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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.

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At least 451 records · Page 25

A Bayesian Approach to Regional Decadal Predictability: Sparse Parameter Estimation in High-Dimensional Linear Inverse Models of High-Latitude Sea Surface Temperature Variability

Stochastic reduced models are an important tool in climate systems whose many spatial and temporal scales cannot be fully discretized or underlying physics may not be fully accounted for. One form of reduced model, the linear inverse model (LIM), has been widely used for regional climate predictability studies—typically focusing more on tropical or midlatitude studies. However, most LIM fitting techniques rely on point estimation techniques deriving from fluctuation–dissipation theory. In this methodological study we explore the use of Bayesian inference techniques for LIM parameter estimation of sea surface temperature (SST), to quantify the skillful decadal predictability of Bayesian LIM models at high latitudes. We show that Bayesian methods, when compared to traditional point estimation methods for LIM-type models, provide better calibrated probabilistic skill, while simultaneously providing better point estimates due to the regularization effect of the prior distribution in high-dimensional problems. We compare the effect of several priors, as well as maximum likelihood estimates, on 1) estimating parameter values on a perfect model experiment and 2) producing calibrated 1-yr SST anomaly forecast distributions using a preindustrial control run of the Community Earth System Model (CESM). Finally, we employ a host of probabilistic skill metrics to determine the extent to which an LIM can forecast SST anomalies at high latitudes. We find that the choice of prior distribution has an appreciable impact on estimation outcomes, and priors that emphasize physically relevant properties enhance the model’s ability to capture variability of SST anomalies.

54 ENVIRONMENTAL SCIENCES↗

Incorporating dynamic recrystallization into a crystal plasticity model for high-temperature deformation of Ti-6Al-4V

During hot deformation of (α + β) titanium alloys, the simultaneous action of strain and temperature in the (α + β) regime facilitates dynamic recovery, dynamic recrystallization (DRX), and phase transformations via non-equilibrium paths. DRX is manifested in the form of fine recrystallized α or β grains. Here, in the present study, a two-phase crystal plasticity finite element framework (CP-DRX) has been developed which incorporates DRX kinetics into the crystal plasticity (CP) model to predict the flow characteristics of Ti-6Al-4V alloys during thermo-mechanical processing. The CP slip system parameters, as well as elastic properties from both α and β phases of Ti, are calibrated for different strain rate conditions. An EBSD-informed two-phase microstructure representation has been utilized in the CP-DRX framework to explore the time-dependent evolution of DRX microstructure and crystal orientation for different strain rate conditions. The proposed CP-DRX can capture the evolution of crystal orientation and plastic flow stress–strain response of polycrystalline Ti-6Al-4V during the deformation process. Furthermore, the proposed model is able to capture the softening behavior, observed in average stress–strain response from experiments performed using a Gleeble thermomechanical simulator and predict the recrystallization texture.

(α+ β)-Titanium (Ti) Alloys↗

Neutralization titer biomarker for antibody-mediated prevention of HIV-1 acquisition

The Antibody Mediated Prevention trials showed that the broadly neutralizing antibody (bnAb) VRC01 prevented acquisition of human immunodeficiency virus-1 (HIV-1) sensitive to VRC01. Using AMP trial data, here we show that the predicted serum neutralization 80% inhibitory dilution titer (PT 80 ) biomarker—which quantifies the neutralization potency of antibodies in an individual’s serum against an HIV-1 isolate—can be used to predict HIV-1 prevention efficacy. Similar to the results of nonhuman primate studies, an average PT 80 of 200 (meaning a bnAb concentration 200-fold higher than that required to reduce infection by 80% in vitro) against a population of probable exposing viruses was estimated to be required for 90% prevention efficacy against acquisition of these viruses. Based on this result, we suggest that the goal of sustained PT 80 <200 against 90% of circulating viruses can be achieved by promising bnAb regimens engineered for long half-lives. We propose the PT 80 biomarker as a surrogate endpoint for evaluatinon of bnAb regimens, and as a tool for benchmarking candidate bnAb-inducing vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

