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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 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mo 3 S 13 Chalcogel: A High-Capacity Electrode for Conversion-Based Li-Ion Batteries

Despite large theoretical energy densities, metal-sulfide electrodes for energy storage systems face several limitations that impact the practical realization. Here, we present the solution-processable, room temperature (RT) synthesis, local structures, and application of a sulfur-rich Mo 3 S 13 chalcogel as a conversion-based electrode for lithium-sulfide batteries (LiSBs). The structure of the amorphous Mo 3 S 13 chalcogel is derived through operando Raman spectroscopy, synchrotron X-ray pair distribution function (PDF), X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) analysis, along with ab initio molecular dynamics (AIMD) simulations. A key feature of the three-dimensional (3D) network is the connection of Mo 3 S 13 units through S–S bonds. Li/Mo 3 S 13 half-cells deliver initial capacity of 1013 mAh g –1 during the first discharge. After the activation cycles, the capacity stabilizes and maintains 312 mAh g –1 at a C/3 rate after 140 cycles, demonstrating sustained performance over subsequent cycling. Such high-capacity and stability are attributed to the high density of (poly)sulfide bonds and the stable Mo–S coordination in Mo 3 S 13 chalcogel. Importantly, these findings showcase the potential of Mo 3 S 13 chalcogels as metal-sulfide electrode materials for LiSBs.

25 ENERGY STORAGE↗
DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advanced data science toolkit for non-data scientists – A user guide

Emerging modern data analytics attracts much attention in materials research and shows great potential for enabling data-driven design. Data populated from the high-throughput CALPHAD approach enables researchers to better understand underlying mechanisms and to facilitate novel hypotheses generation, but the increasing volume of data makes the analysis extremely challenging. Here in this paper, we introduce an easy-to-use, versatile, and open-source data analytics frontend, ASCENDS (Advanced data SCiENce toolkit for Non-Data Scientists), designed with the intent of accelerating data-driven materials research and development. The toolkit is also of value beyond materials science as it can analyze the correlation between input features and target values, train machine learning models, and make predictions from the trained surrogate models of any scientific dataset. Various algorithms implemented in ASCENDS allow users performing quantified correlation analyses and supervised machine learning to explore any datasets of interest without extensive computing and data science background. The detailed usage of ASCENDS is introduced with an example of experimental high-temperature alloy data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Semi-Automated, Object-Based Tomography of Dislocation Structures

The characterization of the three-dimensional arrangement of dislocations is important for many analyses in materials science. Dislocation tomography in transmission electron microscopy is conventionally accomplished through intensity-based reconstruction algorithms. Although such methods work successfully, a disadvantage is that they require many images to be collected over a large tilt range. Here, we present an alternative, semi-automated object-based approach that reduces the data collection requirements by drawing on the prior knowledge that dislocations are line objects. Our approach consists of three steps: (1) initial extraction of dislocation line objects from the individual frames, (2) alignment and matching of these objects across the frames in the tilt series, and (3) tomographic reconstruction to determine the full three-dimensional configuration of the dislocations. Drawing on innovations in graph theory, we employ a node-line segment representation for the dislocation lines and a novel arc-length mapping scheme to relate the dislocations to each other across the images in the tilt series. We demonstrate the method for a dataset collected from a dislocation network imaged by diffraction-contrast scanning transmission electron microscopy. Based on these results and a detailed uncertainty analysis for the algorithm, we discuss opportunities for optimizing data collection and further automating the method.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement

Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules attain the configuration of a “brush”: these PE brushes, due to their ability to form hydrogen bonds (HBs) with water via the PE functional groups, act as a source of soft and active nanoconfinement for the brush-trapped water molecules. In this paper, we study the effects of PE brush-induced confinement on the structure, dynamics and energetics of the water-water and water-PE HBs. Our results indicate a significant weakening of the HBs from bulk to sparsely grafted to densely grafted brushes. i.e., by increasing the degree of brush-induced nanoconfinement. We explain that this weakening of water-water HBs is caused by the disruption of the extended network of water molecules within the brush-induced nanoconfinement. This is confirmed by performing a ring structure analysis of the water molecules, which yields a reduction in the average ring size at higher degrees of brush-induced nanoconfinement (i.e., at higher brush grafting densities). Furthermore, we investigate the role of HB on the orientational dynamics of the water molecules. Here, we observe that the rotational motion of the water molecules becomes sluggish inside the PE brushes. Recent findings have indicated that the water and counterions trapped in brush-induced nanoconfinement demonstrate structures (in combination with the PE functional group) analogous to that in “water-in-salt” electrolytes that have seen extensive recent uses for Li-ion battery applications. However, the rotational dynamics of water molecules inside the brush-induced nanoconfinement is found to be distinctly different from that of conventional “water-in-salt” electrolytes in absence of any confinement; therefore, the present study will provide the necessary platform towards conceptualizing polymer-based nanoconfinement for battery applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Iodine capture with mechanically robust heat-treated Ag-Al-Si-O xerogel sorbents

