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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Improved Throughput and Analysis of Scratch Test Results via Automation and Machine Learning

A data analysis automation interface that incorporates machine learning (ML) has been developed to improve productivity, efficiency, and consistency in identifying and defining critical load values (or other values associated with optically identifiable characteristics) of a coating when a scratch test is performed. In this specific program, the machine learning component of the program has been trained to identify the Critical Load 2 (L C2 ) value by analyzing images of the scratch tracks created in each test. An optical examination of the scratch by a human operator is currently used to determine where this value occurs. However, the vagueness of the standard has led to varying interpretations and nonuniform usage by different operators at different laboratories where the test is implemented, resulting in multiple definitions of the desired parameter. Using a standard set of training and validation images to create the dataset, the critical load can be identified consistently amongst different laboratories using the automation interface without requiring the training of human operators. When the model was used in conjunction with an instrument manufacturer's scratch test software, the model produced accurate and repeatable results and defined L C2 values in as little as half of the time compared to a human operator. When combined with a program that automates other aspects of the scratch testing process usually conducted by a human operator, scratch testing and analysis can occur with little to no intervention from a human beyond initial setup and frees them to complete other work in the lab.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates

The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Informing climate adaptation strategies using ecological simulation models and spatial decision support tools

Introduction: Forest landscapes offer resources and ecosystem services that are vital to the social, economic, and cultural well-being of human communities, but managing for these provisions can require socially and ecologically relevant trade-offs. We designed a spatial decision support model to reveal trade-offs and synergies between ecosystem services in a large eastern Cascade Mountain landscape in Washington State, USA. Methods: We used process-based forest landscape (LANDIS-II) and hydrology (DHSVM) models to compare outcomes associated with 100 years of simulated forest and wildfire dynamics for two management scenarios, Wildfire only and Wildfire + Treatments. We then examined the strength and spatial distribution of potential treatment effects and trends in a set of resources and ecosystem services over the simulation period. Results: We found that wildfire area burned increased over time, but some impacts could be mitigated by adaptation treatments. Treatment benefits were not limited to treated areas. Interestingly, we observed neighborhood benefits where fire spread and severity were reduced not only in treated patches but in adjacent patches and landscapes as well, creating potential synergies among some resource benefits and services. Ordinations provided further evidence for two main kinds of outcomes. Positive ecological effects of treatments were greatest in upper elevation moist and cold forests, while positive benefits to human communities were aligned with drier, low- and mid-elevation forests closer to the wildland urban interface. Discussion: Our results contribute to improved understanding of synergies and tradeoffs linked to adaptation and restoration efforts in fire-prone forests and can be used to inform management aimed at rebuilding resilient, climate-adapted landscapes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

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

Structure of the human SAGA coactivator complex

The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP 6 ) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2023

The drivers and predictability of wildfire re-burns in the western United States (US)

Evidence is mounting that the effectiveness of using prescribed burns as a management tactic may be diminishing due to the higher incidence of wildfire re-burns. The development of predictive models of re-burns is thus essential to better understand their primary drivers so that forest management practices can be updated to account for these events. First, we assess the potential for human activity as a driver of re-burns by evaluating re-burn trends both within and outside of the wildland–urban interface (WUI) of the western US. Next, we investigate the predictability of re-burns through the application of both random forest and the explanatory machine learning non-negative matrix factorization using k-means clustering (NMFk) algorithms to predict re-burn occurrence over California based on a number of climate factors. Our findings indicate that while most states showed increasing trends within the WUI when trends were conducted over longer moving windows (e.g. 20 years), California was the only state where the rate of increase was consistently higher in the WUI, indicating a stronger potential for human activity as a driver in that location. Furthermore, we find model performance was found to be robust over most of California (Testing F1 scores = 0.688), although results were highly variable based on EPA level III Ecoregion (F1 scores = 0.0–0.778). Insights provided from this study will lead to a better understanding of climate and human activity drivers of re-burns and how these vary at broad spatial scales so that improvements in forest management practices can be tuned according to the level of change that is expected for a given region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Designing workflows for materials characterization

