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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 37 records · Page 2

Structural basis of divergent substrate recognition and inhibition of human neurolysin

A zinc metallopeptidase neurolysin (Nln) processes diverse bioactive peptides to regulate signaling in the mammalian nervous system. To understand how Nln interacts with various peptides with dissimilar sequences, we determined crystal structures of Nln in complex with diverse peptides including dynorphins, angiotensin, neurotensin, and bradykinin. The structures show that Nln binds these peptides in a large dumbbell-shaped interior cavity constricted at the active site, making minimal structural changes to accommodate different peptide sequences. The structures also show that Nln readily binds similar peptides with distinct registers, which can determine whether the peptide serves as a substrate or a competitive inhibitor. We analyzed the activities and binding of Nln toward various forms of dynorphin A peptides, which highlights the promiscuous nature of peptide binding and shows how dynorphin A (1–13) potently inhibits the Nln activity while dynorphin A (1–8) is efficiently cleaved. Our work provides insights into the broad substrate specificity of Nln and may aid in the future design of small molecule modulators for Nln.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of a eukaryotic cholinephosphotransferase-1 reveals mechanisms of substrate recognition and catalysis

Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic cell membranes. In eukaryotes, two highly homologous enzymes, cholinephosphotransferase-1 (CHPT1) and choline/ethanolamine phosphotransferase-1 (CEPT1) catalyze the final step of de novo PC synthesis. CHPT1/CEPT1 joins two substrates, cytidine diphosphate-choline (CDP-choline) and diacylglycerol (DAG), to produce PC, and Mg 2+ is required for the reaction. However, mechanisms of substrate recognition and catalysis remain unresolved. Here we report structures of a CHPT1 from Xenopus laevis (xlCHPT1) determined by cryo-electron microscopy to an overall resolution of ~3.2 Å. xlCHPT1 forms a homodimer, and each protomer has 10 transmembrane helices (TMs). The first 6 TMs carve out a cone-shaped enclosure in the membrane in which the catalysis occurs. The enclosure opens to the cytosolic side, where a CDP-choline and two Mg 2+ are coordinated. The structures identify a catalytic site unique to eukaryotic CHPT1/CEPT1 and suggest an entryway for DAG. The structures also reveal an internal pseudo two-fold symmetry between TM3-6 and TM7-10, and suggest that CHPT1/CEPT1 may have evolved from their distant prokaryotic ancestors through gene duplication.

59 BASIC BIOLOGICAL SCIENCES↗

Rescuing Legacy Seismic Data FAIR’ly

The Earth’s interconnected and dynamical systems operate on a spectrum of time scales from millions of years to fractions of a second. While the evolution of the Earth and its deep interior are beyond the time span of human observations, understanding of many natural phenomena operating on human times scales have benefited from direct scientific observation. Continuous processes and those that are repeated over time shape the environment we live in. Furthermore, as we are faced with unprecedented changes to climate, understanding the deeper patterns and trends in natural systems through time have taken on new importance (Research Data Alliance, 2019). The call to reuse data is driven not only by economics but also by the recognition of their complete uniqueness (observations of natural systems are not repeatable) and scientific value in enhancing current understandings as well as potential new discoveries especially in the era of big data. These data are part of the historical record and our scientific heritage (American Geophysical Union, 2019) not only in explicitly recording earth observations but implicitly recording, and thus providing the evidence that addresses the manner in which science was conducted.

58 GEOSCIENCES↗

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗

Noncoordinating Secondary Sphere Ion Modulates Supramolecular Clustering of Lanthanides

The role of counterions in molecular recognition of lanthanides is underexplored, especially when they exhibit weak interactions with the metal cations. Here, we report a complementary and comprehensive investigation integrating theoretical calculations with X-ray absorption fine structure spectroscopy, dynamic light scattering, and small-angle X-ray scattering to reveal atomic-scale structural features beyond the immediate coordination sphere of a system used for rare-earth element separations. Here, our results indicate the formation of an unusual T-shaped outer-sphere lanthanide complex, containing two ligands and two nitrate ions in the first coordination sphere, whereas the third nitrate is weakly coordinated and resides in the second shell. This unique structural arrangement causes inhomogeneous charge distribution, leading to self-assembly of the complexes into larger nanoclusters through sterically directed electrostatic interactions in the nonpolar medium. Our findings point to the importance of "noncoordinating" anions in defining the degree of supramolecular aggregation and ion cluster assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of puromycin-sensitive aminopeptidase and polyglutamine binding

Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Å. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.

