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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 OSTI2015

TlHgInS 3 : An Indirect-Band-Gap Semiconductor with X-ray Photoconductivity Response

The quaternary compound TlHgInS3 crystallizes in a new structure type of space group, C2/c, with cell parameters a = 13.916(3) angstrom, b = 3.9132(8) angstrom, c = 21.403(4) angstrom, beta = 104.16(3)degrees, V = 1130.1(8) angstrom(3), and rho = 7.241 g/cm(3). The structure is a unique three-dimensional framework with parallel tunnels, which is formed by (1)(infinity)[InS33-] infinite chains bridged by linearly coordinated Hg2+ ions. TlHgInS3 is a semiconductor with a band gap of 1.74 eV and a resistivity of similar to 4.32 G Omega cm. TlHgInS3 single crystals exhibit photocurrent response when exposed to Ag X-rays. The mobility-lifetime product (mu tau) of the electrons and holes estimated from the photocurrent measurements are (mu tau)(e) approximate to 3.6 x 10(-4) cm(2)/V and (mu tau)(h) approximate to 2.0 x 10(-4) cm(2)/V. Electronic structure calculations at the density functional theory level indicate an indirect band gap and a relatively small effective mass for both electrons and holes. Based on the photoconductivity data, TlHgInS3 is a potential material for radiation detection applications.

Li, Hao↗
DOE OSTI2025

Probing Hydrogen-Bond Anharmonicity in Cocrystals with Colossal Thermal Expansion

Organic cocrystals with sizable anisotropic thermal expansion (TE) are attractive building blocks for thermally responsive soft actuators. Such materials often display intermolecular H-bonding, whose thermal strength fluctuations are frequently overlooked if displacements and/or conformational changes are visible during TE. In this work, we employed variable-temperature single-crystal synchrotron diffraction to investigate the linear expansion coefficients of two organic cocrystals, 1 and 2, which exhibit colossal thermal expansivity exceeding 140 MK –1 . Despite such pronounced TE, solid-state 2 H and 13 C NMR experiments show no evidence of fast internal reorientations or large-amplitude molecular displacement during expansion. Although nondirectional π–π stacking dominates the colossal TE, our results indicate that hydrogen bonds play a non-negligible role in the anisotropic response. Molecular dynamics simulations reveal a temperature-dependent broadening of H-bond length distributions, which arises from the increased thermal sampling of an anharmonic potential energy surface. Our data support an expansion mechanism based on cooperativity in π-π interactions, accompanied by thermal softening and fluctuation-driven stretching of directional hydrogen bonds in these molecular solids. This mechanism underscores the significance of directional interactions in organic cocrystals, which is a key factor in the design of organic thermoresponsive crystalline materials.

Hernández-Morales, Ernesto A. [Univ. Nacional Auto↗
DOE OSTI2024

Maximizing Marine Carbon Removal by Coupling Electrochemical and Biological Methods

Integrated development of emerging marine decarbonization strategies offers the possibility of lowering CO2 removal costs and enabling their widespread deployment. In this study we examine the feasibility and benefits of coupling electrochemical and biological marine carbon removal strategies. Bipolar membrane electrodialysis (BPMED) is used to generate acid and alkalinity from seawater and electricity, and the alkalinity is returned to the ocean for indirect CO2 removal from the atmosphere, but the acid stream is a waste product. Considering the large-scale of CO2 removal necessary, the acid storage, neutralization, and disposal have prohibitive costs and carbon footprint. Here we investigate the feasibility to valorize the acid stream to enhance the growth and CO2 uptake through photosynthesis in the fast-growing marine phytoplankter Picochlorum celeri. When added to active algae cultures, the BPMED-generated acidified seawater alters the carbonate-bicarbonate equilibrium thereby increasing the bioavailability of CO2 and the observed growth rates. Additions of up to 2 mM H+ from BPMED effluent streams increased algal productivity up to 3-fold. A high-level analysis conducted based on experimental data to estimate the potential of sequestered CO2 emissions when compared to conventional commercial means of acid utilization or disposal, is estimated to be ~30 kgCO2 / kgacid. Through further development and optimization in terms of choice of algal species, growth conditions, acid addition rates, etc. the combined electrochemical-biological approach has the potential to achieve higher net CO2 removal.

