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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Surrogate construction via weight parameterization of residual neural networks

Surrogate model development is a critical step for uncertainty quantification or other sample-intensive tasks for complex computational models. Here, in this work, we develop a multi-output surrogate form using a class of neural networks (NNs) that employ shortcut connections, namely Residual NNs (ResNets). ResNets are known to regularize the surrogate learning problem and improve the efficiency and accuracy of the resulting surrogate. Inspired by the continuous, Neural ODE analogy, we augment ResNets with weight parameterization strategy with respect to ResNet depth. Weight-parameterized ResNets regularize the NN surrogate learning problem and allow better generalization with a drastically reduced number of learnable parameters. We demonstrate that weight-parameterized ResNets are more accurate and efficient than conventional feed-forward multi-layer perceptron networks. We also compare various options for parameterization of the weights as functions of ResNet depth. We demonstrate the results on both synthetic examples and a large scale earth system model of interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Time‐Lapse Image Classification Using a Diffractive Neural Network

Diffractive deep neural networks (D 2 NNs), comprised of spatially engineered passive surfaces, collectively process optical input information at the speed of light propagation through a thin diffractive volume, without any external computing power. Diffractive networks were demonstrated to achieve all‐optical object classification and perform universal linear transformations. Herein, a “time‐lapse” image classification scheme using a diffractive network is demonstrated for the first time, significantly advancing its classification accuracy and generalization performance on complex input objects by using the lateral movements of the input objects and/or the diffractive network, relative to each other. In a different context, such relative movements of the objects and/or the camera are routinely being used for image super‐resolution applications; inspired by their success, a time‐lapse diffractive network is designed to benefit from the complementary information content created by controlled or random lateral shifts. The design space and performance limits of time‐lapse diffractive networks are numerically explored, revealing a blind testing accuracy of 62.03% on the optical classification of objects from the CIFAR‐10 dataset. This constitutes the highest inference accuracy achieved so far using a single diffractive network on the CIFAR‐10 dataset. Time‐lapse diffractive networks will be broadly useful for the spatiotemporal analysis of input signals using all‐optical processors.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Wild Isolates of Neurospora crassa Reveal Three Conidiophore Architectural Phenotypes

The vegetative life cycle in the model filamentous fungus, Neurospora crassa, relies on the development of conidiophores to produce new spores. Environmental, temporal, and genetic components of conidiophore development have been well characterized; however, little is known about their morphological variation. We explored conidiophore architectural variation in a natural population using a wild population collection of 21 strains from Louisiana, United States of America (USA). Our work reveals three novel architectural phenotypes, Wild Type, Bulky, and Wrap, and shows their maintenance throughout the duration of conidiophore development. Furthermore, we present a novel image-classifier using a convolutional neural network specifically developed to assign conidiophore architectural phenotypes in a high-throughput manner. To estimate an inheritance model for this discrete complex trait, crosses between strains of each phenotype were conducted, and conidiophores of subsequent progeny were characterized using the trained classifier. Our model suggests that conidiophore architecture is controlled by at least two genes and has a heritability of 0.23. Additionally, we quantified the number of conidia produced by each conidiophore type and their dispersion distance, suggesting that conidiophore architectural phenotype may impact N. crassa colonization capacity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The trans-regulatory landscape of gene networks in plants

The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative transcriptional effector domains of over 400 Arabidopsis thaliana transcription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how our characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identifying Heterogeneous Micromechanical Properties of Biological Tissues via Physics–Informed Neural Networks

