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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Herein, we present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases. Published by AIP Publishing.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1980

Field size, length, and width distributions based on LACIE ground truth data

The development of agricultural remote sensing systems requires knowledge of agricultural field size distributions so that the sensors, sampling frames, image interpretation schemes, registration systems, and classification systems can be properly designed. Malila et al. (1976) studied the field size distribution for wheat and all other crops in two Kansas LACIE (Large Area Crop Inventory Experiment) intensive test sites using ground observations of the crops and measurements of their field areas based on current year rectified aerial photomaps. The field area and size distributions reported in the present investigation are derived from a representative subset of a stratified random sample of LACIE sample segments. In contrast to previous work, the obtained results indicate that most field-size distributions are not log-normally distributed. The most common field size observed in this study was 10 acres for most crops studied.

Pitts, D. E.↗
DOE OSTI2021

Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study

Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials. A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d -1 (95% CI: 1.06 to 1.27 d -1 ), 0.777 d -1 (0.716 to 0.838 d -1 ), and 0.450 d -1 (0.378 to 0.522 d -1 ) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies). Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome. We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation. In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Cryo-STEM Tomography with Inpainting

Traditionally, microscopists have worked with the Nyquist-Shannon theory of sampling, which states that to be able to reconstruct the image fully it needs to be sampled at a rate of at least twice the highest spatial frequency in the image. This sampling rate assumes that the image is sampled at regular intervals and that every pixel contains information that is crucial for the image (it even assumes that noise is important). Images in general, and especially low dose S/TEM images, contain significantly less information than can be encoded by a grid of pixels (which is why image compression works). Mathematically speaking, the image data has a low dimensional or sparse representation. Through the application of compressive sensing methods [1,2,3] this representation can be found using pre-designed measurements that are usually random for implementation simplicity. These measurements and the compressive sensing reconstruction algorithms have the added benefit of reducing noise. This reconstruction approach can be extended into higher dimensions, whereby the random sampling in each 2-D image can be extended into: a sequence of tomographic projections (i.e. tilt images); a sequence of video frames (i.e. incorporating temporal resolution and dynamics); spectral resolution (i.e. energy filtering an image to see the distribution of elements); and ptychography (i.e. sampling a full diffraction image at each location in a 2-D grid across the sample). This approach has been employed experimentally for materials science samples requiring low-dose imaging [2], and can be readily applied to biological samples. Figure 1 shows the resolution possible in a complex biological system, mouse pancreatic islet beta cells [4], when tomogram slices are reconstructed using subsampling. Reducing the number of pixels (1/6 pix and 1/3*1/3) shows minimal degradation compared to the reconstructions using all pixels (all data and 1/3 tilt). Although subsampling 1/6 of the tilts (1/6 of overall dose) degrades the reconstruction to the point that the cellular structures cannot be identified. Using 1/3 of both the pixels and the tilts provides a high quality image at 1/9 the overall dose even for this most basic and rapid demonstration of the CS methods. Figure 2 demonstrates the theoretical tomogram reconstruction quality (vertical axis) as undersampling (horizontal axis) is increased; we examined subsampling pixels and tilt-angles individually and a combined approach in which both pixels and tilts are sub-sampled. Note that subsampling pixels maintains high quality reconstructions (solid lines). Using the inpainting algorithm to obtain tomograms can automatically reduce the dose applied to the system by an order of magnitude. Perhaps the best way to understand the impact is to consider that by using inpainting (and with minimal hardware changes), a sample that can normally withstand a dose of ~10 e/Å2 can potentially be imaged with an “equivalent quality” to a dose level of 103 e/Å2. To put this in perspective, this is approaching the dose level used for the most advanced images, in terms of spatial resolution, for inorganic systems. While there are issues for biological specimens beyond dose (structural complexity being the most important one), this sampling approach allows the methods that are traditionally used for materials science to be applied to biological systems [5]. References: [1] A Stevens, H Yang, L Carin et al. Microscopy 63(1), (2014), pp. 41. [2] L Kovarik, A Stevens, A Liyu et al. Appl. Phys. Lett. 109, 164102 (2016) [3] A Stevens, L Kovarik, P Abellan et al. Adv. Structural and Chemical Imaging 1(10), (2015), pp. 1. [4] MD Guay, W Czaja, MA Aronova et al. Scientific Reports 6, 27614 (2016) [5] Supported by the Chemical Imaging, Signature Discovery, and Analytics in Motion Initiatives at PNNL. PNNL is operated by Battelle Memorial Inst. for the US DOE; contract DE-AC05-76RL01830.

