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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 649 records · Page 36
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DOE OSTI2022

Progress in Understanding Short-Range Structure in Nuclei: An Experimental Perspective

High-energy electron scattering is a clean, precise probe for measurements of hadronic and nuclear structure and plays a key role in understanding the role of high-momentum nucleons (and quarks) in nuclei. Jefferson Lab has dramatically expanded our knowledge of the high-momentum nucleons generated by short-range correlations, providing sufficient insight to model much of their impact on nuclear structure in neutron stars and in low- to medium-energy scattering observables, including neutrino oscillation measurements. These short-range correlations also seem related to the modification of the quark distributions in nuclei, and efforts to improve our understanding of the internal structure of these short-distance and high-momentum configurations in nuclei will provide important input on a wide range of high-energy observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition

Methylation of the small ribosome subunit rRNA in the ribosomal decoding center results in exceptionally high-level aminoglycoside resistance in bacteria. Enzymes that methylate 16S rRNA on N7 of nucleotide G1405 (m 7 G1405) have been identified in both aminoglycoside-producing and clinically drug-resistant pathogenic bacteria. Using a fluorescence polarization 30S-binding assay and a new crystal structure of the methyltransferase RmtC at 3.14 Å resolution, here we report a structure-guided functional study of 30S substrate recognition by the aminoglycoside resistance-associated 16S rRNA (m 7 G1405) methyltransferases. We found that the binding site for these enzymes in the 30S subunit directly overlaps with that of a second family of aminoglycoside resistance-associated 16S rRNA (m 1 A1408) methyltransferases, suggesting that both groups of enzymes may exploit the same conserved rRNA tertiary surface for docking to the 30S. Within RmtC, we defined an N-terminal domain surface, comprising basic residues from both the N1 and N2 subdomains, that directly contributes to 30S-binding affinity. In contrast, additional residues lining a contiguous adjacent surface on the C-terminal domain were critical for 16S rRNA modification but did not directly contribute to the binding affinity. The results from our experiments define the critical features of m 7 G1405 methyltransferase–substrate recognition and distinguish at least two distinct, functionally critical contributions of the tested enzyme residues: 30S-binding affinity and stabilizing a binding-induced 16S rRNA conformation necessary for G1405 modification. Our study sets the scene for future high-resolution structural studies of the 30S-methyltransferase complex and for potential exploitation of unique aspects of substrate recognition in future therapeutic strategies.

(ribosomal RNA) ribosome RNA methylation↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight

Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD + -dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. Here, we propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.

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

Polyethylene Glycol Surface Modification and Polythiophene Side-Chain Chemistry: A Combined Strategy toward High-Capacity Lithium-Ion Battery Anodes

In the development of high-capacity lithium-ion batteries (LIBs), the combined optimization of active material interfaces and polymer binder chemistry plays a critical role in improving electrode performance and longevity. This work explores a dual design strategy incorporating polyethylene glycol (PEG) surface modification and carboxylated polythiophene side-chain tailoring to enhance the electrochemical behavior of magnetite (Fe 3 O 4 )-based anodes. PEG is employed to improve interfacial stability, while carboxylated polythiophene binders with varying alkyl side-chain lengths─poly[3-(potassium-4-butanoate)thiophene-2,5-diyl] (P3KBT), poly[3-(potassium-5-pentanoate)thiophene-2,5-diyl] (P3KPT), and poly[3-(potassium-6-hexanoate)thiophene-2,5-diyl] (P3KHT)─are used to modulate molecular interactions and ion transport. Among these three analogs, the PEG–Fe 3 O 4 –P3KHT electrode exhibits superior ion-transfer kinetics, the highest capacity retention, and the lowest charge-transfer resistance after extended cycling. Compared to their non-PEG analogs, PEG-coated electrodes demonstrate enhanced structural integrity and electrochemical behavior, emphasizing the synergistic effects of surface modification and side-chain chemistry. These findings highlight the importance of interfacial interactions and molecular design in achieving robust and high-performance composite anodes for next-generation LIBs.

Fe3O4↗
DOE OSTI2025

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase

Abstract The average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3′-CCA end in the active site cannot proceed until the lysyl–adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS–tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium toward the 3′-CCA end “docked” conformation and allosterically increases h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.

