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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 OSTI2026

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗
DOE OSTI2022

Improving Variational Autoencoders for New Physics Detection at the LHC With Normalizing Flows

We investigate how to improve new physics detection strategies exploiting variational autoencoders and normalizing flows for anomaly detection at the Large Hadron Collider. As a working example, we consider the DarkMachines challenge dataset. We show how different design choices (e.g., event representations, anomaly score definitions, network architectures) affect the result on specific benchmark new physics models. Once a baseline is established, we discuss how to improve the anomaly detection accuracy by exploiting normalizing flow layers in the latent space of the variational autoencoder.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1971

Delta modulation

The conclusions of the design research of the song adaptive delta modulator are presented for source encoding voice signals. The variation of output SNR vs input signal power/when 8, 9, and 10 bit internal arithmetic is employed. Voice intelligibility tapes to test the 10-bit system are used. An analysis of a delta modulator is also presented designed to minimize the in-band rms error. This is accomplished by frequency shaping the error signal in the modulator prior to hard limiting. The result is a significant increase in the output SNR measured after low pass filtering.

Schilling, D. L.↗
NASA NTRS1979

Improved reader for magnetically-encoded ID cards

Hybrid demodulator in electronic card reader for magnetically encoded identification cards, accommodates variations in insertion speeds, yet is simpler and less expensive than equivalent all-digital circuits.

Wu, T. T.↗
NASA NTRS2006

Improving Grasp Skills Using Schema Structured Learning

Abstract In the control-based approach to robotics, complex behavior is created by sequencing and combining control primitives. While it is desirable for the robot to autonomously learn the correct control sequence, searching through the large number of potential solutions can be time consuming. This paper constrains this search to variations of a generalized solution encoded in a framework known as an action schema. A new algorithm, SCHEMA STRUCTURED LEARNING, is proposed that repeatedly executes variations of the generalized solution in search of instantiations that satisfy action schema objectives. This approach is tested in a grasping task where Dexter, the UMass humanoid robot, learns which reaching and grasping controllers maximize the probability of grasp success.

Platt, Robert↗
DOE OSTI2024

An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity

Organelle-to-nucleus DNA transfer is an ongoing process playing an important role in the evolution of eukaryotic life. Here, genome-wide association studies (GWAS) of non-photochemical quenching parameters in 743 Populus trichocarpa accessions identified a nuclear-encoded genomic region associated with variation in photosynthesis under fluctuating light. The identified gene, BOOSTER (BSTR), comprises three exons, two with apparent endophytic origin and the third containing a large fragment of plastid-encoded Rubisco large subunit. Higher expression of BSTR facilitated anterograde signaling between nucleus and plastid, which corresponded to enhanced expression of Rubisco, increased photosynthesis, and up to 35% greater plant height and 88% biomass in poplar accessions under field conditions. Overexpression of BSTR in Populus tremula × P. alba achieved up to a 200% in plant height. Similarly, Arabidopsis plants heterologously expressing BSTR gained up to 200% in biomass and up to 50% increase in seed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantum Simulations of Fermionic Hamiltonians with Efficient Encoding and Ansatz Schemes

Here, we propose a computational protocol for quantum simulations of fermionic Hamiltonians on a quantum computer, enabling calculations on spin defect systems which were previously not feasible using conventional encodings and a unitary coupled-cluster ansatz of variational quantum eigensolvers. We combine a qubit-efficient encoding scheme mapping Slater determinants onto qubits with a modified qubitcoupled cluster ansatz and noise-mitigation techniques. Our strategy leads to a substantial improvement in the scaling of circuit gate counts and in the number of required qubits, and to a decrease in the number of required variational parameters, thus increasing the resilience to noise. We present results for spin defects of interest for quantum technologies, going beyond minimum models for the negatively charged nitrogen vacancy center in diamonds and the double vacancy in 4H silicon carbide (4H-SiC) and tackling a defect as complex as negatively charged silicon vacancy in 4H-SiC for the first time.

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

Prime factorization using quantum variational imaginary time evolution

The road to computing on quantum devices has been accelerated by the promises that come from using Shor’s algorithm to reduce the complexity of prime factorization. However, this promise hast not yet been realized due to noisy qubits and lack of robust error correction schemes. Here we explore a promising, alternative method for prime factorization that uses well-established techniques from variational imaginary time evolution. We create a Hamiltonian whose ground state encodes the solution to the problem and use variational techniques to evolve a state iteratively towards these prime factors. We show that the number of circuits evaluated in each iteration scales as \(O(n^{5}d)\) , where n is the bit-length of the number to be factorized and d is the depth of the circuit. We use a single layer of entangling gates to factorize 36 numbers represented using 7, 8, and 9-qubit Hamiltonians. We also verify the method’s performance by implementing it on the IBMQ Lima hardware to factorize 55, 65, 77 and 91 which are greater than the largest number (21) to have been factorized on IBMQ hardware.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Disentangling Coexisting Structural Order Through Phase Lock-In Analysis of Atomic-Resolution STEM Data