Stevens, Andrew↗
NASA NTRS1987

Characterization of fault recovery through fault injection on FTMP

The development of fault-injection procedures and statistical analysis techniques to characterize the fault recovery of fault-tolerant systems is described. Pin-level fault-injection was conducted on a fault-tolerant microprocessor computer in order to generate data to assess the utility of current fault-injection sampling methods. The validity of common reliability-modeling assumptions concerning the statistical distribution of recovery times is investigated. A multiple comparison analysis for detecting behavior variations, and a distribution fitting for determining the best fit for the data were conducted. It is observed that the detection behavior is not homogeneous across all data sets, and that none of the factors under experimental control can account for the observed groupings of behavior. It is determined that no single distribution fits all the data sets, and that stratified random sampling and statistically robust parameter-estimation techniques are required to characterize fault detection time.

Finelli, George B.↗
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Forest Biomass Mapping From Lidar and Radar Synergies

The use of lidar and radar instruments to measure forest structure attributes such as height and biomass at global scales is being considered for a future Earth Observation satellite mission, DESDynI (Deformation, Ecosystem Structure, and Dynamics of Ice). Large footprint lidar makes a direct measurement of the heights of scatterers in the illuminated footprint and can yield accurate information about the vertical profile of the canopy within lidar footprint samples. Synthetic Aperture Radar (SAR) is known to sense the canopy volume, especially at longer wavelengths and provides image data. Methods for biomass mapping by a combination of lidar sampling and radar mapping need to be developed. In this study, several issues in this respect were investigated using aircraft borne lidar and SAR data in Howland, Maine, USA. The stepwise regression selected the height indices rh50 and rh75 of the Laser Vegetation Imaging Sensor (LVIS) data for predicting field measured biomass with a R(exp 2) of 0.71 and RMSE of 31.33 Mg/ha. The above-ground biomass map generated from this regression model was considered to represent the true biomass of the area and used as a reference map since no better biomass map exists for the area. Random samples were taken from the biomass map and the correlation between the sampled biomass and co-located SAR signature was studied. The best models were used to extend the biomass from lidar samples into all forested areas in the study area, which mimics a procedure that could be used for the future DESDYnI Mission. It was found that depending on the data types used (quad-pol or dual-pol) the SAR data can predict the lidar biomass samples with R2 of 0.63-0.71, RMSE of 32.0-28.2 Mg/ha up to biomass levels of 200-250 Mg/ha. The mean biomass of the study area calculated from the biomass maps generated by lidar- SAR synergy 63 was within 10% of the reference biomass map derived from LVIS data. The results from this study are preliminary, but do show the potential of the combined use of lidar samples and radar imagery for forest biomass mapping. Various issues regarding lidar/radar data synergies for biomass mapping are discussed in the paper.

Sun, Guoqing↗
DOE OSTI2021

Cross-national analysis of food security drivers: comparing results based on the Food Insecurity Experience Scale and Global Food Security Index