59 BASIC BIOLOGICAL SCIENCES↗

US Perspectives on the Conventional/Nuclear Interactions and the Impacts on Nuclear Escalation Risks and Future Arms Control Prospects

This short paper is organized around a few discrete questions. How have U.S. perspectives on conventional and nuclear interactions evolved in recent years? How have these changing perspectives shaped U.S. thinking on perceived nuclear escalation risks with Russia, both long standing and newly emerged? And finally, what do these U.S. perceptions of interactions and risks mean for future potential arms control either in the conventional or nuclear arena? The answers to these questions appear to show some promise for future work in this area. Conventional and nuclear interactions are increasing, and thus the two domains cannot be kept as deliberately or artificially separated as in the past. There is a growing mutual recognition regarding the interplay between conventional and nuclear capabilities in the strategic stability equation. There is also an increasingly shared recognition in the United States and Russia that nuclear escalation risks are likely to originate in conventional crises or conflict, placing an imperative on some form of conflict prevention procedures at the lower end of the spectrum. This requirement suggests some potential areas for risk reduction measures outside of those traditionally considered in conventional and nuclear arms control over the past several decades.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Advancing representations of equity and justice in climate mitigation futures

THIS PAPER WAS PRIMARILY COMPLETED PRIOR TO THE AUTHOR JOINING PNNL AND NO DOE FUNDING WAS USED FOR THIS PAPER. In this work, we review how equity and justice issues in global climate mitigation scenarios are addressed within Integrated Assessment Models (IAMs) and propose a new research agenda to strengthen their integration in model development and application. We begin by examining prominent concerns at the science-policy interface. We introduce a typology of equity and justice limitations in climate mitigation scenarios, distinguishing among structural, methodological, and epistemological biases that shape what integrated assessment models can reveal at policy-relevant scales. Reflecting on these concerns, we propose a research agenda that describes new avenues of work and draws together distinct emerging initiatives. This agenda is based on the feasibility and depth of required interventions, from incremental improvements to structural reforms and alternative participatory approaches. Drawing on reflexive insights from integrated assessment practitioners, it addresses the operational challenges of translating justice concepts into metrics, including risks of reductionism, tokenism, and narrow definitions. Underlying this research agenda is a recognition that modeling communities must engage more critically with implicit assumptions in model design and use that have equity and justice implications. Achieving equitable climate futures will require transformative actions that integrate diverse justice concerns, advance sustainable development goals, and confront systemic inequities across both human and ecological dimensions. Although models will never capture all these aspects, they can be significantly enhanced to support more informed discussion and practical application. Our contribution proposes a way forward to achieving this goal.

Pachauri, Shonali↗

A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity

Allergies have become a rising health problem, where plentiful substances can trigger IgE-mediated allergies in humans. While profilins are considered minor allergens, these ubiquitous proteins are primary molecules involved in cross-reactivity and pollen-food allergy syndrome. Here we report the first crystal structures of murine Fab/IgE, with its chains naturally paired, in complex with the allergen profilin from Hevea brasiliensis (Hev b 8). The crystallographic models revealed that the IgE’s six complementarity-determining regions (CDRs) interact with the allergen, comprising a rigid paratope-epitope surface of 926 Å 2 , which includes an extensive network of interactions. Interestingly, we also observed previously unreported flexibility at Fab/IgE’s elbow angle, which did not influence the shape of the paratope. The Fab/IgE exhibits a high affinity for Hev b 8, even when using 1 M NaCl in BLI experiments. Finally, based on the encouraging cross-reactivity assays using two mutants of the maize profilin (Zea m 12), this antibody could be a promising tool in IgE engineering for diagnosis and research applications.