As a real-space technique, atomic-resolution STEM imaging contains both amplitude and geometric phase information about structural order in materials, with the latter encoding important information about local variations and heterogeneities present in crystalline lattices. Such phase information can be extracted using geometric phase analysis (GPA), a method which has generally focused on spatially mapping elastic strain. Here we demonstrate an alternative phase demodulation technique and its application to reveal complex structural phenomena in correlated quantum materials. As with other methods of image phase analysis, the phase lock-in approach can be implemented to extract detailed information about structural order and disorder, including dislocations and compound defects in crystals. Extending the application of this phase analysis to Fourier components that encode periodic modulations of the crystalline lattice, such as superlattice or secondary frequency peaks, we extract the behavior of multiple distinct order parameters within the same image, yielding insights into not only the crystalline heterogeneity but also subtle emergent order parameters such as antipolar displacements. When applied to atomic-resolution images spanning large (~0.5 × 0.5 μm 2 ) fields of view, this approach enables vivid visualizations of the spatial interplay between various structural orders in novel materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗
NASA NTRS1992

More Genetic Engineering With Cloned Hemoglobin Genes

Cells modified to enhance growth and production of proteins. Method for enhancing both growth of micro-organisms in vitro and production of various proteins or metalbolites in these micro-organisms provides for incorporation of selected chromosomal or extrachormosomal deoxyribonucleic acid (DNA) sequences into micro-organisms from other cells or from artificial sources. Incorporated DNA includes parts encoding desired product(s) or characteristic(s) of cells and parts that control expression of productor characteristic-encoding parts in response to variations in environment. Extended method enables increased research into growth of organisms in oxygen-poor environments. Industrial applications found in enhancement of processing steps requiring oxygen in fermentation, enzymatic degradation, treatment of wastes containing toxic chemicals, brewing, and some oxidative chemical reactions.

Bailey, James E.↗
NASA NTRS2007

Symbolic LTL Compilation for Model Checking: Extended Abstract

In Linear Temporal Logic (LTL) model checking, we check LTL formulas representing desired behaviors against a formal model of the system designed to exhibit these behaviors. To accomplish this task, the LTL formulas must be translated into automata [21]. We focus on LTL compilation by investigating LTL satisfiability checking via a reduction to model checking. Having shown that symbolic LTL compilation algorithms are superior to explicit automata construction algorithms for this task [16], we concentrate here on seeking a better symbolic algorithm.We present experimental data comparing algorithmic variations such as normal forms, encoding methods, and variable ordering and examine their effects on performance metrics including processing time and scalability. Safety critical systems, such as air traffic control, life support systems, hazardous environment controls, and automotive control systems, pervade our daily lives, yet testing and simulation alone cannot adequately verify their reliability [3]. Model checking is a promising approach to formal verification for safety critical systems which involves creating a formal mathematical model of the system and translating desired safety properties into a formal specification for this model. The complement of the specification is then checked against the system model. When the model does not satisfy the specification, model-checking tools accompany this negative answer with a counterexample, which points to an inconsistency between the system and the desired behaviors and aids debugging efforts.

Rozier, Kristin Y.↗
NASA NTRSDate not supplied

Image-to-Image Wildfire Detection via Quantum-Compatible Variational Segmentation from Remotely-sensed Data

Over the last decade, the incidence of wildfires has surged, causing widespread destruction globally. To better comprehend and manage these incidents, remote sensing and aerial missions have been implemented in recent efforts. However, this has resulted in an exponential rise in the amount of remote sensing data utilization, leading to a need for intelligent automation of data extraction in wildfire studies. Machine learning provides an accurate automated approach for detecting these natural anomalies and facilitates decision-makers to take prompt actions. To make insightful decisions in wildfire management, it is imperative to move beyond simple detection and explore the potential of probabilistic generative machine learning for creating "what-if" scenarios for various wildfire conditions. Such models offer improved representation of the stochastic nature of wildfire events. However, the optimization of these models can be computationally expensive, especially when using classical computers. Quantum computers have recently emerged as a promising solution to reduce the computational cost of training such models and improve their performance. In this study, we aim to utilize quantum-compatible machine learning techniques to implement our probabilistic generative approach. To that end, we propose a supervised probabilistic variational model consisting of a U-NET-based image-to-image component along with encoder and decoder networks which work as a variational autoencoder (VAE) component. Additionally, we explore the type of latent distribution type in the VAE component and implement different means for modeling the prior distribution. We further investigate the quantum-compatible versions of the model compared to the classical counterpart and benchmark potential benefits of quantum compatibility over the classical model.

