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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 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Combinatorial Biosynthesis of Sulfated Benzenediol Lactones with a Phenolic Sulfotransferase from Fusarium graminearum PH-1

Total biosynthesis or whole-cell biocatalytic production of sulfated small molecules relies on the discovery and implementation of appropriate sulfotransferase enzymes. Although fungi are prominent biocatalysts and have been used to sulfate drug-like phenolics, no gene encoding a sulfotransferase enzyme has been functionally characterized from these organisms. Here, we identify a phenolic sulfotransferase, FgSULT1, by genome mining from the plant-pathogenic fungus Fusarium graminearum PH-1. We expressed FgSULT1 in a Saccharomyces cerevisiae chassis to modify a broad range of benzenediol lactones and their nonmacrocyclic congeners, together with an anthraquinone, with the resulting unnatural natural product (uNP) sulfates displaying increased solubility. FgSULT1 shares low similarity with known animal and plant sulfotransferases. Instead, it forms a sulfotransferase family with putative bacterial and fungal enzymes for phase II detoxification of xenobiotics and allelochemicals. Among fungi, putative FgSULT1 homologues are encoded in the genomes of Fusarium spp. and a few other genera in nonsyntenic regions, some of which may be related to catabolic sulfur recycling. Computational structure modeling combined with site-directed mutagenesis revealed that FgSULT1 retains the key catalytic residues and the typical fold of characterized animal and plant sulfotransferases. Our work opens the way for the discovery of hitherto unknown fungal sulfotransferases and provides a synthetic biological and enzymatic platform that can be adapted to produce bioactive sulfates, together with sulfate ester standards and probes for masked mycotoxins, precarcinogenic toxins, and xenobiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Short-Range Order and Charge Transport in SiO{sub x}: Experiment and Numerical Simulation

The structure of nonstoichiometric silicon oxide (SiO{sub x}) has been studied by the methods of highresolution X-ray photoelectron spectroscopy and fundamental optical-absorption spectroscopy. The conductivity of SiO{sub x} (x = 1.4 and 1.6) films has been measured in a wide range of electric fields and temperatures. Experimental data are described in terms of the proposed SiO{sub x} structure model based on the concept of fluctuating chemical composition leading to nanoscale fluctuations in the electric potential. The maximum amplitude of potential fluctuations amounts to 2.6 eV for electrons and 3.8 eV for holes. In the framework of this model, the observed conductivity of SiO{sub x} is described by the Shklovskii–Efros theory of percolation in inhomogeneous media. The characteristic spatial scale of potential fluctuations in SiO{sub x} films is about 3 nm. The electron-percolation energy in SiO{sub 1.4} and SiO{sub 1.6} films is estimated to be 0.5 and 0.8 eV, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nucleon-induced inelastic scattering with statistical strength functions and the ECIS direct reaction code

Modern theoretical descriptions of inelastic scattering make use of multi-step direct reaction approaches together with transition potentials obtained from sophisticated nuclear structure models. Here we demonstrate how the complexity of such calculations can be reduced to permit simpler ones, also using the ECIS code, but providing an almost equally precise alternative to a much more detailed calculation. We have studied the transition form factors within the random phase approximation (RPA), where these are obtained as linear combinations of particle–hole states. At moderate to high excitation energies, where interference effects tend to disappear, we have proposed an independent particle–hole formalism in which particle–hole states are spread in energy with an appropriate strength function obtained from the RPA. The effects of more complex modes, such as 2p–2h ones, are simulated with widths calculated in a semi-classical context. In this work, we verify the validity of our approximations for pre-equilibrium proton-induced reactions on 90 Zr target. Our calculations provide a good description of the reaction data and point toward a simplification of the description of nucleon-induced reactions based on averages of microscopic details of the projectile–target interaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

I-GCN: A Graph Convolutional Network Accelerator with Runtime Locality Enhancement through Islandization

In this paper, we propose a novel hardware accelerator for GCN inference called I-GCN that significantly improves data locality and reduces unnecessary computation through a new online graph restructuring algorithm we refer to as islandization. The proposed algorithm finds clusters of nodes with strong internal but weak external connections. The islandization process yields two major benefits. First, by processing islands rather than individual nodes, there is better on-chip data reuse and fewer off-chip memory accesses. Second, there is less redundant computation as aggregation for common/shared neighbors in an island can be reused. The parallel search, identification, and leverage of graph islands are all handled purely in hardware at runtime working in an incremental pipelined manner. This is done without any preprocessing of the graph data or adjustment of the GCN model structure.