Improving Solution Accuracy and Convergence for Stochastic Physics Parameterizations with Colored Noise

Stochastic parameterizations are used in numerical weather prediction and climate modeling to help capture the uncertainty in the simulations and improve their statistical properties. Convergence issues can arise when time integration methods originally developed for deterministic differential equations are applied naively to stochastic problems. In previous studies, it has been demonstrated that a correction term, known in stochastic analysis as the Itô correction, can help improve solution accuracy for various deterministic numerical schemes and ensure convergence to the physically relevant solution without substantial computational overhead. The usual formulation of the Itô correction is valid only when the stochasticity is represented by white noise. In this study, a generalized formulation of the Itô correction is derived for noises of any color. The formulation is applied to a test problem described by an advection–diffusion equation forced with a spectrum of fast processes. We present numerical results for cases with both constant and spatially varying advection velocities to show that, for the same time step sizes, the introduction of the generalized Itô correction helps to substantially reduce time integration error and significantly improve the convergence rate of the numerical solutions when the forcing term in the governing equation is rough (fast varying); alternatively, for the same target accuracy, the generalized Itô correction allows for the use of significantly longer time steps and, hence, helps to reduce the computational cost of the numerical simulation.

54 ENVIRONMENTAL SCIENCES↗

Global Precipitation Measurement (GPM) Orbit Design and Autonomous Maneuvers

The NASA Goddard Space Flight Center's Global Precipitation Measurement (GPM) mission will meet a challenge of measuring worldwide precipitation every three hours. The GPM spacecraft, part of a constellation, will be required to maintain a circular orbit in a high drag environment to accomplish this challenge. Analysis by the Flight Dynamics Analysis Branch has shown that the prime orbit altitude of 40% is necessary to prevent ground track repeating. Combined with goals to minimize maneuver impacts to science data collection and enabling reasonable long-term orbit predictions, the GPM project has decided to fly an autonomous maneuver system. This system is a derivative of the successful New Millennium Program technology flown onboard the Earth Observing-1 mission. This paper presents the driving science requirements and goals of the mission and shows how they will be met. Analysis of the orbit optimization and the AV requirements for several ballistic properties are presented. The architecture of the autonomous maneuvering system to meet the goals and requirements is presented along with simulations using a GPM prototype. Additionally, the use of the GPM autonomous system to mitigate possible collision avoidance and to aid other spacecraft systems during navigation outages is explored.

Folta, David↗

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Here we present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

protein complexes↗

A Multi-Season Study of the Effects of MODIS Sea-Surface Temperatures on Operational WRF Forecasts at NWS Miami, FL

Studies at the Short-term Prediction Research and Transition (SPORT) Center have suggested that the use of Moderate Resolution Imaging Spectroradiometer (MODIS) sea-surface temperature (SST) composites in regional weather forecast models can have a significant positive impact on short-term numerical weather prediction in coastal regions. Recent work by LaCasse et al (2007, Monthly Weather Review) highlights lower atmospheric differences in regional numerical simulations over the Florida offshore waters using 2-km SST composites derived from the MODIS instrument aboard the polar-orbiting Aqua and Terra Earth Observing System satellites. To help quantify the value of this impact on NWS Weather Forecast Offices (WFOs), the SPORT Center and the NWS WFO at Miami, FL (MIA) are collaborating on a project to investigate the impact of using the high-resolution MODIS SST fields within the Weather Research and Forecasting (WRF) prediction system. The project's goal is to determine whether more accurate specification of the lower-boundary forcing within WRF will result in improved land/sea fluxes and hence, more accurate evolution of coastal mesoscale circulations and the associated sensible weather elements. The NWS MIA is currently running WRF in real-time to support daily forecast operations, using the National Centers for Environmental Prediction Nonhydrostatic Mesoscale Model dynamical core within the NWS Science and Training Resource Center's Environmental Modeling System (EMS) software. Twenty-seven hour forecasts are run dally initialized at 0300, 0900, 1500, and 2100 UTC on a domain with 4-km grid spacing covering the southern half of Florida and adjacent waters of the Gulf of Mexico and Atlantic Ocean. Each model run is initialized using the Local Analysis and Prediction System (LAPS) analyses available in AWIPS. The SSTs are initialized with the NCEP Real-Time Global (RTG) analyses at 1/12deg resolution (approx.9 km); however, the RTG product does not exhibit fine-scale details consistent with its grid resolution. SPORT is conducting parallel WRF EMS runs identical to the operational runs at NWS MIA except for the use of MODIS SST composites in place of the RTG product as the initial and boundary conditions over water, The MODIS SST composites for initializing the SPORT WRF runs are generated on a 2-km grid four times daily at 0400, 0700, 1600, and 1900 UTC, based on the times of the overhead passes of the Aqua and Terra satellites. The incorporation of the MODIS SST data into the SPORT WRF runs is staggered such that SSTs are updated with a new composite every six hours in each of the WRF runs. From mid-February to July 2007, over 500 parallel WRF simulations have been collected for analysis and verification. This paper will present verification results comparing the NWS MIA operational WRF runs to the SPORT experimental runs, and highlight any substantial differences noted in the predicted mesoscale phenomena for specific cases.

