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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Enhancing the Q-Factor of a Practical Qubit Niobium Three-Dimensional λ/4-Resonator Through Surface Treatment

Quantum computing stands as a revolutionary frontier in information technology, with the potential to solve complex problems far beyond the capacity of classical computers. At the heart of this disruptive innovation are qubits, forming the fundamental backbone of quantum computing. A leading-edge solution for constructing robust, enduring qubits involves embedding a Josephson junction within a high Q-factor, superconducting three-dimensional cavity. Further, our recent innovation lies in developing a uniquely optimized, quarter-wave resonator-based superconducting cavity, functioning at 6 GHz, specifically tailored for quantum computers. In this work, we elucidate our advancement towards elevating the Q-factor tenfold, an achievement made possible through the enhancement of machining precision, the application of rigorous postprocessing techniques—including mechanical, chemical, and surface treatments—as well as the refinement of our testing methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23

Ensemble docking is now commonly used in early-stage in silico drug discovery and can be used to attack difficult problems such as finding lead compounds which can disrupt protein–protein interactions. We give an example of this methodology here, as applied to fibroblast growth factor 23 (FGF23), a protein hormone that is responsible for regulating phosphate homeostasis. The first small-molecule antagonists of FGF23 were recently discovered by combining ensemble docking with extensive experimental target validation data (Science Signaling, 9, 2016, ra113). Here, we provide a detailed account of how ensemble-based high-throughput virtual screening was used to identify the antagonist compounds discovered in reference (Science Signaling, 9, 2016, ra113). Moreover, we perform further calculations, redocking those antagonist compounds identified in reference (Science Signaling, 9, 2016, ra113) that performed well on drug-likeness filters, to predict possible binding regions. These predicted binding modes are rescored with the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) approach to calculate the most likely binding site. Furthermore, our findings suggest that the antagonist compounds antagonize FGF23 through the disruption of protein–protein interactions between FGF23 and fibroblast growth factor receptor (FGFR).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Form factors with q{sup 2} = 0 and Grassmannians in N = 4 Sym theory

In this note we consider tree level form factors of operators from stress tensor supermultiplet with light like operator momentum q{sup 2} = 0. The presentation of form factors in terms of the regulated integral over Grassmannian is given. The conjectured formula is verified by successfully reproducing known answers in the MHV and N{sup k−2}MHV, k ≥ 3 sectors as well as appropriate soft limit behavior.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Form factor of the longitudinal component of weak vector current in pion beta decay

The form factor f{sub -} of the longitudinal component of the weak vector current in pion β-decay is derived using the generalized Ward identity. The form factor is expressed through the pion mass difference and mean-square radii in the channels with angular momenta J = 1, 0 and isospins T = 1, 2.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

On the Power Factor of Bismuth-Telluride-Based Alloys near Topological Phase Transitions at High Pressures

The Seebeck coefficient S and electrical conductivity σ of bismuth-telluride-based alloys with substituents in the Bi and Te sublattices are studied at pressures up to 12 GPa at room temperature. It is shown that the electrical conductivity increases with pressure and, despite a decrease in the Seebeck coefficient, the power factor S{sup 2}σ increases in p-Bi{sub 0.5}Sb{sub 1.5}Te{sub 3} and n-Bi{sub 2}Te{sub 1.65}Se{sub 0.65}S{sub 0.7} alloys. A maximum increase in the power factor is observed for n-Bi{sub 2}Te{sub 1.65}Se{sub 0.65}S{sub 0.7} in the pressure range of 3–4 GPa corresponding to the electronic topological phase transition. The studied alloys are used in modeling the thermoelectric module with adjustable mechanical stress applied to thermoelements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Status of Lattice QCD Determination of Nucleon Form Factors and Their Relevance for the Few-GeV Neutrino Program

Calculations of neutrino–nucleus cross sections begin with the neutrino–nucleon interaction, making the latter critically important to flagship neutrino oscillation experiments despite limited measurements with poor statistics. Alternatively, lattice quantum chromodynamics (LQCD) can be used to determine these interactions from the Standard Model with quantifiable theoretical uncertainties. Recent LQCD results of g A are in excellent agreement with data, and results for the (quasi-)elastic nucleon form factors with full uncertainty budgets are expected within a few years. We review the status of the field and LQCD results for the nucleon axial form factor, F A ( Q 2 ), a major source of uncertainty in modeling sub-GeV neutrino–nucleon interactions. Results from different LQCD calculations are consistent but collectively disagree with existing models, with potential implications for current and future neutrino oscillation experiments. We describe a road map to solidify confidence in the LQCD results and discuss future calculations of more complicated processes, which are important to few-GeV neutrino oscillation experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Understanding Hailstone Temporal Variability and Contributing Factors over the U.S. Southern Great Plains

