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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A genome-scale phylogeny of the kingdom Fungi

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ~85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Finally, our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Even spheres as joint spectra of matrix models

The Clifford spectrum is a form of joint spectrum for noncommuting matrices. This theory has been applied in photonics, condensed matter and string theory. In applications, the Clifford spectrum can be efficiently approximated using numerical methods, but this only is possible in low dimensional example. In this paper we examine the higher-dimensional spheres that can arise from theoretical examples. We also describe a constructive method to generate five real symmetric almost commuting matrices that have a K-theoretical obstruction to being close to commuting matrices. For this, we look to matrix models of topological electric circuits.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Role of reduced precursor and solvolytic reagent molar ratio on preparation and properties of ionogel

In the present study, ionogels have been synthesized by immobilizing IL (1-ethyl-3-methylimidazolium tetrafluoroborate) in silica gel matrices using non-aqueous route. In this process, tetraethyl orho-silane (TEOS) as a precursor to silicon dioxide and formic acid as a solvolytic gelating reagent in reduced molar ratio 1:4 were used. We find that reduced molar concentration of formic acid results the formation of ionogels having less number of closed pores (totally isolated from their neighbours), larger density and stable monolithic form. TEM and SEM measurements are used to visualize the morphology of sample and closed pores present in the sample. N{sub 2}-sorption measurement is used to measure the pore parameters of the silica matrices which shows the mesoporous structure. DSC and TGA results show the change in phase transition temperature and thermal stability of IL upon confinement in silica matrices. Moreover, ionic conductivity of bulk and confined IL is measured using impedance spectroscopy and it has been found that it increases with increasing the temperature as well as concentration of IL in ionogels. Apart from these characterization techniques, ionogels have been characterized using FTIR and fluorescence spectroscopy which exhibit the change in vibrational frequencies and fluorescence behaviour of confined IL. - Highlights: • Synthesis of stable ionogel using non-hydrolytic route with reduced precursor and solvolytic reagent molar ratio. • Ionogels are free from entrapped residual reaction product. • The ionogels synthesized with higher amount of ionic liquids show bulk liquid like electrical behaviour.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Generation of Composite Dose and Biological Effective Dose (BED) Over Multiple Treatment Modalities and Multistage Planning Using Deformable Image Registration

Currently there are no commercially available tools to generate composite plans across different treatment modalities and/or different planning image sets. Without a composite plan, it may be difficult to perform a meaningful dosimetric evaluation of the overall treatment course. In this paper, we introduce a method to generate composite biological effective dose (BED) plans over multiple radiotherapy treatment modalities and/or multistage plans, using deformable image registration. Two cases were used to demonstrate the method. Case I was prostate cancer treated with intensity-modulated radiation therapy (IMRT) and a permanent seed implant. Case II involved lung cancer treated with two treatment plans generated on two separate computed tomography image sets. Thin-plate spline or optical flow methods were used as appropriate to generate deformation matrices. The deformation matrices were then applied to the dose matrices and the resulting physical doses were converted to BED and added to yield the composite plan. Cell proliferation and sublethal repair were considered in the BED calculations. The difference in BED between normal tissues and tumor volumes was accounted for by using different BED models, {alpha}/{beta} values, and cell potential doubling times. The method to generate composite BED plans presented in this paper provides information not available with the traditional simple dose summation or physical dose summation. With the understanding of limitations and uncertainties of the algorithms involved, it may be valuable for the overall treatment plan evaluation.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2018

Part 2: Forensic attribution profiling of Russian VX in food using liquid chromatography-mass spectrometry

This work is part two of a three-part series in this issue of a Sweden-United States collaborative effort towards the understanding of the chemical attribution signatures of Russian VX (VR) in synthesized samples and complex food matrices. We describe the sourcing of VR present in food based on chemical analysis of attribution signatures by liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with multivariate data analysis. Analytical data was acquired from seven different foods spiked with VR batches that were synthesized via six different routes in two separate laboratories. The synthesis products were spiked at a lethal dose into seven food matrices: water, orange juice, apple purée, baby food, pea purée, liquid eggs and hot dog. After acetonitrile sample extraction, the samples were analyzed by LC-MS/MS operated in MRM mode. A multivariate statistical calibration model was built on the chemical attribution profiles from 118 VR spiked food samples. Using the model, an external test-set of the six synthesis routes employed for VR production was correctly identified with no observable major impact of the food matrices to the classification. The overall performance of the statistical models was found to be exceptional (94%) for the test set samples retrospectively classified to their synthesis routes.

