Gene expression differs in codominant prairie grasses under drought
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Biochemistry & Molecular Biology↗
SEARCH · Engineering Papers
Results for “Function analysis”
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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Towards Combined QCD Global Analysis of Polarized and Unpolarized PDFs and Fragmentation Functions
We present a new global QCD analysis of spin-dependent PDFs (SPDF) and fragmentation functions (FF) performed by the JAM (Jefferson Lab Angular Momentum) Collaboration, based on all available data on inclusive spin structure functions from CERN, SLAC, DESY and JLab, and all semi-inclusive hadron production data from electron-positron annihilation experiments, including the most resent measurements from Belle and BaBar. Preliminary results on combined SPDFs and FFs using polarized semi-inclusive data from COMPASS and HERMES will be presented.
Sato, N.↗
Realistic multisite lattice-gas modeling and KMC simulation of catalytic surface reactions: Kinetics and multiscale spatial behavior for CO-oxidation on metal (100) surfaces
A realistic molecular-level description of catalytic reactions on single-crystal metal surfaces can be provided by stochastic multisite lattice-gas (msLG) models. This approach has general applicability, although in this report, we will focus on the example of CO-oxidation on the unreconstructed fcc metal (100) or M(100) surfaces of common catalyst metals M = Pd, Rh, Pt and Ir (i.e., avoiding regimes where Pt and Ir reconstruct). These models can capture the thermodynamics and kinetics of adsorbed layers for the individual reactants species, such as CO/M(100) and O/M(100), as well as the interaction and reaction between different reactant species in mixed adlayers, such as (CO + O)/M(100). The msLG models allow population of any of hollow, bridge, and top sites. This enables a more flexible and realistic description of adsorption and adlayer ordering, as well as of reaction configurations and configuration-dependent barriers. Adspecies adsorption and interaction energies, as well as barriers for various processes, constitute key model input. The choice of these energies is guided by experimental observations, as well as by extensive Density Functional Theory analysis. Model behavior is assessed via Kinetic Monte Carlo (KMC) simulation. We also address the simulation challenges and theoretical ramifications associated with very rapid diffusion and local equilibration of reactant adspecies such as CO. These msLG models are applied to describe adsorption, ordering, and temperature programmed desorption (TPD) for individual CO/M(100) and O/M(100) reactant adlayers. In addition, they are also applied to predict mixed (CO + O)/M(100) adlayer structure on the nanoscale, the complete bifurcation diagram for reactive steady-states under continuous flow conditions, temperature programmed reaction (TPR) spectra, and titration reactions for the CO-oxidation reaction. Extensive and reasonably successful comparison of model predictions is made with experimental data. Furthermore, we discuss the possible transition from traditional mean-field-type bistability and reaction kinetics for lower-pressure to multistability and enhanced fluctuation effects for moderate- or higher-pressure. Behavior in the latter regime reflects a stronger influence of adspecies interactions and also lower diffusivity in the higher-coverage mixed adlayer. We also analyze mesoscale spatiotemporal behavior including the propagation of reaction diffusion fronts between bistable reactive and inactive states, and associated nucleation-mediated transitions between these states. This behavior is controlled by complex surface mass transport processes, specifically chemical diffusion in mixed reactant adlayers for which we provide a precise theoretical formulation. The msLG models together with an appropriate treatment of chemical diffusivity enable equation-free heterogeneous coupled lattice-gas (HCLG) simulations of spatiotemporal behavior. In addition, msLG + HCLG modeling can describe coverage variations across polycrystalline catalysts surfaces, pressure variations across catalyst surfaces in microreactors, and could be incorporated into a multiphysics framework to describe mass and heat transfer limitations for high-pressure catalysis. (C) 2013 Elsevier Ltd. All rights reserved.
36 MATERIALS SCIENCE↗
The Synergy Between Total Scattering and Advanced Simulation Techniques: Quantifying Geopolymer Gel Evolution
With the ever increasing demands for technologically advanced structural materials, together with emerging environmental consciousness due to climate change, geopolymer cement is fast becoming a viable alternative to traditional cements due to proven mechanical engineering characteristics and the reduction in CO2 emitted (approximately 80% less CO2 emitted compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of the molecular changes responsible for nanostructural evolution during the geopolymerization process. Here, in-situ total scattering measurements in the form of X-ray pair distribution function (PDF) analysis are used to quantify the extent of reaction of metakaolin/slag alkali-activated geopolymer binders, including the effects of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerization reaction. Restricting quantification of the kinetics to the initial ten hours of reaction does not enable elucidation of the true extent of the reaction, but using X-ray PDF data obtained after 128 days of reaction enables more accurate determination of the initial extent of reaction. The synergies between the in-situ X-ray PDF data and simulations conducted by multiscale density functional theory-based coarse-grained Monte Carlo analysis are outlined, particularly with regard to the potential for the X-ray data to provide a time scale for kinetic analysis of the extent of reaction obtained from the multiscale simulation methodology.
