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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Recent Advances toward Efficient Calculation of Higher Nuclear Derivatives in Quantum Chemistry

In this article, we provide an overview of state-of-the-art techniques that are being developed for efficient calculation of second and higher nuclear derivatives of quantum mechanical (QM) energy. Calculations of nuclear Hessians and anharmonic terms incur high costs and memory and scale poorly with system size. Three emerging classes of methods—machine learning (ML), automatic differentiation (AD), and matrix completion (MC)—have demonstrated promise in overcoming these challenges. We illustrate studies that employ unsupervised ML methods to reduce the need for multiple Hessian calculations in dynamics simulations and those that utilize supervised ML to construct approximate potential energy surfaces and estimate Hessians and anharmonic terms at reduced cost. By extension, if electronic structure operations could be written in a manner similar to functions underlying ML methods, rapid differentiation or AD routines can be employed to inexpensively calculate higher arbitrary-order derivatives. While ML approaches are typically black-box, we describe methods such as compressed sensing (CS) and MC, which explicitly leverage problem-specific mathematical properties of higher derivatives such as sparsity and low-rank, to complete higher derivative information using only a small, incomplete sample. The three classes of methods facilitate reliable predictions of observables ranging from infrared spectra to thermal conductivity and constitute a promising way forward in accurately capturing otherwise intractable higher-order responses of QM energy to nuclear perturbations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗
DOE OSTI2021

Locating Seismic Events with Local-Distance Data

As the seismic monitoring community advances toward detecting, identifying, and locating ever-smaller natural and anthropogenic events, the need is constantly increasing for higher resolution, higher fidelity data, models, and methods for accurately characterizing events. Local-distance seismic data provide robust constraints on event locations, but also introduce complexity due to the significant geologic heterogeneity of the Earth’s crust and upper mantle, and the relative sparsity of data that often occurs with small events recorded on regional seismic networks. Identifying the critical characteristics for improving local-scale event locations and the factors that impact location accuracy and reliability is an ongoing challenge for the seismic community. Using Utah as a test case, we examine three data sets of varying duration, finesse, and magnitude to investigate the effects of local earth structure and modeling parameters on local-distance event location precision and accuracy. We observe that the most critical elements controlling relocation precision are azimuthal coverage and local-scale velocity structure, with tradeoffs based on event depth, type, location, and range.

42 ENGINEERING↗
DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Dark Energy Survey Year 3 results: Curved-sky weak lensing mass map reconstruction

ABSTRACT We present reconstructed convergence maps, mass maps, from the Dark Energy Survey (DES) third year (Y3) weak gravitational lensing data set. The mass maps are weighted projections of the density field (primarily dark matter) in the foreground of the observed galaxies. We use four reconstruction methods, each is a maximum a posteriori estimate with a different model for the prior probability of the map: Kaiser–Squires, null B-mode prior, Gaussian prior, and a sparsity prior. All methods are implemented on the celestial sphere to accommodate the large sky coverage of the DES Y3 data. We compare the methods using realistic ΛCDM simulations with mock data that are closely matched to the DES Y3 data. We quantify the performance of the methods at the map level and then apply the reconstruction methods to the DES Y3 data, performing tests for systematic error effects. The maps are compared with optical foreground cosmic-web structures and are used to evaluate the lensing signal from cosmic-void profiles. The recovered dark matter map covers the largest sky fraction of any galaxy weak lensing map to date.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Near-zero photon bioimaging by fusing deep learning and ultralow-light microscopy

Enhancing the reliability and reproducibility of optical microscopy by reducing specimen irradiance continues to be an important biotechnology target. As irradiance levels are reduced, however, the particle nature of light is heightened, giving rise to Poisson noise, or photon sparsity that restricts only a few (0.5%) image pixels to comprise a photon. Photon sparsity can be addressed by collecting approximately 200 photons per pixel; this, however, requires long acquisitions and, as such, suboptimal imaging rates. Here, we introduce near-zero photon bioimaging, a method that operates at kHz rates and 10,000-fold lower irradiance than standard microscopy. To achieve this level of performance, we uniquely combined a judiciously designed epifluorescence microscope enabling ultralow background levels and AI that learns to reconstruct biological images from as low as 0.01 photons per pixel. We demonstrate that near-zero photon bioimaging captures the structure of multicellular and subcellular features with high fidelity, including features represented by nearly zero photons. Beyond optical microscopy, the near-zero photon bioimaging paradigm can be applied in remote sensing, covert applications, and biomedical imaging that utilize damaging or quantum light.

