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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.

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

Completeness and coverage of open-access freshwater fish distribution data in the United States

Aim: Primary biodiversity data constitute observations of particular species at given points in space and time. Open-access databases provide unprecedented access to these data, but their utility depends on how complete species inventories are at a given surveying resolution and how uniformly distributed surveys are in space and time. Our aim was to characterize the completeness of freshwater fish data across spatial scales and among habitat types (lotic stream reaches and lentic waterbodies), and assess coverage bias in space and time. Location: Freshwater habitats of the contiguous United States. Methods: We compiled fish occurrence records from the Global Biodiversity Information Facility (GBIF), the Multi-state Aquatic Resources Information Server (MARIS), and three federally-administered surveys (EMAP, NAQWA, NRS). Next, we evaluated survey completeness across seven spatial resolutions representing nested stream catchments, and separately for lotic and lentic habitats. Lastly, we tested for bias in survey coverage along environmental and temporal gradients for each habitat type. Results: A total of 39,855,157 records representing 1925 species were available from 1800 to 2014. The percent of catchments surveyed increased as spatial resolution decreased while the density of occurrence records within surveyed catchments decreased. Species richness also increased with catchment size consistent with putative species–area relationships. Occurrence records were distributed among 72,114 lotic reaches and 3,325 lentic waterbodies throughout the contiguous US. Seven percent (N=5,055) of surveyed lotic reaches and 23% (N=771) of surveyed lentic waterbodies were well-surveyed based on the most conservative thresholds for two completeness indices. Most well-surveyed lotic reaches (95%) and undammed lentic waterbodies (97%) were completed since 1980, and most were surveyed during only one 20-year time interval (83% and 56% for lotic and lentic waterbodies, respectively). Coverage analyses indicated that contemporary and future climates corresponding to regions along the west coast and gulf coast are the most under-represented for both lotic and lentic habitats. Small lentic waterbodies (surface area < 0.1 km2) are also under-represented. Main Conclusions: Contemporary surveys of lotic reaches and, to a lesser extent, lentic waterbodies are plentiful and generally representative of climatic and landscape characteristics. Data compilation efforts should focus on adding historical data to public repositories. Clustering of well-surveyed waterbodies in MARIS-participating states highlights the value of state-agency data and demonstrates the need for dissemination of these data by more state agencies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Long-Term Outcomes Among Patients Who Achieve Complete or Near-Complete Responses After the Induction Phase of Bladder-Preserving Combined-Modality Therapy for Muscle-Invasive Bladder Cancer: A Pooled Analysis of NRG Oncology/RTOG 9906 and 0233

Purpose: To investigate the differences in outcomes among patients with muscle-invasive bladder cancer on NRG Oncology Radiation Therapy Oncology Group protocols 9906 and 0233 who achieved complete response and near-complete response after induction chemoradiation and then completed bladder-preserving therapy with chemoradiation therapy (chemo-RT) to full dose (60-64 Gy). Patients and Methods: A pooled analysis was performed on 119 eligible patients with muscle-invasive bladder cancer enrolled on NRG Oncology Radiation Therapy Oncology Group trials 9906 and 0233, who were classified as having a complete (T0) or near-complete (Ta or Tis) response after induction chemo-RT and completed consolidation with a total RT dose of at least 60 Gy. Bladder recurrence, salvage cystectomy rates, and disease-specific survival were estimated by the cumulative incidence method and bladder-intact and overall survivals by the Kaplan-Meier method. Results: Among the 119 eligible patients, 101 (85%) achieved T0, and 18 (15%) achieved Ta or Tis after induction chemo-RT and proceeded to consolidation. After a median follow-up of 5.9 years, 36 of 101 T0 patients (36%) versus 5 of 18 Ta or Tis patients (28%) experienced bladder recurrence (P=.52). Thirteen patients among complete responders eventually required late salvage cystectomy for tumor recurrence, compared with 1 patient among near-complete responders (P=.63). Disease-specific, bladder-intact, and overall survivals were not significantly different between T0 and Ta/Tis cases. Conclusions: The bladder recurrence and salvage cystectomy rates of the complete and the near-complete responders were similar. Therefore it is reasonable to recommend that patients with Ta or Tis after induction chemo-RT continue with bladder-sparing therapy with consolidation chemo-RT to full dose (60-64 Gy).

