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Results for “Knowledge Discovery”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Ambient-pressure 151-K superconductivity in HgBa 2 Ca 2 Cu 3 O 8+δ via pressure quench

Superconductivity has been a vigorously researched topic since its discovery in 1911. Raising the superconducting transition temperature (T c ) has been the main driving force behind such long-sustained efforts due to its potential for impacting humanity and the fundamental knowledge gained from understanding this macroscopic coherent quantum state at high temperatures. The successful development of high-T c superconductivity will make possible extraordinarily efficient generation, delivery, and utilization of energy and could also enable the development of controlled fusion while impacting other burgeoning fields like quantum computation and quantum electronics. However, progress has been hindered by a longstanding plateau in the record ambient-pressure T c , unchanged since 1993. Subsequent significant advancements in T c have been achieved only under high pressures, preventing the realization of superconductivity’s full potential. To directly address this challenge, we developed a pressure-quench protocol (PQP) to stabilize pressure-induced/-enhanced superconducting states at ambient pressure. Here, we achieve a record ambient-pressure T c of 151 K in the cuprate HgBa 2 Ca 2 Cu 3 O 8+δ via PQP. The experimental results are further supported by synchrotron X-ray diffraction measurements and phonon and electronic structure calculations. This breakthrough opens avenues for stabilizing and exploring ambient-pressure high-T c superconducting states and other quantum states that have been previously only accessible under pressure, paving the way for deeper understanding and practical applications of high-T c superconductivity and beyond.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Predicting the synthesizability of crystalline inorganic materials from the data of known material compositions

Abstract Reliably identifying synthesizable inorganic crystalline materials is an unsolved challenge required for realizing autonomous materials discovery. In this work, we develop a deep learning synthesizability model ( SynthNN ) that leverages the entire space of synthesized inorganic chemical compositions. By reformulating material discovery as a synthesizability classification task, SynthNN identifies synthesizable materials with 7× higher precision than with DFT-calculated formation energies. In a head-to-head material discovery comparison against 20 expert material scientists, SynthNN outperforms all experts, achieves 1.5× higher precision and completes the task five orders of magnitude faster than the best human expert. Remarkably, without any prior chemical knowledge, our experiments indicate that SynthNN learns the chemical principles of charge-balancing, chemical family relationships and ionicity, and utilizes these principles to generate synthesizability predictions. The development of SynthNN will allow for synthesizability constraints to be seamlessly integrated into computational material screening workflows to increase their reliability for identifying synthetically accessible materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

UC LANL Postdoc Entrepreneur Fellowship Cohort Four

Three Laboratory postdoctoral researchers have been selected for this year's cohort of Entrepreneur Fellows. The six-month fellowship program - a joint initiative of the University of California and Los Alamos, now in its fourth year - supports early career scientists explore applications and evaluate market opportunities for their technologies. The Lab selects Entrepreneur Fellows based on the potential for their projects to have both scientific and commercial impact. The fellows receive six months of facilitated training and mentoring, as well as funding to engage in customer discovery, market exploration and technology advancement

36 MATERIALS SCIENCE↗
DOE OSTI2020

Physically Interpretable Neural Networks for the Geosciences: Applications to Earth System Variability

Abstract Neural networks have become increasingly prevalent within the geosciences, although a common limitation of their usage has been a lack of methods to interpret what the networks learn and how they make decisions. As such, neural networks have often been used within the geosciences to most accurately identify a desired output given a set of inputs, with the interpretation of what the network learns used as a secondary metric to ensure the network is making the right decision for the right reason. Neural network interpretation techniques have become more advanced in recent years, however, and we therefore propose that the ultimate objective of using a neural network can also be the interpretation of what the network has learned rather than the output itself. We show that the interpretation of neural networks can enable the discovery of scientifically meaningful connections within geoscientific data. In particular, we use two methods for neural network interpretation called backward optimization and layerwise relevance propagation, both of which project the decision pathways of a network back onto the original input dimensions. To the best of our knowledge, LRP has not yet been applied to geoscientific research, and we believe it has great potential in this area. We show how these interpretation techniques can be used to reliably infer scientifically meaningful information from neural networks by applying them to common climate patterns. These results suggest that combining interpretable neural networks with novel scientific hypotheses will open the door to many new avenues in neural network‐related geoscience research.