Experimental science is enabled by the combination of synthesis, imaging, and functional characterization organized into evolving discovery loop. Synthesis of new material is typically followed by a set of characterization steps aiming to provide feedback for optimization or discover fundamental mechanisms. However, the sequence of synthesis and characterization methods and their interpretation, or research workflow, has traditionally been driven by human intuition and is highly domain specific. Here, we explore concepts of scientific workflows that emerge at the interface between theory, characterization, and imaging. In this study, we discuss the criteria by which these workflows can be constructed for special cases of multiresolution structural imaging and functional characterization, as a part of more general material synthesis workflows. Some considerations for theory–experiment workflows are provided. We further pose that the emergence of user facilities and cloud labs disrupts the classical progression from ideation, orchestration, and execution stages of workflow development. To accelerate this transition, we propose the framework for workflow design, including universal hyperlanguages describing laboratory operation, ontological domain matching, reward functions and their integration between domains, and policy development for workflow optimization. These tools will enable knowledge-based workflow optimization; enable lateral instrumental networks, sequential and parallel orchestration of characterization between dissimilar facilities; and empower distributed research.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Generalized Aerosol/Chemistry Interface (GIANT): A Community Effort to Advance Collaborative Science across Weather and Climate Models

Atmospheric aerosol and chemistry modules are key elements in Earth system models (ESMs), as they predict air pollutant concentrations and properties that can impact human health, weather, and climate. The current uncertainty in climate projections is partly due to the inaccurate representation of aerosol direct and indirect forcing. Aerosol/chemistry parameterizations used within ESMs and other atmospheric models span large structural and parameter uncertainties that are difficult to assess independently of their host models. Moreover, there is a strong need for a standardized interface between aerosol/chemistry modules and the host model to facilitate portability of aerosol/chemistry parameterizations from one model to another, allowing not only a comparison between different parameterizations within the same modeling framework, but also quantifying the impact of different model frameworks on aerosol/chemistry predictions. To address this need, we have initiated a new community effort to coordinate the construction of a Generalized Aerosol/Chemistry Interface (GIANT) for use across weather and climate models. We aim to organize a series of community workshops and hackathons to design and build GIANT, which will serve as the interface between a range of aerosol/chemistry modules and the physics and dynamics components of atmospheric host models. GIANT will leverage ongoing efforts at the U.S. modeling centers focused on building next-generation ESMs and the international AeroCom initiative to implement this common aerosol/chemistry interface. GIANT will create transformative opportunities for scientists and students to conduct innovative research to better characterize structural and parametric uncertainties in aerosol/chemistry modules, and to develop a common set of aerosol/chemistry parameterizations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms

The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1–80) fused to the switch region of troponin I (cTnI; residues 138–162). In both crystal forms, the cTnI residues form a six-turn α-helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative to the cTnC groove and completely blocks the calcium desensitizer binding site of the cTnC–cTnI interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes

Abstract Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography–coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1’) and reveals a surprising role for C1r B loop–interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway–specific inhibition by a human pathogen.

Garrigues, Ryan J. (ORCID:0000000259233250)↗
DOE OSTI2026

Generalizable Web User Interface for Scalable and Streamlined Deployment of Building Energy Management Systems in Small and Medium-Sized Commercial Buildings

Small and medium-sized commercial buildings (SMCBs) comprise 94% of US commercial buildings yet face significant barriers to implementing building energy management systems despite advances in smart device technology. Existing solutions present critical limitations: cloud-based API solutions simplify deployment but create vendor lock-in constraints; commercial integrated software solutions ensure compatibility via standardized protocols but require substantial cost and technical expertise; open-source IoT platforms offer cost-effective vendor independence but provide insufficient standardized protocol support for commercial building automation. This research presents a generalizable web user interface framework that bridges the gap between evolving smart device capabilities and lagging software infrastructure for SMCBs. The proposed system integrates VOLTTRON open-source middleware with an automated configuration converter that transforms unified specifications written in YAML, a human-readable data-serialization format, into system-specific files, streamlining manual setup processes. The vendor-agnostic architecture supports industry-standard protocols (BACnet and Modbus) and semantic building models while providing adaptive web interfaces that dynamically adjust to various building configurations. Demonstrations through simulation-based testing and a field deployment show automatic interface adaptation across heterogeneous HVAC systems and multizone monitoring. The automated configuration converter also substantially reduces labor-intensive setup.

