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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 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Comparative analysis of methicillin-sensitive and resistant Staphylococcus aureus exposed to emodin based on proteomic profiling

Highlights: • Emodin is effective against methicillin-sensitive and resistant Staphylococcus aureus strains. • Global proteomic profiling revealed 145 and 122 significant changes in MSSA and MRSA after emodin treatment, respectively. • Profiling interaction network analysis demonstrated emodin potentially targeted MRSA via multiple mechanisms. Emodin has a strong antibacterial activity, including methicillin-resistant Staphylococcus aureus (MRSA). However, the mechanism by which emodin induces growth inhibition against MRSA remains unclear. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) proteomics approach was used to investigate the modes of action of emodin on a MRSA isolate and methicillin-sensitive S. aureus ATCC29213(MSSA). Proteomic analysis showed that expression levels of 145 and 122 proteins were changed significantly in MRSA and MSSA, respectively, after emodin treatment. Comparative analysis of the functions of differentially expressed proteins between the two strains was performed via bioinformatics tools blast2go and STRING database. Proteins related to pyruvate pathway imbalance induction, protein synthesis inhibition, and DNA synthesis suppression were found in both methicillin-sensitive and resistant strains. Moreover, Interference proteins related to membrane damage mechanism were also observed in MRSA. Our findings indicate that emodin is a potential antibacterial agent targeting MRSA via multiple mechanisms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Prediction of α $IIb$ $β$ 3 integrin structures along its minimum free energy activation pathway

The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but it is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin α IIb β 3 by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of α IIb β 3 integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the α and β subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in α IIb β 3 . Furthermore, these results provide new insights into integrin activation mechanism, and the predicted structures have potential applications in guiding the design of integrin-targeting therapeutics.

Dasetty, Siva [University of Chicago, IL (United S↗
DOE OSTI2018

An atomistic building block description of C-S-H - Towards a realistic C-S-H model

Understanding the atomistic structure of Calcium silicate hydrate (C-S-H), the main product of cement hydration, is of paramount importance to better formulate sustainable cement. The existing atomistic models are not in total agreement with experimental results and fail to explain the nanosized nature of C-S-H. Here, we present a new approach for describing the complexity of these structures at the molecular level, enabling a detailed comparison of C-S-H models. The new methodology encodes a full, large scale atomistic C-S-H structure by a simple, readable string of characters, similar to the way the base sequence in DNA encodes a vast range of different proteins. We then use the methodology to assess 14 Å tobermorite-defect structures and their stabilities using DFT and classical molecular dynamics. Finally we highlight how the model may be extended to develop reliable atomistic C-S-H models for a range of Ca/Si ratios and conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Multisublattice cluster expansion study of short-range ordering in iron-substituted strontium titanate

Owing to the challenges in obtaining realistic atomic configurations in large chemical phase spaces, it is not straightforward to describe structure–property relations in materials exhibiting configurational disorder. One example is iron-substituted strontium titanate (SrTi 1–x Fe x O 3–d , STF), a promising perovskite-derivative cathode material in solid oxide fuel cells that exhibits full solid solubility 0 ≤ x ≤ 1 and a tendency to exhibit short-range order. Here we demonstrate a multisublattice cluster expansion (CE) framework and apply it to STF across the full composition range. The CE approach is distinct from more traditional CE formulations in that clusters are defined explicitly by the chemical species distributed among multiple sublattices, rather than via cluster functions of occupation variables with decoration. The modified CE approach makes it easy to distinguish meaningful chemical interactions that are harder to extract from conventional CE, since for the latter chemical identity in a cluster is expressed as a product of site occupations. The least absolute shrinkage and selection operator (LASSO) is implemented as a regression analysis tool to select key clusters and avoid overfitting. We demonstrate this formulation on STF, and show that it can accurately predict configurational energies in comparison to conventional CE. From the key clusters, we identify that short-range ordering between substitutional Fe and oxygen vacancies (V O ) results in the formation of Fe–VO strings. In addition, we consider the stability of STF through CE-based Monte Carlo (MC) simulations and confirm the presence of superstructures that were previously observed in transmission electron microscopy. In this work, analysis of atomic configurations from MC samples reveals variations in the oxidation state of Fe atoms, which can be explained by the ordering tendency of Fe and V O . The cluster description and selection formalism described here may be applied to other disordered multisublattice systems for accurate and efficient material modeling.