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

The formation of quiescent glomerular endothelial cell monolayer in vitro is strongly dependent on the choice of extracellular matrix coating

Background and aims: Nephropathy involves pathophysiological changes to the glomerulus. The primary glomerular endothelial cells (GEnCs) have emerged as an important tool for studying glomerulosclerotic mechanisms and in the screening process for drug-candidates. The success of the studies is dependent on the quality of the cell model. Therefore, we set out to establish an easy, reproducible model of the quiescent endothelial monolayer with the use of commercially available extracellular matrices (ECMs). Methods: Primary hGEnCs were seeded on various ECMs. Cell adhesion was monitored by an impedance sensing system. The localization of junctional proteins was assessed by immunofluorescence and the barrier function by passage of fluorescent dextrans and magnitude of VEGF response. Results: All ECM matrices except recombinant human laminin 111 (rhLN111) supported comparable cell proliferation. Culturing hGEnCs on rhLN521, rhLN511 or fibronectin resulted in a physiologically relevant barrier to 70 kDa dextrans which was 82% tighter than that formed on collagen type IV. Furthermore, only hGEnCs cultured on rhLN521 or rhLN511 showed plasma-membrane localized zonula occludens-1 and vascular endothelial cadherin indicative of proper tight and adherens junctions (AJ). Conclusion: We recommend culturing hGEnCs on the mature glomerular basement membrane laminin - rhLN521 – which, as the only commercially available ECM, promotes all of the characteristics of the quiescent hGEnC monolayer: cobblestone morphology, well-defined AJs and physiological perm-selectivity. - Highlights: • rhLN521, rhLN511 and hFN assure physiologically relevant permeability. • rhLN521 and rhLN511 ensure best cell morphology and adherens junction formation. • Collagen IV and I based coating results in disorganized hGEnC monolayer. • Physiologically relevant ECM may lead to down-regulation of self-produced matrices.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

An extracellular matrix (ECM) model at high malignant colorectal tumor increases chondroitin sulfate chains to promote epithelial-mesenchymal transition and chemoresistance acquisition

Highlights: • Effect of ECM dynamics in tumor progression on EMT and chemoresistance were assessed. • 5-FU increased EMT genes and ABCB1 expression via TGF-β signaling. • High malignant tumor ECM promoted EMT and ABCB1 expression via TGF-β signaling. • High malignant tumor ECM possessed chondroitin sulfate chains at high level. • Increased chondroitin sulfate promoted EMT genes and ABCB1 expression. Chemoresistance is one of the major barriers for tumor chemotherapy. It is clinically known that chemoresistance increases during tumor progression. Additionally, the extracellular matrix (ECM) is also remodeled during tumor progression. However, it remains unclear how ECM remodeling contributes to chemoresistance acquisition. Recently, it has been reported that epithelial-mesenchymal transition (EMT) contributes to chemoresistance acquisition. Here, how ECM remodeling contributes to 5-fluorouracil (5-FU) resistance acquisition was investigated from the viewpoints of EMT using in vitro ECM models mimicking native ECM in colorectal tumor tissue at three different malignant levels. 5-FU partially induced EMT and increased ABCB1 in colorectal HT-29 cells via TGF-β signaling (an invasive tumor cell model). When HT-29 cells were cultured on an ECM model (high malignant matrices) mimicking native ECM in highly malignant tumor tissues, the cells facilitated TGF-β-induced EMT and increased ABCB1 upregulation compared with that of other ECM models mimicking the low malignant level and normal tissues. High malignant matrices contained more chondroitin sulfate (CS) chains than those of other ECM models. Finally, CS chain-reduced high malignant matrices could not facilitate ABCB1 upregulation and TGF-β-induced EMT. These results demonstrated that ECM remodeling during tumor progression increased CS chains to facilitate EMT and ABCB1 upregulation, contributing to chemoresistance acquisition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A High-Efficiency Delayed Update Algorithm for Evaluating Slater Determinants in Quantum Monte Carlo

For quantum Monte Carlo simulations of molecular systems or supercells with thousands of electrons, matrix operations related to Slater determinants lead the computational cost. McDaniel et al. [J. Chem. Phys. 2017, 147, 174107] proposed a delayed update algorithm to increase computational efficiency by using matrix–matrix multiplication when updating the inverse matrices of Slater determinants. However, preparing intermediate matrices for applying the Sherman–Morrison–Woodbury formula remained a bottleneck. Here, in this work, we introduce an improved algorithm for CPUs and GPUs that (1) reduces this bottleneck by iteratively updating the intermediate matrices and (2) is efficient at any acceptance ratio, with no cost for rejected moves on CPUs and minimal cost on GPUs. We show the full scheme of integrating the delayed update algorithm into a single-electron move. The high efficiency of our algorithm is demonstrated on CPUs and GPUs for a 512 atom/6144 valence electron calculation, with 12× and 2× overall speed-up compared to traditional rank-1 update schemes in diffusion quantum Monte Carlo, respectively.