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Covering complete proteomes with X-ray structures: a current snapshot

The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina equisetifolia Root Nodules

Micromonospora species live in diverse environments and exhibit a broad range of functions, including antibiotic production, biocontrol, and degradation of complex polysaccharides. To learn more about these versatile actinomycetes, we sequenced the genome of strain L5, originally isolated from root nodules of an actinorhizal plant growing in Mexico.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Complex oxide growth using simultaneous in situ reflection high-energy electron diffraction and x-ray reflectivity: When is one layer complete?

During layer-by-layer homoepitaxial growth, both the Reflection High-Energy Electron Diffraction (RHEED) intensity and the x-ray reflection intensity will oscillate, and each complete oscillation indicates the addition of one monolayer of material. However, it is well documented, but not well understood, that the phase of the RHEED oscillations varies from growth to growth and thus the maxima in the RHEED intensity oscillations do not necessarily occur at the completion of a layer. Here, we demonstrate this by using simultaneous in situ x-ray reflectivity and RHEED to characterize layer-by-layer growth of SrTiO 3 . We show that we can control the RHEED oscillation phase by changing the pre-growth substrate annealing conditions, changing the RHEED oscillation phase by as much as 137°. In addition, during growth via pulsed laser deposition, the relaxation times between each laser pulse can be used to determine when a layer is complete, independent of the phase of the RHEED oscillation.

36 MATERIALS SCIENCE↗
DOE OSTI2015

First frontier field constraints on the cosmic star formation rate density AT z ~ 10—the impact of lensing shear on completeness of high-redshift galaxy samples

In this work, we search the complete Hubble Frontier Field data set of Abell 2744 and its parallel field for $z\sim 10$ sources to further refine the evolution of the cosmic star formation rate density (SFRD) between $z\sim 8$ and $z\sim 10$. We independently confirm two images of the recently discovered triply imaged $z\sim 9.8$ source by Zitrin et al. and set an upper limit for similar $z\sim 10$ galaxies with red colors of ${J}_{125}-{H}_{160}\gt 1.2$ in the parallel field of Abell 2744. We utilize extensive simulations to derive the effective selection volume of Lyman-break galaxies at $z\sim 10$, both in the lensed cluster field and in the adjacent parallel field. Particular care is taken to include position-dependent lensing shear to accurately account for the expected sizes and morphologies of highly magnified sources. We show that both source blending and shear reduce the completeness at a given observed magnitude in the cluster, particularly near the critical curves. These effects have a significant, but largely overlooked, impact on the detectability of high-redshift sources behind clusters, and substantially reduce the expected number of highly magnified sources. The detections and limits from both pointings result in an SFRD which is consistent within the uncertainties with previous estimates at $z\sim 10$ from blank fields. The combination of these new results with all other estimates is also consistent with a rapidly declining SFRD in the 170 Myr from $z\sim 8$ to $z\sim 10$ as predicted by cosmological simulations and dark-matter halo evolution in ΛCDM. Once biases introduced by magnification-dependent completeness are accounted for, the full six cluster and parallel Frontier Field program will be an extremely powerful new data set to probe the evolution of the galaxy population at $z\gt 8$ before the advent of the James Webb Space Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble

During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Complete genome sequence of Coriobacterium glomerans type strain (PW2 T ) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

Coriobacterium glomerans Haas and König 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2 T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Towards a More Complete and Accurate Experimental Nuclear Reaction Data Library (EXFOR): International Collaboration Between Nuclear Reaction Data Centres (NRDC)