36 MATERIALS SCIENCE↗
DOE OSTI2024

PlasmoData.jl — A Julia framework for modeling and analyzing complex data as graphs

Datasets encountered in scientific and engineering applications appear in complex formats (e.g., images, multivariate time series, molecules, video, text strings, networks). Graph theory provides a unifying framework to model such datasets and enables the use of powerful tools that can help analyze, visualize, and extract value from data. In this work, we present PlasmoData.jl, an open-source, Julia framework that uses concepts of graph theory to facilitate the modeling and analysis of complex datasets. The core of our framework is a general data modeling abstraction, which we call a DataGraph. We show how the abstraction and software implementation can be used to represent diverse data objects as graphs and to enable the use of tools from topology, graph theory, and machine learning (e.g., graph neural networks) to conduct a variety of tasks. We illustrate the versatility of the framework by using real datasets: (i) an image classification problem using topological data analysis to extract features from the graph model to train machine learning models; (ii) a disease outbreak problem where we model multivariate time series as graphs to detect abnormal events; and (iii) a technology pathway analysis problem where we highlight how we can use graphs to navigate connectivity. Further, our discussion also highlights how PlasmoData.jl leverages native Julia capabilities to enable compact syntax, scalable computations, and interfaces with diverse packages. Overall, we show that the DataGraph abstraction and PlasmoData.jl Julia package are able to model data within graphs and enable useful analysis.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2015

An introduction to PYTHIA 8.2

The Pythia program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. It contains a library of hard processes, models for initial- and final-state parton showers, matching and merging methods between hard processes and parton showers, multiparton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and several interfaces to external programs. Pythia 8.2 is the second main release after the complete rewrite from Fortran to C++, and now has reached such a maturity that it offers a complete replacement for most applications, notably for LHC physics studies. The many new features should allow an improved description of data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

The evens and odds of CMB anomalies

The lack of power of large-angle CMB anisotropies is known to increase its statistical significance at higher Galactic latitudes, where a string-inspired pre-inflationary scale can also be detected. Considering the Planck 2015 data, and relying largely on a Bayesian approach, we show that the effect is mostly driven by the even - harmonic multipoles with , which appear sizably suppressed in a way that is robust with respect to Galactic masking, along with the corresponding detections of . On the other hand, the first odd - multipoles are only suppressed at high Galactic latitudes. We investigate this behavior in different sky masks, constraining through even and odd multipoles, and we elaborate on possible implications. We include low- polarization data which, despite being noise-limited, help in attaining confidence levels of about 3 in the detection of . We also show by direct forecasts that a future all-sky -mode cosmic-variance-limited polarization survey may push the constraining power for beyond 5 .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

A system-level cost-of-energy wind farm layout optimization with landowner modeling

This work applies an enhanced levelized wind farm cost model, including landowner remittance fees, to determine optimal turbine placements under three landowner participation scenarios and two land-plot shapes. Instead of assuming a continuous piece of land is available for the wind farm construction, as in most layout optimizations, the problem formulation represents landowner participation scenarios as a binary string variable, along with the number of turbines. The cost parameters and model are a combination of models from the National Renewable Energy Laboratory (NREL), Lawrence Berkeley National Laboratory, and Windustiy. The system-level cost-of-energy (COE) optimization model is also tested under two land-plot shapes: equally-sized square land plots and unequal rectangle land plots. The optimal COEs results are compared to actual COE data and found to be realistic. The results show that landowner remittances account for approximately 10% of farm operating costs across all cases. Irregular land-plot shapes are easily handled by the model. We find that larger land plots do not necessarily receive higher remittance fees. The model can help site developers identify the most crucial land plots for project success and the optimal positions of turbines, with realistic estimates of costs and profitability. (C) 2013 Elsevier Ltd. All rights reserved.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Memory forensic analysis of a programmable logic controller in industrial control systems

In industrial control systems (ICS), programmable logic controllers (PLCs) are used to automate physical processes such as nuclear plants and power grid stations, and are often subject to cyber attacks. As in conventional IT domain, the memory analysis of the PLCs can help answer important forensic questions about the attack, such as the presence of malicious firmware, injection of modified control logic (the program running on the PLC), and manipulation of I/O devices (e.g., sensors and actuators). Unlike conventional IT domain, PLCs have heterogeneous hardware architecture, proprietary firmware and control software, making it challenging to employ a unified framework for their memory forensics. For merely extracting artifacts of forensic importance, reverse-engineering the firmware is a tedious task, and the effort needs to be repeated for every PLC model. As a community, a step-wise approach to tackle this challenge is to analyze the memory of specific PLCs, and subsequently find a generic framework applicable to all PLCs. Our work is a step forward in this direction. By following a methodology that focuses on the functional layer of PLCs instead of reverse engineering the firmware, we analyze the digital forensic artifacts available in a common PLC, Allen-Bradley ControlLogix 1756-L61. Before diving into the memory dump, we analyze the PLC control software to create a list of important artifacts that are sure to exist in the PLC memory dump. The approach employs a setup where PLC control software RSLogix-5000 is connected to the PLC, and the memory dump can be obtained as and when needed. We create test cases that sequentially highlight each category of artifacts, followed by an examination of the resultant impact on memory. After attaining the listed artifacts, we employ conventional string and known data searches to extract interesting information present in this PLC's memory. The memory analysis profile, presented as a Python library and shared with the community, can help a forensic investigator to readily extract forensic artifacts from the same model's controller. The adopted approach may help researchers in creating memory profile of other PLCs, and ultimately formulating a generic PLC memory analysis framework.