Geng, Tong↗
DOE OSTI2025

Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides

Background: Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored. Results: Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability. Conclusions: We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.

Lipid Signalling↗
DOE OSTI2019

A highly ordered, nonprotective MALAT1 ENE structure is adopted prior to triplex formation

The 3' end of the ~7 kb lncRNA MALAT1 contains an evolutionarily and structurally conserved element for nuclear expression (ENE) which confers protection from cellular degradation pathways. Formation of an ENE triple helix is required to support transcript accumulation, leading to persistent oncogenic activity of MALAT1 in multiple cancer types. Though the specific mechanism of triplex-mediated protection remains unknown, the MALAT1 ENE triplex has been identified as a promising target for therapeutic intervention. Interestingly, a maturation step of the nascent lncRNA 3' end is required prior to triplex formation. We hypothesize that disruption of the maturation or folding process may be a viable mechanism of inhibition. To assess putative cotranscriptional ENE conformations prior to triplex formation, we perform microsecond MD simulations of a partially folded ENE conformation and the ENE triplex. Herein, we identify a highly ordered ENE structure prior to triplex formation. Extensive formation of U•U base pairs within the large U-rich internal loops produces a global rod-like architecture. We present a three-dimensional structure of the isolated ENE motif, the global features of which are consistent with small angle X-ray scattering (SAXS) experiments. Our structural model represents a nonprotective conformation of the MALAT1 ENE, providing a molecular description useful for future mechanistic and inhibition studies. We anticipate that targeting stretches of U•U pairs within the ENE motif will prove advantageous for the design of therapeutics targeting this oncogenic lncRNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods

Several pathways exist to bypass DNA damage during replication. One such pathway is template switching. The Rad5 protein plays two important roles in template switching: it is an E3 ubiquitin ligase that catalyzes PCNA poly-ubiquitylation and it is a helicase that converts replication forks to chicken foot structures. To understand the structure, conformational flexibility, and mechanism of Rad5, we used a full-ensemble hybrid method combining Langevin dynamics simulations and small-angle X-ray scattering. From these studies, we generated the first experimentally validated, high-resolution structural model of Rad5. We found that Rad5 is more compact and less extended than is suggested by its large amount of predicted intrinsic disorder. Thus, Rad5 likely has a novel intra-molecular interaction that limits the range of conformational space it can sample. We provide evidence for a novel interaction between the HIRAN and the helicase domains of Rad5, and we discuss the biological and mechanistic implications of this.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique

A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hicks Pries, Sulman, et al 2018. In situ incubation of 13C-labeled litter in three soil pits at Blodgett Forest, CA from 2013 to 2016

Even though over half of the world's soil organic carbon (SOC) is stored in subsoils (>20 cm deep), and the old ages of subsoil OC indicate its cycling differs from surface SOC, there are few studies examining in situ decomposition processes in deep soils. The purpose of this dataset is to elucidate these processes. In this study we added 13C-labeled fine roots to 15, 55, and 95 cm depths of a well-characterized coniferous forest Alfisol and monitored the amount of root-derived C remaining over 6, 12, and 30 months. We recovered the root-derived C in microbial phospholipid fatty acids (PLFAs) after 6 months and in coarse (>2 mm) particulate, fine (<2 mm) particulate, and dense, mineral-associated pools after 6, 12, and 30 months. Overall, root decomposition in the first 6 months was similar among all depths but significantly diverged at 30 months with faster decomposition at 15 cm than at 95 cm. There were more fungal and Gram negative-associated PLFAs at 15 cm than at 95 cm, and 13C analysis revealed those microbial groups preferred the added root carbon to native SOC. Mineral-associations were not the cause of slower decomposition at depth because similar amounts of applied root C was recovered in the dense fraction at all depths. The largest difference among depths was in the amount of root C recovered in the coarse particulate fraction, which was greater at 95 cm (50%) than at 15 cm (15%). Slower decomposition of the particulate pool at depth likely contributed to the increase in C:N ratios and depletion of δ13C values below 60 cm depth in our soil profiles. Simulations of these soils using the CORPSE model, which incorporates microbial priming effects and mineral stabilization of SOC, reproduced patterns of particulate and mineral-associated SOC over both time and depth and suggested that a lack of priming by root exudates at depth could account for the slower decomposition rate of particulate root material. Decomposition of deep particulate SOC may increase if root exudation or dissolved OC transport to depth increases.This dataset includes (1) characterization of the soil pits prior to litter addition, (2) characterization of how the litter changed after 6, 12, and 30 months, and (3) the CORPSE model structure, parameterization, and output.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Active–Source Seismic Tomography at the Brady Geothermal Field, Nevada, with Dense Nodal and Fiber–Optic Seismic Arrays

