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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Low-rank factorization of electron integral tensors and its application in electronic structure theory

In this letter, we introduce the reverse Cuthill-McKee (RCM) algorithm, which is often used for the bandwidth reduction of sparse tensors, to transform the two-electron integral tensors to their block diagonal forms. By further applying the pivoted Cholesky decomposition (CD) on each of the diagonal blocks, we are able to represent the high-dimensional two-electron integral tensors in terms of permutation matrices and low-rank Cholesky vectors. This representation facilitates the low-rank factorization of the high-dimensional tensor contractions that are usually encountered in post-Hartree-Fock calculations. In this letter, we discuss the second-order Møller-Plesset (MP2) method and linear coupled- cluster model with doubles (L-CCD) as two simple examples to demonstrate the efficiency of the RCM-CD technique in representing two-electron integrals in a compact form.

electronic structure theory↗
DOE OSTI2011

Constructing efficient substructure-based preconditioners for BEM systems of equations

In this work, a generic substructuring algorithm is employed to construct global block-diagonal preconditioners for BEM systems of equations. In this strategy, the allowable fill-in positions are those on-diagonal block matrices corresponding to each BE subregion. As these subsystems are independently assembled, the preconditioner for a particular BE model, after the LU decomposition of all subsystem matrices, is easily formed. So as to highlight the efficiency of the preconditioning proposed, the Bi-CG solver, which presents a quite erratic convergence behavior, is considered. In the particular applications of this paper, 3D representative volume elements (RVEs) of carbon-nanotube (CNT) composites are analyzed. The models contain up to several tens of thousands of degrees of freedom. The efficiency and relevance of the preconditioning technique is also discussed in the context of developing general (parallel) BE codes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Skeletal reaction models for methane combustion

A local-sensitivity-analysis technique is employed to generate new skeletal reaction models for methane combustion from the foundational fuel chemistry model (FFCM-1). Here, the sensitivities of the thermo-chemical variables with respect to the reaction rates are computed via the forced-optimally time dependent (f-OTD) methodology. In this methodology, the large sensitivity matrix containing all local sensitivities is modeled as a product of two low-rank time-dependent matrices. The evolution equations of these matrices are derived from the governing equations of the system. The modeled sensitivities are computed for the auto-ignition of methane at atmospheric and high pressures with different sets of initial temperatures, and equivalence ratios. These sensitivities are then analyzed to rank the most important (sensitive) species. A series of skeletal models with different number of species and levels of accuracy in reproducing the FFCM-1 results are suggested. The performances of the generated models are compared against FFCM-1 in predicting the ignition delay, the laminar flame speed, and the flame extinction. The results of this comparative assessment suggest the skeletal models with 24 and more species generate the FFCM-1 results with an excellent accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Isotope Exchange between Mercuric [Hg(II)] Chloride and Hg(II) Bound to Minerals and Thiolate Ligands: Implications for Enriched Isotope Tracer Studies

Enriched mercury (Hg) stable isotopes have been widely used as tracers in field and laboratory investigations of Hg(II) biogeochemical transformations such as methylation and demethylation. Few studies, however, have considered concurrent isotope exchange reactions between newly spiked and pre-existing Hg(II) in environmental matrices, which may alter redistribution and thus transformation of the spiked and pre-existing Hg(II). Using enriched 198 Hg [as mercuric Hg(II) or HgCl n species], this study investigated isotope exchange between 198 Hg and pre-existing Hg(II) bound to metacinnabar (β-HgS), sediments, low-molecular-weight (LMW) thiols, and dissolved organic matter (DOM). The impact of isotope exchange on methylmercury production in the presence of organic ligands was also evaluated with an iron-reducing bacterium Geobacter sulfurreducens PCA in a phosphate buffered solution (pH 7.4). Here, we found that spiked 198 Hg readily exchanged with mineral-bound ambient Hg(II) despite concurrent Hg(II) adsorption and immobilization on the solids. Rapid exchange (<3 min) was also observed between spiked 198 Hg and 200 Hg pre-equilibrated with LMW thiols and DOM in solution. While the exchange did not cause net changes in Hg(II) chemical speciation, it resulted in redistribution of Hg(II) isotopes bound to the ligands and thus an apparently similar methylation rate and magnitude of the spiked 198 Hg and pre-existing 200 Hg by PCA cells when 198 Hg and 200 Hg were added at 1:1 ratio. These observations underscore the importance of isotope exchange when an enriched Hg isotope is applied in environmental matrices, as the exchange could potentially lead to biased rate calculations of Hg(II) transformation and bioaccumulation and thus risk assessments of new Hg(II) input to the natural ecosystems.

