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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Synthetic antibacterial minerals: harnessing a natural geochemical reaction to combat antibiotic resistance

The overuse of antibiotics in clinical and livestock settings is accelerating the selection of multidrug resistant bacterial pathogens. Antibiotic resistant bacteria result in increased mortality and financial strain on the health care and livestock industry. The development of new antibiotics has stalled, and novel strategies are needed as we enter the age of antibiotic resistance. Certain naturally occurring clays have been shown to have antimicrobial properties and kill antibiotic resistant bacteria. Harnessing the activity of compounds within these clays that harbor antibiotic properties offers new therapeutic opportunities for fighting the potentially devastating effects of the post antibiotic era. However, natural samples are highly heterogenous and exhibit variable antibacterial effectiveness, therefore synthesizing minerals of high purity with reproducible antibacterial activity is needed. Here we describe for the first time synthetic smectite clay minerals and Fe-sulfide microspheres that reproduce the geochemical antibacterial properties observed in natural occurring clays. We show that these mineral formulations are effective at killing the ESKAPE pathogens ( Enterococcus sp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter sp., Pseudomonas aeruginosa and Enterobacter sp.) by maintaining Fe 2+ solubility and reactive oxygen species (ROS) production while buffering solution pH, unlike the application of metals alone. Our results represent the first step in utilizing a geochemical process to treat antibiotic resistant topical or gastrointestinal infections in the age of antibiotic resistance.

58 GEOSCIENCES↗
DOE OSTI2021

Battle of the Defaults: Extracting Performance Characteristics of HDF5 under Production Load

Popular parallel I/O libraries, such as HDF5, provide tuning parameters to obtain superior performance. However, the selection of effective parameters on production systems is complex due to the interdependence of I/O software and file system layers. Hence, application developers typically use the default parameters and often experience poor I/O performance. This work conducts a benchmarking-based analysis on the HDF5 behaviors with a wide variety of I/O patterns to extract performance characteristics under the production workload. To make the analysis well controlled, we exercise I/O benchmarks on POSIX-IO, MPI-IO, and HDF5 using the same I/O patterns and in the same jobs. To address high performance variability in production environments, we repeat the benchmarks across I/O patterns, storage devices, and time intervals. Based on the results, we identified consistent HDF5 behaviors that appropriate configurations and operations on dataset layout and file-metadata placement can improve performance significantly. We apply our findings and evaluate the tuned I/O library on two supercomputers: Summit and Cori. The results show that our tuned parameters can achieve more than 10× I/O performance speedup than that with default parameters on both systems, suggesting the effectiveness, stability, and generality of our solution.

Xie, Bing↗
DOE OSTI2023

Evaluation of Distributed Power Apportioning with Net Load Management Engine in Microgrids Using Power Hardware-in-the-Loop Simulation

This article presents the performance evaluation of ratio consensus-based distributed power apportioning engine along with centralized net load management (NLM) engine that ensures viable and stable operation of an islanded microgrid. Managing net load variability in a microgrid with high penetrations of uncertain renewable generation and ever-changing load demands is a crucial need in order to ensure viable and stable operation of the microgrid. Centralized “dispatch-rule”-based and/or multi-agent-based distributed control of distributed energy resources (DERs) in microgrid are well accepted for microgrid by adapting ANSI/ISA-95-based hierarchical control architecture. In the application where microgrid network has large geographical span with multiple DERs dispersed in the network, high penetration of uncertain renewable energy resources, and ever-changing load demands, a judicious selection of techniques/solutions for managing net-load resources for maintaining viability and stability is required. With this motivation, this article proposes a novel solution to mitigate the challenges by incorporating a mixed centralized NLM engine and distributed power apportioning control of DERs and loads. A power-hardware-in-the-loop (PHIL) -based experiment is conducted with the centralized NLM engine and the distributed power apportioning engine along with two commercial inverters. The experimental results validates the efficacy of the proposed method in ensuring viability and stability of a microgrid.

hardware-in-the-loop simulation↗
DOE OSTI2023

Standard experimental paradigm designs and data exclusion practices in cognitive psychology can inadvertently introduce systematic “shadow” biases in participant samples