We deployed a dense seismic array to image the shallow structure in the injection area of the Brady Hot Springs geothermal power plant in western Nevada. The array was composed of 238 three-component, 5 Hz nodal instruments, 8700 m of distributed acoustic sensing (DAS) fiber-optic cable (FOC) installed horizontally in surface trenches, and 400 m of FOC installed vertically in a borehole. The geophone array had about 60 m instrument spacing in the target zone, whereas DAS channel separations were about 1 m with an averaging (gauge) length of 10 m. The acquisition systems provided 15 days of continuous records, including active-source and ambient noise signals. A large vibroseis truck was operated at 196 locations, exciting a swept-frequency signal from 5 to 80 Hz over 20 s using three vibration modes (vertical, longitudinal, and transverse), with three sweeps per mode at each site. Sweeps were repeated up to four times at each site during four different stages of power plant operation: normal operation, shutdown, high and oscillatory injection and production, and normal operation. After removal of the sweep signal from the raw data, the first P-wave arrivals were automatically picked using a combination of methods. Here, the travel times were then used to invert for the 3D P-wave velocity structure. Models with 100 m horizontal and 20–50 m vertical node spacing were obtained, covering an area 2000 m by 1300 m, with acceptable resolution extending to about 250 m below surface. The travel-time data were fit to a root mean square (rms) misfit of 31 ms, close to our estimated picking uncertainty. Lateral boundaries between high and low velocity zones agree relatively well with the location of local faults from previous studies, and low near-surface velocities are associated with faults and fumarole locations. A sharp increase in velocity from < 1500 to > 2000 m/s at approximately 50 m below the ground surface in many parts of the study area may indicate a shallower water table than expected for the region.

15 GEOTHERMAL ENERGY↗
DOE OSTI2018

Structural Studies of Amorphous Materials by Fluctuation Electron Microscopy

Fluctuation Electron Microscopy (FEM) is a technique that examines the fluctuations in electron scattering across a uniformly thin amorphous sample. The statistics of the intensity fluctuations, mean and variance, reveal any underlying medium-range order present in the structure. The goals of this project were: (1) To determine the fundamentals of the scattering physics that gives rise to the variance signal in fluctuation electron microscopy (FEM); (2) To use these discoveries to find ways to quantify FEM; (3) To apply the FEM method to interesting and technologically important families of amorphous materials, particularly those with important applications in energy-related processes. Excellent progress was made in items (1) and (2). In stage (3) we did not examine the metamict zircons, as proposed. Instead, we examined films of polycrystalline and amorphous semi-conducting diamond. Significant accomplishments are: (1) A Reverse Monte Carlo procedure was successfully implemented to invert FEM data into a structural model. This is computer-intensive, but it demonstrated that diffraction and FEM data from amorphous silicon are most consistent with a paracrystallite model. This means that there is more diamond-like topology present in amorphous silicon than is predicted by the continuous random network model. (2) There is significant displacement decoherence arising in diffraction from amorphous silicon and carbon. The samples are being bombarded by the electron beam and atoms do not stay still while being irradiated – much more than was formerly understood. The atom motions cause the destructive and constructive interferences in the diffraction pattern to fluctuate with time, and it is the time-averaged speckle that is being measured. The variance is reduced by a factor m, 4 ≤ m ≤ 1000, relative to that predicted by kinematical scattering theory. (3) Speckle intensity obeys a gamma distribution, where the mean intensity $ \overline{I}\ $ and m are the two parameters governing the shape of the gamma distribution profile. m is determined by the illumination spatial coherence, which is normally very high, and mostly by the displacement decoherence within the sample. (4) Amorphous materials are more affected by the electron beam than are crystalline materials. Different samples exhibit different disruptibility, as measured by the effective values of m that fit the data. (5) Understanding the origin of the displacement decoherence better should lead to efficient methods for computing the observed variance from amorphous materials.