58 GEOSCIENCES↗
DOE OSTI2023

Tangent functional connectomes uncover more unique phenotypic traits

Functional connectomes (FCs) containing pairwise estimations of functional couplings between pairs of brain regions are commonly represented by correlation matrices. As symmetric positive definite matrices, FCs can be transformed via tangent space projections, resulting into tangent-FCs. Tangent-FCs have led to more accurate models predicting brain conditions or aging. Motivated by the fact that tangent-FCs seem to be better biomarkers than FCs, we hypothesized that tangent-FCs have also a higher fingerprint. We explored the effects of six factors: fMRI condition, scan length, parcellation granularity, reference matrix, main-diagonal regularization, and distance metric. Our results showed that identification rates are systematically higher when using tangent-FCs across the “fingerprint gradient” (here including test-retest, monozygotic and dizygotic twins). Highest identification rates were achieved when minimally (0.01) regularizing FCs while performing tangent space projection using Riemann reference matrix and using correlation distance to compare the resulting tangent-FCs. Such configuration was validated in a second dataset (resting-state).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DOME: Directional medical embedding vectors from Electronic Health Records

Motivation: The increasing availability of Electronic Health Record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data. On the other hand, scalable approaches that only require summary-level data do not incorporate temporal dependencies between concepts. Methods: We introduce a DirectiOnal Medical Embedding (DOME) algorithm to encode temporally directional relationships between medical concepts, using summary-level EHR data. Specifically, DOME first aggregates patient-level EHR data into an asymmetric co-occurrence matrix. Then it computes two Positive Pointwise Mutual Information (PPMI) matrices to correspondingly encode the pairwise prior and posterior dependencies between medical concepts. Following that, a joint matrix factorization is performed on the two PPMI matrices, which results in three vectors for each concept: a semantic embedding and two directional context embeddings. They collectively provide a comprehensive depiction of the temporal relationship between EHR concepts. Results: We highlight the advantages and translational potential of DOME through three sets of validation studies. First, DOME consistently improves existing direction-agnostic embedding vectors for disease risk prediction in several diseases, for example achieving a relative gain of 5.5% in the area under the receiver operating characteristic (AUROC) for lung cancer. Second, DOME excels in directional drug-disease relationship inference by successfully differentiating between drug side effects and indications, correspondingly achieving relative AUROC gain over the state-of-the-art methods by 10.8% and 6.6%. Finally, DOME effectively constructs directional knowledge graphs, which distinguish disease risk factors from comorbidities, thereby revealing disease progression trajectories. The source codes are provided at https://github.com/celehs/Directional-EHRembedding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

High-performance implementation of Chebyshev filter diagonalization for interior eigenvalue computations

We study Chebyshev filter diagonalization as a tool for the computation of many interior eigenvalues of very large sparse symmetric matrices. In this technique the subspace projection onto the target space of wanted eigenvectors is approximated with filter polynomials obtained from Chebyshev expansions of window functions. After the discussion of the conceptual foundations of Chebyshev filter diagonalization we analyze the impact of the choice of the damping kernel, search space size, and filter polynomial degree on the computational accuracy and effort, before we describe the necessary steps towards a parallel high-performance implementation. Because Chebyshev filter diagonalization avoids the need for matrix inversion it can deal with matrices and problem sizes that are presently not accessible with rational function methods based on direct or iterative linear solvers. To demonstrate the potential of Chebyshev filter diagonalization for large-scale problems of this kind we include as an example the computation of the 10{sup 2} innermost eigenpairs of a topological insulator matrix with dimension 10{sup 9} derived from quantum physics applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Higher-order triangular spectral element method with optimized cubature points for seismic wavefield modeling