Silver-loaded heat-treated aluminosilicate xerogels (Ag-HTX) were evaluated as sorbents for iodine [I2(g)] capture. The heat treatment step was performed to help increase the mechanical integrity of the gels. The synthesized xerogels were characterized using powder X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, Brunauer-Emmett-Teller analysis, gravimetric iodine loading, nanoindentation, and dynamic mechanical analysis. The structural and chemical analyses of Ag-HTX showed uniform distribution of Ag throughout the gel network after Ag-exchange. After I2(g) capture, the AgI crystallites were observed in the sorbent verifying chemisorption as the iodine capture mechanism. Iodine loading of this xerogel was 0.43 g g-1 at 150°C over 1 d and 0.52 g g-1 at 22°C over 33 d. The specific surface area of Ag-HTX was 202 m2 g-1 and decreased to 87 m2 g-1 after iodine loading. The hardness of the heat-treated xerogel was 160 times higher than heat-treated aerogel of the same composition. The heat-treatment process increased the modulus value to 40.77 MPa from 6.99 MPa of as-made xerogel, demonstrating the need for this added step in the synthesis process. These results show that Ag-HTX is a promising sorbent for I2(g) capture with good loading capacity and mechanical stability.

xerogels, aerogels, iodine capture, hardness testi↗
DOE OSTI2022

Simulation of the photodetachment spectra of the nitrate anion (NO 3 ₋ ) in the B ~ 2 E' energy range and non-adiabatic electronic population dynamics of NO 3

The photodetachment spectrum of the nitrate anion (NO 3 ₋ ) in the energy range of the NO 3 second excited state is simulated from first principles using quantum wave packet dynamics. The prediction at 10 K and 435 K relies on the use of an accurate full-dimensional fully coupled five state diabatic potential model utilizing an artificial neural network. The ability of this model to reproduce experimental spectra was demonstrated recently for the lower energy range. Analysis of the spectra indicates a weaker Jahn–Teller coupling compared to the first excited state. The detailed non-adiabatic dynamics is studied by computing the population dynamics. An ultra-fast non-statistical radiationless decay is found only among the Jahn–Teller components, which is followed by a slow statistical non-radiative decay among the different state manifolds. The latter is reproduced perfectly by a simple first order kinetics model. The dynamics in the second excited state is not affected by the presence of a conical intersection with the first excited state manifold.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural heterogeneity in non-crystalline Te x Se1−x thin films

Rapid crystallization behavior of amorphous TexSe1−x thin films limits the use of these alloys as coatings and in optoelectronic devices. Understanding the short- and medium-range ordering of the amorphous structure and the fundamental physics governing the crystallization of the films is crucial. Although the lack of long range crystalline order restricts the characterization of the amorphous films, electron microscopy offers a way to extract information about the nanoscale ordering. In this paper, the local ordering of amorphous TexSe1−x thin films with x=0.22, 0.61, 0.70, 0.90, and 1 grown by thermal evaporation is investigated using radial distribution function (RDF) and fluctuation electron microscopy (FEM) analysis. RDF results show that the nearest-neighbor distances of selenium (Se) and tellurium (Te) in their crystalline structure are preserved, and their bond lengths increase with the addition of Te. Density functional theory (DFT) calculations predict structures with interatomic distances similar to those measured experimentally. Additionally, fluctuations in atomic coordination are analyzed. Medium range order (MRO) analysis obtained from FEM and DFT calculations suggests that there are at least two populations within the chain network structure, which are close to the Se–Se and Te–Te intrachain distances. For the binary alloy with x > 0.61, TexSe1−x, Te–Te like populations increase and Te fragments might form, suggesting that the glass forming ability decreases rapidly.

