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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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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Analysis of RNA viral function from metatranscriptomic reads in drought simulated soils

Soil viruses have received increased interest in recent years because of their abundance and unelucidated potential as drivers for organic carbon derived from fungal and bacterial necromass. With decreasing levels of rainfall and climbing instances of unseasonal conditions, it becomes crucial to our goals for negative carbon emissions to understand how soil carbon flux is affected. Here we leveraged metatranscriptomic data from a section of research plot of Hopland Research and Extension in northern California with a suite of viral detection tools: VirSorter, DRAMv, and VContact2. We aimed to cross analyze moisture regiments with viral populations. We find that viral diversity is driven by site, like bacteria. We found that viral diversity at face value showed some differentiation but did not significantly differ by legacy moisture content. Additionally, there was detection of auxiliary metabolic genes in a viral sequence which may further support virus’s direct input into the soil carbon pool.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2011

Age Dating of Mixed SNM--Preliminary Investigations

Recently we investigated the nuclear forensics problem of age determination for mixed special nuclear material (SNM). Through limited computational mixing experiments and interactive age analysis, it was observed that age dating results are generally affected by the mixing of samples with different assays or even by small radioactive material contamination. The mixing and contamination can be detected through interactive age analysis, a function provided by the Decay Interaction, Visualization and Analysis (DIVA) software developed by NSTec. It is observed that for mixed SNM with two components, the age estimators typically fall into two distinct clusters on the time axis. This suggests that averaging or other simple statistical methods may not always be suitable for age dating SNM mixtures. Instead, an interactive age analysis would be more suitable for age determination of material components of such SNM mixtures. This work was supported by the National Center for Nuclear Security (NCNS).

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2014

Gamma Detector Response and Analysis Software - Detector Response Function

GADRAS-DRF uses a Detector Response Function (DRF) to compute the response of gamma-ray detectors incident radiation. The application includes provision for plotting measured and computed spectra and for characterizing detector response parameters based on measurements of a series of calibration sources (e.g., Ba-133, Cs-137, Co-60, and Th-228). An application program interface enables other programs to access the dynamic-link library that is used to compute spectra.

Source record↗
DOE OSTI2024

Infinite quantum signal processing

Quantum signal processing (QSP) represents a real scalar polynomial of degree d using a product of unitary matrices of size 2 × 2 , parameterized by ( d + 1 ) real numbers called the phase factors. This innovative representation of polynomials has a wide range of applications in quantum computation. When the polynomial of interest is obtained by truncating an infinite polynomial series, a natural question is whether the phase factors have a well defined limit as the degree d → ∞ . While the phase factors are generally not unique, we find that there exists a consistent choice of parameterization so that the limit is well defined in the ℓ 1 space. This generalization of QSP, called the infinite quantum signal processing, can be used to represent a large class of non-polynomial functions. Our analysis reveals a surprising connection between the regularity of the target function and the decay properties of the phase factors. Our analysis also inspires a very simple and efficient algorithm to approximately compute the phase factors in the ℓ 1 space. The algorithm uses only double precision arithmetic operations, and provably converges when the ℓ 1 norm of the Chebyshev coefficients of the target function is upper bounded by a constant that is independent of d . This is also the first numerically stable algorithm for finding phase factors with provable performance guarantees in the limit d → ∞ .

Dong, Yulong [Department of Mathematics, Universit↗
DOE OSTI2011

Construction of integrable model Kohn-Sham potentials by analysis of the structure of functional derivatives

A directly approximated exchange-correlation potential should, by construction, be a functional derivative of some density functional in order to avoid unphysical results. Using generalized gradient approximations (GGAs) as an example, we show that functional derivatives of explicit density functionals have a very rigid inner structure, the knowledge of which allows one to build the entire functional derivative from a small part. Based on this analysis, we develop a method for direct construction of integrable Kohn-Sham potentials. As an illustration, we transform the model potential of van Leeuwen and Baerends (which is not a functional derivative) into a semilocal exchange potential that has a parent GGA, yields accurate energies, and is free from the artifacts inherent in existing semilocal potential approximations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Visualisation and outlier detection for probability density function ensembles