Devarkar, Swapnil C. (ORCID:000000029271243X)↗
DOE OSTI2025

Interfacial oxide and other species in trimethylaluminum-pretreated atomic layer deposition-Al 2 O 3 /GaN characterized by sputter-assisted ToF-SIMS

Deposition techniques, like atomic layer deposition (ALD), are used to form high-quality dielectrics for GaN-based metal–oxide–semiconductor (MOS) gate structures due to the lack of a reliable thermal oxide in GaN. Moreover, interfacial GaO x from pre-existing native oxides is thought to adversely impact channel carrier dynamics and induce undesired threshold voltage shifts in GaN-based MOS gate structures. Exposure of the GaN surface to the trimethylaluminum (TMA) precursor prior to standard alumina ALD decreases the native oxide layer on GaN, but the extent of chemical modification has not been well studied in the context of interface composition in a MOS gate structure. Herein, we compare annealed 55 nm Al 2 O 3 dielectric films on GaN grown using either a water-first ALD process or a process including sequential pulses of TMA immediately before the initiation of Al 2 O 3 ALD. Time-of-Flight Secondary Ion Mass Spectrometry measures differences in the interfacial GaO x content between each ALD film. Here, it also detects surface contaminant species like Si, F, S, and C. Furthermore, we report the formation of an AlN species at the Al 2 O 3 /GaN interface, which is more prominent for the film grown using the TMA pre-pulse step. In general, this work demonstrates that the TMA pre-pulse step is an effective strategy for cleaning substrate surfaces prior to ALD.

Atomic layer deposition↗
DOE OSTI2018

Structural insights into the RNA methyltransferase domain of METTL16

N 6 -methyladenosine (m 6 A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m 6 A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3'-terminal RNA triple helix of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Here, we present two X-ray crystal structures of the N-terminal methyltransferase domain (residues 1–291) of human METTL16 (METTL16_291): an apo structure at 1.9 Å resolution and a post-catalytic S-adenosylhomocysteinebound complex at 2.1 Å resolution. The structures revealed a highly conserved Rossmann fold that is characteristic of Class I S-adenosylmethionine-dependent methyltransferases and a large, positively charged groove. This groove likely represents the RNA-binding site and it includes structural elements unique to METTL16. In-depth analysis of the active site led to a model of the methyl transfer reaction catalyzed by METTL16. In contrast to the major m 6 A methyltransferase heterodimer METTL3/ METTL14, full-length METTL16 forms a homodimer and METTL16_291 exists as a monomer based on size-exclusion chromatography. A native gel-shift assay shows that METTL16 binds to the MALAT1 RNA triple helix, but monomeric METTL16_291 does not. Our results provide insights into the molecular structure of METTL16, which is distinct from METTL3/METTL14.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Modification of carbonyl iron particles by carboxyl-containing polydimethylsiloxanes

The possibility of preparing magnetic particles with the “core–shell” structure was demonstrated. The procedure is based on the treatment of carbonyl iron particles with polydimethylsiloxanes (PDMS) containing terminal or distributed over the chain carboxyl groups attached via the alkyl or aryl spacer. The presence of carboxyl-containing PDMS grafted to the surface of carbonyl iron particles was revealed by electron microscopy. Magnetorheological fluids and magnetic elastomers containing magnetic particles with the “core–shell” structure were obtained, and their rheological properties were studied.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Bending and shear improvements in 3D-printed core sandwich composites through modification of resin uptake in the skin/core interphase region

Fused deposition modeling (FDM) printed polymers are rarely used as a structural material due to anisotropic and low mechanical properties compared with conventional composites. In recent years, greater need has been expressed for recycling of materials, such as recyclable FDM, at the end of service life to reduce environmental pollution and manufacture cost. However, how the amount of resin uptake in the skin and skin/core interphase affects the bending and shear performance of the sandwich composites when replacing the low strength and ductile core (conventional core) with a high strength and brittle core (FDM printed PLA (polylactic acid) core) still remains unclear. A new manufacturing routine is needed to improve the incorporation of FDM printed polymers in composite structures. In this work, FDM printed PLA was used as core material and sandwiched between two unidirectional glass fiber reinforced polymer (GFRP) skins to form a sandwich composite by compression-molding (CM) process, which provides a good manufacturing strategy for skin/core interphase modification. The significance of the CM process is proved by investigating the effect of resin uptake on bending and in-plane/out-of-plane shear performances. Current first order shear deformation (FSDT) theory lacks a direct connection between the in-plane shear stress and out-of-shear stress in the core region of sandwich composites. With the help of DIC, a connection between the in-plane shear and the out-of-plane shear strain was built and in-plane shear properties can acquire through out-of-plane shear properties, hence reducing the redundancy of sample preparation or the need for simulation. A significant improvement was found compared with the optimized resin uptake (Optimized resin uptake range: 20.43%–22.86 wt%) 3D-printed PLA core sandwich composite and lowest performance sandwich composite (Improvement: in-plane shear strength (~34%)/modulus (~29%), out-of-plane shear strength (~25%)/modulus (~31%), specific peak bending load (~19%)). Finally, compared with balsa core sandwich composites, the 3D-printed cores are suitable for use in composite sandwich structures in many applications with a satisfactory strength-to-weight ratio.