Sari, Bengisu (ORCID:0000000244217098)↗
DOE OSTI2023

Ferroelectric switching pathways and domain structure of SrBi 2 ⁢(Ta,Nb) 2 ⁢O 9 from first principles

Several families of layered perovskite oxide ferroelectrics exhibit a coupling between polarization and structural order parameters, such as octahedral rotation distortions. This coupling provides opportunities for novel electric field-based manipulation of material properties, and it also stabilizes complex domain patterns and domain-wall vortices. Among layered perovskites with such coupled orders, the Aurivillius-phase oxides SrBi 2 ⁢B 2 ⁢O 9 (B = Ta,Nb) are well-known for their excellent room-temperature ferroelectric performance. This work combines group theoretic analysis with density functional theory calculations to examine the ferroelectric switching processes of SrBi2⁢B2⁢O9. Low-energy two-step ferroelectric switching paths are identified, with polarization reversal facilitated by structural order-parameter rotations. Analysis of the domain structure reveals how the relative energetics of the coupled order parameters translates into a network of several distinct domain-wall types linked by domain-wall vortex structures. Comparisons are made between the ferroelectric switching and domain structure of SrBi 2 ⁢B 2 ⁢O 9 and those of the layered n = 2 Ruddlesden-Popper hybrid improper ferroelectrics. The results provide insight into how ferroelectric properties may be optimized by engineering the complex crystal structures of Aurivillius-phase oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A Deep Learning Pipeline for Optimizing Large-scale Phase Field Simulations

Phase field (PF) simulations are computationally expensive but remain a key analysis tool to understand the complex mechanisms of additive manufacturing (AM) processes. Each PF simulation-aided analysis requires thousands of node hours on leadership-class supercomputers. One of the main goals of these analyses is the study of microstructure evolution during the build process which begins with the onset of nucleation. Nucleation occurs under certain thermomechanical conditions which are not known a priori and many PF simulations are required to identify ranges of input thermo-mechanical parameters that can result in the onset of nucleation. Since many of the simulations do not result in nucleation, an analysis campaign often ends up wasting tremendous amounts of precious computing resources executing nucleation-absent simulations. The goal of this work is to design and train deep learning models to inform a PF simulation about the likelihood of the occurrence of nucleation in a future simulation time-step based on the state summary over a finite number of past time-steps of a running simulation. If the prediction determines that the running simulation is unlikely to reach nucleation in the allotted time, then its execution is stopped immediately ultimately resulting in vast reduction in wasted computations when accrued over all the PF simulations typically performed in a single or multiple analysis campaign(s). The paper presents the performance of a machine learning pipeline that uses a convolutional neural network (CNN) model to learn an embedding which is then used with a self-attention network to build a multi-task deep learning model to predict the likelihood of nucleation. The model also predicts the input parameters used in a simulation. Performance is compared with a baseline pipeline that uses an off-the-shelf LeNet-5 model to learn the initial embedding. Despite their smaller size, performance results indicate significant improvement in accuracy of the proposed models compared to the larger baseline models.

Kannan, Ramakrishnan {ramki}↗
DOE OSTI2020

An Assessment of the Usability of Machine Learning Based Tools for the Security Operations Center

Gartner, a large research and advisory company, anticipates that by 2024 80% of security operation centers (SOCs) will use machine learning (ML) based solutions to enhance their operations. 1 1 https://www.ciodive.com/news/how-data-science-tools-can-lighten-the-load-for-cybersecurity-teams/572209/ In light of such widespread adoption, it is vital for the research community to identify and address usability concerns. This work presents the results of the first in situ usability assessment of ML-based tools. With the support of the US Navy, we leveraged the national cyber range-a large, air-gapped cyber testbed equipped with state-of-the-art network and user emulation capabilities-to study six US Naval SOC analysts' usage of two tools. Our analysis identified several serious usability issues, including multiple violations of established usability heuristics for user interface design. We also discovered that analysts lacked a clear mental model of how these tools generate scores, resulting in mistrust a and/or misuse of the tools themselves. Surprisingly, we found no correlation between analysts' level of education or years of experience and their performance with either tool, suggesting that other factors such as prior background knowledge or personality play a significant role in ML-based tool usage. Our findings demonstrate that ML-based security tool vendors must put a renewed focus on working with analysts, both experienced and inexperienced, to ensure that their systems are usable and useful in real-world security operations settings.