58 GEOSCIENCES↗
DOE OSTI2021

Automating Discovery of Physics-Informed Neural State Space Models via Learning and Evolution

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

genetic algorithms, neural architecture search, ne↗
DOE OSTI2025

Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement

Abstract Wild emmer wheat (Triticum turgidumsubsp.dicoccoides) is the tetraploid progenitor of hexaploid bread wheat (Triticum aestivumL.) and is known to be a valuable source of genetic variation for wheat improvement. However, direct evaluation of wild emmer diversity for agronomic potential has limited value unless performed in the backgrounds of adapted cultivars. Here, we present a genetic characterization of a population of 1601 backcross recombinant inbred lines, with an average genome composition of 75% bread wheat and 25% wild emmer. Low‐coverage whole‐genome sequencing allowed introgressions and aneuploidies to be identified at a relatively low cost per sample. We identified a relatively large proportion of small introgressions (median length 38 Mb), and we found introgressions to be distributed across all chromosomes. Approximately 44% of genotyped progeny carried at least one aneuploidy, with monosomies being by far the most common. This population, which we have denoted as the Great Plains Wild Emmer/Hard Winter Wheat introgression population (GPWEW‐IP), is, to our knowledge, the first introgression population developed through the direct hybridization of wild emmer wheat and US‐adapted hard winter wheat. We believe that this population represents a valuable resource for wheat breeders and will accelerate the discovery and integration of useful variation from wild emmer wheat.

Genetics & Heredity↗
DOE OSTI2024

Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost–benefit oriented decision-making

Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence—from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology—a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease

Rare disease diagnostics and disease gene discovery have been revolutionized by whole-exome and genome sequencing but identifying the causative variant(s) from the millions in each individual remains challenging. The use of deep phenotyping of patients and reference genotype-phenotype knowledge, alongside variant data such as allele frequency, segregation, and predicted pathogenicity, has proved an effective strategy to tackle this issue. Here we review the numerous tools that have been developed to automate this approach and demonstrate the power of such an approach on several thousand diagnosed cases from the 100,000 Genomes Project. Finally, we discuss the challenges that need to be overcome if we are going to improve detection rates and help the majority of patients that still remain without a molecular diagnosis after state-of-the-art genomic interpretation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Secure Collaborative Environment for Seamless Sharing of Scientific Knowledge

In a secure collaborative environment, tera-bytes of data generated from powerful scientific instruments are used to train secure machine learning (ML) models on exascale computing systems, which are then securely shared with internal or external collaborators as cloud-based services. Devising such a secure platform is necessary for seamless scientific knowledge sharing without compromising individual, or institute-level, intellectual property and privacy details. By enabling new computing opportunities with sensitive data, we envision a secure collaborative environment that will play a significant role in accelerating scientific discovery. Several recent technological advancements have made it possible to realize these capabilities. In this paper, we present our efforts at ORNL toward developing a secure computation platform. We present a use case where scientific data generated from complex instruments, like those at the Spallation Neutron Source (SNS), are used to train a differential privacy enabled deep learning (DL) network on Summit, which is then hosted as a secure multi-party computation (MPC) service on ORNL’s Compute and Data Environment for Science (CADES) cloud computing platform for third-party inference. In this feasibility study, we discuss the challenges involved, elaborate on leveraged technologies, analyze relevant performance results and present the future vision of our work to establish secure collaboration capabilities within and outside of ORNL.

Yoginath, Srikanth↗
DOE OSTI2020

Science-Driven Data Management for Multi-Tiered Storage (Final Report)

Scientific discovery at the exascale will not be possible without significant new research in the management, storage and retrieval over the long lifespan of the extreme amounts of data that will be produced. Our thesis is that adding application level knowledge about data to guide the actions of the storage system provides substantial benefits to the organization, storage, and access to extreme scale data, resulting in improved productivity for computational science. In this project we will demonstrate novel techniques to facilitate efficient mapping of data objects, even partitioning individual variables, from the user space onto multiple storage tiers, and enable application-guided data reductions and transformations to address capacity and bandwidth bottlenecks. Our goal is to address the associated Input/ Output (I/O) and storage challenges in the context of current and emerging storage landscapes, and expedite insights into mission critical scientific processes.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Unraveling Emergent Quantum States in Magnetic Topological Insulators using High Pressure Neutron Scattering

This proposal aims to uncover novel quantum phenomena under high pressure and understand the pressure effects on the atomic electronic interactions in magnetic topological materials. This program supports a combined neutron scattering and materials discovery of novel magnetic materials that display the coexistence of magnetism plus other physical phenomena such as a non-trivial electronic band topology under high pressure. The goal of this project is to close a long-standing knowledge gap in quantum materials research by developing a high-pressure neutron scattering (HP-NS) toolbox to systematically determine the magnetic structures and electronic interactions present at high pressure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

The Industry's Long-term, Yet Near-term, Issues: The Need for Radiation Protection Professionals - 20266

Since the discovery of X-rays and radioactivity, the civil use of nuclear technology has thrived for more than a half-century and has matured to be safer and more efficient. A balance between radiological and non-radiological knowledge and experience has been gained and retained through the years. Nevertheless, a slowly developing gap has emerged during the past few decades. National and international data show a declining trend in the existence of health physics programs and associated enrollment and training, which directly impact the pipeline of radiation professionals (i.e., educators, technicians, researchers, and regulators). This decline can be attributed to many factors including the lack of scientific inquisitiveness, declining funding, and the perception that existing protocols are sufficiently protective. Decommissioning and dismantling nuclear facilities is a complex and multi-phased process that generates large quantities of various levels of radioactive waste. With multiple facilities reaching their end of operational life, and others being shut down for economic reasons, the current pipeline for radiation protection experts cannot meet the future's need. Consequently, international organizations have proposed a variety of programs to transfer knowledge of radiation protection principles and practice. While many change-oriented efforts to counteract this trend aim to promote mobility, this is just a partial solution to the actual issue: long-term availability. This paper suggests multidisciplinary collaborations with modern technologies as a path forward to educate young professionals on the diversity of radiation-related applications to retain expert knowledge and foster innovation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