Abstract Standard cognitive psychology research practices can introduce inadvertent sampling biases that reduce the reliability and generalizability of the findings. Researchers commonly acknowledge and understand that any given study sample is not perfectly generalizable, especially when implementing typical experimental constraints (e.g., limiting recruitment to specific age ranges or to individuals with normal color vision). However, less obvious systematic sampling constraints, referred to here as “shadow” biases, can be unintentionally introduced and can easily go unnoticed. For example, many standard cognitive psychology study designs involve lengthy and tedious experiments with simple, repetitive stimuli. Such testing environments may 1) be aversive to some would-be participants (e.g., those high in certain neurodivergent symptoms) who may self-select not to enroll in such studies, or 2) contribute to participant attrition, both of which reduce the sample’s representativeness. Likewise, standard performance-based data exclusion efforts (e.g., minimum accuracy or response time) or attention checks can systematically remove data from participants from subsets of the population (e.g., those low in conscientiousness). This commentary focuses on the theoretical and practical issues behind these non-obvious and often unacknowledged “shadow” biases, offers a simple illustration with real data as a proof of concept of how applying attention checks can systematically skew latent/hidden variables in the included population, and then discusses the broader implications with suggestions for how to manage and reduce, or at a minimum acknowledge, the problem.

Siritzky, Emma M.↗
DOE OSTI2019

Low-Cost Multiparameter Device for Solar Resource Applications

The National Renewable Research Laboratory (NREL) Solar Radiation Research Laboratory (SRRL), in collaboration with Arable Labs Inc., deployed, calibrated, and characterized Arable Lab's Mark low-cost, multiparameter sensor system. Arable Labs was selected by the U.S. Department of Energy for a small business voucher to work with NREL to tap into the knowledge and expertise Arable needs to tailor and evaluate the Mark device for broader solar energy applications. The device is a complete and independent unit. It is a self-powered, off-the-shelf solution for remote solar irradiance and meteorological sensing and data collection. Calibration of devices against the SRRL instruments provides an understanding of the quality of a new instrument compared to peers. The characterization process provides an understanding of the variability compared to high-quality instruments and essentially provides methods to correct the sources of the variabilities.

14 SOLAR ENERGY↗
DOE OSTI2017

Managing variability in algal biomass production through drying and stabilization of feedstock blends

The uncertainty and variability of algal biomass production presents several challenges to the algal biofuel industry including equipment scaling and the ability to provide a consistent feedstock stream for conversion. Blended feedstocks containing both algal and terrestrial biomass may provide a cost-effective method to manage variability of algal biomass production. The hypothesis is that mixing of algae with terrestrial biomass has the potential to create blends with rheologic (flowability) properties similar to terrestrial feedstock and that blends with the consistency of terrestrial biomass can be dried using established low-cost drying systems. To test this hypothesis and its technical feasibility, prototype bench scale simulated drum dyers were designed and tested with blends of algae and ground pine. Scenedesmus dimorphus biomass was used as the algal feedstock, while 2 mm grind pine was used as the terrestrial feedstock. Pine was selected as the representative terrestrial feedstock to leverage independent HTL research using pine feedstock. In these studies, blends up to 60% algae produced drying curves similar to those of pine alone, and reached dryness (2% moisture) much more rapidly than algae alone. Thermogravimetric analyses performed on these feedstocks provided drying curves consistent with the simulated drum dryers. In addition, observable rheologic properties at the time of blending served as an indicator of drying performance, as those blends with texture similar to pine also dried similar to the pine control. Logistics analyses performed to determine cost and availability of feedstock materials for blending at production scale further indicate the potential of this approach. Lastly, our results indicate that blending of algae with terrestrial biomass enables the use of low cost dryers and has the potential to improve overall algal biofuel economics by capturing the value of excess biomass produced during periods of high productivity and by decoupling of algal production farms and conversion facilities.