Oesch, T↗
DOE OSTI2021

Online PMU Missing Value Replacement Via Event-Participation Decomposition

We introduce a new method for online Phasor Measurement Unit (PMU) missing value replacement. Our approach allows us to decompose PMU event responses into a non-dynamic component (denoted the participation factor) that can be inferred directly from the past and a dynamic component that can be inferred directly from all other PMUs (denoted the event strength). When missing values occur, we can use these two components, which do not rely on the missing index, to estimate the correct value. The method is extremely fast and can easily be used for online applications. Furthermore, extensive testing on real power system event data reveals that our approach achieves state-of-the-art performance in terms of Mean Absolute Percent Errors (MAPEs) for PMU data dropped during event periods. Here, the method also yields an interpretable and simplified view of events for further analysis and applications. The method relies only on PMU data and does not take outside information such as network topology.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2021

Recovering the phase and amplitude of X-ray FEL pulses using neural networks and differentiable models

Dynamics experiments are an important use-case for X-ray free-electron lasers (XFELs), but time-domain measurements of the X-ray pulses themselves remain a challenge. Shot-by-shot X-ray diagnostics could enable a new class of simpler and potentially higher-resolution pump-probe experiments. Here, we report training neural networks to combine low-resolution measurements in both the time and frequency domains to recover X-ray pulses at high-resolution. Critically, we also recover the phase, opening the door to coherent-control experiments with XFELs. The model-based generative neural-network architecture can be trained directly on unlabeled experimental data and is fast enough for real-time analysis on the new generation of MHz XFELs.

42 ENGINEERING↗
DOE OSTI2019

Characterizing Vulnerabilities Associated with Connected Lighting: Exploring Authorization Protocols

Cities are upgrading their infrastructure and converting traditional indoor and outdoor luminaires to Connected Lighting Systems equipped with sensors in an aggressive effort to reduce energy consumption, increase sustainability, and improve the quality of life. When you take something seemingly benign like a lighting system and connect it to the internet, if improperly secured a potential attack vector for hackers is created. Hackers could then access sensitive information, pivot into other networks, shut down services, or enslave devices to do their bidding. In attempt to close this attack vector and secure these systems, this paper extends previous work that investigated, compared and contrasted authentication vulnerabilities in Connected Lighting Systems that identified the need for additional testing and improved test method documentation. One additional authentication test and four new authorization tests were developed utilizing the Open Web Application Security Project (OWASP) as a test development and documentation guide. The new tests were integrated with the previous work to develop an updated test method with a focus on describing test procedures to make them easy to understand and repeat. In addition, a first Connected Lighting System use case was established to begin developing threat profiles that will aid in the identification of vulnerabilities whose focus areas extend beyond authentication and authorization. This use case describes the generation and flow of CLS data which assists in specifying methods to harden CLSs from outside interference and exploitation that can be implemented immediately on existing CLSs and as new products come to market.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Verification of Triso Fuel Burnup Using Machine Learning Algorithms

Pebble Bed Reactors are fueled with fuel pebbles that are circulated multiple times through the reactor vessel before discharge. During the normal operation of a PBR, ejected pebbles are returned to the reactor or discharged depending on the fuel burnup and physical condition of the pebbles. The burnup measurement is usually based on detected radiation signatures of fission products accumulated in the pebble fuel over burnup. Previous research has shown that height of photopeaks of fission products, such as 134 Cs, 137 Cs, 154 Eu, etc., can be used independently or in combination to infer or predict the level of burnup in the fuel. However, it remains challenging to measure such complex sources due to self-shielding effects, strong radiation background and intervening materials. Another operational challenge is the required high throughput of burnup measurement, which necessitates limited measurement time and thus impacts quality of measured gamma-ray spectra. Hence, advanced spectral analysis methods are needed to analyze the noisy gamma spectra and predict the burnup values. We propose to use machine learning (ML) method to interpret gamma-ray spectra and predict the burnup values of the pebbles. ML has achieved widespread success and adoption across a few domains that require pattern recognition and analysis in varied data types. In this work, we apply three proven ML approaches - multilayer perceptrons, convolutional neural networks, and transformers - to the task of predicting fuel burnup from measured gamma spectra, and compile a dataset of simulated spectra for training and validation of the ML models. In this paper, we will discuss the network architecture of these three ML approaches and compare the performance of the simplest of these (MLP) to a standard linear regression.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