The mass-lumped method avoids the cost of inverting the mass matrix and simultaneously maintains spatial accuracy by adopting additional interior integration points, known as cubature points. To date, such points are only known analytically in tensor domains, such as quadrilateral or hexahedral elements. Thus, the diagonal-mass-matrix spectral element method (SEM) in non-tensor domains always relies on numerically computed interpolation points or quadrature points. However, only the cubature points for degrees 1 to 6 are known, which is the reason that we have developed a p-norm-based optimization algorithm to obtain higher-order cubature points. In this way, we obtain and tabulate new cubature points with all positive integration weights for degrees 7 to 9. The dispersion analysis illustrates that the dispersion relation determined from the new optimized cubature points is comparable to that of the mass and stiffness matrices obtained by exact integration. Simultaneously, the Lebesgue constant for the new optimized cubature points indicates its surprisingly good interpolation properties. As a result, such points provide both good interpolation properties and integration accuracy. The Courant–Friedrichs–Lewy (CFL) numbers are tabulated for the conventional Fekete-based triangular spectral element (TSEM), the TSEM with exact integration, and the optimized cubature-based TSEM (OTSEM). A complementary study demonstrates the spectral convergence of the OTSEM. A numerical example conducted on a half-space model demonstrates that the OTSEM improves the accuracy by approximately one order of magnitude compared to the conventional Fekete-based TSEM. In particular, the accuracy of the 7th-order OTSEM is even higher than that of the 14th-order Fekete-based TSEM. Furthermore, the OTSEM produces a result that can compete in accuracy with the quadrilateral SEM (QSEM). The high accuracy of the OTSEM is also tested with a non-flat topography model. In terms of computational efficiency, the OTSEM is more efficient than the Fekete-based TSEM, although it is slightly costlier than the QSEM when a comparable numerical accuracy is required. - Highlights: • Higher-order cubature points for degrees 7 to 9 are developed. • The effects of quadrature rule on the mass and stiffness matrices has been conducted. • The cubature points have always positive integration weights. • Freeing from the inversion of a wide bandwidth mass matrix. • The accuracy of the TSEM has been improved in about one order of magnitude.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Accelerating eigenvalue computation for nuclear structure calculations via perturbative corrections

Subspace projection methods utilizing perturbative corrections have been proposed for computing the lowest few eigenvalues and corresponding eigenvectors of large Hamiltonian matrices. In this paper, we build upon these methods and introduce the term Subspace Projection with Perturbative Corrections (SPPC) method to refer to this approach. We tailor the SPPC for nuclear many-body Hamiltonians represented in a truncated configuration interaction subspace, i.e., the no-core shell model (NCSM). We use the hierarchical structure of the NCSM Hamiltonian to partition the Hamiltonian as the sum of two matrices. The first matrix corresponds to the Hamiltonian represented in a small configuration space, whereas the second is viewed as the perturbation to the first matrix. Eigenvalues and eigenvectors of the first matrix can be computed efficiently. Because of the split, perturbative corrections to the eigenvectors of the first matrix can be obtained efficiently from the solutions of a sequence of linear systems of equations defined in the small configuration space. These correction vectors can be combined with the approximate eigenvectors of the first matrix to construct a subspace from which more accurate approximations of the desired eigenpairs can be obtained. We show by numerical examples that the SPPC method can be more efficient than conventional iterative methods for solving large-scale eigenvalue problems such as the Lanczos, block Lanczos and the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The method can also be combined with other methods to avoid convergence stagnation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Testing and signal identification for two-sample high-dimensional covariances via multi-level thresholding