The heterogeneous micromechanical properties of biological tissues have profound implications across diverse medical and engineering domains. However, identifying full-field heterogeneous elastic properties of soft materials using traditional engineering approaches is fundamentally challenging due to difficulties in estimating local stress fields. Recently, there has been a growing interest in data-driven models for learning full-field mechanical responses, such as displacement and strain, from experimental or synthetic data. However, research studies on inferring full-field elastic properties of materials, a more challenging problem, are scarce, particularly for large deformation, hyperelastic materials. Here, a physics-informed machine learning approach is proposed to identify the elasticity map in nonlinear, large deformation hyperelastic materials. This study reports the prediction accuracies and computational efficiency of physics-informed neural networks (PINNs) in inferring the heterogeneous elasticity maps across materials with structural complexity that closely resemble real tissue microstructure, such as brain, tricuspid valve, and breast cancer tissues. Further, the improved architecture is applied to three hyperelastic constitutive models: Neo-Hookean, Mooney Rivlin, and Gent. Furthermore, the improved network architecture consistently produces accurate estimations of heterogeneous elasticity maps, even when there is up to 10% noise present in the training data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants

Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein–DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein–DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. Finally, this chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recent advances in ink-based additive manufacturing for porous structures

The use of porous structures is an ancient wisdom, people found its importance ever since we began to understand nature. The evolution of porous structure gives rise to multi-scale (combined nano-, micro-, and macro-) porous networks. Traditional manufacturing technologies have challenges in creating shape-complex and conformable porous structures for real-world applications. Additive manufacturing (AM) with the capability of assembling various materials with complex and customized architectures is rapidly developing. With the advancement of material development, the integration of AM and porous structure offers unparalleled and emerging opportunities for concept-to-design-to-fabrication of multi-scale porous networks, enabling the multi-functionalities of the 3D printed specimen and broadening its applications. In this work, we provide a comprehensive review of the state-of-the-art ink-based AM techniques for 3D printing porous structures. The ink design principle, ink composition, and printability are thoroughly discussed. The methodologies of various AM technologies for porous structures are analyzed. Readers can find a clear experimental guidance toward 3D printing multi-scale porous structures. The synergistic and collective merits of additive manufacturing and porous structure are highlighted and systematically discussed in this review. The challenges and promises of this field for future research are also outlined.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A requirement for an active proton delivery network supports a compound I-mediated C–C bond cleavage in CYP51 catalysis

CYP51 enzymes (sterol 14α-demethylases) are cytochromes P450 that catalyze multistep reactions. The CYP51 reaction occurs in all biological kingdoms and is essential in sterol biosynthesis. It removes the 14α-methyl group from cyclized sterol precursors by first forming an alcohol, then an aldehyde, and finally eliminating formic acid with the introduction of a Δ14–15 double bond in the sterol core. The first two steps are typical hydroxylations, mediated by an electrophilic compound I mechanism. The third step, C–C bond cleavage, has been proposed to involve either compound I (i.e. FeO 3+ ) or, alternatively, a proton transfer-independent nucleophilic ferric peroxo anion (compound 0, i.e. Fe 3+ O 2 – ). In this work, using comparative crystallographic and biochemical analyses of WT human CYP51 (CYP51A1) and its D231A/H314A mutant, whose proton delivery network is destroyed (as evidenced in a 1.98-Å X-ray structure in complex with lanosterol), we demonstrate that deformylation of the 14α-carboxaldehyde intermediate requires an active proton relay network to drive the catalysis. These results indicate a unified, compound I-based mechanism for all three steps of the CYP51 reaction, as previously established for CYP11A1 and CYP19A1. We anticipate that our approach can be applied to mechanistic studies of other P450s that catalyze multistep reactions, such as C–C bond cleavage.

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

Unified Universal Control and Coordination of Inverter-Based Resources, and Validation for a PV + Battery Hybrid Plant

