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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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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗
DOE OSTI2022

Group structure selection with random forests

Choosing an appropriate group structure for multigroup transport is far from an exact science. For some applications, one blindly uses a group structure developed years ago by forgotten methods. Furthermore, one sometimes uses the same group structure for a variety of problems, even if the group structure was originally developed with a certain application in mind. In this work, we create optimized group structures with simulated annealing for critical assembly test problems and apply a random forest regressor with bagging to choose the best group structure based on parameters of the different test problems. The optimized group structures were generated using a simulated annealing optimizer for several simple, spherical, and unreflected problems. The optimization was performed to minimize a cost function that included fission rate, absorption rate, leakage, and k{sub eff}. A random forest regressor was then trained on a set of International Criticality Safety Benchmark Evaluation Project inputs and used to select one of these six group structures. The trained machine learning model chose the best group structure 65% of the time, and one of the three best 89% of the time. Furthermore, it decreased the L2 error over all test problems by a factor of 25 when compared to the standard Los Alamos 70-group structure. In other words, the model chose group structure that were far more appropriate for the test problems than the traditional LANL group structure. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Serving Verifiable, Device-Independent Randomness to the Public

Device-independent random number generators can be certified unhackable simply by the impossibility of superluminal signaling. We demonstrate a novel protocol to transparently operationalize this security through a public randomness beacon service.

Kavuri, Gautam A.↗
DOE OSTI2022

Randomized probe imaging through deep k-learning

Randomized probe imaging (RPI) is a single-frame diffractive imaging method that uses highly randomized light to reconstruct the spatial features of a scattering object. The reconstruction process, known as phase retrieval, aims to recover a unique solution for the object without measuring the far-field phase information. Typically, reconstruction is done via time-consuming iterative algorithms. In this work, we propose a fast and efficient deep learning based method to reconstruct phase objects from RPI data. The method, which we call deep k-learning, applies the physical propagation operator to generate an approximation of the object as an input to the neural network. This way, the network no longer needs to parametrize the far-field diffraction physics, dramatically improving the results. Deep k-learning is shown to be computationally efficient and robust to Poisson noise. The advantages provided by our method may enable the analysis of far larger datasets in photon starved conditions, with important applications to the study of dynamic phenomena in physical science and biological engineering.

Guo, Zhen (ORCID:0000000213473451)↗
DOE OSTI2022

Random adaptive tool path for zonal optics fabrication

Deterministic optics fabrication using sub-aperture tools has been vital for manufacturing precision optical surfaces. The fabrication process requires the tool influence function and the tool path to calculate the dwell time that guides the tool to bring surface quality within tight design tolerances. Widely used spiral and raster paths may leave excess waviness from the tool path, and the unavoidable constant removal layer is added to obtain positive dwell time. This waviness can be removed by either using smaller tools sequentially or randomizing the tool path. However, the existing tool-path solutions can hardly adapt to different surface aperture shapes and localized surface errors. Process efficiency and accuracy are also not well considered in tool-path planning. We propose an innovative zonal Random Adaptive Path (RAP) to solve these problems in this study. Firstly, RAP can be flexibly adapted to different surface aperture shapes by introducing part boundary. Secondly, an average threshold strategy is used in the RAP planning to improve efficiency, enabling the surface errors to be selectively corrected. Finally, the threshold is performed in several passes within one processing cycle, each with its RAP, until the desired residual is achieved. The performance of the proposed RAP is studied by comparing it with the conventional tool paths. The results demonstrated that RAP takes the least processing time and achieves the best surface quality, which verifies the effectiveness of RAP in deterministic optics fabrication.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Single-shot imaging with randomized structured illumination at a free electron laser

Stroboscopic nanoscale imaging with free electron laser light is revolutionizing our understanding of fast dynamics in heterogeneous systems. The short wavelength of X-ray and extreme ultraviolet radiation makes it possible to achieve nanoscale resolution, while resonance with atomic transitions gives access to electronic and magnetic degrees of freedom. Here, we report on our implementation of a recently developed imaging method, randomized probe imaging, at a free electron laser. The advantage of randomized probe imaging over existing methods is its compatibility with extended and strongly scattering samples. Our implementation delivers robust single-shot reconstructions at up to a full-pitch resolution of 400 nm over a field of view with a 40 µm diameter. We also demonstrate single-shot imaging of magnetic domain structures using circular dichroism at resonance, paving the way to future time-resolved studies of magnetic dynamics, shock physics, and the dynamics of collective electronic phases.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Neuromorphic scaling advantages for energy-efficient random walk computations