The paper considers testing and signal identification for covariance matrices from two populations of marginally sub-Gaussian distributed. A multi-level thresholding procedure is proposed for testing the equality of two high-dimensional covariance matrices, which is designed to detect sparse and faint differences between the covariances. A novel -statistic composition is developed to establish the asymptotic distribution of the thresholding statistics in conjunction with the matrix blocking and the coupling techniques. It is shown that the proposed test is more powerful than the existing tests in detecting sparse and weak signals in covariances. Multiple testing procedures are constructed to discover different covariances and the sub-groups of variables with different covariance structures between the two populations. The proposed procedures are based on the multi-level thresholding test, which are able to control the false discovery proportion () with high power. Simulation experiments and a case study on the returns of the S&P 500 stocks before and after the COVID-19 pandemic are conducted to demonstrate and compare the utilities of the proposed methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2010

Selective Capture of Cesium and Thallium from Natural Waters and Simulated Wastes with Copper Ferrocyanide Functionalized Mesoporous Silica

Copper(II) ferrocyanide immobilized inside mesoporous silica MCM-41 supports (Cu-FC-EDA-SAMMSTM) has been evaluated against iron(III) hexacyanoferrate(II) (insoluble Prussian blue) for the sorption of cesium (Cs+) and thallium (Tl+) from natural waters and simulated wastes. The affinities (in term of distribution coefficients, Kd) of both sorbents for Cs and Tl were measured as a function of solution pH, competing cations, and matrices. For the entire pH studied (pH 0.1 to 7.3), Cu-FC-EDA-SAMMS had higher affinities for Cs and Tl (one to two orders of magnitude higher Kd) than Prussian blue and was less negatively impacted by the solution pH, competing cations, and matrices. The adsorption isotherms and kinetics of the two sorbents for Cs and/or Tl were also determined in seawater and simulated acid and alkaline wastes. SAMMS outperformed Prussian blue in terms of maximum adsorption capacity (e.g., 21.7 versus 2.6 mg Cs/g in acid waste stimulant, pH 1.1), and rate (e.g., over 95 wt% of Cs was removed after 2 minutes with SAMMS, while only 75 wt% was removed with Prussian blue). The lower affinity, capacity, and rate of Cs and Tl sorption on Prussian blue than those on Cu-FC-EDA-SAMMS were attributed to the molecular pore sizes, which restrict mass transport, and the insoluble Cs abducts of the Prussian blue, which restrict the ability of neighboring binding sites to further bind Cs ions. On the other hand, the large pores of SAMMS not only enable faster diffusion and faster binding chemistry, but they also allow isolation of binding sites so that one Cs binding event does not impact further Cs binding. In addition, iron (Fe) dissolved from insoluble Prussian blue over 10-fold of that from Cu-FC-EDA-SAMMS after 24 hours of contact time, indicating poorer material stability of Prussian blue.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Immobilization of cesium and iodine into Cs 3 Bi 2 I 9 perovskite-silica composites and core-shell waste forms with high waste loadings and chemical durability

Cs$_3$Bi$_2$I$_9$, a defect perovskite derivative, is a potential host phase to immobilize iodine and cesium with high waste loadings. In this work, two strategies were explored to form Cs$_3$Bi$_2$I$_9$-silica composites and a core-shell structure in order to improve chemical durability of waste form materials meanwhile maintaining high waste loadings. Cs$_3$Bi$_2$I$_9$ loadings as high as 70 wt.% were incorporated into a silica matrix to form silica-ceramic composites, and 20 wt.% Cs$_3$Bi$_2$I$_9$ was encapsulated into silica to form a core–shell structure by low temperature spark plasma sintering. Chemical durability of the composite and core-shell waste forms was evaluated by semi-dynamic leaching experiments, and Cs and I were incongruently released from waste form matrices. A BiOI alteration layer formed, acting as a passivation layer to reduce the release of radionuclides. The long-term iodine release rate was low (30 mg m$^{-2}$ day$^{-1}$) for the 70 wt.%Cs$_3$Bi$_2$I$_9$–silica composite leached in deionized water at 90 °C, which can be further reduced to 5 × 10$^{-3}$ mg m$^{-2}$ day$^{-1}$ for the 20 wt.% core-shell structure. This work highlights a robust way to immobilize the highly mobile radionuclides with high waste loadings through encapsulation into durable matrices and a surface passivating mechanism that can greatly reduce the elemental transport from waste form materials and significantly enhance their chemical durability.

