Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequencing experiments”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Eu speciation in apatite at 1 bar: An experimental study of valence-state partitioning by XANES, lattice strain, and Eu/Eu* in basaltic systems

Abstract Partition coefficients for rare earth elements (REEs) between apatite and basaltic melt were determined as a function of oxygen fugacity (fO2; iron-wüstite to hematite-magnetite buffers) at 1 bar and between 1110 and 1175 °C. Apatite-melt partitioning data for REE3+ (La, Sm, Gd, Lu) show near constant values at all experimental conditions, while bulk Eu becomes more incompatible (with an increasing negative anomaly) with decreasing fO2. Experiments define three apatite calibrations that can theoretically be used as redox sensors. The first, a XANES calibration that directly measures Eu valence in apatite, requires saturation at similar temperature-composition conditions to experiments and is defined by: ( E u 3 + ∑ E u ) Apatite = 1 1 + 10 - 0.10 ± 0.01 × l o g ⁡ ( f o 2 ) - 1.63 ± 0.16 . The second technique involves analysis of Sm, Eu, and Gd in both apatite and coexisting basaltic melt (glass), and is defined by: ( Eu E u * ) D Sm × Gd = 1 1 + 10 - 0.15 ± 0.03 × l o g ⁡ ( f o 2 ) - 2.46 ± 0.41 . The third technique is based on the lattice strain model and also requires analysis of REE in both apatite and basalt. This calibration is defined by ( Eu E u * ) D lattice strain = 1 1 + 10 - 0.20 ± 0.03 × l o g ⁡ ( f o 2 ) - 3.03 ± 0.42 . The Eu valence-state partitioning techniques based on (Sm×Gd) and lattice strain are virtually indistinguishable, such that either methodology is valid. Application of any of these calibrations is best carried out in systems where both apatite and coexisting glass are present and in direct contact with one another. In holocrystalline rocks, whole rock analyses can be used as a guide to melt composition, but considerations and corrections must be made to either the lattice strain or Sm×Gd techniques to ensure that the effect of plagioclase crystallization either prior to or during apatite growth can be removed. Similarly, if the melt source has an inherited either a positive or negative Eu anomaly, appropriate corrections must also be made to lattice strain or Sm×Gd techniques that are based on whole rock analyses. This being the case, if apatite is primary and saturates from the parent melt early during the crystallization sequence, these corrections may be minimal. The partition coefficients for the REE between apatite and melt range from a maximum DEu3+ = 1.67 ± 0.25 (as determined by lattice strain) to DLu3+ = 0.69 ± 0.10. The REE partition coefficient pattern, as observed in the Onuma diagram, is in a fortuitous situation where the most compatible REE (Eu3+) is also the polyvalent element used to monitor fO2. These experiments provide a quantitative means of assessing Eu anomalies in apatite and how they be used to constrain the oxygen fugacity of silicate melts.

Geochemistry & Geophysics↗
DOE OSTI2015

Four-Dimensional Magnetic Resonance Imaging With 3-Dimensional Radial Sampling and Self-Gating–Based K-Space Sorting: Early Clinical Experience on Pancreatic Cancer Patients