As renewable energy deployment grows, hybrid power plants (HPPs) combining photovoltaic (PV) and battery systems must evolve to offer both energy and grid stability services. These systems typically include a mix of grid-following (GFL) and grid-forming (GFM) inverters, presenting unique coordination and control challenges. This Department of Energy–funded project developed and validated a Unified Universal Control and Coordination (UUCC) framework for such PV + battery hybrid plants, enabling seamless and stable operation, including ultrafast black start, autonomous synchronization, and robust frequency and voltage regulation, under different grid conditions. The project significantly advanced the understanding of inverter-based resource (IBR) control by developing and validating three complementary system-level approaches for hybrid GFL/GFM operation: 1. A combined Virtual Resistance (VR)-based GFL and Virtual Oscillator Control (VOC)-based GFM method, where each inverter type is governed by a specialized control strategy. Together, these achieve stable, fast-response coordination, eliminating inrush current and enabling smooth black start and grid synchronization across a wide range of grid strengths. 2. A Deadbeat-based UUCC strategy, which uses discrete-time, switching-cycle-level control for both GFL and GFM inverters. This approach replaces traditional PI/PLL control with a control parameter-free, high-bandwidth framework that supports stable LVRT and instantaneous synchronization under all conditions. 3. A benchmark comparison with Siemens’ commercial GFM microgrid controller, which provided a fast baseline platform. The commercial approach decoupled v & f control was implemented on a commercial microgrid controller.The baseline commercial benchmark helped highlight superior transient response and black start performance offered by the deadbeat and VOC approaches. These technical contributions offer substantial improvements over conventional inverter control schemes, which often rely on slow phase-locked loop (PLL)-based synchronization, require careful control parameters tuning, and prone to unstable in weak grids with GFL inverters and in stiff grid with GFM inverters therefore challenging for hybrid GFL+GFM under all grid conditions. The deadbeat-based UUCC framework enables simpler, faster, and more robust operation of hybrid IBR systems using wide-bandgap (WBG) devices such as SiC power semiconductors. The rapid expansion of hybrid distributed energy resources (DERs), including residential and commercial PV-BESS installations such as Tesla Powerwall, PV with vehicle-to-grid (V2G) capability, and other integrated configurations, presents complex operational challenges for medium-voltage radial distribution feeders. These networks are subject to frequent disturbances such as faults, switching operations, rapid reclosing sequences, and feeder reconfigurations, all of which introduce dynamic stress on IBRs. In addition, planned feeder segmentation and deliberate islanding for resilience will require DERs that can autonomously perform blackstart, establish voltage and frequency references, and resynchronize with the main grid. The advanced deadbeat-based UUCC control and blackstart functionalities developed in this project directly address these requirements, enabling decentralized and autonomous operation of inverter-dominated DERs in distribution systems under a wide range of fault and reconfiguration scenarios. From a public benefit perspective, these innovations enable more reliable and cost-effective integration of renewable energy into distribution networks. The ability to autonomously black start and stabilize grids under varying grid conditions support accelerates recovery from outages and support decentralized resilient energy systems. By reducing system complexity and improving performance, this project lays critical groundwork for future inverter-dominated power grids that are clean, reliable, and accessible to all.

14 SOLAR ENERGY↗
DOE OSTI2023

Topological structure of complex predictions

Abstract Current complex prediction models are the result of fitting deep neural networks, graph convolutional networks or transducers to a set of training data. A key challenge with these models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into a simplified topological view of the prediction landscape. The result is a map of the predictions that enables inspection of the model results with more specificity than dimensionality-reduction methods such as tSNE and UMAP. The methods scale up to large datasets across different domains. We present a case study of a transformer-based model previously designed to predict expression levels of a piece of DNA in thousands of genomic tracks. When the model is used to study mutations in the BRCA1 gene, our topological analysis shows that it is sensitive to the location of a mutation and the exon structure of BRCA1 in ways that cannot be found with tools based on dimensionality reduction. Moreover, the topological framework offers multiple ways to inspect results, including an error estimate that is more accurate than model uncertainty. Further studies show how these ideas produce useful results in graph-based learning and image classification.

Computer Science↗
DOE OSTI2025

Deep Point Cloud Building Envelope Segmentation (DeeP-CuBES) using Deep Learning

Building Information Modeling (BIM) plays an important role in building design and construction, particularly for achieving energy-efficient retrofits. Building envelope retrofits using panelized prefabricated system, such as those popularized by the Energiesprong program, need accurate as-built dimensions of facade features (windows, doors, etc.) to achieve the desired thermal and air tightness. Traditionally, building surveying is done manually, resulting in a time-consuming and labor-intensive process. Recently, 3D point clouds from terrestrial LiDAR have been used to automate the generation of as-built dimensions of existing buildings. However, automated BIM using LiDAR relies on solving the point cloud semantic segmentation (PCSS) problem. In this work, we propose a robust pipeline for solving the PCSS problem using deep neural networks, focusing on overcoming challenges posed by imbalanced datasets and complex architectural features. We introduce the first high-density, labeled, and validated building envelope point cloud dataset derived from multiple building scans, specifically curated to tackle challenges in facade-level segmentation. Results from the trained neural networks show that advanced attention-based architectures and incorporating radiometry (light intensity and RGB) features significantly boost segmentation accuracy for windows and doors.

