output of general circulation models to observations is essential for assessing and improving the quality of models. While numerical weather prediction models are routinely assessed against a large array of observations, comparing climate models and observations usually requires long time series to build robust statistics. Here, we show that by nudging the large-scale atmospheric circulation in coupled climate models, model output can be compared to local observations for individual days. We illustrate this for three climate models during a period in April 2020 when a warm air intrusion reached the MOSAiC (Multidisciplinary drifting Observatory for the Study of Arctic Climate) expedition in the central Arctic. Radiosondes, cloud remote sensing and surface flux observations from the MOSAiC expedition serve as reference observations. The climate models AWI-CM1/ECHAM and AWI-CM3/IFS miss the diurnal cycle of surface temperature in spring, likely because both models assume the snowpack on ice to have a uniform temperature. CAM6, a model that uses three layers to represent snow temperature, represents the diurnal cycle more realistically. During a cold and dry period with pervasive thin mixed-phase clouds, AWI-CM1/ECHAM only produces partial cloud cover and overestimates downwelling shortwave radiation at the surface. AWI-CM3/IFS produces a closed cloud cover but misses cloud liquid water. Our results show that nudging the large-scale circulation to the observed state allows a meaningful comparison of climate model output even to short-term observational campaigns. We suggest that nudging can simplify and accelerate the pathway from observations to climate model improvements and substantially extends the range of observations suitable for model evaluation.
54 ENVIRONMENTAL SCIENCES↗