The International Network of Nuclear Reaction Data Centres (NRDC) coordinated by the IAEA Nuclear Data Section (NDS) successfully collaborates in the maintenance and development of the EXFOR library. As the scope of published data expands (e.g. to higher energy, to heavier projectile) to meet the needs of research and applications, it has become a challenging task to maintain both the completeness and accuracy of the EXFOR library. Evolution of the library highlighting recent developments is described.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework

Driven by major scientific advances in analytical methods, biomonitoring, and computational exposure assessment, and a newly articulated vision for a greater impact in public health, the field of exposure science is undergoing a rapid transition from a field of observation to a field of prediction. Deployment of an organizational and predictive framework for exposure science analogous to the computationally enabled “systems approaches” used in the biological sciences is a necessary step in this evolution. Here we propose the aggregate exposure pathway (AEP) concept as the natural and complementary companion in the exposure sciences to the adverse outcome pathway (AOP) concept in the toxicological sciences. The AEP framework offers an intuitive approach to successful organization of exposure science data within individual units of prediction common to the field, setting the stage for exposure forecasting. Looking farther ahead, we envision direct linkages between aggregate exposure pathway and adverse outcome pathways, completing the source to outcome continuum and setting the stage for more efficient integration of exposure science and toxicity testing information. Together these frameworks form and inform a decision making framework with the flexibility for risk-based, hazard-based or exposure-based decisions.

Teeguarden, Justin G.↗
DOE OSTI2019

Time-Dependent Complete Active Space Embedded in Polarizable Force Field

Electron correlation and environmental effects play important roles in electron dynamics and spectroscopic observables of chemical systems in condensed phase. In this paper, we present a time-dependent complete active space configuration interaction (TD-CASCI) approach embedded in a polaraizable force filed, MMPol. The present implementation of TD-CASCI/MMPol utilizes a direct matrix-vector contraction, allowing studies of large systems. This scheme is used to study the solvatochromic shift of coumarin 153 in methanol. The TD-CASCI/MMPol approach captures the double excitation character in the excited state wave function and accurately predicts the solvatochromic red-shift of coumarin 153 dye within the experimental range, outperforming linear response time-dependent density functional theory. The effect of using different reference orbitals for the TD-CASCI/MMPol simulation is also investigated, highlighting the need for an unbiased treatment of all electronic states in the energy range of interest.

Liu, Hongbin↗
DOE OSTI2015

A model for dark matter, naturalness and a complete gauge unification

We consider dark matter in a minimal extension of the Standard Model (SM) which breaks electroweak symmetry dynamically and leads to a complete unification of the SM and technicolor coupling constants. The unification scale is determined to be M{sub U}≈2.2×10{sup 15} GeV and the unified coupling α{sub U}≈0.0304. Moreover, unification strongly suggest that the technicolor sector of the model must become strong at the scale of O(TeV). The model also contains a tightly constrained sector of mixing neutral fields stabilized by a discrete symmetry. We find the lightest of these states can be DM with a mass in the range m{sub DM}≈30–800 GeV. We find a large set of parameters that satisfy all available constraints from colliders and from dark matter search experiments. However, most of the available parameter space is within the reach of the next generation of DM search experiments. The model is also sensitive to a modest improvement in the measurement of the precision electroweak parameters.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Asymmetric dark matter and CP violating scatterings in a UV complete model

We explore possible asymmetric dark matter models using CP violating scatterings to generate an asymmetry. In particular, we introduce a new model, based on DM fields coupling to the SM Higgs and lepton doublets, a neutrino portal, and explore its UV completions. We study the CP violation and asymmetry formation of this model, to demonstrate that it is capable of producing the correct abundance of dark matter and the observed matter-antimatter asymmetry. Crucial to achieving this is the introduction of interactions which violate CP with a T{sup 2} dependence.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