Luo, Ye [Argonne National Laboratory (ANL), Argonn↗
DOE OSTI2021

Nonlinear Architectures Can Alter the Dynamics of Polymer–Nanoparticle Composites

Polymer nanocomposites exhibit remarkable physical properties that are attractive for many applications. These systems have been so far investigated by using linear polymer chains; the role of polymer matrix architecture on local dynamics, bulk rheology and nanoparticle motion remains unexplored. Here, using quasielastic neutron scattering, bulk rheology and x-ray photon correlation spectroscopy, we investigated nanocomposites with spherical silica nanoparticles well dispersed in poly (ethylene oxide) matrices having different architectures (specifically linear, stars and hyperbranched). The results reveal that the mechanical reinforcement of the nanocomposites with the nonlinear polymers can be altered by orders of magnitude with respect to the conventional nanocomposite with the linear polymer. Additionally, the polymer compactness and inter-penetrability are found to play crucial roles in determining their bulk rheology. At microscopic level, average segmental dynamics is remarkably slowed down by the attractive NPs in the matrices of high degree of branching whereas no significant effect is observed in linear polymer matrix at the same NP loading. In addition, the nanoscale dynamics of particles in the compact nonlinear matrices exhibit strong decoupling from the bulk viscoelasticity, allowing their fast relaxation even at ≈ 30% by volume. These results provide an experimental evidence that macromolecular architecture is a powerful new tool for tuning the bulk rheological properties as well as the nanoscale dynamics of PNCs without the need for changing polymer molecular weight, nanoparticle size, shape, loading or dispersion state.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Design of Heterogeneous Chalcogenide Nanostructures with Pressure-Tunable Gaps and without Electronic Trap States

Heterogeneous nanostructures, such as quantum dots (QDs) embedded in solid matrices or core–shell nanoparticles, are promising platforms for a wide variety of applications, including phosphors with increased quantum yield, photocatalysis, and solar energy conversion. However, characterizing and controlling their interfacial morphology and defects, which greatly influence their electronic properties, have proven difficult in numerous cases. Here we carried out atomistic calculations on chalcogenide nanostructured materials, i.e., PbSe QDs in CdSe matrices and CdSe embedded in PbSe, and we established how interfacial and core structures affect their electronic properties. In particular, we showed that defects present at interfaces of PbSe nanoparticles and CdSe matrices give rise to detrimental intragap states, degrading the performance of photovoltaic devices. Instead, the electronic gaps of the inverted system (CdSe dots in PbSe) are clean, indicating that this material has superior electronic properties for solar applications. In addition, our calculations predicted that the core structure of CdSe and in turn its band gap may be tuned by applying pressure to the PbSe matrix, providing a means to engineering the properties of new functional materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Contentious relationships in phylogenomic studies can be driven by a handful of genes

Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. In conclusion, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, for which examination of the distributions of gene-wise and site-wise phylogenetic signal across eight data matrices consistently supports ctenophores as the sister group to all other metazoans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Trimethyloxonium-mediated methylation strategies for the rapid and simultaneous analysis of chlorinated phenols in various soils by electron impact gas chromatography–mass spectrometry

Abstract The efficient methylation of a panel of five industrial and environmentally-relevant chlorophenols (CPs) employing trimethyloxonium tetrafluoroborate (TMO) for their qualitative detection and identification by electron impact gas chromatography–mass spectrometry (EI-GC–MS) is presented. The protocol’s execution is simple and smoothly converts the phenols into their O-methylated counterparts conveniently at ambient temperature. The efficiency of two versions of the protocol was successfully tested in their ability to simultaneously derivatize five CPs (2-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, pentachlorophenol and triclosan) in six distinct, separate soil matrices (Nebraska EPA standard soil, Virginia Type A soil, Ottawa sand, Baker sand, Silt and Georgia EPA standard soil) when present at low levels (~ 10 μgg −1 ). The first version involves the direct derivatization of the spiked soils with the methylating salt while the second one involves an initial soil extraction step of the CPs followed by methylation. The MDL values for each methylated CP were determined and lower values were found (4.1–13.2 ng . mL −1 ) for both sand matrices (Ottawa and Baker) as well as for the Georgia EPA standard soil, while larger values (8.2–21.8 ng . mL −1 ) were found for the Virginia Type soil, Nebraska EPA standard soil and Silt. The presented protocol offers a safer and more practical alternative to the universally employed diazomethane method and can be readily applicable to matrices other than soils. Furthermore, the protocols described herein may find applicability to the methylation of other analytes bearing acidic protons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A universal variational quantum eigensolver for non-Hermitian systems