Rais, Muhammad Haris↗
DOE OSTI2019

pH-Responsive crude oil-in-water Pickering emulsion stabilized by polyacrylamide nanogels

Oil-in-water (o/w) Pickering emulsions stabilized by polyacrylamide (PAM) and poly(acrylamide-co-acrylic acid) nano-sized crosslinked polymeric particles (nanogels) under various conditions are described herein. Nanogels with different crosslinking and charge degree were synthesized through suspension polymerization and characterized at various salinities and pH using dynamic light scattering (DLS) and scanning electron microscopy (SEM). The PAM nanogel-stabilized o/w Pickering emulsions were quickly demulsified in alkaline solutions whereas they showed markedly stability in brines and under acidic conditions. A small amount of nanogels were sufficient for the formation of Pickering emulsions. The average diameter of oil droplets was no longer decreasing with nanogel concentration increment above 1000 mg/L. In addition, the average diameter of oil drops was independent of sonication period in the range of 15–240 s. Interestingly, the string-like structures of nanogel aggregations were found in the aromatic hydrocarbons/water Pickering emulsions, which significantly enhanced the emulsion stability. Compared to the crude oil, the corresponding Pickering emulsions showed excellent flowability at various shear rates. The crude oil/water Pickering emulsions could be broken using alkali as a trigger, which suggests the potential utility for the recovery of crude oil.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Deuterium pellet fueling in type-III ELMy H-mode plasmas on EAST superconducting tokamak

Type-III ELMy H-mode plasmas are a valuable operating scenario, as they may simultaneously achieve fusion power gain of Q = 10 and acceptable steady-state and peak power fluxes to the plasma-facing components. It is important to investigate cryogenic deuterium pellet injection fueling in this kind of H-mode plasma since it has been chosen as a main plasma fueling technique for ITER. Recently, pellet fueling experiments have been successfully carried out on EAST, an ITER-like tokamak. A maximum electron density of 0.73 × n GW has been obtained. It is found that ELM behavior was modified immediately and a string of small ELMs were induced when pellets were injected at a low velocity from ¯40 cm above the mid-plane on the low field side, which is different from the fact that pellets trigger signal ELMs in Type-I ELMy H-mode plasmas in other tokamaks. Furthermore, the decreased edge temperature caused by the cryogenic pellet was proposed as the reason for this ELM modification. These results will provide a useful reference for the pellet fueling in a Type-III ELMy H-mode plasma on ITER in the future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization

Objective: The growing availability of electronic health records (EHR) data opens opportunities for integrative analysis of multi-institutional EHR to produce generalizable knowledge. A key barrier to such integrative analyses is the lack of semantic interoperability across different institutions due to coding differences. We propose a Multiview Incomplete Knowledge Graph Integration (MIKGI) algorithm to integrate information from multiple sources with partially overlapping EHR concept codes to enable translations between healthcare systems. Methods: The MIKGI algorithm combines knowledge graph information from (i) embeddings trained from the co-occurrence patterns of medical codes within each EHR system and (ii) semantic embeddings of the textual strings of all medical codes obtained from the Self-Aligning Pretrained BERT (SAPBERT) algorithm. Due to the heterogeneity in the coding across healthcare systems, each EHR source provides partial coverage of the available codes. MIKGI synthesizes the incomplete knowledge graphs derived from these multi-source embeddings by minimizing a spherical loss function that combines the pairwise directional similarities of embeddings computed from all available sources. MIKGI outputs harmonized semantic embedding vectors for all EHR codes, which improves the quality of the embeddings and enables direct assessment of both similarity and relatedness between any pair of codes from multiple healthcare systems. Results: With EHR co-occurrence data from Veteran Affairs (VA) healthcare and Mass General Brigham (MGB), MIKGI algorithm produces high quality embeddings for a variety of downstream tasks including detecting known similar or related entity pairs and mapping VA local codes to the relevant EHR codes used at MGB. Based on the cosine similarity of the MIKGI trained embeddings, the AUC was 0.918 for detecting similar entity pairs and 0.809 for detecting related pairs. For cross-institutional medical code mapping, the top 1 and top 5 accuracy were 91.0% and 97.5% when mapping medication codes at VA to RxNorm medication codes at MGB; 59.1% and 75.8% when mapping VA local laboratory codes to LOINC hierarchy. When trained with 500 labels, the lab code mapping attained top 1 and 5 accuracy at 77.7% and 87.9%. MIKGI also attained best performance in selecting VA local lab codes for desired laboratory tests and COVID-19 related features for COVID EHR studies. Compared to existing methods, MIKGI attained the most robust performance with accuracy the highest or near the highest across all tasks. Conclusions: The proposed MIKGI algorithm can effectively integrate incomplete summary data from biomedical text and EHR data to generate harmonized embeddings for EHR codes for knowledge graph modeling and cross-institutional translation of EHR codes.

