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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 127 records · Page 7

Shock wave formation from head-on collision of two subsonic vortex rings

Vortex ring collisions have attracted intense interest in both water and air studies (Baird in Proc R Soc Lond Ser Math Phys Sci 409:59–65, 1987, Poudel et al. in Phys Fluids 33:096105, 2021, Lim and Nickels in Nature 357:225, 1992, New et al. in Exp Fluids 57:109, 2016, Suzuki et al. in Geophys Res Lett 34, 2007, Yan et al. in J Fluids Eng 140:054502, 2018, New et al. in J Fluid Mech 899, 2020, Cheng et al. in Phys Fluids 31:067107, 2019, Hernández and Reyes in 29:103604, 2017, Mishra et al. in Phys Rev Fluids, 2021, Zednikova et al. in Chem Eng Technol 42:843–850, 2019, Kwon et al. in Nature 600:64–69, 2021). These toroidal structures spin around a central axis and travel in the original direction of impulse while spinning around the core until inertial forces become predominant causing the vortex flow to spontaneously decay to turbulence (Vortex Rings, https://projects.iq.harvard.edu/smrlab/vortex-rings). Previous studies have shown the collision of subsonic vortex rings resulting in reconnected vortex rings, but the production of a shock wave from the collision has not been demonstrated visibly (Lim and Nickels in Nature 357:225, 1992, Cheng et al. in Phys Fluids 31:067107, 2019). Here we present the formation of a shock wave due to the collision of explosively formed subsonic vortex rings. As the vortex rings travel at Mach 0.66 toward the collision point, they begin to trap high pressure air between them. Upon collision, high pressure air was imploded and released radially away from the axis of the collision, generating a visible shock wave traveling through and away from the colliding vortices at Mach 1.22. Our results demonstrate a pressure gradient with high pressure release creating a shock wave. We anticipate our study to be a starting point for more explosively formed vortex collisions. For example, explosives with different velocities of detonation could be tested to produce vortex rings of varying velocities.

42 ENGINEERING↗

Optical recognition of constructs using hyperspectral imaging and detection (ORCHID)

Abstract Challenges to deep sample imaging have necessitated the development of special techniques such as spatially offset optical spectroscopy to collect signals that have travelled through several layers of tissue. However, these techniques provide only spectral information in one dimension (i.e., depth). Here, we describe a general and practical method, referred to as Optical Recognition of Constructs Using Hyperspectral Imaging and Detection (ORCHID). The sensing strategy integrates (1) the spatial offset detection concept by computationally binning 2D optical data associated with digital offsets based on selected radial pixel distances from the excitation source; (2) hyperspectral imaging using tunable filter; and (3) digital image binding and collation. ORCHID is a versatile modality that is designed to collect optical signals deep inside samples across three spatial (X, Y, Z) as well as spectral dimensions. The ORCHID method is applicable to various optical techniques that exhibit narrow-band structures, from Raman scattering to quantum dot luminescence. Samples containing surface-enhanced Raman scattering (SERS)-active gold nanostar probes and quantum dots embedded in gel were used to show a proof of principle for the ORCHID concept. The resulting hyperspectral data cube is shown to spatially locate target emitting nanoparticle volumes and provide spectral information for in-depth 3D imaging.

47 OTHER INSTRUMENTATION↗

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Seamless integration of commercial Clouds with ATLAS Distributed Computing

The CERN ATLAS Experiment successfully uses a worldwide dis-tributed computing Grid infrastructure to support its physics programme at the Large Hadron Collider (LHC). The Grid workflow system PanDA routinely manages up to 700,000 concurrently running production and analysis jobs to process simulation and detector data. In total more than 500 PB of data are distributed over more than 150 sites in the WLCG and handled by the ATLAS data management system Rucio. To prepare for the ever growing data rate in future LHC runs new developments are underway to embrace industry accepted protocols and technologies, and utilize opportunistic resources in a standard way. This paper reviews how the Google and Amazon Cloud computing ser-vices have been seamlessly integrated as a Grid site within PanDA and Rucio. Performance and brief cost evaluations will be discussed. Such setups could offer advanced Cloud tool-sets and provide added value for analysis facilities that are under discussions for LHC Run-4.

