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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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27 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Nuclear Theory from First Principles to Forefront Experiments (Final Report for DE-SC0018638)

The Lee research group is a part of the Nuclear Lattice Effective Field Theory Collaboration, which has developed and performed ab initio lattice simulations of nuclear structure, scattering, reactions, and many-body systems. The other senior members of the collaboration include Ulf-G. Meißner at Bonn/Julich, Evgeny Epelbaum and Hermann Krebs at Bochum, Timo Lahde and Thomas Luu at Julich, and Gautam Rupak at Mississippi State. Our letter “Ab initio alpha-alpha scattering” was featured in a Nature News and Views article. Another letter “Nuclear binding near a quantum phase transition” was highlighted in a Viewpoint article in the online APS journal Physics as well as a news article in the IOP publication Physics World (September 21, 2016). Our letter “Eigenvector continuation with subspace learning” was also highlighted a Synopsis article in Physics. There are many promising ab initio approaches being used to calculate the properties of few-and many-nucleon systems. This includes the no-core shell model, symmetry-adapted no-core shell model quantum Monte Carlo, auxiliary-field diffusion Monte Carlo, self-consistent Green’s functions, many-body perturbation theory, in-medium similarity renormalization group, and coupled cluster methods. Lattice effective field theory is another ab initio approach which combines the framework of effective field theory with lattice Monte Carlo methods to allow favorable scaling from few- to many-body systems. Perhaps the most important aspect of lattice effective field theory is that its strengths and weaknesses are orthogonal to that of other ab initio methods. For example, lattice effective field theory has little difficulty in probing cluster structures and collectivity, while such features are much more difficult using other methods. Furthermore it can be used to compute superfluid condensate fractions as well as the phase diagram of strongly matter and the density and temperature dependence of clustering. Lattice effective field theory was first used in simulations of infinite nuclear matter and infinite neutron matter with pions and without pions. In addition to the efforts by our collaboration, there have been recent efforts by other groups as well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

N 5 -Scaling Excited-State-Specific Perturbation Theory

In this paper, we show that by working in a basis similar to that of the natural transition orbitals and using a modified zeroth-order Hamiltonian, the cost of a recently introduced perturbative correction to excited-state mean field theory can be reduced from seventh to fifth order in the system size. The (occupied) 2 (virtual) 3 asymptotic scaling matches that of ground-state second-order Møller-Plesset theory but with a significantly higher prefactor because the bottleneck is iterative: it appears in the Krylov-subspace-based solution of the linear equation that yields the first-order wave function. Here, we discuss the details of the modified zeroth-order Hamiltonian we use to reduce the cost and the automatic code generation process we used to derive and verify the cost scaling of the different terms. Overall, we find that our modifications have little impact on the method's accuracy, which remains competitive with singles and doubles equation-of-motion coupled cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Quantum Filtering and Analysis of Multiplicities in Eigenvalue Spectra

Fine-grained spectral properties of quantum Hamiltonians, including both eigenvalues and their multiplicities, provide useful information for characterizing many-body quantum systems as well as for understanding phenomena such as topological order. Extracting such information with small additive error is #BQP-complete in the worst case. In this work, we introduce QFAMES (quantum filtering and analysis of multiplicities in eigenvalue spectra), a quantum algorithm that efficiently identifies clusters of closely spaced dominant eigenvalues and determines their multiplicities under physically motivated assumptions, which allows us to bypass worst-case complexity barriers. QFAMES also enables the estimation of observable expectation values within targeted energy clusters, providing a powerful tool for studying quantum phase transitions and other physical properties. We validate the effectiveness of QFAMES through numerical demonstrations, including its applications to characterizing quantum phases in the transverse-field Ising model and estimating the ground-state degeneracy of a topologically ordered phase in the two-dimensional toric code model. We also generalize QFAMES to the setting of mixed initial states. Our approach offers rigorous theoretical guarantees and significant advantages over existing subspace-based quantum spectral analysis methods, particularly in terms of the sample complexity and the ability to resolve degeneracies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A Shift Selection Strategy for Parallel Shift-invert Spectrum Slicing in Symmetric Self-consistent Eigenvalue Computation