Case, Jonathan L.↗

Predicting boron coordination in multicomponent borate and borosilicate glasses using analytical models and machine learning

Accurate prediction of boron coordination in multicomponent glasses is critical in glass science and technology as it strongly affects the properties of borate and borosilicate glasses. We have collected a dataset containing 657 glasses from literature with boron coordination values and developed models using analytical functions based on the well accepted Dell, Xiao and Bray model. Good prediction of boron coordination with a R 2 value higher than 0.8 was obtained. The large variation of boron coordination from experiments, originated from sample preparations and characterizations, led to difficulties in obtaining models with better prediction performance. Various machine learning (ML) algorithms were evaluated and slightly better prediction performance was observed; however, interpretation of the ML models is less straight forward. In conclusion, this study developed various models capable of providing quantitative boron coordination predictions, providing insights into its structural roles in multi-component glasses, and suggesting fruitful areas for future research.

36 MATERIALS SCIENCE↗

Toward Comprehensive Uncertainty Predictions for Remote Imaging Spectroscopy

Remote imaging spectroscopy’s role in Earth science will grow in the coming decade as a series of globe-spanning spectroscopy missions launch from NASA, ESA, and other agencies. The nature of remote imaging spectroscopy will change, advancing from short regional studies to address global multi-year questions. The diversity of data will also grow with exposure to a wider range of biomes and atmospheric conditions. To execute these new investigations we must reconcile diverse observing conditions to derive consistent global maps. To this end, rig- orous uncertainty quantification and propagation enables an optimal synthesis of data accounting for observing conditions and data quality. Understanding data uncertainties is also important for principled hypothesis testing, information content assessment, and informed decision making by end users. We survey prior efforts in uncer- tainty quantification for imaging spectroscopy, and describe methods for validating the accuracy of uncertainty predictions. We conclude with a discussion of remaining challenges and promising avenues for future research.

Susiluoto, Jouni↗

Toward a Climate OSSE Framework for Satellite Mission Design

The rich history of observing system simulation experiments (OSSEs) does not yet include a well-established framework for using climate models. The need for a climate OSSE is triggered by the need to quantify the value of a particular measurement for reducing the uncertainty in climate predictions, which differ from numerical weather predictions in that they depend on future atmospheric composition rather than the current state of the weather. However, both weather and climate modeling communities share a need for motivating major observing system investments. Here, we outline a new framework for climate OSSEs that leverages the use of machine learning to calibrate climate model physics against existing satellite data. We demonstrate its application using NASA’s GISS-E3 model to objectively quantify the value of potential future improvements in spaceborne measurements of Earth’s planetary boundary layer. A mature climate OSSE framework should be able to quantitatively compare the ability of proposed observing system architectures to answer a climate-related question, thus offering added value throughout the mission design process, which is subject to increasingly rapid advances in instrument and satellite technology. Technical considerations include selection of observational benchmarks and climate projection metrics, approaches to pinpoint the sources of model physics uncertainty that dominate uncertainty in projections, and the use of instrument simulators. Community and policy-making considerations include the potential to interface with an established culture of model intercomparison projects and a growing need to economically assess the value-driven efficiency of social spending on Earth observations.