36 MATERIALS SCIENCE↗
First Simultaneous Extraction of Spin-Dependent Parton Distributions and Fragmentation Functions from a Global QCD Analysis
In this paper, we perform the first global QCD analysis of polarized inclusive and semi-inclusive deep-inelastic scattering and single-inclusive $e^+e^-$ annihilation data, simultaneously fitting the parton distribution and fragmentation functions using the iterative Monte Carlo method. Without imposing SU(3) symmetry relations, we find the strange polarization to be very small, consistent with zero for both inclusive and semi-inclusive data, which provides a resolution to the strange quark polarization puzzle. Finally, the combined analysis also allows the direct extraction from data of the isovector and octet axial charges, and is consistent with a small SU(2) flavor asymmetry in the polarized sea.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
In silico analysis of stomach lineage specific gene set expression pattern in gastric cancer
Highlights: •Identified stomach lineage specific gene set (SLSGS) was found to be under expressed in gastric tumors. •Elevated expression of SLSGS in gastric tumor is a molecular predictor of metabolic type gastric cancer. •In silico pathway scanning identified estrogen-α signaling is a putative regulator of SLSGS in gastric cancer. •Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. -- Abstract: Stomach lineage specific gene products act as a protective barrier in the normal stomach and their expression maintains the normal physiological processes, cellular integrity and morphology of the gastric wall. However, the regulation of stomach lineage specific genes in gastric cancer (GC) is far less clear. In the present study, we sought to investigate the role and regulation of stomach lineage specific gene set (SLSGS) in GC. SLSGS was identified by comparing the mRNA expression profiles of normal stomach tissue with other organ tissue. The obtained SLSGS was found to be under expressed in gastric tumors. Functional annotation analysis revealed that the SLSGS was enriched for digestive function and gastric epithelial maintenance. Employing a single sample prediction method across GC mRNA expression profiles identified the under expression of SLSGS in proliferative type and invasive type gastric tumors compared to the metabolic type gastric tumors. Integrative pathway activation prediction analysis revealed a close association between estrogen-α signaling and SLSGS expression pattern in GC. Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. In conclusion, our results highlight that estrogen mediated regulation of SLSGS in gastric tumor is a molecular predictor of metabolic type GC and prognostic factor in GC.
60 APPLIED LIFE SCIENCES↗
Spectroscopic investigation of nitrogen-functionalized carbon materials: Spectroscopic investigation of nitrogen-functionalized carbon
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Wood, Kevin N.↗
Short and medium range structure in elastic deformation of metallic and covalent glasses
Here, we present a concise methodology to analyze structural response to the applied stress in amorphous solids, including metallic glasses (MG), glassy selenium, silica and polycarbonate, using high energy x-ray diffraction and atomic pair distribution function (PDF) analysis. To assess the structural anisotropy induced by applied axial stress, diffraction data were expanded into spherical harmonics. Using Bessel transformation, components of the structure function were converted into isotropic and anisotropic PDFs. The PDFs were compared to the expected model behavior for ideal elastic deformation to separate homogeneous affine strain from local non-affine strains. In metallic glass the range of non-affine deformation is limited to the nearest neighbor shell, suggesting local strain relaxation under stress that occurs even in the elastic regime. Beyond the second atomic shell strain is uniform. However, in glassy silica, polycarbonate and selenium strong local bonding inhibits local displacements and strain in short range order is accommodated by rotation of local units. Interestingly, beyond a molecular unit, deformation in covalent systems is similar to MG, and response of the medium range order scales with the macroscopic stress.