Purpose: To apply a novel self-gating k-space sorted 4-dimensional MRI (SG-KS-4D-MRI) method to overcome limitations due to anisotropic resolution and rebinning artifacts and to monitor pancreatic tumor motion. Methods and Materials: Ten patients were imaged using 4D-CT, cine 2-dimensional MRI (2D-MRI), and the SG-KS-4D-MRI, which is a spoiled gradient recalled echo sequence with 3-dimensional radial-sampling k-space projections and 1-dimensional projection-based self-gating. Tumor volumes were defined on all phases in both 4D-MRI and 4D-CT and then compared. Results: An isotropic resolution of 1.56 mm was achieved in the SG-KS-4D-MRI images, which showed superior soft-tissue contrast to 4D-CT and appeared to be free of stitching artifacts. The tumor motion trajectory cross-correlations (mean ± SD) between SG-KS-4D-MRI and cine 2D-MRI in superior–inferior, anterior–posterior, and medial–lateral directions were 0.93 ± 0.03, 0.83 ± 0.10, and 0.74 ± 0.18, respectively. The tumor motion trajectories cross-correlations between SG-KS-4D-MRI and 4D-CT in superior–inferior, anterior–posterior, and medial–lateral directions were 0.91 ± 0.06, 0.72 ± 0.16, and 0.44 ± 0.24, respectively. The average standard deviation of gross tumor volume calculated from the 10 breathing phases was 0.81 cm{sup 3} and 1.02 cm{sup 3} for SG-KS-4D-MRI and 4D-CT, respectively (P=.012). Conclusions: A novel SG-KS-4D-MRI acquisition method capable of reconstructing rebinning artifact–free, high-resolution 4D-MRI images was used to quantify pancreas tumor motion. The resultant pancreatic tumor motion trajectories agreed well with 2D-cine-MRI and 4D-CT. The pancreatic tumor volumes shown in the different phases for the SG-KS-4D-MRI were statistically significantly more consistent than those in the 4D-CT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

How Good Is Your Location? Comparing and Understanding the Uncertainties in Location for the 1993 Rock Valley Sequence

Accurate event locations are important for many endeavors in seismology, and understanding the factors that contribute to uncertainties in those locations is complex. In this article, we present a case study that takes an in-depth look at the accuracy and precision possible for locating nine shallow earthquakes in the Rock Valley fault zone in southern Nevada. These events are targeted by the Rock Valley Direct Comparison phase of the Source Physics Experiment, as candidates for the colocation of a chemical explosion with an earthquake hypocenter to directly compare earthquake and explosion sources. For this comparison, it is necessary to determine earthquake hypocenters as accurately as possible so that different source types have nearly identical locations. Our investigations include uncertainty analysis from different sets of phase arrivals, stations, velocity models, and location algorithms. For a common set of phase arrivals and stations, we find that epicentral locations from different combinations of velocity models and algorithms are within 600 m of one another in most cases. Event depths exhibit greater uncertainties, but focusing on the S-P times at the nearest station allows for estimates within approximately 500 m.

58 GEOSCIENCES↗
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The RAVE-on Catalog of Stellar Atmospheric Parameters and Chemical Abundances for Chemo-dynamic Studies in the Gaia Era

The orbits, atmospheric parameters, chemical abundances, and ages of individual stars in the Milky Way provide the most comprehensive illustration of galaxy formation available. The Tycho- Gaia Astrometric Solution (TGAS) will deliver astrometric parameters for the largest ever sample of Milky Way stars, though its full potential cannot be realized without the addition of complementary spectroscopy. Among existing spectroscopic surveys, the RAdial Velocity Experiment (RAVE) has the largest overlap with TGAS (≳200,000 stars). We present a data-driven re-analysis of 520,781 RAVE spectra using The Cannon . For red giants, we build our model using high-fidelity APOGEE stellar parameters and abundances for stars that overlap with RAVE. For main sequence and sub-giant stars, our model uses stellar parameters from the K2/EPIC . We derive and validate effective temperature T {sub eff}, surface gravity log g , and chemical abundances of up to seven elements (O, Mg, Al, Si, Ca, Fe, and Ni). We report a total of 1,685,851 elemental abundances with a typical precision of 0.07 dex, a substantial improvement over previous RAVE data releases. The synthesis of RAVE-on and TGAS is the most powerful data set for chemo-dynamic analyses of the Milky Way ever produced.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Sci-Fri AM: MRI and Diagnostic Imaging - 01: Estimating the Transverse Relaxation Time of Taurine Protons in Rat Brain at 9.4 T with Optimized PRESS Sequence Timings