Abstract The second UN Sustainable Development Goal establishes food security as a priority for governments, multilateral organizations, and NGOs. These institutions track national-level food security performance with an array of metrics and weigh intervention options considering the leverage of many possible drivers. We studied the relationships between several candidate drivers and two response variables based on prominent measures of national food security: the 2019 Global Food Security Index (GFSI) and the Food Insecurity Experience Scale’s (FIES) estimate of the percentage of a nation’s population experiencing food security or mild food insecurity (FI ). We compared the contributions of explanatory variables in regressions predicting both response variables, and we further tested the stability of our results to changes in explanatory variable selection and in the countries included in regression model training and testing. At the cross-national level, the quantity and quality of a nation’s agricultural land were not predictive of either food security metric. We found mixed evidence that per-capita cereal production, per-hectare cereal yield, an aggregate governance metric, logistics performance, and extent of paid employment work were predictive of national food security. Household spending as measured by per-capita final consumption expenditure (HFCE) was consistently the strongest driver among those studied, alone explaining a median of 92% and 70% of variation (based on out-of-sample R 2 ) in GFSI and FI , respectively. The relative strength of HFCE as a predictor was observed for both response variables and was independent of the countries used for model training, the transformations applied to the explanatory variables prior to model training, and the variable selection technique used to specify multivariate regressions. The results of this cross-national analysis reinforce previous research supportive of a causal mechanism where, in the absence of exceptional local factors, an increase in income drives increase in food security. However, the strength of this effect varies depending on the countries included in regression model fitting. We demonstrate that using multiple response metrics, repeated random sampling of input data, and iterative variable selection facilitates a convergence of evidence approach to analyzing food security drivers.

42 ENGINEERING↗
DOE OSTI2017

Stellar clusterings around 'isolated' Massive YSOs in the LMC

Observations suggest that there is a significant fraction of O stars in the field of the Milky Way that appear to have formed in isolation or in low-mass clusters (<100 M{sub ⊙}). The existence of these high-mass stars that apparently formed in the field challenges the generally accepted paradigm, which requires star formation to occur in clustered environments. In order to understand the physical conditions for the formation of these stars, it is necessary to observe isolated high-mass stars while they are still forming. With the Hubble Space Telescope, we observe the seven most isolated massive (>8 M{sub ⊙}) young stellar objects (MYSOs) in the Large Magellanic Cloud. The observations show that while these MYSOs are remote from other MYSOs, OB associations, and even known giant molecular clouds, they are actually not isolated at all. Imaging reveals ∼100 to several hundred pre-main-sequence (PMS) stars in the vicinity of each MYSO. These previously undetected PMS stars form prominent compact clusters around the MYSOs, and in most cases they are also distributed sparsely across the observed regions. Contrary to what previous high-mass field star studies show, these observations suggest that high-mass stars may not be able to form in clusters with masses less than 100 M{sub ⊙}. If these MYSOs are indeed the best candidates for isolated high-mass star formation, then the lack of isolation is at odds with random sampling of the initial mass function. Moreover, while isolated MYSOs may not exist, we find evidence that isolated clusters containing O stars can exist, which in itself is rare.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Megadrought: A Series of Unfortunate La Niña Events?

Megadroughts are multidecadal periods of aridity more persistent than most droughts during the instrumental period. Paleoclimate evidence suggests that megadroughts occur in many parts of the world, including North America, Central America, western Europe, eastern Asia, and northern Africa. It remains unclear to what extent such megadroughts require external forcing or whether they can arise from internal climate variability alone. A novel statistical–dynamical approach is used to evaluate the possibility that such events arise solely as a function of interannual tropical sea surface temperature (SST) variations. A statistical emulator of tropical SST variations is constructed by using an empirical moving-blocks bootstrap approach that randomly samples multiyear sequences of the observational SST record. This approach preserves the power spectrum, seasonal cycle, and spatial pattern of El Niño-Southern Oscillation (ENSO) but removes longer timescale fluctuations embedded in the observational record. These resampled SST anomalies are then used to force an atmospheric model (the Community Atmosphere Model Version 5). As megadroughts emerge in this run, they should, therefore, be solely a consequence of La Niña sequences combined with internal atmospheric variability and persistence driven by soil moisture storage and other land-surface processes. We indeed find that megadroughts in this simulation have an amplitude-duration rate that is generally indistinguishable from the rate documented in paleoclimate records of the western United States. Our findings support the idea that megadroughts may occur randomly when the unforced climate system evolves freely over a sufficiently long period of time, implying that an unforced unusual but statistically plausible series of La Niña events may be sufficient to generate megadrought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Recent Progress on the Stochastic Objective Decision Aide (SODA) Application