quantum machine learning↗
DOE OSTI2022

Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks

Background Genome-wide Association Studies (GWAS) aims to uncover the link between genomic variation and phenotype. They have been actively applied in cancer biology to investigate associations between variations and cancer phenotypes, such as susceptibility to certain types of cancer and predisposed responsiveness to specific treatments. Since GWAS primarily focuses on finding associations between individual genomic variations and cancer phenotypes, there are limitations in understanding the mechanisms by which cancer phenotypes are cooperatively affected by more than one genomic variation. Results This paper proposes a network representation learning approach to learn associations among genomic variations using a prostate cancer cohort. The learned associations are encoded into representations that can be used to identify functional modules of genomic variations within genes associated with early- and late-onset prostate cancer. The proposed method was applied to a prostate cancer cohort provided by the Veterans Administration’s Million Veteran Program to identify candidates for functional modules associated with early-onset prostate cancer. The cohort included 33,159 prostate cancer patients, 3181 early-onset patients, and 29,978 late-onset patients. The reproducibility of the proposed approach clearly showed that the proposed approach can improve the model performance in terms of robustness. Conclusions To our knowledge, this is the first attempt to use a network representation learning approach to learn associations among genomic variations within genes. Associations learned in this way can lead to an understanding of the underlying mechanisms of how genomic variations cooperatively affect each cancer phenotype. This method can reveal unknown knowledge in the field of cancer biology and can be utilized to design more advanced cancer-targeted therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Three‐Dimensional Permeability Inversion Using Convolutional Neural Networks and Positron Emission Tomography

Abstract Quantification of heterogeneous multiscale permeability in geologic porous media is key for understanding and predicting flow and transport processes in the subsurface. Recent utilization of in situ imaging, specifically positron emission tomography (PET), enables the measurement of three‐dimensional (3‐D) time‐lapse radiotracer solute transport in geologic media. However, accurate and computationally efficient characterization of the permeability distribution that controls the solute transport process remains challenging. Leveraging the relationship between local permeability variation and solute advection behavior, an encoder‐decoder based convolutional neural network (CNN) is implemented as a permeability inversion scheme using a single PET scan of a radiotracer pulse injection experiment as input. The CNN can accurately capture the 3‐D spatial correlation between the permeability and the radiotracer solute arrival time difference maps in geologic cores. We first test the inversion accuracy using synthetic test datasets and then test the accuracy on a suite of experimental PET imaging datasets acquired on four different geologic cores. The network‐predicted permeability maps from the geologic cores are used to parameterize forward numerical models that are directly compared with the experimental PET imaging data. The results indicate that a single trained network can generate robust 3‐D permeability inversion maps in seconds. Numerical models parameterized with these permeability maps closely capture the experimentally observed solute arrival time behavior. This work provides an unprecedented approach for efficiently characterizing multiscale permeability heterogeneity in complex geologic samples.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Optimizing training trajectories in variational autoencoders via latent Bayesian optimization approach *

Unsupervised and semi-supervised ML methods such as variational autoencoders (VAE) have become widely adopted across multiple areas of physics, chemistry, and materials sciences due to their capability in disentangling representations and ability to find latent manifolds for classification and/or regression of complex experimental data. Like other ML problems, VAEs require hyperparameter tuning, e.g. balancing the Kullback–Leibler and reconstruction terms. However, the training process and resulting manifold topology and connectivity depend not only on hyperparameters, but also their evolution during training. Because of the inefficiency of exhaustive search in a high-dimensional hyperparameter space for the expensive-to-train models, here we have explored a latent Bayesian optimization (zBO) approach for the hyperparameter trajectory optimization for the unsupervised and semi-supervised ML and demonstrated for joint-VAE with rotational invariances. We have demonstrated an application of this method for finding joint discrete and continuous rotationally invariant representations for modified national institute of standards and technology database (MNIST) and experimental data of a plasmonic nanoparticles material system. The performance of the proposed approach has been discussed extensively, where it allows for any high dimensional hyperparameter trajectory optimization of other ML models.

42 ENGINEERING↗
DOE OSTI2024

Acoustic sensing and autoencoder approach for abnormal gas detection in a spent nuclear fuel canister mock-up

Currently, spent nuclear fuel (SNF) from commercial nuclear power plants is stored in stainless-steel canisters for interim dry storage. To provide an inert environment, these canisters are backfilled with helium after vacuum drying. However, the helium environment may be contaminated during extended storage because of the material degradation. For example, the heavier fission gas xenon may be released from the fuel rods into the canister cavity should the fuel cladding be breached. Other gases such as air and water vapor may also be present as a result of leakage caused by chloride-induced stress corrosion cracking on the canister walls or by insufficient vacuum drying. Therefore, monitoring the gas composition can provide critical information about the health of SNF canisters. In this study, noninvasive testing was conducted on a 2/3-scaled SNF canister mock-up using acoustic sensing. Ultrasonic transducers were placed on the exterior surface of the canister to probe the gas composition. A dataset was collected by sealing the canister mock-up and introducing up to 1.53% argon or 1.29% air into the helium background gas. Three methods were used to detect changes in the gas composition: the time-of-flight (TOF) method, the differential method, and the autoencoder method. Results showed that the TOF method had sufficient resolution to detect abnormal gas concentrations of less than 1.0%. The differential method demonstrated a periodic in-phase and out-of-phase behavior between the benchmark (i.e., pure helium) and abnormal (i.e., with argon or air) state signals. The variational autoencoder (VAE) and the Wasserstein autoencoder (WAE) were trained on the benchmark data and were applied directly to the abnormal state data. It was found that both the unsupervised VAE and the WAE were able to distinguish the benchmark and abnormal states of the canister mock-up based on the reconstruction error.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