97 MATHEMATICS AND COMPUTING↗

Demagnetization analysis of an 18 GHz electron cyclotron resonance ion source permanent magnet hexapole

An upgrade of ECR2 at the Argonne Tandem Linac Accelerator System is under way, focusing on increasing the intensity capabilities of the facility. ECR2 is a room temperature electron cyclotron resonance ion source, and the upgrade has strict requirements to retain radial access to the plasma chamber and keep the ion source operating without the use of superconducting magnets. The upgrade design with respect to the magnet arrangement and magnetization vectors has recently been presented [R. C. Vondrasek, J. McLain, and R. H. Scott, J. Phys.: Conf. Ser. 2743 , 012044 (2024)] using the same magnetic material as the current ECR2 hexapole. A thorough exploration of the demagnetization potential of this hexapole was carried out, and the risk of demagnetization was deemed too high, despite the magnetic performance meeting the requirements for the upgrade. Additional permanent magnet materials are considered with their respective performance evaluated. Magnet strength and demagnetization resistance are investigated and optimized with the final room temperature design demonstrating a high temperature transient demagnetization resistance and a radial magnetic field of 1.18 T at the plasma chamber wall. Finally, the simulations of this hexapole suggest that it will be sufficient to optimize intensity with a 14.5 GHz driving frequency and will allow 18 GHz operation, while keeping a high safety margin for maintaining magnet performance.

Argonne Tandem Linac Accelerator System↗

A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization

Epitope III, a highly conserved amino acid motif of 524 APTYSW 529 on the hepatitis C virus (HCV) E2 glycoprotein, resides in the critical loop that binds to the host receptor CD81, thus making it one of the most important antibody targets for blocking HCV infections. Here, we have determined the X-ray crystal structure of epitope III at a 2.0-Å resolution when it was captured by a site-specific neutralizing antibody, monoclonal antibody 1H8 (mAb1H8). The snapshot of this complex revealed that epitope III has a relatively rigid structure when confined in the binding grooves of mAb1H8, which confers the residue specificity at both ends of the epitope. Such a high shape complementarity is reminiscent of the “lock and key” mode of action, which is reinforced by the incompatibility of an antibody binding with an epitope bearing specific mutations. By subtly positioning the side chains on the three residues of Tyr 527 , Ser 528 , and Trp 529 while preserving the spatial rigidity of the rest, epitope III in this cocrystal complex adopts a unique conformation that is different from previously described E2 structures. With further analyses of molecular docking and phage display–based peptide interactions, we recognized that it is the arrangements of two separate sets of residues within epitope III that create these discrete conformations for the epitope to interact selectively with either mAb1H8 or CD81. These observations thus raise the possibility that local epitope III conformational dynamics, in conjunction with sequence variations, may act as a regulatory mechanism to coordinate “mAb1H8-like” antibody-mediated immune defenses with CD81-initiated HCV infections.

59 BASIC BIOLOGICAL SCIENCES↗

The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants

Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Empirical scaling of the L–H threshold power for metal wall tokamaks using a multi-device database

The empirical scaling for the H-mode power threshold in tokamaks has been revisited using a database with threshold data from machines with a metallic first wall as part of International Tokamak Physics Activity (ITPA) task TC-26. The database contains discharges from ASDEX Upgrade (AUG) (W), JET (Be/W) and Alcator C-Mod (Mo). This was motivated by reports that in like-for-like discharges the power threshold was reduced by approximately 30% after the change from carbon based to metallic first wall materials on AUG (Ryter et al 2013 Nucl. Fusion 53 113003) and JET (Maggi et al 2014 Nucl. Fusion 54 023007). The database contains L–H transition data for all hydrogen isotopes and mixtures, including T and DT from the recent JET campaigns. Compared to the ITPA 2008 scaling (Martin et al 2008 J. Phys.: Conf. Ser. 123 012033), the metal wall scaling has a smaller magnetic field exponent but a larger density exponent. We present an additional parameter to capture the strong dependence of the L–H power threshold (approx. factor 2) on the magnetic configuration in the divertor on JET. The scaling recovers the approximate inverse isotope mass scaling of the threshold power. Alternative scalings involving the plasma current and poloidal magnetic field are explored. Despite the reduction in threshold observed earlier, the scalings based on the metal wall database do not necessarily extrapolate to a lower threshold for ITER compared to the ITPA 2008 scaling, especially at high density. The divertor configuration effect induces the largest uncertainty in the extrapolation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

59 BASIC BIOLOGICAL SCIENCES↗

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗

A Closer Look at Acyl-ACPs in Lipid Metabolism

Acyl lipids are a wide range of compounds that have diverse functions in membrane synthesis, energy storage, and signal transduction. Fatty acids are key building blocks of acyl lipids that are synthesized by the fatty acid synthase complex via sequential condensation of two-carbon units to reach lengths of up to 18 carbons (Li-Beisson et al., 2013). During this process, the elongating acyl chains are attached to Acyl Carrier Proteins (ACPs) through a phosphopantetheine group linked to a Ser residue of ACPs to form acyl-ACPs, which are central components in de novo fatty acid synthesis. However, the roles of acyl-ACPs in lipid metabolism are rarely studied due to a lack of methods to accurately quantify individual acyl-ACPs and their cargoes.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.