Idaho State University, in collaboration with Idaho National Laboratory, is engaged in development of a simple to use software application that utilizes stochastic techniques for the calculation of radiation doses associated with hypothetical radioactive material releases. This work is being performed through a grant from the U.S. Department of Energy (DOE) Nuclear Safety Research and Development (NSR and D) Program. Initial progress on the application was reported previously. Recent additions to the application are reported here. The Stochastic Objective Decision Aide (SODA) provides an easy to use software application to help decision makers support their judgment about the need or lack of need for safety structures, systems, and components. SODA is not intended to replace traditional design basis accident dose calculation methodology, nor is it intended to replace existing software used to perform formal dose consequence calculations. Rather, SODA is intended to supplement information obtained from existing codes to give a decision maker more information about an accident scenario. SODA also provides a simple method to perform parametric or sensitivity studies on individual input parameters. Non-reactor nuclear facilities operated under the approval authority of the US DOE use unmitigated hazard evaluations to determine if potential radiological doses associated with design basis events challenge dose evaluation guidelines. Unmitigated events that sufficiently challenge dose evaluation guidelines merit the selection of safety structures, systems, or components (SSCs) to prevent or mitigate the hazard. Dose consequence calculations traditionally involve use of the 'five-factor' formula: ST = MAR.DR.ARF.RF.LPF where ST is the source term (Bq), MAR is the total available material-at-risk (Bq), DR is the damage ratio (no units), ARF is the airborne release fraction (no units), RF is the respirable fraction (no units), and LPF is the leak path factor (no units). Potential radiation doses are then calculated using: CED = χ/Q.BR.ST.DCF (2) where CED is the committed effective dose (Sv), χ/Q is the plume dispersion (s/m{sup 3}), BR is the breathing rate (m{sup 3}/s), ST is the source term (Bq), and DCF is the dose conversion factor (Sv/Bq). Conservative single value input parameters are typically used to represent ARF, RF, LPF and BR. The traditional methodology, while conservative, can lead to skewed conclusions in the balance between cost and risk reduction resulting in over engineered systems with greater design, construction and operating costs. Rather than using a bounding single point value for each parameter in the dose consequence calculation, SODA uses distributions for some or all of the parameters. Each input parameter distribution is stochastically sampled and the resulting dose consequence calculation is repeated many times to develop a dose consequence distribution. The resulting distribution provides more information for the decision maker to rely upon when determining the need for safety SSCs. The SODA application was developed using MATLAB and it incorporates the use of Monte Carlo techniques as well as a graphical user interface (GUI). The application includes user selection of the governing distribution for parameters such as the MAR, DR, ARF, RF, LPF,χ/Q, BR, and DCF. While MATLAB was used for the development work, the application is distributed as a self-contained executable program. Features of the application include pull down menus with available distributions for the various parameters. The user has the option to plot the input parameter distribution that results from the random sampling process. The resulting dose consequence distribution is automatically analyzed to determine its similarity to well know distributions. This was done using the Bayesian Information Criterion method. If the resulting distribution is sufficiently similar to a well-known distribution, the application provides information about the distributions such as the mean value and other parameters. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