Purpose: To investigate the response of taurine (Tau) protons as a function of PRESS echo times, TE{sub 1} and TE{sub 2}, to determine two TE combinations that can be employed to estimate the T{sub 2} (transverse relaxation) value of Tau at 9.4 T. The Tau protons are involved in J-coupling interactions; therefore, the two timing combinations should result in similar signal losses due to J-coupling. Methods: Experiments were performed with a 9.4 T animal MRI scanner. Numerical calculations of the response of Tau as a function of PRESS TE{sub 1} and TE{sub 2} were calculated and two TE combinations that yield a similar area for the 3.42 ppm Tau resonance were selected as optimal. The timings were verified on a 50 mM Tau/10 mM Cr (creatine) phantom. In-vivo experiments were performed on four rats. Spectra were acquired with the timings from a voxel placed in the rat brain and Tau peak areas were fit to monoexponentially decaying functions to obtain T{sub 2} values. Results: The PRESS TE combinations selected for Tau T{sub 2} determination are (TE{sub 1}, TE{sub 2}) = (17 ms, 10 ms) and (80 ms, 70 ms); the signal yield for the two timings differs by 5 % theoretically. The average Tau T{sub 2} for the four rats was found to be 106 ms with a standard deviation of 12 ms. Conclusions: We have demonstrated that acquiring PRESS spectra with (TE{sub 1}, TE{sub 2}) = (17 ms, 10 ms) and (TE{sub 1}, TE{sub 2}) = (80 ms, 70 ms) enables T{sub 2} corrected measures of Tau to be obtained at 9.4 T.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2015

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time–decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Torsion-rotation-vibration effects in the ground and first excited states of methacrolein, a major atmospheric oxidation product of isoprene

Methacrolein is a major oxidation product of isoprene emitted in the troposphere. New spectroscopy information is provided with the aim to allow unambiguous identification of this complex molecule, characterized by a large amplitude motion associated with the methyl top. State-of-the-art millimeter-wave spectroscopy experiments coupled to quantum chemical calculations have been performed. For the most stable s-trans conformer of atmospheric interest, the torsional and rotational structures have been characterized for the ground state, the first excited methyl torsional state (ν{sub 27}), and the first excited skeletal torsional state (ν{sub 26}). The inverse sequence of A and E tunneling sub-states as well as anomalous A-E splittings observed for the rotational lines of v{sub 26} = 1 state clearly indicates a coupling between methyl torsion and skeletal torsion. A comprehensive set of molecular parameters has been obtained. The far infrared spectrum of Durig et al. [Spectrochim. Acta, Part A 42, 89–103 (1986)] was reproduced, and a Fermi interaction between ν{sub 25} and 2ν{sub 27} was evidenced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Unlocking preservation bias in the amber insect fossil record through experimental decay

Fossils entombed in amber are a unique resource for reconstructing forest ecosystems, and resolving relationships of modern taxa. Such fossils are famous for their perfect, life-like appearance. However, preservation quality is vast with many sites showing only cuticular preservation, or no fossils. The taphonomic processes that control this range are largely unknown; as such, we know little about potential bias in this important record. Here we employ actualistic experiments, using, fruit flies and modern tree resin to determine whether resin type, gut microbiota, and dehydration prior to entombment affects decay. We used solid phase microextraction gas chromatography-mass spectrometry (SPME GC-MS) to confirm distinct tree resin chemistry; gut microbiota of flies was modified using antibiotics and categorized though sequencing. Decay was assessed using phase contrast synchrotron tomography. Resin type demonstrates a significant control on decay rate. The composition of the gut microbiota was also influential, with minor changes in composition affecting decay rate. Dehydration prior to entombment, contrary to expectations, enhanced decay. Our analyses show that there is potential significant bias in the amber fossil record, especially between sites with different resin types where ecological completeness and preservational fidelity are likely affected.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

HUBBLE TARANTULA TREASURY PROJECT. III. PHOTOMETRIC CATALOG AND RESULTING CONSTRAINTS ON THE PROGRESSION OF STAR FORMATION IN THE 30 DORADUS REGION