09 BIOMASS FUELS↗
DOE OSTI2018

A massively-parallel, unstructured overset method for mesh connectivity

Here we present a method that dynamically and efficiently performs connectivity calculations between many O(10 5 ) moving, unstructured overset meshes in parallel. In order to connect overset meshes, elements exterior to the solution domain must be removed from the simulation. In regions with many overlapping meshes, elements must be selectively removed to reduce redundancy while maintaining a solution over the entire domain. Around masked regions interpolation partner pairing is required between meshes to provide boundary conditions. For general unstructured meshes, these steps involve challenging computational geometry calculations which must be efficient and automatic. For many moving meshes each step must be massively parallelized and scalable to large numbers of computational cores. To establish communication patterns a parallelized master/slave algorithm is used which minimizes global communication and storage. To remove elements a parallel ‘Forest Fire’ flood-fill algorithm is used to set a masking variable. For interpolation partner pairing, and other necessary searches, k-dimensional tree data structures (k-d trees) are extensively used. Often in a calculation, the connectivity between overset meshes remains largely the same between time steps. The temporal coherence of the various objects in the connectivity calculation is directly used to only update necessary information with time, resulting in substantial cost savings. Details of the different algorithms are presented. Resulting connectivity and timings are shown for complex geometries. Parallel scaling is demonstrated for 100,000 spherical particles within a channel up to 492,000 processors.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Identification of Metal Stresses in Arabidopsis thaliana Using Hyperspectral Reflectance Imaging

Industrial accidents, such as the Fukushima and Chernobyl disasters, release harmful chemicals into the environment, covering large geographical areas. Natural flora may serve as biological sensors for detecting metal contamination, such as cesium. Spectral detection of plant stresses typically employs a few select wavelengths and often cannot distinguish between different stress phenotypes. In this study, we apply hyperspectral reflectance imaging in the visible and near-infrared along with multivariate curve resolution (MCR) analysis to identify unique spectral signatures of three stresses in Arabidopsis thaliana : salt, copper, and cesium. While all stress conditions result in common stress physiology, hyperspectral reflectance imaging and MCR analysis produced unique spectral signatures that enabled classification of each stress. As the level of potassium was previously shown to affect cesium stress in plants, the response of A. thaliana to cesium stress under variable levels of potassium was also investigated. Increased levels of potassium reduced the spectral response of A. thaliana to cesium and prevented changes to chloroplast cellular organization. While metal stress mechanisms may vary under different environmental conditions, this study demonstrates that hyperspectral reflectance imaging with MCR analysis can distinguish metal stress phenotypes, providing the potential to detect metal contamination across large geographical areas.

multivariate curve resolution↗
DOE OSTI2024

Model and remote-sensing-guided experimental design and hypothesis generation for monitoring snow-soil–plant interactions

In this study, we develop a machine-learning (ML)-enabled strategy for selecting hillslope-scale ecohydrological monitoring sites within snow-dominated mountainous watersheds, with a particular focus on snow-soil–plant interactions. Data layers rely on spatial data layers from both remote sensing and hydrological model simulations. Specifically, a Landsat-based foresummer drought sensitivity index is used to define the dependency of the annual peak plant productivity on the Palmer drought severity index in the early growing season. Hydrological simulations provide the spatiotemporal dynamics of near-surface soil moisture and snow depth. In this framework, a regression analysis identifies the key hydrological variables relevant to the spatial heterogeneity of drought sensitivity. We then apply unsupervised clustering to these key variables, using the Gaussian mixture model, to group hillslopes into several zones that have divergent relationships regarding soil moisture, snow dynamics, and drought sensitivity. Using the datasets collected in the East River Watershed (Crested Butte, Colorado, United States), results show that drought sensitivity is significantly correlated with model-derived soil moisture and snow-free timing over space and time. The relationship is, however, non-linear, such that the correlation decreases above a threshold elevation and in a heavy snow year due to large snowpacks, lateral flow, and soil storage limitations. Clustering is then able to define the zones that have high or low sensitivity to drought, as well as the mid-elevation regions where sensitivity is associated with the topographic aspect and net potential radiation. In addition, the algorithm identifies the most representative hillslopes with road/trail access within each zone for installing monitoring sites. Our method also aims to significantly increase the use of ML and model-simulation results to guide critical zone and watershed monitoring activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Selection of Sampling and Surrogate Modeling Methods for State-Point Evaluations of an AGN-201M Reactor

Nuclear reactor digital twins (DTs) have been proposed for use as a safeguards technology to efficiently monitor new and novel reactors as they come online. A safeguards DT needs to be capable of detecting misuse and diversion as they occur, requiring physics models to be accurate and efficient. Mathematical surrogate models are capable of achieving the necessary efficiency and can largely maintain the accuracy of higher-order models given a quality training sample. The Multiphysics Object-Oriented Simulation Environment (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models. Utilizing an operational AGN-201M reactor’s specifications, two surrogate types were trained on samples of variable size, and using Cartesian products, Latin hypercube sampling, and quadrature sampling, each was compared and evaluated on accuracy when compared to a full-order Monte Carlo model. Both surrogate types were able to capture reactivity changes within 0.05 $ of the Monte Carlo model while reducing the computation costs by eight orders of magnitude.