The central importance of large-scale eigenvalue problems in scientific computation necessitates the development of massively parallel algorithms for their solution. Recent advances in dense numerical linear algebra have enabled the routine treatment of eigenvalue problems with dimensions on the order of hundreds of thousands on the world’s largest supercomputers. In cases where dense treatments are not feasible, Krylov subspace methods offer an attractive alternative due to the fact that they do not require storage of the problem matrices. However, demonstration of scalability of either of these classes of eigenvalue algorithms on computing architectures capable of expressing massive parallelism is non-trivial due to communication requirements and serial bottlenecks, respectively. In this work, we introduce the SISLICE method: a parallel shift-invert algorithm for the solution of the symmetric self-consistent field (SCF) eigenvalue problem. The SISLICE method drastically reduces the communication requirement of current parallel shift-invert eigenvalue algorithms through various shift selection and migration techniques based on density of states estimation and k-means clustering, respectively. This work demonstrates the robustness and parallel performance of the SISLICE method on a representative set of SCF eigenvalue problems and outlines research directions that will be explored in future work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Reduced-basis method for few-body bound-state emulation

Recent advances in both theoretical and computational methods have enabled large-scale, precision calculations of the properties of atomic nuclei. With the growing complexity of modern nuclear theory, however, also comes the need for novel methods to perform systematic studies and quantify the uncertainties of models when confronted with experimental data. Here, this study presents an application of such an approach, the reduced basis method, to substantially lower computational costs by constructing a significantly smaller Hamiltonian subspace informed by previous solutions. Our method shows comparable efficiency and accuracy to other dimensionality reduction techniques on an artificial three-body bound system while providing a richer representation of physical information in its projection and training subspace. This methodological advancement can be applied in other contexts and has the potential to greatly improve our ability to systematically explore theoretical models and thus enhance our understanding of the fundamental properties of nuclear systems.

cluster models↗
DOE OSTI2023

Local Excitations of a Charged Nitrogen Vacancy in Diamond with Multireference Density Matrix Embedding Theory

Here, we investigate the negatively charged nitrogen-vacancy center in diamond using periodic density matrix embedding theory (pDMET). To describe the strongly correlated excited states of this system, the complete active space self-consistent field (CASSCF) followed by n-electron valence state second-order perturbation theory (NEVPT2) was used as the impurity solver. Since the NEVPT2-DMET energies show a linear dependence on the inverse of the size of the embedding subspace, we performed an extrapolation of the excitation energies to the nonembedding limit using a linear regression. The extrapolated NEVPT2-DMET first triplet–triplet excitation energy is 2.31 eV and that for the optically inactive singlet–singlet transition is 1.02 eV, both in agreement with the experimentally observed vertical excitation energies of ∼2.18 eV and ∼1.26 eV, respectively. This is the first application of pDMET to a charged periodic system and the first investigation of the NV – defect using NEVPT2 for periodic supercell models.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A novel cosmic filament catalogue from SDSS data

Here, in this work, we present a new catalogue of cosmic filaments obtained from the latest Sloan Digital Sky Survey (SDSS) public data. In order to detect filaments, we implement a version of the Subspace-Constrained Mean-Shift algorithm that is boosted by machine learning techniques. This allows us to detect cosmic filaments as one-dimensional maxima in the galaxy density distribution. Our filament catalogue uses the cosmological sample of SDSS, including Data Release 16, and therefore inherits its sky footprint (aside from small border effects) and redshift coverage. In particular, this means that, taking advantage of the quasar sample, our filament reconstruction covers redshifts up to z = 2.2, making it one of the deepest filament reconstructions to our knowledge. We follow a tomographic approach and slice the galaxy data in 269 shells at different redshift. The reconstruction algorithm is applied to 2D spherical maps. The catalogue provides the position and uncertainty of each detection for each redshift slice. The quality of our detections, which we assess with several metrics, show improvement with respect to previous public catalogues obtained with similar methods. We also detect a highly significant correlation between our filament catalogue and galaxy cluster catalogues built from microwave observations of the Planck Satellite and the Atacama Cosmology Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A circuit-generated quantum subspace algorithm for the variational quantum eigensolver

Recent research has shown that wavefunction evolution in real and imaginary time can generate quantum subspaces with significant utility for obtaining accurate ground state energies. Inspired by these methods, we propose combining quantum subspace techniques with the variational quantum eigensolver (VQE). In our approach, the parameterized quantum circuit is divided into a series of smaller subcircuits. The sequential application of these subcircuits to an initial state generates a set of wavefunctions that we use as a quantum subspace to obtain high-accuracy groundstate energies. We call this technique the circuit subspace variational quantum eigensolver (CSVQE) algorithm. By benchmarking CSVQE on a range of quantum chemistry problems, we show that it can achieve significant error reduction in the best case compared to conventional VQE, particularly for poorly optimized circuits, greatly improving convergence rates. Furthermore, we demonstrate that when applied to circuits trapped at local minima, CSVQE can produce energies close to the global minimum of the energy landscape, making it a potentially powerful tool for diagnosing local minima.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