Computing stands to be radically improved by neuromorphic computing (NMC) approaches inspired by the brain's incredible efficiency and capabilities. Most NMC research, which aims to replicate the brain's computational structure and architecture in man-made hardware, has focused on artificial intelligence; however, less explored is whether this brain-inspired hardware can provide value beyond cognitive tasks. We demonstrate that high-degree parallelism and configurability of spiking neuromorphic architectures makes them well-suited to implement random walks via discrete time Markov chains. Such random walks are useful in Monte Carlo methods, which represent a fundamental computational tool for solving a wide range of numerical computing tasks. Additionally, we show how the mathematical basis for a probabilistic solution involving a class of stochastic differential equations can leverage those simulations to provide solutions for a range of broadly applicable computational tasks. Despite being in an early development stage, we find that NMC platforms, at a sufficient scale, can drastically reduce the energy demands of high-performance computing platforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Transport in Stochastic Media with Random Chord Length Distributions

Thermal radiation transport computations in binary Markovian random mixtures rely almost exclusively on the Levermore-Pomraning (LP) model which is obtained by applying a heuristic closure to the ensemble averaged random medium transport equation. The validity of this model has been extensively tested by comparing numerical results over a broad parameter range (material types and mixing parameters) against benchmark solutions in planar geometry. The conditions under which the LP-model provides useful results and when it breaks down are now well established, but work to date has been largely restricted to homogeneous mixing statistics, i.e., the mean chord lengths of both materials are taken to be spatially constant. In recent work, this limitation was relaxed by allowing the mean chord lengths and, in a consistent fashion, the volume fractions in the LP-model to vary spatially and in a follow-up investigation benchmark solutions were obtained by ensemble averaging results over material realizations sampled from a nonhomogeneous Poisson process (NHPP). Numerical experiments in rod geometry with specifically linear and quadratic spatial dependence of chord lengths showed that the material averaged radiation intensities vary nonmonotonically with depth into the medium, in stark contrast to solutions obtained assuming uniform chord lengths. Moreover, depending on the local optical thickness and strength of scattering, the LP-model results showed locally more nuanced deviations from the benchmark solutions than was the case with constant chord lengths. These limited numerical investigations highlight the nontrivial qualitative and quantitative consequences of nonhomogeneous mixing statistics, in particular that closure approximations may not be uniformly valid or invalid over the problem domain.

42 ENGINEERING↗
DOE OSTI2024

Controlling radioisotope proportions when randomly sampling from Dirichlet distributions in PyRIID

As machine learning models for radioisotope quantification become more powerful, likewise the need for high-quality synthetic training data grows as well. For problem spaces that involve estimating the relative isotopic proportions of various sources in gamma spectra it is necessary to generate training data that accurately represents the variance of proportions encountered. In this report, we aim to provide guidance on how to target a desired variance of proportions which are randomly when using the PyRIID Seed Mixer, which samples from a Dirichlet distribution. We provide a method for properly parameterizing the Dirichlet distribution in order to maintain a constant variance across an arbitrary number of dimensions, where each dimension represents a distinct source template being mixed. We demonstrate that our method successfully parameterizes the Dirichlet distribution to target a specific variance of proportions, provided that several conditions are met. This allows us to follow a principled technique for controlling how random mixture proportions are generated which are then used downstream in the synthesis process to produce the final, noisy gamma spectra.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

A Contextually-Aware Sensitivity Analysis to Guide the Design of Randomized Least Squares Solvers in Applications

Our work on the DOE-sponsored project “A Contextually-Aware Sensitivity Analysis to Guide the Design of Randomized Least Squares Solvers in Applications,” was an effort to address critical challenges in nu merical computing and its applications to optimization. The increasing demand for robust and scalable solutions to large-scale linear algebra problems has highlighted the limitations of traditional approaches, particularly in heterogeneous and extreme-scale computing environments. Randomized Numerical Linear Algebra (RandNLA) offers a promising framework to address these challenges, and this proposal builds on this foundation by introducing innovations in sensitivity analysis and computational adaptability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Diabetes-specific formula with standard of care improves glycemic control, body composition, and cardiometabolic risk factors in overweight and obese adults with type 2 diabetes: results from a randomized controlled trial