36 MATERIALS SCIENCE↗
DOE OSTI2018

“Graphene-Wrapped” Complex Hydrides as High-Capacity, Regenerable Hydrogen Storage Materials

This project focused on the development of a new class of hydrogen storage material, hydride@graphene, for the next-generation H 2 powered fuel cell vehicles. The new approach was based on a recent technology breakthrough through the collaboration between Argonne National Laboratory (ANL) and Shanghai Jiao Tong University (SJTU). A “nanoencapsulated” sodium borohydride-graphene composite, NaBH 4 @graphene, was successfully synthesized using a simple solvent-based method. The new composite offers regenerable high H 2 storage capacity in multiple dehydrogenation and rehydrogenation cycles. Under this short project, we successfully synthesized catalyst-doped NaBH 4 @graphene composite and demonstrated five dehydrogenation (DH) and rehydrogenation (RH) cycles with measured gravimetric capacity > 7.4 wt% at 406 ºC. We also successfully demonstrated the improvement in hydrogen release kinetics by lowering DH temperature of 320 degree over bulk NaBH 4 or 138 degree over NaBH 4 @G as the benchmark at the beginning of the project. We collaborated with members of the Hydrogen Materials – Advanced Research Consortium (HyMARC) team in computational modeling, structural characterization and performance measurement.

08 HYDROGEN↗
DOE OSTI2019

Electric Form Factor of the Neutron from Asymmetry Measurements

The overwhelming majority of visible mass in the universe is composed of protons and neutrons, collectively known as nucleons, which are arguably the most important strongly interacting systems to study. A nucleon may naively be thought of as a composite object built out of three non-interacting sub-objects, known as quarks, in the large energy limit; however, the structure of the nucleon is much more complicated, and consequently far richer, than a simple valence-quark picture. There are sea quarks in addition to valence quarks that interact strongly via the exchange of gluons resulting in a complex vacuum structure, and the collective system must give rise to the observed properties of the nucleon, e.g. the radius and mass. The nucleon is the most well-studied hadron and yet there are still unresolved complexities in the calculation of properties from first principles of QCD; this represents a central problem in nuclear physics. The theoretical difficulty with the nucleon requires experimentation, which is steadily increasing the knowledge of nucleon structure and the strong interaction. The subject of this thesis pertains to nucleon electromagnetic form factors which are fundamental quantities containing information on the spatial and momentum distributions of charge and current within the nucleon. Nucleon form factors may be accessed through well-understood leading order electromagnetic processes with a leptonic probe, and provide strong constraints on testing non-perturbative QCD and nuclear structure models. The form factor ratio of the neutron has been extracted via a beam-target helicity asymmetry measurement. The Jefferson Lab Hall A experiment E02-013 ran in 2006 utilizing the 6 GeV CEBAF for its high-duty, longitudinally polarized electron beam. The double-arm coincidence experiment detected the quasielastically scattered electrons in a large angular and momentum acceptance spectrometer. The recoiling nucleons were detected and momentum analyzed in a large scintillator-iron based neutron detector. The analysis of a previously unpublished extraction of the electric form factor of the neutron is presented.