3D-printed core sandwich composite↗
DOE OSTI2026

PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thiol redox proteomics: Characterization of thiol-based post-translational modifications

Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Probing the Short-Distance Structure of the Quark-Gluon Plasma with Energy Correlators

Energy-energy correlators (EECs) are promising observables to study the dynamics of jet evolution in the quark-gluon plasma (QGP) through its imprint on angular scales in the energy flux of final-state particles. We carry out the first complete calculation of EECs using realistic simulations of high-energy heavy-ion collisions and dissect the different dynamics underlying the final distribution through analyses of jet propagation in a uniform medium. The EECs of γ -jets in heavy-ion collisions are found to be enhanced by the medium response from elastic scatterings instead of induced gluon radiation at large angles. In the meantime, EECs are suppressed at small angles due to energy loss and transverse momentum broadening of jet shower partons. These modifications are further shown to be sensitive to the angular scale of the in-medium interaction, as characterized by the Debye screening mass. Experimental verification and measurement of such modifications will shed light on this scale and the short-distance structure of the QGP in heavy-ion collisions. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Collisional enhancement of energetic particle Alfvénic resonance width in tokamaks

The phase-space structure of resonances between fast ions and an Alfvénic mode and the associated modification of density profiles in tokamaks are studied as a function of particle collisions. Guiding-center simulations in a realistic tokamak equilibrium are employed to address the resonance broadening parametric dependencies with respect to changes in the pitch-angle scattering rate. The rate of collisional replenishment, along with resonance strength, given by the combination of eigenmode and resonance structures and equilibrium parameters, determines saturation amplitudes for a given damping rate. As seen from the distribution function flattening, collisions have an effect of broadening the resonances, while the absolute value of δf decreases with increasing collisionality. It is observed that the collisional broadening can be comparable to the collisionless resonance width due to the mode amplitude alone. The resonance broadening coefficients are compared with the existing theory based on analytically expected saturation levels, showing fair agreement. Furthermore the results can be useful in assisting reduced kinetic models, such as quasilinear models, when prescribing the effective resonance phase-space width, i.e., the mode-particle interaction platform, due to collisional or turbulent processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial α-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation

Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg 2+ -free structures of KRAS with flexible N-termini. In the Mg 2+ -free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg 2+ -free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg 2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg 2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg 2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Possible reason for the numerical value of the fine-structure constant

A simple picture of the electron emerges if there is a cross section of πλ 2 for vacuum virtual photons to stimulate an isolated electron to emit an additional virtual photon. This reaction mechanism leads to the storage of the rest-mass energy in the surrounding cloud of virtual photons. The Lamb shift can be obtained if one out of every 1/α of the stimulated emissions is preceded by the absorption and re-emission of the incident vacuum virtual photon including the corresponding electron recoil. This suggests a “doorway” cross section of απλ 2 plays a key role in some QED processes. Additional support for this suggestion is obtained via a simple semi-classical picture of Compton scattering. Several speculative semi-classical reaction mechanism choices, including near-field effects, give the anomalous magnetic moment of the free electron. These choices are partially justified by their ability to give the magnetic moment of electrons in hydrogen-like atoms as a function of the atomic number of the corresponding nucleus, close to the correct result. The stimulated-emission process used to obtain the rest-mass energy allows for the possibility that stimulated virtual photons can be exchanged between an electron pair. This exchange can be used to estimate a repulsive force between electrons, and thus allows for a calculation of the fine-structure constant. A result near to the experimental value is obtained with minor modifications to the assumptions that give the rest mass, Lamb shift, and anomalous magnetic moment of the electron. Additional studies are required to confirm or negate the suggestions made here.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Strongly Modified Scaling of CO Hydrogenation in Metal Supported TiO Nanostripes

The boundary between a metal-oxide and its metal support (metal-oxide|support) provides an intriguing structural interface for heterogeneous catalysis. The hydrogenation of CO is a reaction step believed to be rate limiting in electro-chemical CO2 reduction. Density functional theory (DFT) calculations were performed to study this reaction step for a class of catalytic material: metal supported TiO nanostripe. The most stable adsorption sites were identified for all metal supports which showed a striking difference in adsorbate geometry between the strong and weak binding metal supports. The modified CO hydrogenation scaling shows a significant strengthening over (111) and (211) transition metal surfaces. Such enhancement can be attributed to a combination of geometrical effects and metal-oxide|support electronic interactions. A correlation analysis was performed to identify the key features needed to accurately predict *CO and *CHO adsorption energies on the TiO nanostripes and to further validate our physical analysis of the results. This structural motif seems to be a promising avenue to explore scaling modification in other metal-oxide materials and reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