Phylodynamic Inference across Epidemic Scales

Within-host genetic diversity and large transmission bottlenecks confound phylodynamic inference of epidemiological dynamics. Conventional phylodynamic approaches assume that nodes in a time-scaled pathogen phylogeny correspond closely to the time of transmission between hosts that are ancestral to the sample. However, when hosts harbor diverse pathogen populations, node times can substantially pre-date infection times. Imperfect bottlenecks can cause lineages sampled in different individuals to coalesce in unexpected patterns. To address realistic violations of standard phylodynamic assumptions we developed a new inference approach based on a multi-scale coalescent model, accounting for nonlinear epidemiological dynamics, heterogeneous sampling through time, non-negligible genetic diversity of pathogens within hosts, and imperfect transmission bottlenecks. We apply this method to HIV-1 and Ebola virus (EBOV) outbreak sequence data, illustrating how and when conventional phylodynamic inference may give misleading results. Within-host diversity of HIV-1 causes substantial upwards bias in the number of infected hosts using conventional coalescent models, but estimates using the multi-scale model have greater consistency with reported number of diagnoses through time. In contrast, we find that within-host diversity of EBOV has little influence on estimated numbers of infected hosts or reproduction numbers, and estimates are highly consistent with the reported number of diagnoses through time. The multi-scale coalescent also enables estimation of within-host effective population size using single sequences from a random sample of patients. We find within-host population genetic diversity of HIV-1 p17 to be 2Nμ=0.012 (95% CI 0.0066–0.023), which is lower than estimates based on HIV envelope serial sequencing of individual patients.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2007

Potential of VIIRS Time Series Data for Aiding the USDA Forest Service Early Warning System for Forest Health Threats: A Gypsy Moth Defoliation Case Study