carbon dioxide, marine, marine algae↗
DOE OSTI2024

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Pipe Parity Analysis of Seawater Desalination in the United States: Exploring Costs, Energy, and Reliability via Case Studies and Scenarios of Emerging Technology

As climate change-induced variables exacerbate water scarcities, the use of seawater reverse osmosis (SWRO) membrane desalination technology for treating seawater could potentially provide a long-term drought-proof source of drinking water. This study carried out a technoeconomic assessment (TEA) for three SWRO desalination plants in the U.S. and one in Israel to set baselines for the cost and energy consumption for seawater desalination. In addition, a breakeven curve for implementing SWRO desalination was estimated in relation to the cost of water conservation measures to meet drought-induced reduction of the traditional water supply. The results show that the cost of SWRO water production scales with the plant capacity while energy intensity is not dramatically different across the plants. The higher cost in some U.S. plants is due to high capital investment, including land acquisition and permitting. Variations in plant capacity utilization have the greatest impact on the levelized cost of water (LCOW) over the plant service life, suggesting the importance of reducing fouling and maintenance-related downtime. Scenario analysis of fixed labor cost reduction through process automation indicates investments in automation and sensing technology could result in long-term savings. Breakeven analysis shows the decision to adopt SWRO is highly dependent on the local cost associated with water conservation to meet water supply reduction. Moreover, a small reduction in SWRO cost can influence a shift toward the adoption of SWRO over water conservation measures. Incorporation of future water demand, water conservation potential, and water stress data around the nation indicates SWRO desalination could be an important contributor to the future municipal drinking water portfolio in the U.S.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2017

Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe 4 S 4 ] Site in EndoIII and MutY

S K-edge X-ray absorption spectroscopy (XAS) was used to study the [Fe 4 S 4 ] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe–S bond covalencies (i.e., the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron–thiolate and iron–sulfide bonds would stabilize the oxidized state of the [Fe 4 S 4 ] clusters. Our results are compared to those on previously studied [Fe 4 S 4 ] model complexes, ferredoxin (Fd), and to new data on high-potential iron–sulfur protein (HiPIP). A limited decrease in covalency is observed upon removal of solvent water from EndoIII and MutY, opposite to the significant increase observed for Fd, where the [Fe 4 S 4 ] cluster is solvent exposed. Importantly, in EndoIII and MutY, a large increase in covalency is observed upon DNA binding, which is due to the effect of its negative charge on the iron–sulfur bonds. Furthermore, in EndoIII, this change in covalency can be quantified and makes a significant contribution to the observed decrease in reduction potential found experimentally in DNA repair proteins, enabling their HiPIP-like redox behavior.

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

Streamflow in the Columbia River Basin: Quantifying Changes Over the Period 1951-2008 and Determining the Drivers of Those Changes

Trend, detection, and attribution analyses were performed using naturalized streamflow observations and routed land surface model runoff for 10 subbasins in the Columbia River Basin during water years 1951–2008. The Energy Exascale Earth System land-surface model (ELM) version 1.0 and the Routing Application for Parallel computatIon of Discharge (RAPID) routing model were used to conduct semi-factorial simulations driven by multiple sets of bias-corrected forcing data sets. Four main potential drivers, including climate change (CLMT), CO 2 concentration (CO 2 ), nitrogen deposition (NDEP), and land use and land cover change (LULCC), were analyzed during the assessment. All subbasins showed significant (α = 0.10) declines in the observed amount of annual total streamflow, except for the Middle and Upper Snake and Upper Columbia Subbasins. These declines were led by significant decreases in June–October streamflow, which also directly led to significant decreases in peak and summer streamflow. Except for the Snake River Subbasins, LULCC had the same pattern of declines in monthly streamflow, but the period was shifted to May–September. NDEP also had significant trends in June–October; however, rather than decreases, the trends showed significant increases in streamflow. While there were significant trends in CO 2 , NDEP, and LULCC, their signals of change were weak in comparison to the signal in CLMT and the natural internal variability found in streamflow. Overall, the detection and attribution analysis showed that the historical changes found in annual total, center of timing of, and summer mean streamflow could be attributed to changing climate and variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

An Analysis of Abandoned Oil Well Characteristics Affecting Methane Emissions Estimates in the Cherokee Platform in Eastern Oklahoma