Abstract Exploratory data analysis (EDA) for functional data—data objects where observations are entire functions—is a difficult problem that has seen significant attention in recent literature. This surge in interest is motivated by the ubiquitous nature of functional data, which are prevalent in applications across fields such as meteorology, biology, medicine and engineering. Empirical probability density functions (PDFs) can be viewed as constrained functional data objects that must integrate to one and be nonnegative. They show up in contexts such as yearly income distributions, zooplankton size structure in oceanography and in connectivity patterns in the brain, among others. While PDF data are certainly common in modern research, little attention has been given to EDA specifically for PDFs. In this paper, we extend several methods for EDA on functional data for PDFs and compare them on simulated data that exhibit different types of variation, designed to mimic that seen in real‐world applications. We then use our new methods to perform EDA on the breakthrough curves observed in gas transport simulations for underground fracture networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Genomic Encyclopedia of Fungi

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Wavefunction stability analysis without analytical electronic Hessians: application to orbital-optimised second-order Møller–Plesset theory and VV10-containing density functionals

Wavefunction stability analysis is commonly applied to converged self-consistent field (SCF) solutions to verify whether the electronic energy is a local minimum with respect to second-order variations in the orbitals. By iterative diagonalisation, the procedure calculates the lowest eigenvalue of the stability matrix or electronic Hessian. However, analytical expressions for the electronic Hessian are unavailable for most advanced post-Hartree-Fock (HF) wave function methods and even some Kohn-Sham (KS) density functionals. To address such cases, here we formulate the Hessian-vector product within the iterative diagonalisation procedure as a finite difference of the electronic gradient with respect to orbital perturbations in the direction of the vector. As a model application, following the lowest eigenvalue of the orbital-optimised second-order Møller-Plesset perturbation theory (OOMP2) Hessian during H 2 dissociation reveals the surprising stability of the spin-restricted solution at all separations, with a second independent unrestricted solution. We show that a single stable solution can be recovered by using the regularised OOMP2 method (δ-OOMP2), which contains a level shift. Internal and external stability analyses are also performed for SCF solutions of a recently developed range-separated hybrid density functional, ωB97X-V, for which the analytical Hessian is not yet available due to the complexity of its long-range non-local VV10 correlation functional.

Brueckner orbitals↗
DOE OSTI2022

Role of SaPCR2 in Zn Uptake in the Root Elongation Zone of the Zn/Cd Hyperaccumulator Sedum alfredii

Zn pollution is a potential toxicant for agriculture and the environment. Sedum alfredii is a Zn/Cd hyperaccumulator found in China and has been proven as a useful resource for the phytoremediation of Zn-contaminated sites. However, the molecular mechanism of Zn uptake in S. alfredii is limited. In this study, the function of SaPCR2 on Zn uptake in S. alfredii was identified by gene expression analysis, yeast function assays, Zn accumulation and root morphology analysis in transgenic lines to further elucidate the mechanisms of uptake and translocation of Zn in S. alfredii. The results showed that SaPCR2 was highly expressed in the root elongation zone of the hyperaccumulating ecotype (HE) S. alfredii, and high Zn exposure downregulated the expression of SaPCR2 in the HE S. alfredii root. The heterologous expression of SaPCR2 in yeast suggested that SaPCR2 was responsible for Zn influx. The overexpression of SaPCR2 in the non-hyperaccumulating ecotype (NHE) S. alfredii significantly increased the root uptake of Zn, but did not influence Mn, Cu or Fe. SR-μ-XRF technology showed that more Zn was distributed in the vascular buddle tissues, as well as in the cortex and epidermis in the transgenic lines. Root morphology was also altered after SaPCR2 overexpression, and a severe inhibition was observed. In the transgenic lines, the meristematic and elongation zones of the root were lower compared to the WT, and Zn accumulation in meristem cells was also reduced. These results indicate that SaPCR2 is responsible for Zn uptake, and mainly functions in the root elongation zone. This research on SaPCR2 could provide a theoretical basis for the use of genetic engineering technology in the modification of crops for their safe production and biological enhancement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Method to Measure the Unbiased Decorrelation Timescale of the AGN Variable Signal from Structure Functions

A simple, model-independent method to quantify the stochastic variability of active galactic nuclei (AGNs) is the structure function (SF) analysis. If the SF for the timescales shorter than the decorrelation timescale τ is a single power law and for the longer ones becomes flat (i.e., white noise), then the auto-correlation function (ACF) of the signal can have the form of the power exponential (PE). We show that the signal decorrelation timescale can be measured directly from the SF as the timescale matching the amplitude 0.795 of the flat SF part (at long timescales), and only then is the measurement independent of the ACF PE power. Typically, the timescale has been measured at an arbitrarily fixed SF amplitude, but as we prove, this approach provides biased results, because the AGN SF/power spectral density slopes, and thus the ACF shape, are not constant and depend on either the AGN luminosity and/or the black hole mass. In particular, we show that using such a method for the simulated SFs that includes a combination of empirically known dependencies between the AGN luminosity L and both the SF amplitude and the PE power, and having no intrinsic τ–L dependence, produces a fake τ∝L{sup κ} relation with 0.3≲κ≲0.6, which otherwise is expected from theoretical works (κ≡0.5). Our method provides an alternative means for analyzing AGN variability to the standard SF fitting. The caveats, for both methods, are that the light curves must be sufficiently long (with a several year rest frame) and the ensemble SF assumes AGNs to have the same underlying variability process.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Position-specific isotope effects during alkaline hydrolysis of 2,4-dinitroanisole resolved by compound-specific isotope analysis, 13 C NMR, and density-functional theory