We present and describe the astro-photometric catalog of more than 800,000 sources found in the Hubble Tarantula Treasury Project (HTTP). HTTP is a Hubble Space Telescope Treasury program designed to image the entire 30 Doradus region down to the sub-solar (∼0.5 M{sub ⊙}) mass regime using the Wide Field Camera 3 and the Advanced Camera for Surveys. We observed 30 Doradus in the near-ultraviolet (F275W, F336W), optical (F555W, F658N, F775W), and near-infrared (F110W, F160W) wavelengths. The stellar photometry was measured using point-spread function fitting across all bands simultaneously. The relative astrometric accuracy of the catalog is 0.4 mas. The astro-photometric catalog, results from artificial star experiments, and the mosaics for all the filters are available for download. Color–magnitude diagrams are presented showing the spatial distributions and ages of stars within 30 Dor as well as in the surrounding fields. HTTP provides the first rich and statistically significant sample of intermediate- and low-mass pre-main sequence candidates and allows us to trace how star formation has been developing through the region. The depth and high spatial resolution of our analysis highlight the dual role of stellar feedback in quenching and triggering star formation on the giant H ii region scale. Our results are consistent with stellar sub-clustering in a partially filled gaseous nebula that is offset toward our side of the Large Magellanic Cloud.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

TBECH, 1,2-dibromo-4-(1,2 dibromoethyl) cyclohexane, alters androgen receptor regulation in response to mutations associated with prostate cancer

Point mutations in the AR ligand-binding domain (LBD) can result in altered AR structures leading to changes of ligand specificity and functions. AR mutations associated to prostate cancer (PCa) have been shown to result in receptor activation by non-androgenic substances and anti-androgenic drugs. Two AR mutations known to alter the function of anti-androgens are the AR{sub T877A} mutation, which is frequently detected mutation in PCa tumors and the AR{sub W741C} that is rare and has been derived in vitro following exposure of cells to the anti-androgen bicalutamide. AR activation by non-androgenic environmental substances has been suggested to affect PCa progression. In the present study we investigated the effect of AR mutations (AR{sub W741C} and AR{sub T877A}) on the transcriptional activation following exposure of cells to an androgenic brominated flame retardant, 1,2-dibromo-4-(1,2 dibromoethyl) cyclohexane (TBECH, also named DBE-DBCH). The AR mutations resulted in higher interaction energies and increased transcriptional activation in response to TBECH diastereomer exposures. The AR{sub T877A} mutation rendered AR highly responsive to low levels of DHT and TBECH and led to increased AR nuclear translocation. Gene expression analysis showed a stronger induction of AR target genes in LNCaP cells (AR{sub T877A}) compared to T-47D cells (AR{sub WT}) following TBECH exposure. Furthermore, AR knockdown experiments confirmed the AR dependency of these responses. The higher sensitivity of AR{sub T877A} and AR{sub W741C} to low levels of TBECH suggests that cells with these AR mutations are more susceptible to androgenic endocrine disrupters. - Highlights: • TBECH, is an endocrine disrupting compound that differ in activity depending on AR structure and sequence. • TBECH interaction with the human AR-LBD containing the mutations W741C and T877A is increased compared to the wild type receptor • The mutations, W741C and T877A, are more potent than the wild type receptor at inducing AR nuclear translocation and transcriptional activation following TBECH exposure. • TBECH mediates action on androgen response genes via AR signaling.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Protein crystal structure from non-oriented, single-axis sparse X-ray data

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that are kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using the EMC algorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using the EMC algorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases where the data are sparse.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Tailoring Charge Reactivity Using In-Cylinder Generated Reformate for Gasoline Compression Ignition Strategies