AI↗
DOE OSTI2024

Diffusion model approach to simulating electron-proton scattering events

Generative artificial intelligence is a fast-growing area of research offering various avenues for exploration in high-energy nuclear physics. In this work, we explore the use of generative models for simulating electron-proton collisions relevant to experiments like the Continuous Electron Beam Accelerator Facility and the future Electron-Ion Collider (EIC). These experiments play a critical role in advancing our understanding of nucleons and nuclei in terms of quark and gluon degrees of freedom. The use of generative models for simulating collider events faces several challenges such as the sparsity of the data, the presence of global or eventwide constraints, and steeply falling particle distributions. In this work, we focus on the implementation of diffusion models for the simulation of electron-proton scattering events at EIC energies. Our results demonstrate that diffusion models can reproduce relevant observables such as momentum distributions and correlations of particles, momentum sum rules, and the leading electron kinematics, all of which are of particular interest in electron-proton collisions. Although the sampling process is relatively slow compared to other machine-learning architectures, we find diffusion models can generate high-quality samples. We foresee various applications of our work including inference for nuclear structure, interpretable generative machine learning, and searches of physics beyond the Standard Model. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Observed Relationships Between Cloud Droplet Effective Radius and Biogenic Gas Concentrations in Summertime Marine Stratocumulus Over the Eastern North Atlantic

Abstract Biogenic gases are a prominent component of the summertime marine boundary layer (MBL) over the Eastern North Atlantic. One of these gases, dimethyl sulfide (DMS), can produce sulfate cloud condensation nuclei (CCN) that, in theory, can brighten clouds through photolysis, and produces a reaction product, methane sulfonic acid (MSA). It is also possible that DMS can interact with sea‐salt or other marine aerosols changing their CCN activation spectrum, which could also modify cloud microphysical structure. Data collected aboard the G1 aircraft during the Aerosol Cloud Experiment Eastern North Atlantic (ACE‐ENA) in well‐mixed and decoupled marine boundary layers (MBLs) were used to examine relationships between the cloud droplet effective radii, , and the concentrations of DMS and MSA in constant cloud liquid water content (LWC) bins. A weak but statistically significant negative correlation was observed between CCN concentration and in most LWC bins, regardless of the source of the CCN, while a weak but statistically significant positive correlation between and DMS was observed. No correlation between the cloud droplet number concentration and DMS was found. The presence of MSA indicated that DMS‐to‐sulfate photolysis was likely occurring, but data sparsity prevented a statistically significant conclusion regarding the relationship between MSA and . Data sparsity in decoupled conditions also prevented statistically significant conclusions. To properly address biogenic gas impacts on cloud microphysics, it is recommended that aircraft data be supplemented by long‐term biogenic gas measurements at the surface in marine locations with appropriate remote and in‐situ cloud sensing capabilities, and the analysis limited to well‐mixed MBL's.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Reinforcement Learning Configuration Interaction

Selected configuration interaction (sCI) methods exploit the sparsity of the full configuration interaction (FCI) wave function, yielding significant computational savings and wave function compression without sacrificing the accuracy. Despite recent advances in sCI methods, the selection of important determinants remains an open problem. Furthermore, we explore the possibility of utilizing reinforcement learning approaches to solve the sCI problem. By mapping the configuration interaction problem onto a sequential decision-making process, the agent learns on-the-fly which determinants to include and which to ignore, yielding a compressed wave function at near-FCI accuracy. This method, which we call reinforcement-learned configuration interaction, adds another weapon to the sCI arsenal and highlights how reinforcement learning approaches can potentially help solve challenging problems in electronic structure theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Bit-GraphBLAS: Bit-Level Optimizations of Matrix-Centric Graph Processing on GPU

In the graph data structure like adjacency matrix, the connectivity of two nodes can be sufficiently represented using only 1 bit, but they are generally treated as 32-bit full-precision in state-of-the-art graph frameworks to adopt common sparse format such as CSR. Meanwhile, bit-level parallelism has recently be explored to have high-performance potential and low storage requirement on GPUs with dense bit-tiles. To fill the gap, our solution is a hierarchical storage format that contains the bit-indexing base and dense bit-tile units. Inherently, the granularity of the bit-tile is an essential factor in achieving both storage compression and GPU parallelism. How to find a sweet spot that trades off between avoiding sparsity and exploiting is comprehensively researched in this work. In the experiment, we evaluate the proposed storage format and algorithms on modern generation GPUs, including Pascal and Volta, to figure out critical software co-designs in conjunction with existing hardware-specific optimization.