Chung, Jihoon [ORNL] (ORCID:0000000184880815)↗
DOE OSTI2022

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Entry and Disposition of Zika Virus Immune Complexes in a Tissue Culture Model of the Maternal-Fetal Interface

Zika virus (ZIKV) infections have been associated with an increased incidence of severe microcephaly and other neurodevelopmental disorders in newborn babies. Passive immunization with anti-ZIKV neutralizing antibodies has the potential to become a feasible treatment or prophylaxis option during pregnancy. Prior to clinical use, such antibodies should be assessed for their ability to block ZIKV passage to the fetus. We used human placental and mammalian cell monolayers that express FcRn and laboratory preparations of anti-ZIKV antibodies as a model system to investigate the disposition of ZIKV/antibody immune complexes (ICs) at the maternal-fetal interface. We further characterized solution properties of the ICs to evaluate whether these are related to in vitro effects. We found that both ZIKV and ZIKV envelope glycoprotein can enter and passage through epithelial cells, especially those that overexpress FcRn. In the presence of ZIKV antibodies, Zika virus entry was bimodal, with reduced entry at the lowest (0.3–3 ng/mL) and highest (µg/mL) antibody concentrations. Intermediate concentrations attenuated inhibition or enhanced viral entry. With respect to anti-ZIKV antibodies, we found that their degradation was accelerated when presented as ICs containing increased amounts of ZIKV immunogen. Of the two monoclonal antibodies tested, the preparation with higher aggregation also exhibited higher degradation. Our studies confirm that intact Zika virus and its envelope immunogen have the potential to enter and be transferred across placental and other epithelial cells that express FcRn. Presence of anti-ZIKV IgG antibodies can either block or enhance cellular entry, with the antibody concentration playing a complex role in this process. Physicochemical properties of IgG antibodies can influence their degradation in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Employing Eye Trackers to Reduce Nuisance Alarms

When process operators anticipate an alarm prior to its annunciation, that alarm loses information value and becomes a nuisance. This study investigated using eye trackers to measure and adjust the salience of alarms with three methods of gaze-based acknowledgement (GBA) of alarms that estimate operator anticipation. When these methods detected possible alarm anticipation, the alarm’s audio and visual salience was reduced. A total of 24 engineering students (male = 14, female = 10) aged between 18 and 45 were recruited to predict alarms and control a process parameter in three scenario types (parameter near threshold, trending, or fluctuating). The study evaluated whether behaviors of the monitored parameter affected how frequently the three GBA methods were utilized and whether reducing alarm salience improved control task performance. The results did not show significant task improvement with any GBA methods (F(3,69) = 1.357, p = 0.263, partial η 2 = 0.056). However, the scenario type affected which GBA method was more utilized (X 2 (2, N = 432) = 30.147, p < 0.001). Alarm prediction hits with gaze-based acknowledgements coincided more frequently than alarm prediction hits without gaze-based acknowledgements (X 2 (1, N = 432) = 23.802, p < 0.001, OR = 3.877, 95% CI 2.25–6.68, p < 0.05). Participant ratings indicated an overall preference for the three GBA methods over a standard alarm design (F(3,63) = 3.745, p = 0.015, partial η 2 = 0.151). This study provides empirical evidence for the potential of eye tracking in alarm management but highlights the need for additional research to increase validity for inferring alarm anticipation.

99 - GENERAL AND MISCELLANEOUS↗