Abstract Many quantum algorithms are developed to evaluate eigenvalues for Hermitian matrices. However, few practical approach exists for the eigenanalysis of non-Hermintian ones, such as arising from modern power systems. The main difficulty lies in the fact that, as the eigenvector matrix of a general matrix can be non-unitary, solving a general eigenvalue problem is inherently incompatible with existing unitary-gate-based quantum methods. To fill this gap, this paper introduces a Variational Quantum Universal Eigensolver (VQUE), which is deployable on noisy intermediate scale quantum computers. Our new contributions include: (1) The first universal variational quantum algorithm capable of evaluating the eigenvalues of non-Hermitian matrices—Inspired by Schur’s triangularization theory, VQUE unitarizes the eigenvalue problem to a procedure of searching unitary transformation matrices via quantum devices; (2) A Quantum Process Snapshot technique is devised to make VQUE maintain the potential quantum advantage inherited from the original variational quantum eigensolver—With additional $$O(log_{2}{N})$$ O ( l o g 2 N ) quantum gates, this method efficiently identifies whether a unitary operator is triangular with respect to a given basis; (3) Successful deployment and validation of VQUE on a real noisy quantum computer, which demonstrates the algorithm’s feasibility. We also undertake a comprehensive parametric study to validate VQUE’s scalability, generality, and performance in realistic applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Planck 2015 results: VI. LFI mapmaking

This article describes the mapmaking procedure applied to Planck Low Frequency Instrument (LFI) data. The mapmaking step takes as input the calibrated timelines and pointing information. The main products are sky maps of I, Q, and U Stokes components. For the first time, we present polarization maps at LFI frequencies. The mapmaking algorithm is based on a destriping technique, which is enhanced with a noise prior. The Galactic region is masked to reduce errors arising from bandpass mismatch and high signal gradients. We apply horn-uniform radiometer weights to reduce the effects of beam-shape mismatch. The algorithm is the same as used for the 2013 release, apart from small changes in parameter settings. We validate the procedure through simulations. Special emphasis is put on the control of systematics, which is particularly important for accurate polarization analysis. We also produce low-resolution versions of the maps and corresponding noise covariance matrices. These serve as input in later analysis steps and parameter estimation. The noise covariance matrices are validated through noise Monte Carlo simulations. The residual noise in the map products is characterized through analysis of half-ring maps, noise covariance matrices, and simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

DESI mock challenge: Halo and galaxy catalogues with the bias assignment method

We present a novel approach to the construction of mock galaxy catalogues for large-scale structure analysis based on the distribution of dark matter halos obtained with effective bias models at the field level. We aim to produce mock galaxy catalogues capable of generating accurate covariance matrices for a number of cosmological probes that are expected to be measured in current and forthcoming galaxy redshift surveys (e.g. two- and three-point statistics). The construction of the catalogues shown in this paper is part of a mock-comparison project within the Dark Energy Spectroscopic Instrument (DESI) collaboration. We use the bias assignment method ( BAM ) to model the statistics of halo distribution through a learning algorithm using a few detailed N-body simulations, and approximated gravity solvers based on Lagrangian perturbation theory. We introduce cosmic-web-dependent corrections to modelling redshift-space distortions at the N-body level – both in the halo and galaxy distributions –, as well as a multi-scale approach for accurate assignment of halo properties. Using specific models of halo occupation distributions to populate halos, we generate galaxy mocks with the expected number density and central-satellite fraction of emission-line galaxies, which are a key target of the DESI experiment. BAM generates mock catalogues with per cent accuracy in a number of summary statistics, such as the abundance, the two- and three-point statistics of halo distributions, both in real and redshift space. In particular, the mock galaxy catalogues display ~3%-10% accuracy in the multipoles of the power spectrum up to scales of k ~ 0.4 h -1 Mpc. We show that covariance matrices of two- and three-point statistics obtained with BAM display a similar structure to the reference simulation. BAM offers an efficient way to produce mock halo catalogues with accurate two- and three-point statistics and is able to generate a variety of multi-tracer catalogues with precise covariance matrices of several cosmological probes. We discuss future developments of the algorithm towards mock production in DESI and other galaxy-redshift surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

In situ synchrotron X-ray diffraction study of deformation behavior and load transfer in a Ti{sub 2}Ni-NiTi composite

The deformation behavior and load transfer of a dual-phase composite composed of martensite NiTi embedded in brittle Ti{sub 2}Ni matrices were investigated by using in situ synchrotron x-ray diffraction during compression. The composite exhibits a stage-wise deformation feature and a double-yielding phenomenon, which were caused by the interaction between Ti{sub 2}Ni and NiTi with alternative microscopic deformation mechanism. No load transfer occurs from the soft NiTi dendrites to the hard Ti{sub 2}Ni matrices during the pseudoplastic deformation (detwinning) of NiTi, which is significantly different from that previously reported in bulk metallic glasses matrices composites.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