Anthropogenic activities increase methane emissions, contributing to greenhouse gas levels and adversely affecting the environment. Abandoned oil and gas wells potentially leak methane, but data are limited. We analyze methane emissions from abandoned wells (n = 179) in the Cherokee Platform in Oklahoma, a previously unaccounted basin, and compare emissions factors (EFs) to those in the Greenhouse Gas Inventory. We compare the contribution of various characteristics to the propensity for leakage. Higher emissions were observed with shallower wells and with unplugged wells. Plugged wells (n = 20) had an average EF of 96 ± 429 g/day and 65 ± 294 g/day for unplugged wells (n = 159). The majority of wells had no detectable leak. We calculated ethane EFs based on geochemical analysis of gas samples, finding higher EFs for unplugged (1.2 ± 5.5 g/day) versus plugged (0.9 ± 4.6 g/day) wells. The data indicate that in addition to the location of abandoned wells, physical characteristics are necessary to consider in estimating methane emissions.

58 GEOSCIENCES↗
DOE OSTI2024

Machine Learning Classification Strategy to Improve Streamflow Estimates in Diverse River Basins in the Colorado River Basin

Streamflow in the Colorado River Basin (CRB) is significantly altered by human activities including land use/cover alterations, reservoir operation, irrigation, and water exports. Climate is also highly varied across the CRB which contains snowpack-dominated watersheds and arid, precipitation-dominated basins. Recently, machine learning methods have improved the generalizability and accuracy of streamflow models. Previous successes with LSTM modeling have primarily focused on unimpacted basins, and few studies have included human impacted systems in either regional or single-basin modeling. We demonstrate that the diverse hydrological behavior of river basins in the CRB are too difficult to model with a single, regional model. We propose a method to delineate catchments into categories based on the level of predictability, hydrological characteristics, and the level of human influence. Lastly, we model streamflow in each category with climate and anthropogenic proxy data sets and use feature importance methods to assess whether model performance improves with additional relevant data. Overall, land use cover data at a low temporal resolution was not sufficient to capture the irregular patterns of reservoir releases, demonstrating the importance of having high-resolution reservoir release data sets at a global scale. On the other hand, the classification approach reduced the complexity of the data and has the potential to improve streamflow forecasts in human-altered regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Enhancing gene regulatory network inference through data integration with markov random fields

Here, a gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization scheme to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Origin of short- and medium-range order in supercooled liquid Ge 3 Sb 2 Te 6 from ab initio molecular dynamics simulations

Phase-change materials such as Ge–Sb–Te compounds have attracted much attention due to their potential value in electrical data storage. In contrast to the amorphous and crystalline phases, supercooled liquids are far from being deeply understood despite their inevitable role in both amorphization and crystallization processes. To this end, we have studied the dynamics properties and structural characteristics of liquid and supercooled liquid Ge 3 Sb 2 Te 6 during the fast cooling process. As the temperature decreases, chemical bonds become more homogeneous, but coordination numbers of Ge, Sb and Te atoms change very little. Meanwhile, the structural order of short-range configuration is obviously enhanced. Further studies suggest that Ge-centered, Sb-centered and Te-centered configurations change to the more ordered defective octahedrons mainly by adjusting the bond-angle relationship and bond length, rather than just by changing the coordination environment. It is the more ordered octahedrons that promote the formation of medium-range order. Our findings provide a deep insight into the origin of local structural order in supercooled liquid Ge 3 Sb 2 Te 6 , which is of great importance for the comprehensive understanding of amorphization and crystallization processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design

Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Quantum mechanical force field for water with explicit electronic polarization

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10{sup 6} self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Note: On the generation of sub-300 keV flash-X-rays using rod-pinch diode: An experimental investigation

Generation of flash X-rays (FXRs) at less than 500 keV is described with emphasis on experimental investigation. The pulser is a Tesla transformer-Water transmission line based pulsed power generator operating in double resonance mode to power a rod-pinch diode. The configuration of aspect ratio reported here falls much below the normally reported ratios for the rod-pinch diode operation. Experimental investigation at such low pulsed voltage has revealed “flowering” of the anode tip and “pitting” of the perspex window. A possible explanation in terms of Lorentz body force is discussed rather than the pinch mechanism generally suggested in literature. The experimental investigation for the FXR generation is corroborated by measuring the radiation dose using CaSO{sub 4} (Dy) thermo luminescent dosimeters.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