54 ENVIRONMENTAL SCIENCES↗

Ensemble transfer learning for the prediction of anti-cancer drug response

Abstract Transfer learning, which transfers patterns learned on a source dataset to a related target dataset for constructing prediction models, has been shown effective in many applications. In this paper, we investigate whether transfer learning can be used to improve the performance of anti-cancer drug response prediction models. Previous transfer learning studies for drug response prediction focused on building models to predict the response of tumor cells to a specific drug treatment. We target the more challenging task of building general prediction models that can make predictions for both new tumor cells and new drugs. Uniquely, we investigate the power of transfer learning for three drug response prediction applications including drug repurposing, precision oncology, and new drug development, through different data partition schemes in cross-validation. We extend the classic transfer learning framework through ensemble and demonstrate its general utility with three representative prediction algorithms including a gradient boosting model and two deep neural networks. The ensemble transfer learning framework is tested on benchmark in vitro drug screening datasets. The results demonstrate that our framework broadly improves the prediction performance in all three drug response prediction applications with all three prediction algorithms.

60 APPLIED LIFE SCIENCES↗

CONFLUX: A standardized framework to calculate reactor antineutrino flux

Nuclear fission reactors are abundant sources of antineutrinos for neutrino physics experiments. The flux and spectrum of antineutrinos emitted by a reactor can indicate its activity and composition, suggesting potential applications of neutrino measurements beyond fundamental scientific studies that may be valuable to society. The utility of reactor antineutrinos for applications and fundamental science is dependent on the availability of precise predictions of these emissions. For example, in the last decade, disagreements between reactor antineutrino measurements and models have inspired revision of reactor antineutrino calculations and standard nuclear databases as well as searches for new fundamental particles not predicted by the Standard Model of particle physics. Past predictions and descriptions of the methods used to generate them are documented to varying degrees in the literature, with different modeling teams incorporating a range of methods, input data, and assumptions. The resulting difficulty in accessing or reproducing past models and reconciling results from differing approaches complicates the future study and application of reactor antineutrinos. The CONFLUX (Calculation Of Neutrino FLUX) software framework is a neutrino prediction tool built with the goal of simplifying, standardizing, and democratizing the process of reactor antineutrino flux calculations. CONFLUX includes three primary methods for calculating the antineutrino emissions of nuclear reactors or individual beta decays that incorporate common nuclear data and beta decay theory. The software is prepackaged with the current nuclear databases, including ENDF.B/VIII, JEFF-3.3, and ENSDF, and it includes the capability to predict time-dependent reactor emissions, adjust nuclear database or beta decay inputs/assumptions, and propagate related sources of uncertainty. Here, this paper describes the CONFLUX software structure, details the methods used for flux and spectrum calculations, and provides examples of potential use cases.

Zhang, Xianyi [Lawrence Livermore National Laborat↗

Clinically applicable 53-Gene prognostic assay predicts chemotherapy benefit in gastric cancer: A multicenter study