Obrecht, Richard↗
DOE OSTI2018

Voltron Compatible Whole Building Root-Fault Detection and Diagnosis

Buildings consume more than 40% of primary energy in the U.S. Malfunctioning sensors, components, and control systems, as well as degrading components in Heating, Ventilating and Air-conditioning (HVAC) and lighting systems are main reasons for energy waste and unsatisfactory indoor environment. Field studies have shown that an energy saving of 5-30% of total building energy consumption and improved indoor air quality can be achieved by simply applying automated fault detection and diagnosis (AFDD), followed by corrections even if these are not done in real time. Extensive research has been made on the development of component level AFDD tools in the past two decades. However, in recent years, the development of method for a whole building level AFDD has received much attention. Here, a whole building fault refers to a fault happening in one subsystem but impact on more than one subsystems, or has a significant impact on building performances, such as building’s energy consumption. Existing component level AFDD tools could fail to detect or give false alarm for faults that trigger abnormalities in multiple subsystems. Isolating such whole building faults, which have impacts on multiple subsystems, is also challenging by simply using component based AFDD solutions. On the other hand, it might be more cost-effective for medium- or small-sized commercial buildings that have subsystems (e.g. primary cooling subsystem, air loop subsystem, heating subsystem, lighting subsystem, etc.) to install one whole building level AFDD tool, rather than many component level AFDD tools, to focus on significant faults. The focus of this project is firstly to provide training opportunities in building AFDD research area for undergraduate students and to develop a workforce pipeline in building sciences. The objective of the proposed research activities is to develop cost-effective and scalable AFDD solutions for whole building level faults. The developed AFDD solution is VOLTTRONTM compatible to further increase its plug-n-play capacity and the market penetration. VOLTTRONTM is an open-source innovative distributed control and sensing software platform developed by the Pacific Northwest National Laboratory. A VOLTTRONTM compatible AFDD tool brings the benefits such as low-cost deployment, and better building to grid integration, etc. The performance of the developed whole building AFDD tools is evaluated using data collected from a mixed-use medium-sized university campus building. Another significant goal of this project is to engage undergraduate students in research activities and expose them to building control and AFDD fields. A demonstration building – Nesbitt Hall at Drexel University is identified for this study. This demonstration building has a typical HVAC system configuration, which includes a water-cooled chiller system, three variable air volume (VAV) air handling unit (AHU) systems, and a hydronic heating system. Faults, that are expected to have a whole building level impact, are artificially implemented in this demonstration building for three different seasons. Building data have been collected in this project, which include fault free building automation system (BAS) data and BAS data that contain system behaviors caused by artificially implemented and naturally occurred faults. These collected data are used to evaluate the developed whole building AFDD tools. A data-driven method, which includes a weather and schedule-based pattern matching (WPM) method and Feature based Principal Component Analysis (FPCA) method, is developed for whole building level fault detection. Parameter sensitivity tests, including snapshot window size, data sample searching pool size, etc., are implemented to evaluate the impacts of various WPM-FPCA parameters. A data-driven and expert knowledge/rule-based method using Bayesian Network (BN) and WPM is developed for whole building level fault diagnosis. The developed WPM-BN method, which includes a two-layer BN structure model and BN parameters, are either learned from baseline data or developed from expert knowledge. The developed whole building AFDD tools are evaluated using BAS data collected from the demonstration building. Using the evaluation data set, the WPM-FPCA fault detection method is evaluated under two different Principle Component (PC) retention rates, i.e., 0.65 retention rate and 0.95 retention rate. It is observed that when using 0.65 PC retention rate, the WPM-FPCA fault detection method achieves a 79% fault detection rate (this rate reaches to 85% when including the six make-up fault test cases discussed in the next bullet), while when using 0.95 PC retention rate, the WPM-FPCA fault detection method achieves 100% fault detection rate (this rate remains to be 100% when including the six make-up fault test cases). Under both PC retention rates, the WPM-FPCA fault detection method demonstrates 0% false alarm rates. Using the evaluation data set, the developed WPM-BN fault diagnosis method has successfully diagnosed thirteen (13) faults out of the fourteen (14) fault test cases. The one mis-diagnosed case exhibits fewer fault symptoms in different subsystems, when compared with other fault test cases. Overall speaking, the developed whole building AFDD solutions demonstrate satisfactory fault detection/diagnosis accuracy with very low false alarm rate. Lastly, a survey and market study has been performed to understand the existing AFDD market, including its gaps and needs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2019