Compound-specific isotope analysis (CSIA), position-specific isotope analysis (PSIA), and computational modeling (e.g., quantum mechanical models; reactive-transport models) are increasingly being used to monitor and predict biotic and abiotic transformations of organic contaminants in the field. However, identifying the isotope effect(s) associated with a specific transformation remains challenging in many cases. We describe and interpret the position-specific isotope effects of C and N associated with a SN 2 Ar reaction mechanism by a combination of CSIA and PSIA using quantitative 13 C nuclear magnetic resonance spectrometry, and density-functional theory, using 2,4-dinitroanisole (DNAN) as a model compound. The position-specific 13 C enrichment factor of O–C 1 bond at the methoxy group attachment site (ε C1 ) was found to be approximately -41‰, a diagnostic value for transformation of DNAN to its reaction products 2,4-dinitrophenol and methanol. Theoretical kinetic isotope effects calculated for DNAN isotopologues agreed well with the position-specific isotope effects measured by CSIA and PSIA. This combination of measurements and theoretical predictions demonstrates a useful tool for evaluating degradation efficiencies and/or mechanisms of organic contaminants and may promote new and improved applications of isotope analysis in laboratory and field investigations.

13C NMR↗
DOE OSTI2025

Hydrogen Bond Benchmark: Focal‐Point Analysis and Assessment of DFT Functionals

We performed a hierarchical, convergent ab initio benchmark study and systematically analyzed the performance of density functional approximations for describing hydrogen bonds in small neutral, cationic, and anionic complexes, as well as in larger systems involving amide, urea, deltamide, and squaramide moieties. Focal point analyses (FPA), extrapolating to the ab initio limit, were carried out using correlated wave function methods up to CCSDT(Q) for the small complexes and CCSD(T) for the larger systems, together with correlation-consistent Gaussian basis sets up to the complete basis set limit. Optimized geometries and vibrational frequencies were obtained at the CCSD(T) level. The resulting FPA hydrogen-bond energies converge within a few tenths of a kcal mol −1 . These reference data were used to evaluate 60 density functionals (including 12 dispersion-corrected), spanning the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. Overall, the meta-hybrid M06-2X provides the best performance for both hydrogen bond energies and geometries, while the dispersion-corrected GGAs BLYP-D3(BJ) and BLYP-D4 also yield accurate hydrogen-bond data and can serve as cost-effective options for studying large and complex systems.

coupled cluster theory↗
DOE OSTI2025

Non-stoichiometry Governs the Pathway from Amorphous to Crystalline Calcium Carbonate

The controlled crystallization of calcium carbonate underlies the elaborate architectures of marine corals, the design of biomimetic materials, and the global carbon cycle. Despite its ubiquity, the chemical mechanisms that govern the crystallization of calcium carbonate from its amorphous precursor, amorphous calcium carbonate (ACC), remain elusive, largely due to the difficulty in resolving the structure and chemistry of this transient amorphous state. Here, we use time-lapse photography, image analysis, spatially resolved pH determination, in situ synchrotron pair distribution function (PDF) analysis, and dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) spectroscopy to reveal pervasive compositional variability in ACC that underpins its metastability and crystallization. By evaluating the kinetics of the amorphous-to-crystalline transition across different solution chemistries, we demonstrate that ACC is non-stoichiometric and CO 3 -deficient. Counterions from the precursor (e.g., NO 3 - from Ca(NO 3 ) 2 ) substitute into the ACC network, displacing CO 3 ions and mediating both ACC stability and transformation. Crystallization proceeds through refinement of the stoichiometry toward CaCO 3 and uptake of free CO 3 2- anions. Furthermore, these findings are consistent across a wide range of concentrations and different carbonate sources, explaining the diverse behaviors observed for ACC and providing a chemical framework for controlling calcium carbonate crystallization.

77 NANOSCIENCE AND NANOTECHNOLOGY↗