Selvakumar, Balaji [ORNL]↗
DOE OSTI2022

Network Models of Active Degradation Mechanisms and Pathways for Service Life Prediction of Indoor and Outdoor PV Modules

ct: PV service lifetime prediction (SLP) enables accurate calculation of levelized cost of energy (LCOE), which is crucial to rationalizing PV investment and installation. However, SLP is challeging since PV reliability in the field is affected by many combined factors, including various environmental stresses and module quality. In order to map out the active degradation mechanisms and pathways that best resemble real world conditions, we introduce the framework of a study protocol and use network models fitted to data, to enable analysis and SLP of complex PV systems with multiple active degradation mechanisms. The study protocol is the experimental design, including module variants and different exposure conditions, selection of evaluation methods, time-series data acquisition and training of network models to these data. We present SLP of minimodules in the lab and PV systems in the field. For lab SLP, minimodules with 8 variants based on manufacturer, architecture, and encapsulation were prepared and aged in modified damp heat with or without full spectrum light exposure. Stepwise I-V and Suns-Voc data acquisition tracks changes in electrical properties including Rs,IV, Isc,IV, Vmp,PIV providing insights into power loss of minimodules. Network structural equation modeling (netSEM) was utilized to construct degradation pathway models that identify active degradation mechanisms and predict power loss over time. For field SLP, datastreams of Pmp values and I-V curve datastreams of two types of modules installed in three distinctly different Köppen-Geiger climate zones for 9 years were acquired. With power loss modes corresponding to uniform current loss (ΔPIsc), recombination (ΔPVoc), series resistance (ΔPRs), and current mismatch (ΔPImis) determined, the performance loss rates (PLR) were determined using PVplr. We show how to establish a study protocol framework to ensure appropriate parametric variations and valid data collection from the variants of your complex systems. Then the data-driven netSEM model fitting provides a comprehensive mapping of multiple active degradation mechanisms, and accurate service life prediction.

network model, degradation, photovoltaic, solar↗
DOE OSTI2021

Efficient Contingency Analysis in Power Systems via Network Trigger Nodes

Modeling failure dynamics within a power system is a complex and challenging process due to multiple inter-dependencies and convoluted inter-domain relationships. Subject matter experts (SMEs) are interested in understanding these failure dynamics for reducing the impact from future disasters (i.e., losses or failures of power system components, such as transmission lines). Contingency analysis (CA) tools enable such ’what-if’ scenario analyses to evaluate the impacts on the power system. Analyzing all possible contingencies among N system components can be computationally expensive. An important step for performing CA is identifying a set of k ‘trigger’ components, which when failed initially can significantly impact the overall system by causing multiple failures. Currently SMEs focus on identifying these trigger components by running expensive simulations on all possible subsets, which quickly becomes infeasible. Hence finding a relevant set of trigger components (contingencies) rapidly to enable efficient and useful CA is crucial.In a collaboration between computer scientists and power system experts, we propose an efficient method for performing CA by exploiting network inter-dependencies in power system components. First, we construct a network with multiple electric grid infrastructure components and dependencies as connections among them. We reformulate the problem of finding a set of trigger components as a problem of identifying critical nodes in the network, which can cascade power failures through connected nodes and cause significant damage to the network. To guide the practical CA tools, we develop a network-based model with a probabilistic edge-weights setup using intricate domain rules. Then we conduct an empirical study on real power system data in the US for both regional and national levels. Firstly, we use power system datasets for the US to create a national-scale domain-driven model. Secondly, we demonstrate that network-based model outperforms the outputs from a real CA tool and show on average 25 × improved selection of contingencies, thereby showcasing practical benefits to the power experts.