Coupling Chemical Energy with Protein Conformational Changes to Translocate Small Molecules Across Membranes

EmrE is a small, homodimeric membrane transporter that exploits the established pH gradient across the E. coli inner membrane to export polyaromatic cations that might otherwise inhibit cellular growth. While herculean efforts through experimental studies have established many fundamental facts about the specificity and rate of substrate transport in EmrE, the low resolution of the available structures have hampered efforts to tie those findings to the EmrE coupling mechanism between proton and small molecule substrates. Here we present a full three-dimensional structure of EmrE optimized against available cyro-EM data to delineate the critical interactions by which EmrE regulates its conformation. We use the generated structural model to conduct equilibrium and nonequilibrium molecular dynamics simulations to probe EmrE dynamics under different substrate loading states, representing different states in the transport cycle. The model is stable under extended simulation, and reveals that water dynamics within the EmrE lumen change substantially with the loading state. The water dynamics cause hydrogen bonding networks to shift radically when the protonation states change for a pair of solvent-exposed glutamate residues (E14) within the lumen of the transporter, which are proposed to act as proton binding sites during the transport cycle. One specific hydrogen bond from a tyrosine (Y60) of one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. Furthermore, the hydrogen bond provided by Y60 lowers the pK a of the interacting glutamate relative to its partner on the opposite monomer such that it will protonate second, establishing the need for both glutamates to be protonated for the hydrogen bond to break and a substrate-free transition to take place.

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

Measurement of the (e,e') cross section for12C, 48Ti, 27Al and 40Ar

Many experiments have found that neutrinos have three different flavors, and they can transform from each other. Each flavor is a mixture of three nonzero mass states. In neutrino oscillation experiments, the uncertainty of the extracted oscillation parameters is dependent on the neutrino-nucleus cross section. In recent years various experiments provided precise neutrino and anti-neutrino cross section measurements and they have shown the inability of current Monte Carlo simulations to reproduce the data. A more accurate nuclear structure model of the target employed in neutrino detector is urgently needed to improve the precision of long baseline neutrino experiments. Electron scattering has been one of the most powerful methods of obtaining information about cross sections in the past. In the upcoming deep underground neutrino experiment (DUNE), Liquid Argon Time Projection Chambers (LArTPCs) will be used as the detector technology and argon will be used as the nuclear target. There are very few data available on argon and there is not an accurate nuclear model that describes them accurately, at ~5% level. We have performed an electron-argon scattering experiment at Jefferson Lab (E12-14-012) to provide accurate data that will help build a reliable nuclear model for describing neutrino-argon scattering. The JLab E12-14-012 experiment has successfully taken data in Hall A at the Thomas Jefferson National Accelerator Facility between February and March of 2017. We collected data for the inclusive (e,e') and exclusive (e,e'p) processes for a variety of targets (argon, titanium, aluminum, carbon) at a wide range of kinematic settings. This thesis will present the results of the inclusive double differential cross sections for carbon, titanium, aluminum and argon at beam energy E = 2:222 GeV and scattering angle theta = 15:541 deg with total uncertainties smaller than 5%. The kinematic settings covered a broad range of energy transfers, including deep inelastic scattering (DIS), delta production, and quasielastic scattering.

Dai, Hongxia↗
DOE OSTI2020

Treatment of Tilted Sonar Data for Salt Cavern Analysis

Structural modeling and visualization of salt caverns requires three-dimensional representations. These representations are typically produced from sonar surveys conducted by companies that then produce a report of depths, distances, and volumes. There are multiple formats that are vendor dependent, and, as technology improves, there have been changes from only horizontal surveys to inclined shots for ceilings and floors to mid-cavern inclined shots. For geomechanical modeling, leaching predictions, and cavern stability visualizations, Sandia has previously written in-house software, called SONAR8, that created a consistent geometry format from the processed sonar reports. However, the increase in the need for mid-cavern inclined surveys led to the discovery of certain limitations in that code. This report describes methods used to process the multiple different formats to handle inclined shots in a consistent and accurate manner in our modeling efforts. A set of file formats and a database schema that was developed for this work is also documented in the appendices.

02 PETROLEUM↗