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Results for “Human in the Loop”

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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5

Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.

affinity-maturation↗
DOE OSTI2019

Structure and regulation of human epithelial cell transforming 2 protein

Epithelial cell transforming 2 (Ect2) protein activates Rho GTPases and controls cytokinesis and many other cellular processes. Dysregulation of Ect2 is associated with various cancers. Here, we report the crystal structure of human Ect2 and complementary mechanistic analyses. The data show the C-terminal PH domain of Ect2 folds back and blocks the canonical RhoA-binding site at the catalytic center of the DH domain, providing a mechanism of Ect2 autoinhibition. Ect2 is activated by binding of GTP-bound RhoA to the PH domain, which suggests an allosteric mechanism of Ect2 activation and a positive-feedback loop reinforcing RhoA signaling. Furthermore this bimodal RhoA binding of Ect2 is unusual and was confirmed with Förster resonance energy transfer (FRET) and hydrogen–deuterium exchange mass spectrometry (HDX-MS) analyses. Several recurrent cancer-associated mutations map to the catalytic and regulatory interfaces, and dysregulate Ect2 in vitro and in vivo. Together, our findings provide mechanistic insights into Ect2 regulation in normal cells and under disease conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

In-situ irradiation-induced studies of grain growth kinetics of nanocrystalline UO 2

The thermal conductivity of UO 2 fuel needs to be high enough to dissipate the heat generated from the fission reaction. Since grain size affects thermal conductivity and grain size can evolve with irradiation, it is critical to understand in-reactor UO 2 grain growth. Most studies of grain growth in UO 2 are based on thermally driven processes at elevated temperatures. However, studies have shown that grain growth can occur even at cryogenic temperatures by ballistic processes. Such irradiation-induced grain growth in UO 2 is yet to be studied. Advanced in-situ Kr ion irradiation and transmission electron microscopy were systematically performed on nanocrystalline UO 2 thin films at temperatures ranging from 50 K to 1073 K; grain growth was observed at all temperatures. A combination of manual and machine learning techniques was used to measure and plot grain size evolution against irradiation fluence at various irradiation temperatures. The machine learning method has significantly improved the analysis efficiency and reduced human labors. The grain diameter data were fitted using classical grain growth and thermal spike models to describe grain growth kinetics with and without irradiation effect. Grain growth during low temperature irradiation (≤ 475 K) can be well described by the thermal spike model. Above 475 K, there were additional thermally assisted processes that further accelerate the grain growth. At the highest irradiation temperature about 1075 K, both irradiation-induced dislocation loops and cavities/bubbles were observed to form in the UO 2 . In this report, the effects of irradiation-induced defects on grain growth kinetics are discussed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins

We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Machine learning with knowledge constraints for process optimization of open-air perovskite solar cell manufacturing

Perovskite photovoltaics (PV) have achieved rapid development in the past decade in terms of power conversion efficiency of small-area lab-scale devices; however, successful commercialization still requires further development of low-cost, scalable, and high-throughput manufacturing techniques. One of the critical challenges of developing a new fabrication technique is the high-dimensional parameter space for optimization, but machine learning (ML) can readily be used to accelerate perovskite PV scaling. Herein, we present an ML-guided framework of sequential learning for manufacturing process optimization. We apply our methodology to the Rapid Spray Plasma Processing (RSPP) technique for perovskite thin films in ambient conditions. With a limited experimental budget of screening 100 process conditions, we demonstrated an efficiency improvement to 18.5% as the best-in-our-lab device fabricated by RSPP, and we also experimentally found 10 unique process conditions to produce the top-performing devices of more than 17% efficiency, which is 5 times higher rate of success than the control experiments with pseudo-random Latin hypercube sampling. Our model is enabled by three innovations: (a) flexible knowledge transfer between experimental processes by incorporating data from prior experimental data as a probabilistic constraint; (b) incorporation of both subjective human observations and ML insights when selecting next experiments; (c) adaptive strategy of locating the region of interest using Bayesian optimization first, and then conducting local exploration for high-efficiency devices. Furthermore, in virtual benchmarking, our framework achieves faster improvements with limited experimental budgets than traditional design-of-experiments methods (e.g., one-variable-at-a-time sampling). This framework shows the capability of incorporating researchers’ domain knowledge into the ML-guided optimization loop; therefore, it has the potential to facilitate the wider adoption of ML in scaling to perovskite PV manufacturing.

14 SOLAR ENERGY↗
DOE OSTI2022

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively ‘featureless’ surface dominated by the peptide’s backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Structure of the human cation–chloride cotransport KCC1 in an outward-open state

Cation–chloride cotransporters (CCCs) catalyze electroneutral symport of Cl - with Na + and/or K + across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl - concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K + –Cl - cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid–polyamine–organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds.