In-cylinder reforming of injected fuel during a negative valve overlap (NVO) recompression period can be used to optimize main-cycle combustion phasing for low-load low-temperature gasoline combustion (LTGC). The objective of this work is to examine the effects of reformate composition on main-cycle engine performance. An alternate-fire sequence was used to generate a common exhaust temperature and composition boundary condition for a cycle-of-interest, with performance metrics measured for these custom cycles. NVO reformate was also separately collected using a dump valve apparatus and characterized by both gas chromatography and photoionization mass spectroscopy. To facilitate gas sample analysis, sampling experiments were conducted using a five-component gasoline surrogate (isooctane, n-heptane, ethanol, 1-hexene, and toluene) that matched the molecular composition, 50% boiling point, and ignition characteristics of the research gasoline. For the gasoline, it was found that an advance of the NVO start-of-injection (SOI) led to a corresponding advance in main-period combustion phasing as the combination of longer residence times and lower amounts of liquid spray piston impingement led to a greater degree of fuel decomposition. The effect was more pronounced as the fraction of total fuel injected in the NVO period increased. Main-period combustion phasing was also found to advance as the main-period fueling decreased. Slower kinetics for leaner mixtures were offset by a combination of increased bulk-gas temperature from higher charge specific heat ratios and increased fuel reactivity due to higher charge reformate fractions.

42 ENGINEERING↗
DOE OSTI2015

The Biosynthesis of UDP- D -QuiNAc in Bacillus cereus ATCC 14579

N-acetylquinovosamine (2-acetamido-2,6-di-deoxy-D-glucose, QuiNAc) is a relatively rare amino sugar residue found in glycans of few pathogenic gram-negative bacteria where it can play a role in infection. However, little is known about QuiNAc-related polysaccharides in gram-positive bacteria. In a routine screen for bacillus glycan grown at defined medium, it was surprising to identify a QuiNAc residue in polysaccharides isolated from this grampositive bacterium. To gain insight into the biosynthesis of these glycans, we report the identification of an operon in Bacillus cereus ATCC 14579 that contains two genes encoding activities not previously described in gram-positive bacteria. One gene encodes a UDP-N-acetylglucosamine C4,6-dehydratase, (abbreviated Pdeg) that converts UDPGlcNAc to UDP-4-keto-4,6-D-deoxy-GlcNAc (UDP-2-acetamido-2,6-dideoxy-α-D-xylo-4- hexulose); and the second encodes a UDP-4-reductase (abbr. Preq) that converts UDP-4- keto-4,6-D-deoxy-GlcNAc to UDP-N-acetyl-quinovosamine in the presence of NADPH. Biochemical studies established that the sequential Pdeg and Preq reaction product is UDP-D-QuiNAc as determined by mass spectrometry and one- and two-dimensional NMR experiments. Also, unambiguous evidence for the conversions of the dehydratase product, UDP-α-D-4-keto-4,6-deoxy-GlcNAc, to UDP-α-D-QuiNAc was obtained using real-time 1 HNMR spectroscopy and mass spectrometry. The two genes overlap by 4 nucleotides and similar operon organization and identical gene sequences were also identified in a few other Bacillus species suggesting they may have similar roles in the lifecycle of this class of bacteria important to human health. Our results provide new information about the ability of Bacilli to form UDP-QuiNAc and will provide insight to evaluate their role in the biology of Bacillus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Experiments at Scale with In-Situ Visualization Using ParaView/Catalyst in RAGE

In this paper I describe some numerical experiments performed using the ParaView/Catalyst in-situ visualization infrastructure deployed in the Los Alamos RAGE radiation-hydrodynamics code to produce images from a running large scale 3D ICF simulation on the Cielo supercomputer at Los Alamos. The detailed procedures for the creation of the visualizations using ParaView/Catalyst are discussed and several images sequences from the ICF simulation problem produced with the in-situ method are presented. My impressions and conclusions concerning the use of the in-situ visualization method in RAGE are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Update of CEA DES Criticality-Safety Activities and Perspectives [Slides]

Neutronics staff at CEA DES are in charge of a whole set of modeling and simulation tools for neutronics: nuclear data evaluation and processing, transport codes development, calculation sequences edition, verification, validation and uncertainty analysis. Advanced user groups are in charge of specific nuclear analysis in reactor physics, fuel cycle, criticality-safety, radiation shielding and nuclear instrumentation for CEA and its partners, at all stages of nuclear facilities life cycle. CEA is willing to participate/collaborate on the following issues: detector design, experiments, analysis and evaluation, DH validation by combining TAGS measurements with Fission Yield variance-covariance matrices.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