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

Structure and luminescence properties of Dy 2 O 3 doped bismuth-borate glasses

In this study heavy bismuth-borate glasses were studied as host matrices of Dy 2 O 3 rare earth, for potential application as scintillator materials in high energy physics experiments and in general radiation detection systems. Glass matrices were prepared from 20BaO-xBi 2 O 3 -(80-x)B 2 O 3 (x = 20, 30, 40 mol%) ternary systems and synthesized by the melt-quenching method at different temperatures in order to obtain high density and high transparency in the UV/Vis range. Particularly, the glass manifesting the higher transparency and with sufficiently high density was doped with Dy 2 O 3 (2.5 and 5 mol%) in order to induce the luminescence characteristics. The effects of Bi 2 O 3 and Dy 2 O 3 on density, thermal behaviour, transmission as well as luminescence properties under UV excitation, were investigated. The experimental results show that the synthesized glasses can be considered promising candidate materials as dense scintillators, due to the Dy 3 + centres emission.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Reconstructing householder vectors from Tall-Skinny QR

The Tall-Skinny QR (TSQR) algorithm is more communication efficient than the standard Householder algorithm for QR decomposition of matrices with many more rows than columns. However, TSQR produces a different representation of the orthogonal factor and therefore requires more software development to support the new representation. Further, implicitly applying the orthogonal factor to the trailing matrix in the context of factoring a square matrix is more complicated and costly than with the Householder representation. We show how to perform TSQR and then reconstruct the Householder vector representation with the same asymptotic communication efficiency and little extra computational cost. We demonstrate the high performance and numerical stability of this algorithm both theoretically and empirically. The new Householder reconstruction algorithm allows us to design more efficient parallel QR algorithms, with significantly lower latency cost compared to Householder QR and lower bandwidth and latency costs compared with Communication-Avoiding QR (CAQR) algorithm. Experiments on supercomputers demonstrate the benefits of the communication cost improvements: in particular, our experiments show substantial improvements over tuned library implementations for tall-and-skinny matrices. Furthermore, we also provide algorithmic improvements to the Householder QR and CAQR algorithms, and we investigate several alternatives to the Householder reconstruction algorithm that sacrifice guarantees on numerical stability in some cases in order to obtain higher performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2010

The study of the crystalline phosphates of kosnarite type structure containing different alkali metals

The incorporation possibilities of different alkali elements into crystalline phosphates A{sub 1-x}A'{sub x}Hf{sub 2}(PO{sub 4}){sub 3} (A=Li, Na, K, Rb, Cs) were studied, the formation regions of kosnarite solid solutions were determined. Na{sub 0.5}K{sub 0.5}Hf{sub 2}(PO{sub 4}){sub 3} crystal structure was studied by powder X-ray diffraction, and the distribution of alkali metals in kosnarite structure was found out. The phosphate crystallizes in the space group R3c, with a=8.7295(1) A, c=23.2023(4) A, V=1531.24(4) A{sup 3}, Z=6; R{sub wp}=6.15, R{sub p}=4.43. The concentration region knowledge of the kosnarite phase existence and peculiarities of their phase formation in the A{sub 1-x}A'{sub x}M{sub 2}(PO{sub 4}){sub 3} (M=Ti, Zr, Hf) systems allow us to choose phosphate matrice compositions suitable for solidification of reprocessing wastes of spent U-Pu nuclear fuels. - Graphical abstract: The incorporation possibilities of different alkali elements into crystalline phosphates A{sub 1-x}A'{sub x}Hf{sub 2}(PO{sub 4}){sub 3} (A=Li, Na, K, Rb, Cs) were studied, the formation regions of kosnarite solid solutions were determined. Na{sub 0.5}K{sub 0.5}Hf{sub 2}(PO{sub 4}){sub 3} crystal structure was studied by powder X-ray diffraction, and the distribution of alkali metals in kosnarite structure was found out. The phosphate crystallizes in the space group R3c, with a=8.7295(1) A, c=23.2023(4) A, V=1531.24(4) A{sup 3}, Z=6; R{sub wp}=6.15, R{sub p}=4.43. The concentration region knowledge of the kosnarite phase existence and peculiarities of their phase formation in the A{sub 1-x}A'{sub x}M{sub 2}(PO{sub 4}){sub 3} (M=Ti, Zr, Hf) systems allow us to choose phosphate matrice compositions suitable for solidification of reprocessing wastes of spent U-Pu nuclear fuels.