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

Experimentally Driven Automated Machine-Learned Interatomic Potential for a Refractory Oxide

Understanding the structure and properties of refractory oxides is critical for high temperature applications. In this work, a combined experimental and simulation approach uses an automated closed loop via an active learner, which is initialized by x-ray and neutron diffraction measurements, and sequentially improves a machine-learning model until the experimentally predetermined phase space is covered. Furthermore, a multiphase potential is generated for a canonical example of the archetypal refractory oxide, HfO 2 , by drawing a minimum number of training configurations from room temperature to the liquid state at similar to 2900 degrees C. The method significantly reduces model development time and human effort.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, in this study, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ~20–50 cm –1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Deep Learning for Intelligent Bubble Size Detection in the Spallation Neutron Source Visual Target

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) will undergo proton power upgrade (PPU), increasing the proton beam power from 1.4 MW to 2.8 MW. From 2.8 MW, 2.0 MW will go to the current First Target Station and the rest will go to the future Second Target Station (STS). The First Target Station uses a liquid mercury target that is contained in a 316L stainless steel vessel. The proton beam is pulsed at 60 Hz, with a pulse of about 0.7μs. When the proton beam hits the target, the intense energy deposition leads to a rapid rise in temperature in the mercury. This temperature rise creates pressure waves that propagate through the mercury and cause cavitation erosion. The power upgrade will cause stronger pressure waves that will further increase damage because of cavitation. Injecting small helium bubbles in the mercury has been an efficient method of mitigating the pressure wave at 1.4 MW. However, at higher power, additional mitigation is necessary. Therefore, the 2 MW target vessel will be equipped with swirl bubblers and an additional gas injection port near the nose to inject more gas in the target. To develop a gas injection strategy and design, flow visualization in water with a transparent prototypical target (“visual target”) was performed. Bubble sizes and their spatial distribution in the flow loop are crucial to understanding the effectiveness of the bubbles in mitigating pressure waves. Bubbles were generated in the visual target under varied conditions of input pressures with helium and air. Images were captured using a high-speed camera at varied frame rates at different positions away from the swirl bubbler and different depths in the flow loop under varying lighting conditions. Initially, methods such as circular Hough transforms were applied after a series of images processing to obtain a general distribution of bubble sizes. Bubbles smaller than 500 μm are preferred to effectively mitigate the effect of pressure waves, which demands an accurate bubble detection and sizing system. Intelligent detection and identification of bubble sizes alleviate misdetection and improves accuracies. Employing neural networks, intelligent detection of bubble sizes and their distribution was developed and provides a robust alternative to traditional techniques. Human intervention was employed to label in-focus and out-of-focus bubbles in the set of training images. An object detection network using a pretrained convolutional neural network was created that extracted the features from the training images. Data augmentation was used to improve network accuracy through a random transformation of the original data.

Rasheed, Fayaz↗
DOE OSTI2023

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Advocating Feedback Control for Human-Earth System Applications

This paper proposes a feedback control perspective for Human-Earth Systems (HESs) which essentially are complex systems that capture the interactions between humans and nature. Recent attention in HES research has been directed towards devising strategies for climate change mitigation and adaptation, aimed at achieving environmental and societal objectives. However, existing approaches heavily rely on HES models, which inherently suffer from inaccuracies due to the complexity of the system. Moreover, overly detailed models often prove impractical for optimization tasks. We propose a framework inheriting from feedback control strategies the robustness against model errors, because inaccuracies are mitigated using measurements retrieved from the field. The framework comprises two nested control loops. The outer loop computes the optimal inputs to the HES, which are then implemented by actuators controlled in the inner loop. Potential fields of applications are also identified and a numerical example is provided.

biological system modeling↗
DOE OSTI2021

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity

To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements (MGEs) encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic acid–binding proteins. Based on mutational analyses and functional assays, we deduced that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and MGEs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Computationally Selected Multivalent HIV-1 Subtype C Vaccine Protects Against Heterologous SHIV Challenge