glassy structure↗
Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state
Background: Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results: The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Conclusions: Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
59 BASIC BIOLOGICAL SCIENCES↗
Probing the Local Site Disorder and Distortion in Pyrochlore High-Entropy Oxides
High-entropy oxides (HEOs) have attracted great interest in diverse fields because of their inherent opportunities to tailor and combine materials functionalities. The control of local order/disorder in the class is by extension a grand challenge toward realizing their vast potential. In this paper, we report the first examples of pyrochlore HEOs with five M-site cations, for Nd 2 M 2 O 7 , in which the local structure has been investigated by neutron diffraction and pair distribution function (PDF) analysis. The average structure of the pyrochlores is found to be orthorhombic Imma, in agreement with radius-ratio rules governing the structural archetype. The computed PDFs from density functional theory relaxed special quasirandom structure models are compared with real space PDFs in this work to evaluate M-site order/disorder. Reverse Monte Carlo combined with ab initio molecular dynamics and Metropolis Monte Carlo simulations demonstrates that Nd 2 (Ta 0.2 Sc 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7 is synthesized with its M-site local to nanoscale order highly randomized/disordered, while Nd 2 (Ti 0.2 Nb 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7+x exhibits a strong distortion of the TiO 6 octahedron and small degree of Ti chemical short-range order (SRO) on the subnanometer scale. Calculations suggest that this may be intrinsic, energetically favored SRO rather than due to sample processing. These results offer an important demonstration that the engineered variation of participating ions in HEOs, even among those with very similar radii, provides richly diverse opportunities to control local order/disorder motifs—and therefore materials properties for future designs. This work also hints at the exquisite level of detail that may be needed in computational and experimental data analysis to guide structure–property tuning in the emerging HEO materials class.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Precise cosmological constraints from BOSS galaxy clustering with a simulation-based emulator of the wavelet scattering transform
For this study, we perform a reanalysis of the BOSS CMASS DR12 galaxy dataset using a simulation-based emulator for the wavelet scattering transform (WST) coefficients. Moving beyond our previous works, which laid the foundation for the first galaxy clustering application of this estimator, we construct a neural net-based emulator for the cosmological dependence of the WST coefficients and the 2-point correlation function multipoles, trained from the state-of-the-art suite of abacussummit simulations combined with a flexible halo occupation distribution (HOD) galaxy model. In order to confirm the accuracy of our pipeline, we subject it to a series of thorough internal and external mock parameter recovery tests, before applying it to reanalyze the CMASS observations in the redshift range 0.46 < z < 0.57. We find that a joint WST+2-point correlation function likelihood analysis allows us to obtain marginalized 1σ errors on the Λ CDM parameters that are tighter by a factor of 2.5–6, compared to the 2-point correlation function, and by a factor of 1.4–2.5 compared to the WST-only results. This corresponds to a competitive 0.9%, 2.3% and 1% level of determination for parameters ω c , σ 8 &n s , respectively, and also to a 0.7% and 2.5% constraint on derived parameters h and ƒ(z)σ 8 (z), in agreement with the Planck 2018 results. Our results reaffirm the constraining power of the WST and highlight the exciting prospect of employing higher-order statistics in order to fully exploit the power of upcoming stage-IV spectroscopic observations.
79 ASTRONOMY AND ASTROPHYSICS↗
Synthesis of manganese stearate for high density polyethylene (HDPE) and its biodegradation
An oxidant additive is one type of additive used for oxo-biodegradable polymers. This additive was prepared by reaction multivalent transition metals and fatty acids to accelerate the degradation process of polymers by providing a thermal treatment or irradiation with light. This study focused on the synthesis of manganese stearate as an additive for application in High Density Polyethylene (HDPE), and the influence of manganese stearate on the characteristics of HDPE including their biodegradability. Manganese stearate was synthesized by the reaction of stearic acid with sodium hydroxide, and sodium stearate formed was reacted with manganese chloride tetrahydrate to form manganese stearate with a melting point of 100-110 °C. Based on the FTIR spectrum showed absorption peak at wave number around 1560 cm{sup −1} which is an asymmetric vibration of CO functional group that binds to the manganese. The films of oxo-biodegradable polymer were prepared by blending HDPE and manganese stearate additives at various concentrations with using the polymer melting method, followed heating at a temperature of 50°C and 70°C for 10 days. The characterizations of the oxo-biodegradable polymers were carried out by analysis the functional groups (FTIR and ATR),thermal properties (TGA), surface properties (SEM), as well as analysis of the biodegradability (the biodegradation test by using activated sludge, % weight loss). Based on COi indicate that the additive of manganese stearate is active in oxidizing polymer by heating treatment. Results of biodegradation by microorganisms from activated sludge showed that the percentage weight loss of polymers increase with the increasing incubation time and the concentration of manganese stearate in HDPE. Biodegradability of HDPE with the addition of manganese stearate and followed by heating at a higher temperature was better observed. The highest percentage weight loss was obtained at the polymer with concentration of 0.2% manganese stearate, and followed by thermal treatment at a temperature of 70 °C and the incubation time for 45 days in the activated sludge.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