This report details one of three experiments performed during FY 2007 for the NASA RPC (Rapid Prototyping Capability) at Stennis Space Center. This RPC experiment assesses the potential of VIIRS (Visible/Infrared Imager/Radiometer Suite) and MODIS (Moderate Resolution Imaging Spectroradiometer) data for detecting and monitoring forest defoliation from the non-native Eurasian gypsy moth (Lymantria dispar). The intent of the RPC experiment was to assess the degree to which VIIRS data can provide forest disturbance monitoring information as an input to a forest threat EWS (Early Warning System) as compared to the level of information that can be obtained from MODIS data. The USDA Forest Service (USFS) plans to use MODIS products for generating broad-scaled, regional monitoring products as input to an EWS for forest health threat assessment. NASA SSC is helping the USFS to evaluate and integrate currently available satellite remote sensing technologies and data products for the EWS, including the use of MODIS products for regional monitoring of forest disturbance. Gypsy moth defoliation of the mid-Appalachian highland region was selected as a case study. Gypsy moth is one of eight major forest insect threats listed in the Healthy Forest Restoration Act (HFRA) of 2003; the gypsy moth threatens eastern U.S. hardwood forests, which are also a concern highlighted in the HFRA of 2003. This region was selected for the project because extensive gypsy moth defoliation occurred there over multiple years during the MODIS operational period. This RPC experiment is relevant to several nationally important mapping applications, including agricultural efficiency, coastal management, ecological forecasting, disaster management, and carbon management. In this experiment, MODIS data and VIIRS data simulated from MODIS were assessed for their ability to contribute broad, regional geospatial information on gypsy moth defoliation. Landsat and ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) data were used to assess the quality of gypsy moth defoliation mapping products derived from MODIS data and from simulated VIIRS data. The project focused on use of data from MODIS Terra as opposed to MODIS Aqua mainly because only MODIS Terra data was collected during 2000 and 2001-years with comparatively high amounts of gypsy moth defoliation within the study area. The project assessed the quality of VIIRS data simulation products. Hyperion data was employed to assess the quality of MODIS-based VIIRS simulation datasets using image correlation analysis techniques. The ART (Application Research Toolbox) software was used for data simulation. Correlation analysis between MODIS-simulated VIIRS data and Hyperion-simulated VIIRS data for red, NIR (near-infrared), and NDVI (Normalized Difference Vegetation Index) image data products collectively indicate that useful, effective VIIRS simulations can be produced using Hyperion and MODIS data sources. The r(exp 2) for red, NIR, and NDVI products were 0.56, 0.63, and 0.62, respectively, indicating a moderately high correlation between the 2 data sources. Temporal decorrelation from different data acquisition times and image misregistration may have lowered correlation results. The RPC experiment also generated MODIS-based time series data products using the TSPT (Time Series Product Tool) software. Time series of simulated VIIRS NDVI products were produced at approximately 400-meter resolution GSD (Ground Sampling Distance) at nadir for comparison to MODIS NDVI products at either 250- or 500-meter GSD. The project also computed MODIS (MOD02) NDMI (Normalized Difference Moisture Index) products at 500-meter GSD for comparison to NDVI-based products. For each year during 2000-2006, MODIS and VIIRS (simulated from MOD02) time series were computed during the peak gypsy moth defoliation time frame in the study area (approximately June 10 through July 27). Gypsy moth defoliation mapping products from simated VIIRS and MOD02 time series were produced using multiple methods, including image classification and change detection via image differencing. The latter enabled an automated defoliation detection product computed using percent change in maximum NDVI for a peak defoliation period during 2001 compared to maximum NDVI across the entire 2000-2006 time frame. Final gypsy moth defoliation mapping products were assessed for accuracy using randomly sampled locations found on available geospatial reference data (Landsat and ASTER data in conjunction with defoliation map data from the USFS). Extensive gypsy moth defoliation patches were evident on screen displays of multitemporal color composites derived from MODIS data and from simulated VIIRS vegetation index data. Such defoliation was particularly evident for 2001, although widespread denuded forests were also seen for 2000 and 2003. These visualizations were validated using aforementioned reference data. Defoliation patches were visible on displays of MODIS-based NDVI and NDMI data. The viewing of apparent defoliation patches on all of these products necessitated adoption of a specialized temporal data processing method (e.g., maximum NDVI during the peak defoliation time frame). The frequency of cloud cover necessitated this approach. Multitemporal simulated VIIRS and MODIS Terra data both produced effective general classifications of defoliated forest versus other land cover. For 2001, the MOD02-simulated VIIRS 400-meter NDVI classification produced a similar yet slightly lower overall accuracy (87.28 percent with 0.72 Kappa) than the MOD02 250-meter NDVI classification (88.44 percent with 0.75 Kappa). The MOD13 250-meter NDVI classification had a lower overall accuracy (79.13 percent) and a much lower Kappa (0.46). The report discusses accuracy assessment results in much more detail, comparing overall classification and individual class accuracy statistics for simulated VIIRS 400-meter NDVI, MOD02 250-meter NDVI, MOD02-500 meter NDVI, MOD13 250-meter NDVI, and MOD02 500-meter NDMI classifications. Automated defoliation detection products from simulated VIIRS and MOD02 data for 2001 also yielded similar, relatively high overall classification accuracy (85.55 percent for the VIIRS 400-meter NDVI versus 87.28 percent for the MOD02 250-meter NDVI). In contrast, the USFS aerial sketch map of gypsy moth defoliation showed a lower overall classification accuracy at 73.64 percent. The overall classification Kappa values were also similar for the VIIRS (approximately 0.67 Kappa) versus the MOD02 (approximately 0.72 Kappa) automated defoliation detection product, which were much higher than the values exhibited by the USFS sketch map product (overall Kappa of approximately 0.47). The report provides additional details on the accuracy of automated gypsy moth defoliation detection products compared with USFS sketch maps. The results suggest that VIIRS data can be effectively simulated from MODIS data and that VIIRS data will produce gypsy moth defoliation mapping products that are similar to MODIS-based products. The results of the RPC experiment indicate that VIIRS and MODIS data products have good potential for integration into the forest threat EWS. The accuracy assessment was performed only for 2001 because of time constraints and a relative scarcity of cloud-free Landsat and ASTER data for the peak defoliation period of the other years in the 2000-2006 time series. Additional work should be performed to assess the accuracy of gypsy moth defoliation detection products for additional years.The study area (mid-Appalachian highlands) and application (gypsy moth forest defoliation) are not necessarily representative of all forested regions and of all forest threat disturbance agents. Additional work should be performed on other inland and coastal regions as well as for other major forest threats.