MOOSE↗
DOE OSTI2023

Estimating and Calibrating DER Model Parameters Using Levenberg–Marquardt Algorithm in Renewable Rich Power Grid

The proliferation of inverter-based distributed energy resources (IBDERs) has increased the number of control variables and dynamic interactions, leading to new grid control challenges. For stability analysis and designing appropriate protection controls, it is important that IBDER models are accurate. This paper focuses on the accurate estimation and parameter calibration of DER_A, a recently proposed aggregated IBDER model. In particular, we focus on the parameters of the reactive power–voltage regulation module. We formulate the problem of parameter tuning as a non-linear least square minimization problem and solve it using the Levenberg–Marquardt (LM) method. The LM method is primarily chosen due to its flexibility in adaptively selecting between the steepest descent and Gauss–Newton methods through a damping parameter. The LM approach is used to minimize the error between the actual measurements and the estimated response of the model. Further, the computational challenges posed by the numerical calculation of the Jacobian are tackled using a quasi-Newton root-finding approach. The proposed method is validated on a real feeder model in the northeastern part of the United States. The feeder is modeled in OpenDSS and the measurements thus obtained are fed to the DER_A model for calibration. The simulation results indicate that our approach is able to successfully calibrate the relevant model parameters quickly and with high accuracy, with a total sum of square error of 3.57 × 10 –7 .

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Low flow characteristics for regulated and unregulated streams in North Carolina and prediction using climate signals

In this work, low flow statistics of regulated and unregulated streams in the state of North Carolina were updated with streamflow data through 2019. About 22% of the streams considered show a significant downward trend, but considerable low-frequency variability confounding trends. The relationship between regional index time series of groundwater-depth low flow and the Atlantic Multidecadal Oscillation (AMO) was examined to determine whether low-frequency climate modes can account for the long-term pattern in low flows. Consequently, a significant correlation was found between AMO and groundwater-depth low flow, such that positive AMO is associated with lower groundwater-depth low flow and vice versa, particularly for the Piedmont region. Predictive equations for annual low flows at the ecoregion level shows that springtime average streamflow and AMO were selected as the primary predictors of low flow for coastal and Piedmont regions, whereas springtime average streamflow and the November–December–January average Oceanic Niño Index were used as the primary predictors for the mountain region. The relative root mean square error (RMSE) of the disaggregated predictions to US Geologic Survey gauge locations was <23% at 79% of the stations, between 24% and 43% at 10% of the stations, and greater than 44% at 1% of the stations. The remaining 10% of stations showed large RMSEs. This latter percentage is characterized by smaller drainage basins and intermittent flows, suggesting the prediction models are not applicable to drainage basins smaller than roughly 20 square km and intermittent streams.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Rainfall erosivity in Slovenia: Sensitivity estimation and trend detection

Highlights: • Rainfall erosivity for 10 rainfall stations located in Slovenia was evaluated. • Rainfall erosivity trends are mostly positive while mostly statistically insignificant. • The maximum rainfall erosivity is obtained under Alpine climate. • Monthly rainfall erosivity was computed. • Sensitivity analyses were carried out. Slovenia is one of the EU countries with the largest values and largest amounts of variability in rainfall erosivity, with maximum annual values exceeding 10,000 MJ mm ha{sup -1} h{sup -1} yr{sup -1}. Five-minute rainfall data was analysed from 10 Slovenian rainfall stations with data-length availability longer than 25 years with a maximum data length of 69 years and a total data-station length equal to 443 years. Trends in the rainfall erosivity R-factor were detected for four different sub-samples using monthly, half-year, and annual rainfall erosivity values. The results indicate that rainfall erosivity trends for the selected Slovenian stations are mostly statistically insignificant, with the selected significance level of 0.05. However, a larger share of identified trends are positive than negative. The maximum annual rainfall erosivity values were obtained for one specific mountain station. Furthermore, a sensitivity analysis regarding the rainfall erosivity factor R calculation showed that the rainfall threshold parameter (12.7 mm) that is used to remove the small-magnitude rainfall events in order to reduce the computational burden can attribute up to 10% of the average annual R-values in cases where this threshold is not used. Other parameters have, on average, a smaller impact on the calculated rainfall erosivity. Furthermore, the application of local kinetic energy equations resulted in, on average, about 20% higher annual rainfall erosivity values compared to the equation that is proposed by the Revised Universal Soil Loss Equation (RUSLE) manual and was not developed specifically for this region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Optical and X-ray GRB Fundamental Planes as cosmological distance indicators