Abstract Hailstones are a natural hazard that pose a significant threat to property and are responsible for significant economic losses each year in the United States. Detailed understanding of their characteristics is essential to mitigate their impact. Identifying the dynamic and physical factors contributing to hail formation and hailstone sizes is of great importance to weather and climate prediction and policymakers. In this study, we have analyzed the temporal and spatial variabilities of severe hail occurrences over the U.S. southern Great Plains (SGP) states from 2004 to 2016 using two hail datasets: hail reports from the Storm Prediction Center and the newly developed radar-retrieved maximum expected size of hail (MESH). It is found that severe and significant severe hail occurrences have a considerable year-to-year temporal variability in the SGP region. The interannual variabilities have a strong correspondence with sea surface temperature anomalies over the northern Gulf of Mexico and there is no outlier. The year 2016 is identified as an outlier for the correlations with both El Niño–Southern Oscillation (ENSO) and aerosol loading. The correlations with ENSO and aerosol loading are not statistically robust to inclusion of the outlier 2016. Statistical analysis without the outlier 2016 shows that 1) aerosols that may be mainly from northern Mexico have the largest correlation with hail interannual variability among the three factors and 2) meteorological covariation does not significantly contribute to the high correlation. These analyses warrant further investigations of aerosol impacts on hail occurrence.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Surface-Enhanced Raman Scattering (SERS) Studies of Disc-on-Pillar (DOP) Arrays: Contrasting Enhancement Factor with Analytical Performance

The use of nanomachining methods capable of reproducible construction of nano-arrayed devices have revolutionized the field of plasmonic sensing by the introduction of a diversity of rationally engineered designs. Significant strides have been made to fabricate plasmonic platforms with tailored interparticle gaps to improve their performance for surface-enhanced Raman scattering (SERS) applications. Over time, a dichotomy has emerged in the implementation of SERS for analytical applications, the construction of substrates, optimization of interparticle spacing as a means to optimize electromagnetic field enhancement at the localized surface plasmon level, and the substrate sensitivity over extended areas to achieve quantitative performance. Here, we assessed the enhancement factor of plasmonic Ag/SiO 2 /Si disc-on-pillar (DOP) arrays of variable pitch with its analytical performance for quantitative applications. Experimental data were compared with those from finite-difference time-domain (FDTD) simulations used in the optimization of the array dimensions. A self-assembled monolayer (SAM) of benzenethiol rendered highly reproducible signals (RSD ~4–10%) and SERS substrate enhancement factor (SSEF) values in the orders of 10 6 –10 8 for all pitches. Furthermore, spectra corresponding to rhodamine 6G (R6G) and 4-aminobenzoic acid demonstrated the advantages of using the more densely packed DOP arrays with a 160 nm pitch (gap= 40 nm) for quantitation in spite of the strongest SSEF was attained for a pitch of 520 nm corresponding to a 400 nm gap.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor

Background: Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes. To date, little is known about the key transcriptional regulators driving these changes, and the aim of the present study was to delineate and functionally characterize the transcription factor (TF) repertoire of the model ECM fungus Laccaria bicolor. Results: We curated the L. bicolor gene models coding for transcription factors and assessed their expression and regulation in Poplar and Douglas fir ectomycorrhizae. We identified 285 TFs, 191 of which share a significant similarity with known transcriptional regulators. Expression profiling of the corresponding transcripts identified TF-encoding fungal genes differentially expressed in the ECM root tips of both host plants. The L. bicolor core set of differentially expressed TFs consists of 12 and 22 genes that are, respectively, upregulated and downregulated in symbiotic tissues. These TFs resemble known fungal regulators involved in the control of fungal invasive growth, fungal cell wall integrity, carbon and nitrogen metabolism, invasive stress response and fruiting-body development. However, this core set of mycorrhiza-regulated TFs seems to be characteristic of L. bicolor and our data suggest that each mycorrhizal fungus has evolved its own set of ECM development regulators. A subset of the above TFs was functionally validated with the use of a heterologous, transcription activation assay in yeast, which also allowed the identification of previously unknown, transcriptionally active yet secreted polypeptides designated as Secreted Transcriptional Activator Proteins (STAPs). Conclusions: Transcriptional regulators required for ECM symbiosis development in L. bicolor have been uncovered and classified through genome-wide analysis. This study also identifies the STAPs as a new class of potential ECM effectors, highly expressed in mycorrhizae, which may be involved in the control of the symbiotic root transcriptome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of Ammonium and Iodine Decontamination Factors for Hanford's Waste Treatment and Immobilization Plant Feed in the Effluent Treatment Facility