Spruce, Joseph P.↗
DOE OSTI2026

Statistics of base polytopes in F-theory

We propose a new statistical ensemble of toric bases for elliptic Calabi-Yaus used in F-theory models, by focusing on only the convex hull of the base, i.e., the base polytope. This physically motivated coarse-graining greatly simplifies the combinatorial complexity of the part of the 4d F-theory landscape with toric bases. We develop a Monte Carlo approach that randomly samples the base polytopes within fixed boxes, with proper statistical weights. We first apply the algorithm to the set of 2d base polytopes, generating an enlarged set of toric 2d bases that include certain types of codimension-two (4,6) points, and we validate our approach against exact numbers. We then explore the set of 3d base polytopes which fit in a set of “maximal” 3d boxes, and estimate the total number of inequivalent 3d base polytopes to be 10 85 –10 90 . We provide statistical data such as the distribution of non-Higgsable gauge groups on these bases. Amusingly, a similar method can also be applied to generate reflexive polytopes in various dimensions. In both the reflexive and base polytope cases, the number of relevant polytopes obeys a Gaussian distribution as a function of the number of vertices, which can be understood in terms of other results on random polytopes in the math literature.

Differential and algebraic geometry↗
DOE OSTI2018

Metropolis–Hastings Monte Carlo Method for Neutron Emissivity Tomographic Inversion in Tokamak Plasma

The article presents a new approach to plasma neutron emissivity reconstruction based on the Metropolis–Hastings Monte Carlo algorithm. The algorithm is based on a biased random walk. A dedicated computer code generates pseudo-random samples within the domain that contains the solution. The properly chosen objective function ensures convergence to the desired solution. The method allows to overcome the problem of trapping in local minima by accepting, with some finite probability, changes in the direction opposite to that indicated by the objective function. The developed method was tested using a synthetic data set. The results show that the method provides reliable reconstructions and thus can be used as an alternative or complementary method to the commonly applied ones. The method capabilities were also tested against noise present in the line-integrated projections.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Real classical shadows

Efficiently learning expectation values of a quantum state using classical shadow tomography has become a fundamental task in quantum information theory. In a classical shadows protocol, one measures a state in a chosen basis $\mathcal{W}$ after it has evolved under a unitary transformation randomly sampled from a chosen distribution $\mathcal{U}$. In this work we study the case where $\mathcal{U}$ corresponds to either local or global orthogonal Clifford gates, and $\mathcal{W}$ consists of real-valued vectors. Our results show that for various situations of interest, this ‘real’ classical shadow protocol improves the sample complexity over the standard scheme based on general Clifford unitaries. For example, when one is interested in estimating the expectation values of arbitrary real-valued observables, global orthogonal Cliffords typically decrease the required number of samples by a factor of two. More dramatically, for k-local observables composed only of real-valued Pauli operators, sampling local orthogonal Cliffords leads to a reduction by an exponential-in-k factor in the sample complexity over local unitary Cliffords. Finally, we show that by measuring in a basis containing complex-valued vectors, orthogonal shadows can, in the limit of large system size, exactly reproduce the original unitary shadows protocol.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics

Computational methods for creating in silico libraries of molecular descriptors (e.g., collision cross sections) are becoming increasingly prevalent due to the limited number of authentic reference materials available for traditional library building. These so-called “reference-free metabolomics” methods require sampling sets of molecular conformers in order to produce high accuracy property predictions. Due to the computational cost of the subsequent calculations for each conformer, there is a need to sample the most relevant subset and avoid repeating calculations on conformers that are nearly identical. The goal of this study is to introduce a heuristic method of finding the most dissimilar conformers from a larger population in order to help speed up reference-free calculation methods and maintain a high property prediction accuracy. Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population size grows large. Because there exists a pairwise relationship between each item and all other items in the population, finding the set of the n most dissimilar items is different than simply sorting an array of numbers. For instance, if you have a set of the most dissimilar n = 4 items, one or more of the items from n = 4 might not be in the set n = 5. An exact solution would have to search all possible combinations of size n in the population exhaustively. We present an open-source software called similarity downselection (SDS), written in Python and freely available on GitHub. SDS implements a heuristic algorithm for quickly finding the approximate set(s) of the n most dissimilar items. We benchmark SDS against a Monte Carlo method, which attempts to find the exact solution through repeated random sampling. We show that for SDS to find the set of n most dissimilar conformers, our method is not only orders of magnitude faster, but it is also more accurate than running Monte Carlo for 1,000,000 iterations, each searching for set sizes n = 3–7 out of a population of 50,000. We also benchmark SDS against the exact solution for example small populations, showing that SDS produces a solution close to the exact solution in these instances. Using theoretical approaches, we also demonstrate the constraints of the greedy algorithm and its efficacy as a ratio to the exact solution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Modeled and observed properties related to the direct aerosol radiative effect of biomass burning aerosol over the southeastern Atlantic