ABSTRACT Gamma-ray bursts (GRBs), can be employed as standardized candles, extending the distance ladder beyond Type Ia supernovae (SNe Ia, z = 2.26). We standardize GRBs using the three-dimensional (3D) Fundamental Plane relation (the Dainotti relation) among the rest-frame end time of the X-ray plateau emission, its corresponding luminosity, and the peak prompt luminosity. Combining SNe Ia and GRBs, we constrain ΩM = 0.299 ± 0.009 assuming a flat Λ cold dark matter (ΛCDM) cosmology with and without correcting GRBs for selection biases and redshift evolution. Using a 3D optical Dainotti correlation, we find this sample is as efficacious in the determination of ΩM as the X-ray sample. We trimmed our GRB samples to achieve tighter planes to simulate additional GRBs. We determined how many GRBs are needed as stand-alone probes to achieve a comparable precision on ΩM to the one obtained by SNe Ia only. We reach the same error measurements derived using SNe Ia in 2011 and 2014 with 142 and 284 simulated optical GRBs, respectively, considering the error bars on the variables halved. These error limits will be reached in 2038 and in 2047, respectively. Using a doubled sample (obtained by future machine learning approaches allowing a light-curve reconstruction and the estimates of GRB redshifts when z is unknown) compared to the current sample, with error bars halved we will reach the same precision as SNe Ia in 2011 and 2014, now and in 2026, respectively. If we consider the current SNe precision, this will be reached with 390 optical GRBs by 2054.

Dainotti, M. G.↗
DOE OSTI2023

Chaconne: A Statistical Approach to Nonlocal Compression for Supervised Learning, Semi-Supervised Learning, and Anomaly Detection

This project developed a novel statistical understanding of compression analytics (CA), which has challenged and clarified some core assumptions about CA, and enabled the development of novel techniques that address vital challenges of national security. Specifically, this project has yielded the development of novel capabilities including 1. Principled metrics for model selection in CA, 2. Techniques for deriving/applying optimal classification rules and decision theory to supervised CA, including how to properly handle class imbalance and differing costs of misclassification, 3. Two techniques for handling nonlocal information in CA, 4. A novel technique for unsupervised CA that is agnostic with regard to the underlying compression algorithm, 5. A framework for semisupervised CA when a small number of labels are known in an otherwise large unlabeled dataset. 6. The academic alliance component of this project has focused on the development of a novel exemplar-based Bayesian technique for estimating variable length Markov models (closely related to PPM [prediction by partial matching] compression techniques). We have developed examples illustrating the application of our work to text, video, genetic sequences, and unstructured cybersecurity log files.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Time Evolution and Diurnal Variability of the Parametric Sensitivity of Turbine-Height Winds in the MYNN-EDMF Parameterization

The Mellor-Yamada-Nakanishi-Niino (MYNN) parameterization applied in the Weather Research and Forecasting (WRF) model has been augmented to include the Eddy-Diffusion Mass-Flux (EDMF) approach to better represent transport by boundary-layer eddies. This change includes the addition of new parameters associated with convective updrafts and boundary-layer clouds. These additions lead to new parametric sensitivities in the hub-height wind speed compared to simulations using the standard MYNN parameterization that were explored previously. This work builds on efforts focused on WRF’s MYNN parameterization by examining the sensitivity of hub-height wind speed to parameters in the MYNN-EDMF parameterization as a function of simulation lead time. Summer and winter periods were selected from the second Wind Forecast Improvement Project (WFIP2). Five sets of simulations were completed for each season, with lead times ranging from 2 to 6 days. The results show that the sensitivity to the new parameters associated with the EDMF scheme is generally small compared to other parameters, with the largest impact in convective boundary layers. The spread in the perturbed parameter ensembles was found to grow quickly over the first 8 to 19 hours in the summer simulations and 17 to 24 hours in the winter simulations with little change after that, regardless of the simulation length. A strong diurnal cycle in the parameter sensitivity was also found associated with changes in the atmospheric stability, as well as an increase in the sensitivity to the entrainment parameter used in the EDMF parameterization that is associated with increasing fractional areas covered by plumes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability

Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