BACKGROUND:We previously established a 53-gene prognostic signature for overall survival (OS) of gastric cancer patients. This retrospective multi-center study aimed to develop a clinically applicable gene expression detection assay and to investigate the prognostic value of this signature. METHODS:A TCGA gastric adenocarcinoma cohort (TCGA-STAD) was used for comparing 53-gene signature with other gene signatures. A high-throughput mRNA hybridization gene expression assay was developed to quantify the expression of 53-genes in formalin-fixed paraffin-embedded tissues of 540 patients enrolled from three hospitals. 180 patents were randomly selected from two hospitals to build a prognostic prediction model based on the 53-gene signature using leave-p-out (one-third out) cross-validation method together with Cox regression and Kaplan-Meier analysis, and the model was assessed on three validation cohorts. FINDINGS:In the evaluation phase, studies based on TCGA-STAD showed that the 53-gene signature was significantly superior to other three prognostic signatures and was independent of TCGA molecular subtypes and clinical factors. For clinical validation and utility, the prognostic scores were generated using the newly developed assay, which was reliable and sensitive, in 100 sampling training sets and were significantly associated with OS in 100 sampling validation sets. The scores were significantly associated with OS in three independent and combined validation cohorts, and in patients with stages II and III/IV. The multivariate Cox regression demonstrated that the prognostic power of the score was independent of clinical factors, consistent with those findings in the TCGA dataset. Finally, patients with good prognostic scores exhibited significantly a better 5-year OS rate from adjuvant FOLFOX chemotherapy after surgery than from other chemotherapies. INTERPRETATION:The 53-gene prognostic score system is clinically applicable for predicting the OS of patients independent of clinical factors in gastric cancers, which could also be a promising predictive biomarker for FOLFOX regimen. FUNDING:Chinese National Science and Technology, National Natural Science Foundation and Natural Science Foundation of Jiangsu Province.

60 APPLIED LIFE SCIENCES↗

Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces

As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and nanoporous materials, and (3) simple functional form which facilitates incorporation into a variety of simulation codes. Here, we review applications of Clayff to model bulk phases and interfaces not included in the original parameter set and recent modifications for modeling surface terminations such as hydroxylated nanoparticle edges. Overall, we conclude with a discussion of expectations for future developments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phenological shifts in lake stratification under climate change

One of the most important physical characteristics driving lifecycle events in lakes is stratification. Already subtle variations in the timing of stratification onset and break-up (phenology) are known to have major ecological effects, mainly by determining the availability of light, nutrients, carbon and oxygen to organisms. Despite its ecological importance, historic and future global changes in stratification phenology are unknown. Here, we used a lake-climate model ensemble and long-term observational data, to investigate changes in lake stratification phenology across the Northern Hemisphere from 1901 to 2099. Under the high-greenhouse-gas-emission scenario, stratification will begin 22.0 ± 7.0 days earlier and end 11.3 ± 4.7 days later by the end of this century. It is very likely that this 33.3 ± 11.7 day prolongation in stratification will accelerate lake deoxygenation with subsequent effects on nutrient mineralization and phosphorus release from lake sediments. Further misalignment of lifecycle events, with possible irreversible changes for lake ecosystems, is also likely.

54 ENVIRONMENTAL SCIENCES↗

SARS-CoV2 billion-compound docking

Abstract This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens.

60 APPLIED LIFE SCIENCES↗

Spatial pattern of lake evaporation increases under global warming linked to regional hydroclimate change

Abstract Lakes are critical natural resources that are vulnerable to climate change. In a warmer climate, lake evaporation is projected to increase globally, but with substantial variation between regions. Here, based on ensemble projections of climate and lake models and an attribution method, we show that future lake evaporation increase is strongly modulated by regional hydroclimate change. Specifically, a drying hydroclimate will amplify evaporation increase by enlarging surface vapor pressure deficit and reducing cloud shortwave reflection. Future lake evaporation increase is amplified in tropical America, the Mediterranean and Southeast China with drier future hydroclimates, and dampened in high latitudes and the Tibetan Plateau with wetter future hydroclimates. Such spatially coupled changes in lake evaporation and hydroclimate have important implications on regional lake water balance and volume change, which can aggravate water scarcity and flood risks.

54 ENVIRONMENTAL SCIENCES↗

From Optimization to Sampling Through Gradient Flows

Optimization and sampling algorithms play a central role in science and engineering as they enable finding optimal predictions, policies, and recommendations, as well as expected and equilibrium states of complex systems. The notion of “optimality” is formalized by the choice of an objective function, while the notion of an “expected” state is specified by a probabilistic model for the distribution of states. Optimizing rugged objective functions and sampling multimodal distributions is computationally challenging, especially in high-dimensional problems. Here, for this reason, many optimization and sampling methods have been developed by researchers working in disparate fields such as Bayesian statistics, molecular dynamics, genetics, quantum chemistry, machine learning, weather forecasting, econometrics, and medical imaging.

Trillos, N. García↗