Biochemistry & Molecular Biology↗

Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree

Hydroxynitrile lyase fromHevea brasiliensis(HbHNL) and the esterase SABP2 fromNicotiana tabacumshare the α/β-hydrolase fold, a Ser–His–Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions inHbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineeredHbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C α atoms, and even smaller r.m.s.d.s within the active-site region. Both HNL40 and HNL71 show a restored oxyanion hole and an additional tunnel connecting the active site to the protein surface. This work demonstrates the essential role of distant, indirectly acting residues to catalysis in α/β-hydrolase enzymes.

Biochemistry & Molecular Biology↗

Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila

Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila , can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidase enzyme OgpA, which cleaves peptide bonds at the N-terminus of serine (Ser) or threonine (Thr) residues carrying O-glycan substitutions, with selectivity influenced by the O-glycan functional groups. Using molecular dynamics (MD) simulations and quantum chemistry calculations, we explored how different O-glycan groups affect OgpA's selectivity. Our results show that peptides bind to the enzyme via hydrogen bonds, π–π interactions, van der Waals forces and electrostatic interactions, with key residues, including Tyr90, Val138, Gly176, Tyr210 and Glu91, playing important roles. The primary determinant of selectivity is the interaction between the peptide's functional group and the enzyme's binding cavity, while peptide–enzyme interface interactions are secondary. Quantum chemistry calculations reveal that OgpA prefers peptides with a lower electrophilic character. This study provides new insights into mucin degradation by gut microbiota enzymes, advancing our understanding of this critical biological process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neutron diffraction reveals protonation states in pyridoxal‐5′‐phosphate‐free and glycine external aldimine‐bound serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT) is a critical enzyme in the one-carbon (1C) metabolism pathway catalyzing the reversible conversion of L-Ser into Gly and concurrent transfer of 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF), which is used in the downstream syntheses of biomolecules critical for cell proliferation. The cellular 1C metabolism is hijacked by many cancer types to support cancer cell proliferation, making SHMT a promising target for the design and development of novel small-molecule antimetabolite chemotherapies. To advance structure-assisted drug design, knowledge of SHMT catalysis is crucial, but can only be fully realized when the atomic details of each reaction step governed by the acid–base catalysis are elucidated by visualizing active site hydrogen atoms. Here, we used room-temperature neutron crystallography to directly determine protonation states in Thermus thermophilus SHMT (TthSHMT), capturing protomer A in the apo form lacking the coenzyme pyridoxal 5′-phosphate (PLP), and protomer B as a ternary complex with PLP–Gly-external aldimine and (6S)-5-methyltetrahydrofolate (5MTHF). We observed protonation of the Schiff base nitrogen in PLP–Gly and neutrality of the catalytic Lys226 side chain in the ternary complex, whereas Lys226 is protonated and positively charged in the apo-active site. Furthermore, we obtained an X-ray structure of TthSHMT in complex with the substrate THF, which binds identically as 5MTHF at the peripheral binding site. In conclusion, the unique structural and functional information provided by neutron crystallography, in combination with X-ray structures, can be employed in the rational design of SHMT inhibitors.

X-ray crystallography↗

Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance

Most of the world’s biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS) 26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.

59 BASIC BIOLOGICAL SCIENCES↗

Research three-dimensional hierarchical graphite architectures for anodes for fast charging

With current lithium ion batteries optimized for performance under relatively low charge rate conditions, implementation of XFC has been hindered by drawbacks including Li plating, kinetic polarization, and heat dissipation. This project will utilize model-informed design of 3-D hierarchical electrodes to tune key XFCrelated variables like 1) bulk porosity/tortuosity 2) vertical pore diameter, spacing, and lattice 3) crystallographic orientation of graphite particles relative to exposed surfaces 4) interfacial chemistry of the graphite surfaces through "artificial sEr' formation using ALD 5) current collector surface roughness (aspect ratio, roughness factor, etc.). A key aspect of implementing novel electrodes is characterizing them in relevant settings. For this project, ultimately led out of University of Michigan by Neil Dasgupta, that includes both coin cell and 2+ Ah pouch cell testing, as well as comparison testing against baselines. Sandia National Labs will be conducting detailed cell characterization on iterative versions/improvements of the model-based hierarchical electrodes, as well as COTS cells for baseline comparisons. Key metrics include performance under fast charge conditions, as well as the absence or degree of lithium plating. Sandia will use their unique high precision cycling and rapid EIS capabilities to accurately characterize performance and any lithium plating during 6C charging and beyond, coupling electrochemical observations with cell teardown. Sandia will also design custom fixturing to cool cells during rapid charge, to decouple any kinetic effects brought about by cell heating and allow comparisons between different cells and charge rates. Using these techniques, Sandia will assess HOH electrodes from the University of Michigan, as well as aiding in iterative model and electrode design.

25 ENERGY STORAGE↗