Chen, Jou-An↗
DOE OSTI2024

Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units

Atomic structure prediction and associated property calculations are the bedrock of chemical physics. Since high-fidelity ab initio modeling techniques for computing the structure and properties can be prohibitively expensive, this motivates the development of machine-learning (ML) models that make these predictions more efficiently. Training graph neural networks over large atomistic databases introduces unique computational challenges such as the need to process millions of small graphs with variable size and support communication patterns that are distinct from learning over large graphs such as social networks. We demonstrate a novel hardware-software co-design approach to scale up the training of atomistic graph neural networks (GNN) for structure and property prediction. First, to eliminate redundant computation and memory associated with alternative padding techniques and to improve throughput via minimizing communication, we formulate the effective coalescing of the batches of variable-size atomistic graphs as the bin packing problem and introduce a hardware-agnostic algorithm to pack these batches. In addition, we propose hardware-specific optimizations including a planner and vectorization for the gather-scatter operations targeted for Graphcore’s Intelligence Processing Unit (IPU), as well as model-specific optimizations such as merged communication collectives and optimized softplus. Putting these all together, we demonstrate the effectiveness of the proposed co-design approach by providing an implementation of a well-established atomistic GNN on the Graphcore IPUs. We evaluate the training performance on multiple atomistic graph databases with varying degrees of graph counts, sizes and sparsity. Here, we demonstrate that such a co-design approach can reduce the training time of atomistic GNNs and can improve the performance by up to 1.5× compared to the baseline implementation of the model on the IPUs. Additionally, we compare our IPU implementation with a Nvidia GPU-based implementation and show that our atomistic GNN implementation on the IPUs can run 1.8× faster on average compared to the execution time on the GPUs.

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

Sparse regression for plasma physics

Many scientific problems can be formulated as sparse regression, i.e., regression onto a set of parameters when there is a desire or expectation that some of the parameters are exactly zero or do not substantially contribute. This includes many problems in signal and image processing, system identification, optimization, and parameter estimation methods such as Gaussian process regression. Sparsity facilitates exploring high-dimensional spaces while finding parsimonious and interpretable solutions. In the present work, we illustrate some of the important ways in which sparse regression appears in plasma physics and point out recent contributions and remaining challenges to solving these problems in this field. Further, a brief review is provided for the optimization problem and the state-of-the-art solvers, especially for constrained and high-dimensional sparse regression.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Enhanced Tensor Completion Based Approaches for State Estimation in Distribution Systems

Grid state estimation is essential for effective control and management of distribution systems. While weighted least squares has been the conventional method for state estimation, sparsity-aware methods have become popular due to their superior performance with limited data. Matrix completion and compressed sensing-based state estimation approaches exploit the underlying smoothness in the state variables. However, classic matrix completion methods do not take into account the temporal correlation of system states. Compressed sensing methods, on the other hand, require an appropriate choice of sparsifying basis that may not be easy to identify. This paper proposes a blocktensor completion based framework which uses an alternative approach to estimate voltage phasor, power injections and branch currents. This approach utilizes the temporal correlation of the system states in a tensor trace-norm minimization formulation with power flow equations as constraints. Herein, feature scaling is introduced in the problem formulation to benefit from the improved sensitivity of the tensor trace norm to the matrix columns in the scaled unfoldings of the tensor. Weighted tensor norm is utilized to exploit the structures of the different unfoldings of the state measurement tensor to improve the voltage estimation. The estimation accuracy is further improved by alternatively estimating the tensor columns and increasing the available data at each stage in the tensor completion process. The proposed methods are evaluated on the IEEE-33, 37 test systems and a 100- node test system. The proposed methods are shown to provide significant performance gains relative to the classic matrix and tensor completion based approaches.

24 POWER TRANSMISSION AND DISTRIBUTION↗