Background and aims Medical nutrition therapy is important for diabetes management. This randomized controlled trial investigated the effects of a diabetes-specific formula (DSF) on glycemic control and cardiometabolic risk factors in adults with type 2 diabetes (T2D). Methods Participants ( n = 235) were randomized to either DSF with standard of care (SOC) (DSF group; n = 117) or SOC only (control group; n = 118). The DSF group consumed one or two DSF servings daily as meal replacement or partial meal replacement. The assessments were done at baseline, on day 45, and on day 90. Results There were significant reductions in glycated hemoglobin (−0.44% vs. –0.26%, p = 0.015, at day 45; −0.50% vs. −0.21%, p = 0.002, at day 90) and fasting blood glucose (−0.14 mmol/L vs. +0.32 mmol/L, p = 0.036, at day 90), as well as twofold greater weight loss (−1.30 kg vs. –0.61 kg, p < 0.001, at day 45; −1.74 kg vs. –0.76 kg, p < 0.001, at day 90) in the DSF group compared with the control group. The decrease in percent body fat and increase in percent fat-free mass at day 90 in the DSF group were almost twice that of the control group (1.44% vs. 0.79%, p = 0.047). In addition, the percent change in visceral adipose tissue at day 90 in the DSF group was several-fold lower than in the control group (−6.52% vs. –0.95%, p < 0.001). The DSF group also showed smaller waist and hip circumferences, and lower diastolic blood pressure than the control group (all overall p ≤ 0.045). Conclusion DSF with SOC yielded significantly greater improvements than only SOC in glycemic control, body composition, and cardiometabolic risk factors in adults with T2D.

Tey, Siew Ling↗
DOE OSTI2022

Effect of High-Protein Diets on Integrated Myofibrillar Protein Synthesis before Anterior Cruciate Ligament Reconstruction: A Randomized Controlled Pilot Study

Increasing dietary protein intake during periods of muscle disuse may mitigate the resulting decline in muscle protein synthesis (MPS). The purpose of this randomized pilot study was to determine the effect of increased protein intake during periods of disuse before anterior cruciate ligament (ACL) reconstruction on myofibrillar protein synthesis (MyoPS), and proteolytic and myogenic gene expression. Six healthy, young males (30 ± 9 y) were randomized to consume a high-quality, optimal protein diet (OP; 1.9 g·kg−1·d−1) or adequate protein diet (AP; 1.2 g·kg−1·d−1) for two weeks before ACL reconstruction. Muscle biopsies collected during surgery were used to measure integrated MyoPS during the intervention (via daily deuterium oxide ingestion) and gene expression at the time of surgery. MyoPS tended to be higher, with a large effect size in OP compared to AP (0.71 ± 0.1 and 0.54 ± 0.1%·d−1; p = 0.076; g = 1.56). Markers of proteolysis and myogenesis were not different between groups (p > 0.05); however, participants with greater MyoPS exhibited lower levels of MuRF1 gene expression compared to those with lower MyoPS (r = −0.82, p = 0.047). The data from this pilot study reveal a potential stimulatory effect of increased daily protein intake on MyoPS during injury-mediated disuse conditions that warrants further investigation.