Zhou, Doudou↗
DOE OSTI2023

Even spheres as joint spectra of matrix models

The Clifford spectrum is a form of joint spectrum for noncommuting matrices. This theory has been applied in photonics, condensed matter and string theory. In applications, the Clifford spectrum can be efficiently approximated using numerical methods, but this only is possible in low dimensional example. In this paper we examine the higher-dimensional spheres that can arise from theoretical examples. We also describe a constructive method to generate five real symmetric almost commuting matrices that have a K-theoretical obstruction to being close to commuting matrices. For this, we look to matrix models of topological electric circuits.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Microstructural evolution of a silicon carbide-carbon coated nanostructured ferritic alloy composite during in-situ Kr ion irradiation at 300°C 450°C

This work focuses on irradiation behaviors of a novel silicon carbide and carbon coated nanostructured ferritic alloy (SiC-C@NFA) composite for potential applications as a cladding and structural material for next generation nuclear reactors. The SiC-C@NFA samples were irradiated with 1 MeV Kr ions up to 10 dpa at 300 and 450 °C. Microstructures and defect evolution were studied in-situ at the IVEM-Tandem facility at Argonne National Laboratory. The effects of ion irradiation on various phases such as α-ferrite matrix, (Fe,Cr) 7 C 3 , and (Ti,W)C precipitates were evaluated. The α-ferrite matrix showed a continuous increase in dislocation density along with spatial ordering of dislocation loops (or loop strings) at >5 dpa. The size of the dislocation loops at 450 °C was larger than that at 300 °C. The nucleation and growth of new (Ti,W)C precipitates in α-ferrite grains were enhanced with the ion dose at 450 °C. This study provides new insight into the irradiation resistance of the SiC-C@NFA system.

(FeCr)(7)C-3↗
DOE OSTI2018

The effect of Mn/Ni on thermodynamic properties of critical nucleus in Fe-Cu-Mn (Ni) ternary alloys

The aging- or radiation-induced hardening of Cu/Mn/Ni precipitates in Fe alloys is one of property degradation mechanisms in structural materials in nuclear reactors. Experiments show that aging or radiation leads the formation of Cu-rich precipitates, and the addition of Mn or Ni elements enhances the precipitation kinetics. In this study, the phase-field model coupled with the constrained string method have been applied to investigate the thermodynamic properties of critical nuclei such as the minimum energy path of Cu/Mn/Ni precipitation in Fe-Cu-Mn and Fe-Cu-Ni ternary alloys. The chemical free energies used in the model are taken from CALPHAD. The simulation results show that the formation of Cu/Mn/Ni clusters needs to overcome an energy barrier, and the precipitate has a Core-Shell structure. The thermodynamic properties of the critical nucleus are influenced by temperature and Cu/Mn/Ni overall concentrations, which are in accordance with the simulation results as well as the experimental observations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2012

The complex metal-rich boride Ti{sub 1+x}Rh{sub 2-x+y}Ir{sub 3-y}B{sub 3} (x=0.68, y=1.06) with a new structure type containing B{sub 4} zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

Polycrystalline samples and single crystals of the new complex boride Ti{sub 1+x}Rh{sub 2-x+y}Ir{sub 3-y}B{sub 3} (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B{sub 4} fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) A, b=14.995(2) A and c=3.234(1) A. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B{sub 4} fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior. - graphical abstract: The structure of Ti{sub 1.68(2)}Rh{sub 2.38(6)}Ir{sub 1.94(4)} B{sub 3}, a new structure type containing planar trans zigzag B{sub 4} units, is another example which illustrates the tendency of metal-rich borides to form B-B bonds with increasing boron content. Beside the B{sub 4} fragment it exhibits one-dimensional chains of titanium atoms and hold one-dimensional strings of face-sharing empty tetrahedral and square pyramidal clusters (see figure). Highlights: Black-Right-Pointing-Pointer Synthesis of a new metal-rich complex boride. Black-Right-Pointing-Pointer New structure type containing isolated boron and trans zigzag B{sub 4} units. Black-Right-Pointing-Pointer Crystallographic parameters and bond length well reproduced by theory. Black-Right-Pointing-Pointer Strong boron-boron and metal-boron interactions responsible for structural stability. Black-Right-Pointing-Pointer Three-dimensional metallic network responsible for metallic behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