Background: The RV144 trial in Thailand is the only HIV-1 vaccine efficacy trial to date to demonstrate any efficacy. Genetic signatures suggested that antibodies targeting the variable loop 2 (V2) of the HIV-1 envelope played an important protective role. The ALVAC prime and protein boost follow-up trial in southern Africa (HVTN702) failed to show any efficacy. One hypothesis for this is the greater diversity of subtype C viruses in southern Africa relative to CRF01_AE in Thailand. Methods: Here, we determined whether an ALVAC prime with computationally selected gp120 boost immunogens maximizing coverage of diversity of subtype C viruses in the variable V1 and V2 regions (V1V2) improved the protection of non-human primates (NHPs) from a heterologous subtype C SHIV challenge compared to more traditional regimens. Results: An ALVAC prime with Trivalent subtype C gp120 boosts resulted in statistically significant protection from repeated intrarectal SHIV challenges compared to the control. Evaluation of the immunogenicity of each vaccine regimen at the time of challenge demonstrated that different gp120 combination boosts elicited similar high magnitudes of gp120 and breadth of V1V2-binding antibodies, as well as strong Fc-mediated immune responses. Low-to-no neutralization of the challenge virus was detected. A Cox proportional hazard analysis of five pre-selected immune parameters at the time of challenge identified ADCC against the challenge envelope as a correlate of protection. Systems serology analysis revealed that immune responses elicited by the different vaccine regimens were distinct and identified further correlates of resistance to infection. Conclusions: Computationally designed vaccines with maximized subtype C V1V2 coverage mediated protection of NHPs from a heterologous Tier-2 subtype C SHIV challenge.

Immunology↗
DOE OSTI2025

Radiation‐Resistant Aluminum Alloy for Space Missions in the Extreme Environment of the Solar System

Future human exploration of the solar system demands advanced materials capable of withstanding extreme environments, particularly exposure to solar energetic particle radiation. Current material selection criteria for space applications prioritize a high strength-to-weight ratio, high corrosion resistance and manufacturability, favoring age-hardenable Al-based alloys. However, conventional precipitation-hardened Al alloys suffer from irradiation-assisted dissolution of strengthening phases at doses as low as 0.2 displacements-per-atom (dpa), undermining their performance. Furthermore, these alloys develop radiation-induced defects, such as dislocation loops and voids, even at low doses. This study presents a novel ultrafine-grained (UFG) Al-based alloy, designed using the crossover alloying concept and strengthened by T-phase precipitates, featuring a chemically-complex structure with 162 atoms in its unit cell composed of Mg 32 (Zn,Al) 49 . It is showed that T-phase precipitates have exceptional radiation tolerance up to 24 dpa. Owing to the nanoscale UFG structure, dislocation loops are suppressed, and voids are only observed beyond 75 dpa. Microtensile tests up to 20 dpa confirm the preservation of mechanical performance under irradiation. The results underline the potential of this alloy as a radiation-resistant, lightweight material for future space applications. Three key strategies enable this performance: (i) stabilization of a UFG microstructure, (ii) T-phase precipitation featuring a highly negative Gibbs free energy and chemically-complex giant unit cell, and (iii) precise process control to prevent grain growth during heat treatment and irradiation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Modular Autonomous Experimentation for Biological Applications (Full Report)

The Modular Autonomous Research System (MARS) was developed to address the pressing need for faster, more reliable, and more adaptable scientific discovery. Traditional experimentation is limited by manual labor, long cycle times, and fragmented data streams, which constrain the ability to explore complex chemical and materials design spaces. To overcome these limitations, we created an integrated, modular platform that combines laboratory robotics, diverse measurement instruments, and a central data infrastructure with artificial intelligence–driven decision-making. The system links liquid handling robots, robotic arms, and optical plate readers into a closed loop where experiments are executed automatically, data is analyzed in real time, and subsequent experimental conditions are adaptively chosen to maximize information gain. Over the course of the project, MARS was validated on two primary test cases—spectroscopic metal–ligand binding assays and peptide-directed mineralization—which highlighted the system’s ability to handle uncertainty and variability in experimental measurements. To further demonstrate modularity and extensibility, we also established additional testbeds in electrochemistry for catalyst discovery and electrolyte formulation for advanced batteries. The results show that MARS can reliably conduct autonomous campaigns with minimal human intervention, adapt to distinct scientific domains, and provide a scalable model for future self-driving laboratories. This work establishes new capabilities for modular, uncertainty-aware automation and directly supports the need for advanced, data-driven research platforms capable of accelerating discovery across a wide range of scientific and national security missions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germ line-encoded monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and determined its structure in complex with the spike glycoprotein by electron cryomicroscopy (cryo-EM). We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its heavy complementarity-determining region 3 (HCDR3) loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that, because of the conserved nature of the epitope, the mAb maintains binding to viral variants B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron). Our study describes a novel conserved epitope on the NTD that is readily targeted by vaccine-induced antibody responses.

59 BASIC BIOLOGICAL SCIENCES↗