59 BASIC BIOLOGICAL SCIENCES↗

Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Fenwick, Michael K↗

Unconventional Materials Processing Using Spark Plasma Sintering

Spark plasma sintering (SPS) has gained recognition in the last 20 years for its rapid densification of hard-to-sinter conventional and advanced materials, including metals, ceramics, polymers, and composites. Herein, we describe the unconventional usages of the SPS technique developed in the field. The potential of various new modifications in the SPS technique, from pressureless to the integration of a novel gas quenching system to extrusion, has led to SPS’ evolution into a completely new manufacturing tool. The SPS technique’s modifications have broadened its usability from merely a densification tool to the fabrication of complex-shaped components, advanced functional materials, functionally gradient materials, interconnected materials, and porous filter materials for real-life applications. The broader application achieved by modification of the SPS technique can provide an alternative to conventional powder metallurgy methods as a scalable manufacturing process. The future challenges and opportunities in this emerging research field have also been identified and presented.

36 MATERIALS SCIENCE↗

Technical Issues in the Comprehensive Nuclear Test Ban Treaty (CTBT) Ratification Debate: A 20 Year Retrospective

Two decades after the U.S. Senate declined in 1999 to give its consent to ratification of the Comprehensive Nuclear Test Ban Treaty (CTBT), the treaty remains in legal and political limbo. Legally, the treaty cannot enter into force without U.S. ratification. However, the Senate’s rejection does not strip the treaty of its force as an element of customary international law or alter the will of other signatories to see it enter into force. Politically, the debate over the virtues and flaws of the treaty remains as strong as ever, with some CTBT advocates pushing energetically for U.S. re-review while some opponents seek ways to “un-sign” the treaty. Meanwhile, despite the Senate’s rejection of the treaty, the United States acts in a manner consistent with its main obligations by maintaining a moratorium on explosive nuclear testing and providing financial support (as well as technical expertise) to the CTBT Organization (CTBTO)—in particular the CTBTO’s International Monitoring System (IMS). The CTBT may well remain in such limbo for a long time to come, unless some catalytic event comes along to re-shape national perceptions and priorities, one way or the other. The treaty’s future, whatever it might be, will be determined in part by how much perspectives might have changed in light of interim developments. Our purpose is to shed light on some of those developments and to assess their relevance. The 1999 ratification debate addressed a large number of issues. Rejection was driven by various policy and technical judgments. The purpose of this paper is to re-examine those technical judgments in light of what has been learned over the following two decades. On some technical matters, there was explicit recognition of extant uncertainties, as well as a conviction and hope that time would dispel them. To be doubly clear, our purpose is not to recommend a way forward on CTBT ratification. The policy judgments of 1999 and 2020 are beyond the scope of this paper. This technical re-examination proceeds as follows. It begins with a short background section to introduce the key technical matters in discussion in the U.S. ratification process. Then it moves systematically through each of those topics with a review of relevant background information, a discussion of key points in debate, an analysis of subsequent experience, and a current assessment. The historical analysis draws on many sources including the primary documents of the Congressional debate, the official article-by-article interpretation by the Department of State, and the statements of key players in the process. We also relied on key technical reports and publications by subject matter experts that have addressed in more detail many of the issues in our focus. These sources include the 2002 and 2012 reports of the National Academy of Sciences as well as publications by senior technical staff of Lawrence Livermore National Laboratory (LLNL) who were actively involved in the ratification debate, including then-Laboratory Director Bruce Tarter. We also conducted several interviews with government officials from the 1990s, past laboratory directors, and other members of the scientific community. But, except where individuals are specifically cited by name, the judgments offered here are our own and should not be attributed to any other individual or to LLNL as such.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

59 BASIC BIOLOGICAL SCIENCES↗

Shape‐Dependent Multi‐Weight Magnetic Artificial Synapses for Neuromorphic Computing