Howard, Emily E. (ORCID:0000000179791236)↗
DOE OSTI2020

JWST Noise Floor. I. Random Error Sources in JWST NIRCam Time Series

James Webb Space Telescope (JWST) transmission and emission spectra will provide invaluable glimpses of transiting exoplanet atmospheres, including possible biosignatures. This promising science from JWST, however, will require exquisite precision and understanding of systematic errors that can impact the time series of planets crossing in front of and behind their host stars. Here, we provide estimates of the random noise sources affecting JWST Near-Infrared Camera (NIRCam) time-series data on the integration-to-integration level. We find that 1/f noise can limit the precision of grism time series for two groups (230–1000 ppm depending on the extraction method and extraction parameters), but will average down like the square root of N frames/reads. The current NIRCam grism time-series mode is especially affected by 1/f noise because its GRISMR dispersion direction is parallel to the detector fast-read direction, but could be alleviated in the GRISMC direction. Care should be taken to include as many frames as possible per visit to reduce this 1/f noise source: thus, we recommend the smallest detector subarray sizes one can tolerate, four output channels, and readout modes that minimize the number of skipped frames (RAPID or BRIGHT2). We also describe a covariance-weighting scheme that can significantly lower the contributions from 1/f noise as compared to sum extraction. We evaluate the noise introduced by pre-amplifier offsets, random telegraph noise, and high dark current resistor capacitor (RC) pixels and find that these are correctable below 10 ppm once background subtraction and pixel masking are performed. We explore systematic error sources in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Random Forests as a Viable Method to Select and Discover High-redshift Quasars

We present a method of selecting quasars up to redshift ≈6 with random forests, a supervised machine-learning method, applied to Pan-STARRS1 and WISE data. We find that, thanks to the increasing set of known quasars, we can assemble a training set that enables supervised machine-learning algorithms to become a competitive alternative to other methods up to this redshift. We present a candidate set for the redshift range 4.8–6.3, which includes the region around z = 5.5 where selecting quasars is difficult due to their photometric similarity to red and brown dwarfs. We demonstrate that, under our survey restrictions, we can reach a high completeness (66% ± 7% below redshift 5.6/83{sub -9}{sup +6}% above redshift 5.6) while maintaining a high selection efficiency (78{sub -8}{sup +10}%/94{sub -8}{sup +5}%). Our selection efficiency is estimated via a novel method based on the different distributions of quasars and contaminants on the sky. The final catalog of 515 candidates includes 225 known quasars. We predict the candidate catalog to contain additional 148{sub -33}{sup +41} new quasars below redshift 5.6 and 45{sub -8}{sup +5} above, and we make the catalog publicly available. Spectroscopic follow-up observations of 37 candidates led us to discover 20 new high redshift quasars (18 at 4.6 ≤ z ≤ 5.5, 2 z ~ 5.7). These observations are consistent with our predictions on efficiency. We argue that random forests can lead to higher completeness because our candidate set contains a number of objects that would be rejected by common color cuts, including one of the newly discovered redshift 5.7 quasars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Augmented Gaussian random field: Theory and computation

We propose the novel augmented Gaussian random field (AGRF), which is a universal framework incorporating the data of observable and derivatives of any order. Rigorous theory is established. We prove that under certain conditions, the observable and its derivatives of any order are governed by a single Gaussian random field, which is the aforementioned AGRF. As a corollary, the statement "the derivative of a Gaussian process remains a Gaussian process" is validated, since the derivative is represented by a part of the AGRF. Moreover, a computational method corresponding to the universal AGRF framework is constructed. Both noiseless and noisy scenarios are considered. Formulas of the posterior distributions are deduced in a nice closed form. A significant advantage of our computational method is that the universal AGRF framework provides a natural way to incorporate arbitrary order derivatives and deal with missing data. We use four numerical examples to demonstrate the effectiveness of the computational method. The numerical examples are composite function, damped harmonic oscillator, Korteweg-De Vries equation, and Burgers' equation.

Mathematics↗
DOE OSTI2025

A Cascaded Random Access Quantum Memory

Dynamic random access memory is critical to classical computing but notably absent in experimental quantum computers. Here we realize an 8-bit cascaded random access quantum memory using superconducting circuits and cavities and showcase the ability to perform arbitrary gate operations on it. In addition to individual error channels such as photon loss, quantum memories can also experience decoherence from many-body self-interaction. We characterize the origin and contributions of many-body infidelity throughout the memory cycle. We find that individual modes can be accessed with $\lesssim 1.5\%$ infidelity per mode and that the entire memory can be accessed in arbitrary order with an error rate below the depolarization threshold of the surface code, paving the way for fault-tolerant quantum memories.

Li, Ziqian [Stanford U., Appl. Phys. Dept.; Stanfo↗
DOE OSTI2021

Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement

Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed fractional Brownian motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR interference sequencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii. Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

79 ASTRONOMY AND ASTROPHYSICS↗