X-ray Emission Spectroscopy of Mn Coordination Complexes Toward Interpreting the Electronic Structure of the Oxygen-Evolving Complex of Photosystem II
X-ray emission (XES) spectroscopy is an attractive technique for analysis of the electronic structure of molecules, materials, and metalloproteins. However, a better understanding of XES results is required. Using a combination of experiment and ground-state density functional theory analysis, we rationalize differences in the X-ray emission spectra of multinuclear Mn complexes. Model compounds, including dinuclear [Mn 2 O 2 L' 4 ](ClO 4 ) 3 (L'= 2,2'-bipyridyl, [1]) and two examples from the Mn 4 O 4 L 6 “cubane” family of model compounds (L = (p-R-C 6 H 4 )PO 2 – , R = OCH 3 [2], CH3 [3] ), were compared with the Oxygen Evolving Complex of Photosystem II. Our analysis demonstrates that changes in the structure of the Mn complexes, resulting in changes to the spin polarization, can introduce significant spectral shifts in compounds of the same formal redox state. The implications of changes in spin polarization for understanding photosynthetic water-splitting catalysis is discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Local and long-range atomic/magnetic structure of non-stoichiometric spinel iron oxide nanocrystallites
Spinel iron oxide nanoparticles of different mean sizes in the range 10–25 nm have been prepared by surfactant-free up-scalable near- and super-critical hydrothermal synthesis pathways and characterized using a wide range of advanced structural characterization methods to provide a highly detailed structural description. The atomic structure is examined by combined Rietveld analysis of synchrotron powder X-ray diffraction (PXRD) data and time-of-flight neutron powder-diffraction (NPD) data. The local atomic ordering is further analysed by pair distribution function (PDF) analysis of both X-ray and neutron total-scattering data. It is observed that a non-stoichiometric structural model based on a tetragonal γ-Fe 2 O 3 phase with vacancy ordering in the structure (space group P 4 3 2 1 2) yields the best fit to the PXRD and total-scattering data. Detailed peak-profile analysis reveals a shorter coherence length for the superstructure, which may be attributed to the vacancy-ordered domains being smaller than the size of the crystallites and/or the presence of anti-phase boundaries, faulting or other disorder effects. The intermediate stoichiometry between that of γ-Fe 2 O 3 and Fe 3 O 4 is confirmed by refinement of the Fe/O stoichiometry in the scattering data and quantitative analysis of Mössbauer spectra. The structural characterization is complemented by nano/micro-structural analysis using transmission electron microscopy (TEM), elemental mapping using scanning TEM, energy-dispersive X-ray spectroscopy and the measurement of macroscopic magnetic properties using vibrating sample magnetometry. Notably, no evidence is found of a Fe 3 O 4 /γ-Fe 2 O 3 core-shell nanostructure being present, which had previously been suggested for non-stoichiometric spinel iron oxide nanoparticles. Finally, the study is concluded using the magnetic PDF (mPDF) method to model the neutron total-scattering data and determine the local magnetic ordering and magnetic domain sizes in the iron oxide nanoparticles. The mPDF data analysis reveals ferrimagnetic collinear ordering of the spins in the structure and the magnetic domain sizes to be ∼60–70% of the total nanoparticle sizes. The present study is the first in which mPDF analysis has been applied to magnetic nanoparticles, establishing a successful precedent for future studies of magnetic nanoparticles using this technique.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NanoSIP: Developing Community Imaging for Phylogenetic and Functional Characterization Using Cyanobacterial Mats
This project was to develop and optimize the following technologies: stable isotope probing + NanoSIMS analysis (nanoSIP), FISH, functional gene analysis, H2 production measurements, culturing, and metatranscriptomics for specific use in microbial mat systems. The larger goal was to further develop these methodologies in a way that facilitates their linkage, high fidelity 3-D correlation to location specific environmental change integrating geochemical characterization, such that ability to see and characterize microbial community responses to normal daily fluctuations and further ecological manipulations, in different locations of the mat communities is optimized.
59 BASIC BIOLOGICAL SCIENCES↗
Bounding uncertainty in functional data: A case study
Functional data are fast becoming a preeminent source of information across a wide range of industries. A particularly challenging aspect of functional data is bounding uncertainty. In this unique case study, we present our attempts at creating bounding functions for selected applications at Sandia National Laboratories (SNL). The first attempt involved a simple extension of functional principal component analysis (fPCA) to incorporate covariates. Though this method was straightforward, the extension was plagued by poor coverage accuracy for the bounding curve. This led to a second attempt utilizing elastic methodology which yielded more accurate coverage at the cost of more complexity.
97 MATHEMATICS AND COMPUTING↗
Density driven structural transformations in amorphous semiconductor clathrates
Abstract not provided
Tulk, C. A.↗
Characterizing quasiconvex functions in terms of the Kronrod's tree of a function
As an application of Kronrod's construction of the tree of a function to convex analysis, a characterization of quasiconvex functions is obtained. Namely, a function is quasiconvex if and only if the associated function defined on the tree of the original function is quasiconvex. A new proof of one of the existence lemmas in Kronrod's construction of the tree of a function (the original proof of which turned out to be incorrect) is given. Bibliography: 4 titles. (paper)
97 MATHEMATICS AND COMPUTING↗