36 MATERIALS SCIENCE↗
DOE OSTI2012

K{sub 2}NaOsO{sub 5.5} and K{sub 3}NaOs{sub 2}O{sub 9}: The first osmium perovskites containing alkali cations at the 'A' site

K{sub 2}NaOsO{sub 5.5} and K{sub 3}NaOs{sub 2}O{sub 9} were obtained from solid-state reactions of potassium superoxide, sodium peroxide and osmium metal at elevated oxygen pressures. K{sub 2}NaOsO{sub 5.5} crystallizes as an oxygen-deficient cubic double perovskite in space group Fm3{sup Macron }m with a=8.4184(5) A and contains isolated OsO{sub 6} octahedra. K{sub 3}NaOs{sub 2}O{sub 9} crystallizes hexagonally in P6{sub 3}/mmc with a=5.9998(4) A and c=14.3053(14) A. K{sub 3}NaOs{sub 2}O{sub 9} consists of face sharing Os{sub 2}O{sub 9} pairs of octahedra. According to magnetic measurements K{sub 2}NaOsO{sub 5.5} is diamagnetic, whereas K{sub 3}NaOs{sub 2}O{sub 9} displays strong antiferromagnetic coupling (T{sub N}=140 K), indicating enhanced magnetic interactions within the octahedral pair. - Graphical abstract: High oxidation states of Os, obtained by high oxygen pressure synthesis, are accommodated in double and triple perovskite matrices. K{sub 3}NaOs{sub 2}O{sub 9} displays enhanced magnetic interactions. Highlights: Black-Right-Pointing-Pointer New osmates containing highly oxidized Os were obtained by high O{sub 2} pressure synthesis. Black-Right-Pointing-Pointer High oxidation states of Os are accommodated in double and triple perovskite matrices. Black-Right-Pointing-Pointer Both compounds represent the first Os perovskites with an alkali metal at the A site. Black-Right-Pointing-Pointer K{sub 3}NaOs{sub 2}O{sub 9} displays enhanced magnetic interactions within the octahedral pair.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Microstructural evolution of P92 ferritic/martensitic steel under argon ion irradiation

Microstructural evolution of P92 ferritic/martensitic steel irradiated by Ar{sup +} ion beams at doses from 0.6 to 230 displacements per atom (dpa) at room temperature was investigated with conventional transmission electron microscope technique. Selected-area electron diffraction combined with bright-field and dark-field contrast image indicated that carbide/matrix interfaces were more easily damaged. The carbide peripheries became partly amorphous at irradiation dose of 2.3 dpa and were almost complete amorphous at the dose of 11.5 dpa. The small carbides would re-precipitate in matrices at 34.5 dpa. Energy dispersive X-ray analysis revealed that segregation of Cr and W and depletion of Fe in carbides occurred under irradiation. With the irradiation dose increasing, the irradiation induced segregation and depletion became more severe, which would influence mechanical properties of the steel. - Research Highlights: {yields} Carbide/matrix interfaces in P92 ferritic/martensitic steel were easily damaged. {yields} Small carbides re-precipitated in matrices after higher dose irradiation. {yields} Segregation of Cr and W and depletion of Fe in carbides occurred after irradiation.

36 MATERIALS SCIENCE↗