Tabassum, Anika↗
DOE OSTI2021

Crystal structures of inhibitor complexes of M‐PMV protease with visible flap loops

Abstract Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P 1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P 2 1 crystal structures and is similar to a rarely occurring system in HIV‐1 PR.

Wosicki, Stanislaw↗
DOE OSTI2020

Verification benchmarks for single-phase flow in three-dimensional fractured porous media

Flow in fractured porous media occurs in the earth’s subsurface, in biological tissues, and in man-made materials. Fractures have a dominating influence on flow processes, and the last decade has seen an extensive development of models and numerical methods that explicitly account for their presence. To support these developments, four benchmark cases for single-phase flow in three-dimensional fractured porous media are presented. Furthermore, the cases are specifically designed to test the methods’ capabilities in handling various complexities common to the geometrical structures of fracture networks. Based on an open call for participation, results obtained with 17 numerical methods were collected. This paper presents the underlying mathematical model, an overview of the features of the participating numerical methods, and their performance in solving the benchmark cases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Closing transdisciplinary collaboration gaps of food-energy-water nexus research

The nexus of food, energy, and water (FEW) systems is key to ensuring global sustainability in the face of climate change, population growth, and urbanization. To address FEW resources inequity among different regions and countries, transdisciplinary research networking becomes increasingly important for tackling this intractable, complex grand challenge. In contrast to interdisciplinary or multidisciplinary research, transdisciplinary research emphasizes the interactions of scientific, cognitive, and social factors from a top-down view. Intellectual and strategic integrations entail weaving scientific, socioeconomic, and political perspectives together into a new convergence model and fostering a shared vision and comparable assessment, though these goals might not be realistically achievable in the short term. This article summarizes major barriers to transdisciplinary research on FEW nexus grand challenges and possible solutions to be implemented at multiple levels of distinct social systems. Implementation of the solutions relies on not only top-down incentives of governments but also bottom-up initiatives of academic communities and individual researchers. The relevance of shared interests and visions between the research communities and the public is emphasized.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

What are mycorrhizal traits?

Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. Here we propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location – plant, fungus, or the symbiosis – which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Segmental Dynamics and Vitrification in Associating Copolymer Melts: Role of Cluster Formation, Microdomains, and Cross-Linking

A microscopic statistical mechanical theory of the structure, self-assembly, and activated segmental relaxation is employed to study associating copolymer melts with high attractive sticker fractions, local clustering, and disordered microphase ordering. The stickers are dynamically pinned in a manner that does not affect equilibrium structure which mimics the much slower physical bond breaking process or postassembly cross-linking of sticky monomers. Local sticker clustering and microdomain spatial correlations significantly modify the activated relaxation of nonstickers and glass transition temperature, T g . A re-entrant glass-melting feature is predicted as sticker attraction strength is initially increased corresponding to a speed up of segmental relaxation, and hence reduction of T g relative to the cross-linked homopolymer network. A mechanistic analysis reveals three competing effects: a purely kinetic slowing down of nonstickers down due to cross-linking, disordering of the nonsticker local cage and weakening of effective forces they experience due to sticker physical clustering, and a longer range impact of microdomain scale correlations that results in nonmonotonic dynamical effects. At high enough attraction strength, a qualitative change emerges corresponding to a sticker fraction dependent elevation of T g , which eventually surpasses that of the cross-linked homopolymer network. Dynamically, the new physics arises from a complex evolution of the amplitude of the collective elastic field that dresses the large amplitude mobile segment hopping within a coupled local-nonlocal description of the alpha relaxation. Furthermore, the results are qualitatively consistent with recent experiments on associating PDMS and PPG telechelics of fixed sticker fraction but with chemically different end groups of variable attraction strengths. Finally, possible tests using simulation and the influence of material or model specific interaction potentials and other real world complications are discussed.

Copolymers↗