Abstract In neuromorphic computing, artificial synapses provide a multi‐weight (MW) conductance state that is set based on inputs from neurons, analogous to the brain. Herein, artificial synapses based on magnetic materials that use a magnetic tunnel junction (MTJ) and a magnetic domain wall (DW) are explored. By fabricating lithographic notches in a DW track underneath a single MTJ, 3–5 stable resistance states that can be repeatably controlled electrically using spin‐orbit torque are achieved. The effect of geometry on the synapse behavior is explored, showing that a trapezoidal device has asymmetric weight updates with high controllability, while a rectangular device has higher stochasticity, but with stable resistance levels. The device data is input into neuromorphic computing simulators to show the usefulness of application‐specific synaptic functions. Implementing an artificial neural network (NN) applied to streamed Fashion‐MNIST data, the trapezoidal magnetic synapse can be used as a metaplastic function for efficient online learning. Implementing a convolutional NN for CIFAR‐100 image recognition, the rectangular magnetic synapse achieves near‐ideal inference accuracy, due to the stability of its resistance levels. This work shows MW magnetic synapses are a feasible technology for neuromorphic computing and provides design guidelines for emerging artificial synapse technologies.

Leonard, Thomas↗

Symmetry-Breaking Dendrimer Synthons in Colloidal Crystal Engineering with DNA

Breaking symmetry in colloidal crystals is challenging due to the inherent chemical and structural isotropy of many nanoscale building blocks. If a non-particle component could be used to anisotropically encode such building blocks with orthogonal recognition properties, one could expand the scope of structural and compositional possibilities of colloidal crystals beyond what is thus far possible with purely particle-based systems. In this work, we report the synthesis and characterization of novel DNA dendrimers that function as symmetry-breaking synthons, capable of programming anisotropic and orthogonal interactions within colloidal crystals. When the DNA dendrimers have identical sticky ends, they hybridize with DNA-functionalized nanoparticles to yield three distinct colloidal crystals, dictated by dendrimer size, including a structure not previously reported in the field of colloidal crystal engineering, Si 2 Sr. When used as symmetry-breaking synthons (when the sticky ends deliberately consist of orthogonal sequences), the synthesis of binary and ternary colloidal alloys with structures that can only be realized through directional interactions is possible. Furthermore, by modulating the extent of shape anisotropy within the DNA dendrimers, the local distribution of the nanoparticles within the crystals can be directed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automated Threat Recognition For Aviation Security Applications

We have developed a framework for automated threat recognition (ATR) of explosive threat materials for both single-energy and dual-energy X-ray CT systems. Under this framework, two different types of ATR have been developed. The first type of ATR employs supervised machine learning with statistical characterization of target materials for threat identification training. The reliance only on statistical characterization information for threat training uniquely enables this style of ATR to adapt quickly to evolving threats. The second type of ATR employs deep learning through convolutional neural networks. Convolutional neural networks are attractive due to their human-like capacity for learning and strong ability to identify trends and patterns. Although this method is more powerful than the first type, it requires large amounts of training data and therefore is less agile. Each ATR performs threat characterization at the voxel neighborhood level. This approach avoids the use of threat shape as a detection criterion, which is prohibited by DHS and TSA guidelines.

97 MATHEMATICS AND COMPUTING↗

Machine learning approach to pattern recognition in nuclear dynamics from the ab initio symmetry-adapted no-core shell model

A novel machine learning approach is used to provide further insight into atomic nuclei and to detect orderly patterns amid a vast data of large-scale calculations. The method utilizes a neural network that is trained on ab initio results from the symmetry-adapted no-core shell model (SA-NCSM) for light nuclei. We show that the SA-NCSM, which expands ab initio applications up to medium-mass nuclei by using dominant symmetries of nuclear dynamics, can reach heavier nuclei when coupled with the machine learning approach. In particular, we find that a neural network trained on probability amplitudes for s- and p-shell nuclear wave functions not only predicts dominant configurations for heavier nuclei but in addition, when tested for the 20 Ne ground state, accurately reproduces the probability distribution. The non-negligible configurations predicted by the network provide an important input to the SA-NCSM for reducing ultralarge model spaces to manageable sizes that can be, in turn, utilized in SA-NCSM calculations to obtain accurate observables. The neural network is capable of describing nuclear deformation and is used to track the shape evolution along the 20-42 Mg isotopic chain, suggesting a shape coexistence that is more pronounced toward the very neutron-rich isotopes. We provide first descriptions of the structure and deformation of 24 Si and 40 Mg of interest to x-ray burst nucleosynthesis, and even of the extremely heavy nuclei such as 166,168 Er and 236 U, that build on first-principles considerations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