Biomass burning smoke is advected over the southeastern Atlantic Ocean between July and October of each year. This smoke plume overlies and mixes into a region of persistent low marine clouds. Model calculations of climate forcing by this plume vary significantly in both magnitude and sign. NASA EVS-2 (Earth Venture Suborbital-2) ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) had deployments for field campaigns off the west coast of Africa in 3 consecutive years (September 2016, August 2017, and October 2018) with the goal of better characterizing this plume as a function of the monthly evolution by measuring the parameters necessary to calculate the direct aerosol radiative effect. Here, this dataset and satellite retrievals of cloud properties are used to test the representation of the smoke plume and the underlying cloud layer in two regional models (WRF-CAM5 and CNRM-ALADIN) and two global models (GEOS and UM-UKCA). The focus is on the comparisons of those aerosol and cloud properties that are the primary determinants of the direct aerosol radiative effect and on the vertical distribution of the plume and its properties. The representativeness of the observations to monthly averages are tested for each field campaign, with the sampled mean aerosol light extinction generally found to be within 20 % of the monthly mean at plume altitudes. When compared to the observations, in all models, the simulated plume is too vertically diffuse and has smaller vertical gradients, and in two of the models (GEOS and UM-UKCA), the plume core is displaced lower than in the observations. Plume carbon monoxide, black carbon, and organic aerosol masses indicate underestimates in modeled plume concentrations, leading, in general, to underestimates in mid-visible aerosol extinction and optical depth. Biases in mid-visible single scatter albedo are both positive and negative across the models. Observed vertical gradients in single scatter albedo are not captured by the models, but the models do capture the coarse temporal evolution, correctly simulating higher values in October (2018) than in August (2017) and September (2016). Uncertainties in the measured absorption Ångstrom exponent were large but propagate into a negligible (<4 %) uncertainty in integrated solar absorption by the aerosol and, therefore, in the aerosol direct radiative effect. Model biases in cloud fraction, and, therefore, the scene albedo below the plume, vary significantly across the four models. The optical thickness of clouds is, on average, well simulated in the WRF-CAM5 and ALADIN models in the stratocumulus region and is underestimated in the GEOS model; UM-UKCA simulates cloud optical thickness that is significantly too high. Overall, the study demonstrates the utility of repeated, semi-random sampling across multiple years that can give insights into model biases and how these biases affect modeled climate forcing. The combined impact of these aerosol and cloud biases on the direct aerosol radiative effect (DARE) is estimated using a first-order approximation for a subset of five comparison grid boxes. A significant finding is that the observed grid box average aerosol and cloud properties yield a positive (warming) aerosol direct radiative effect for all five grid boxes, whereas DARE using the grid-box-averaged modeled properties ranges from much larger positive values to small, negative values. It is shown quantitatively how model biases can offset each other, so that model improvements that reduce biases in only one property (e.g., single scatter albedo but not cloud fraction) would lead to even greater biases in DARE. Across the models, biases in aerosol extinction and in cloud fraction and optical depth contribute the largest biases in DARE, with aerosol single scatter albedo also making a significant contribution.

54 ENVIRONMENTAL SCIENCES↗