Savannah River National Laboratory (SRNL) reviewed the unit operations in the Effluent Treatment Facility (FTP) at the Hanford site to estimate the partitioning of iodine and ammonia when processing Waste Treatments and Immobilization Plant (WTP) feed. The evaluation consisted of literature and vendor data reviews and no experiments were performed. A list of the unit operations reviewed, along with estimated decontamination factors (DFs) for both iodine and ammonium are shown in the table below. With the exception of the Peroxide Decomposer, reasonable estimations of the decontamination factors for all operations are provided.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

The softening factor c b of commercial titanium alloy wires

The strain-rate sensitivity exponent m and activation volume υ* are often used to characterize the strain-rate sensitivity of strength behavior in metals and alloys. Complications can arise when the m and υ* values become indeterminate, due to factors such as an inherent scatter in the mechanical property data. Here, the study of commercial Ti-alloy wires is considered wherein to overcome this limitation, the formulation of the Kocks–Mecking (K–M) model is modified to provide a parameter c b that characterizes the microstructural scale responsible for the observed plasticity and work hardening behavior. The softening factor c b is found to be independent of strain-rate for the Ti-alloy wires of this study. It is proposed that c b !can offer a versatile and complementary computation to the activation volume υ* since its formulation includes the yield and ultimate strength values along with the plastic strain. For the tensile testing of Ti-alloy wires, a low c b -value of 14 is calculated for Ti-6Al-4V that is consistent with >10 % plasticity during work hardening whereas a high c b -value of 135 for Ti-6Al-7Nb corresponds with <4 % plasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A

The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stable binding to phosphatidylserine-containing membranes requires conserved arginine residues in tandem C domains of blood coagulation factor VIII

At sites of vascular damage, factor VIII (fVIII) is proteolytically activated by thrombin and binds to activated platelet surfaces with activated factor IX (fIXa) to form the intrinsic “tenase” complex. Previous structural and mutational studies of fVIII have identified the C1 and C2 domains in binding to negatively charged membrane surfaces through β-hairpin loops with solvent-exposed hydrophobic residues and a ring of positively charged basic residues. Several hemophilia A-associated mutations within the C domains are suggested to disrupt lipid binding, preventing formation of the intrinsic tenase complex. In this study, we devised a novel platform for generating recombinant C1, C2, and C1C2 domain constructs and performed mutagenesis of several charged residues proximal to the putative membrane binding region of each C domain. Binding measurements between phosphatidylserine (PS)-containing lipid membrane surfaces and fVIII C domains demonstrated an ionic strength dependence on membrane binding affinity. Mutations to basic residues adjacent to the surface-exposed hydrophobic regions of C1 and C2 differentially disrupted membrane binding, with abrogation of binding occurring for mutations to conserved arginine residues in the C1 (R2163) and C2 (R2320) domains. Lastly, we determined the X-ray crystal structure of the porcine fVIII C2 domain bound to o-phospho-L-serine, the polar headgroup of PS, which binds to a basic cleft and makes charge-charge contact with R2320. We conclude that basic clefts in the fVIII C domains bind to PS-containing membranes through conserved arginine residues via a C domain modularity, where each C domain possesses modest electrostatic-dependent affinity and tandem C domains are required for high affinity binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The association between neighborhood obesogenic factors and prostate cancer risk and mortality: the Southern Community Cohort Study

Background: Prostate cancer is one of the leading causes of cancer-related mortality among men in the United States. We examined the role of neighborhood obesogenic attributes on prostate cancer risk and mortality in the Southern Community Cohort Study (SCCS). Methods: From the total of 34,166 SCCS male participants, 28,356 were included in the analysis. We assessed the relationship between neighborhood obesogenic factors [neighborhood socioeconomic status (nSES) and neighborhood obesogenic environment indices including the restaurant environment index, the retail food environment index, parks, recreational facilities, and businesses] and prostate cancer risk and mortality by controlling for individual-level factors using a multivariable Cox proportional hazards model. We further stratified prostate cancer risk analysis by race and body mass index (BMI). Results: Median follow-up time was 133 months [interquartile range (IQR): 103, 152], and the mean age was 51.62 (SD: ± 8.42) years. There were 1,524 (5.37%) prostate cancer diagnoses and 98 (6.43%) prostate cancer deaths during follow-up. Compared to participants residing in the wealthiest quintile, those residing in the poorest quintile had a higher risk of prostate cancer (aHR = 1.32, 95% CI 1.12–1.57, p = 0.001), particularly among non-obese men with a BMI < 30 (aHR = 1.46, 95% CI 1.07–1.98, p = 0.016). The restaurant environment index was associated with a higher prostate cancer risk in overweight (BMI ≥ 25) White men (aHR = 3.37, 95% CI 1.04–10.94, p = 0.043, quintile 1 vs. None). Obese Black individuals without any neighborhood recreational facilities had a 42% higher risk (aHR = 1.42, 95% CI 1.04–1.94, p = 0.026) compared to those with any access. Compared to residents in the wealthiest quintile and most walkable area, those residing within the poorest quintile (aHR = 3.43, 95% CI 1.54–7.64, p = 0.003) or the least walkable area (aHR = 3.45, 95% CI 1.22–9.78, p = 0.020) had a higher risk of prostate cancer death. Conclusion: Living in a lower-nSES area was associated with a higher prostate cancer risk, particularly among Black men. Restaurant and retail food environment indices were also associated with a higher prostate cancer risk, with stronger associations within overweight White individuals. Finally, residing in a low-SES neighborhood or the least walkable areas were associated with a higher risk of prostate cancer mortality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes

Evidence suggests that exposure to elevated concentrations of air pollution during pregnancy is associated with increased risks of birth defects and other adverse birth outcomes. While current regulations put limits on total PM2.5 concentrations, there are many speciated pollutants within this size class that likely have distinct effects on perinatal health. However, due to correlations between these speciated pollutants, it can be difficult to decipher their effects in a model for birth outcomes. To combat this difficulty, we develop a multivariate spatio-temporal Bayesian model for speciated particulate matter using dynamic spatial factors. These spatial factors can then be interpolated to the pregnant women’s homes to be used to model birth defects. The birth defect model allows the impact of pollutants to vary across different weeks of the pregnancy in order to identify susceptible periods. Here, the proposed methodology is illustrated using pollutant monitoring data from the Environmental Protection Agency and birth records from the National Birth Defect Prevention Study.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

What Factors Drive Air Pollutants in China? An Analysis from the Perspective of Regional Difference Using a Combined Method of Production Decomposition Analysis and Logarithmic Mean Divisia Index

Air pollution in China attracts the world’s attention, so it is important to study its driving factors for air pollutants. The combined Production Decomposition Analysis and Logarithmic Mean Divisia Index (PDA–LMDI) model is applied to construct a regional contribution index in this study to explore the regional differences in factors affecting sulfur dioxide (SO 2 ), nitrogen oxides (NO x ), and particulate matter with diameter not greater than 2.5 µm (PM 2.5 ) from 2005 to 2015 in China. The regional emission coefficient had a great inhibitory effect, which reduced SO 2 , NO x , and PM 2.5 by 25,364.9, 10,449.3, and 11,295.3 kilotons (kt) from 2005 to 2015, respectively. For this inhibitory effect, the degree to emission reduction was great for North and East China, followed by South and Central China, and small for Southwest. Northwest. and Northeast China. The regional technical efficiency, technology improvement, capital-energy substitution and labor-energy substitution effects each reduced SO 2 , NO x , and PM 2.5 by about 3500, 3100, and 1500 kt from 2005 to 2015, respectively. For the regional technical efficiency and technology improvement effects, the degree to emission reduction was great in East and Central China, and small in South Northwest and Northeast China. For the regional capital- and labor-energy substitution effects, the degree of emission reduction was great for North East and Central China, and small for Northwest and South China. The regional output proportion effect increased SO 2 , NO x , and PM 2.5 by 1211.2, 320.1, and 277.8 kt from 2005 to 2015, respectively. The national economic growth had a relatively great promoting effect and increased SO 2 , NO x , and PM 2.5 by 26,445.5, 23,827.5, and 11,925.5 kt from 2005 to 2015, respectively. Each region should formulate relevant policies and measures for emission reduction according to local conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Efficient Application of the Factorized form of the Unitary Coupled-Cluster Ansatz for the Variational Quantum Eigensolver Algorithm by Using Linear Combination of Unitaries

The variational quantum eigensolver is one of the most promising algorithms for near-term quantum computers. It has the potential to solve quantum chemistry problems involving strongly correlated electrons with relatively low-depth circuits, which are otherwise difficult to solve on classical computers. The variational eigenstate is constructed from a number of factorized unitary coupled-cluster terms applied onto an initial (single-reference) state. Current algorithms for applying one of these operators to a quantum state require a number of operations that scale exponentially with the rank of the operator. We exploit a hidden SU(2) symmetry to allow us to employ the linear combination of unitaries approach, Our Prepare subroutine uses n+2 ancilla qubits for a rank-n operator. Our Select (U) scheme uses O(n) Cnot gates. This results in a full algorithm that scales like the cube of the rank of the operator n 3 , a significant reduction in complexity for rank five or higher operators. This approach, when combined with other algorithms for lower-rank operators (when compared to the standard implementation), will make the factorized form of the unitary coupled-cluster approach much more efficient to implement on all types of quantum computers.

97 MATHEMATICS AND COMPUTING↗