SANE: strategic autonomous non-smooth exploration for multiple optima discovery in multi-modal and non-differentiable black-box functions

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and multimodal parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, material structure image spaces, and molecular embedding spaces. Often these systems are black-boxes and time-consuming to evaluate, which resulted in strong interest towards active learning methods such as Bayesian optimization (BO). However, these systems are often noisy which make the black box function severely multi-modal and non-differentiable, where a vanilla BO can get overly focused near a single or faux optimum, deviating from the broader goal of scientific discovery. To address these limitations, here we developed Strategic Autonomous Non-Smooth Exploration (SANE) to facilitate an intelligent Bayesian optimized navigation with a proposed cost-driven probabilistic acquisition function to find multiple global and local optimal regions, avoiding the tendency to becoming trapped in a single optimum. To distinguish between a true and false optimal region due to noisy experimental measurements, a human (domain) knowledge driven dynamic surrogate gate is integrated with SANE. We implemented the gate-SANE into pre-acquired piezoresponse spectroscopy data of a ferroelectric combinatorial library with high noise levels in specific regions, and piezoresponse force microscopy (PFM) hyperspectral data. SANE demonstrated better performance than classical BO to facilitate the exploration of multiple optimal regions and thereby prioritized learning with higher coverage of scientific values in autonomous experiments. Our work showcases the potential application of this method to real-world experiments, where such combined strategic and human intervening approaches can be critical to unlocking new discoveries in autonomous research.

Biswas, Arpan [University of Tennessee, Knoxville,↗
DOE OSTI2021

DOE Energy Frontier Research Centers Center for Direct Catalytic Conversion of Biomass to Biofuels (C3Bio)

New capabilities to predict, design and control the chemistries of carbon could answer a global imperative to transition from fossil-based to sustainable transportation fuels. While the use of inexpensive hydrocarbons has been an unparalleled achievement and enabler of economic prosperity for many nations, singular dependence upon crude oil has given rise to systemic vulnerabilities in climate, energy, economic, and national security. Lignocellulosic biomass, a renewable and carbon-neutral resource, has the potential to displace an estimated annual equivalent of three billion barrels of oil in the U.S. alone (National Research Council 2009, U. S. Department of Energy, 2011). However, biomass has only one-third the energy density of crude oil (Agrawal and Singh 2009, Richard 2010) and lacks petroleum’s versatility as a feedstock for fuels and chemicals. These limitations keep biomass conversion below the efficiency level needed for strategic impact while the scientific challenge of routing carbon from one molecular context to another remains unmet. In 2009, the Center for Direct Catalytic Conversion of Biomass to Biofuels (C3Bio) recognized the potential of chemical catalysis and fast pyrolysis to overcome such limitations by transforming the main components of biomass (cellulose, xylan, and lignin) from grasses and trees directly to liquid hydrocarbons and aromatic co-products. Enabled by the EFRC high-risk, high-reward approach to grand challenge science, C3Bio researchers have been key national players in disrupting the conventional paradigm of the cellulosic biorefinery into a new future of “no carbon left behind”—the full utilization of carbon from plant cell walls in energy-dense fuels (Fig. 1). We identified catalytic and fast-pyrolytic pathways that utilize cellulose, xylan and, most significantly, lignin. We developed catalytic processes that deoxygenate and transform monomers and isolated polymers into useful products and tested their use with intact biomass. We gained control of lignin synthesis within plants and initiated tailoring biomass to its end-use through the tools of plant molecular biology and genetic engineering. C3Bio breakthroughs have increased the energy density of biomass-derived substrates via catalytic and pyrolytic conversions into products such as benzoquinones, furfural and hydroxymethylfurfural, levoglucosan and levulinic acid, methoxypropylphenols and propylbenzene. Such advances in biomass conversion would not have been possible without simultaneous advances in analytical instrumentation and methodologies, and imaging technologies and applications. The legacy science developed by C3Bio enables design and control strategies for achieving a targeted product portfolio of fuel and chemical feedstocks from a diverse range of native and tailored biomass. Our research provides the knowledge base required for a bio-economy with product streams as diverse in functionality as those of the petrochemical industry. Coupling targeted computational modeling with experimentation, we achieved: (1) fundamental understanding of biopolymers and cell wall architecture assembly, (2) discovery of new chemistries that allow the development of highly selective pathways to fuels and desirable chemicals, and (3) an integrated systems-level understanding to control catalytic and pyrolytic pathways.

09 BIOMASS FUELS↗