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DOE OSTI2023

Universal Utility Data Exchange (UUDEX): Information Exchange Models for Solar DER (Rev. 1)

This report describes how the Universal Utility Data Exchange (UUDEX) can encapsulate and exchange information about distributed energy resources (DER) within UUDEX-formatted JSON documents. It proposes to use the existing extensible markup language (XML) information exchange format described in IEEE Std 2030.5, IEEE Standard for Smart Energy Profile Application Protocol but not other information exchange provisions of IEEE 2030.5, rather, relying on equivalent mechanisms in UUDEX. This will allow adoption of the UUDEX exchanges with minimal changes to the structure of the information exchanged and will not require a modification to the UUDEX documentation if IEEE 2030.5 makes changes to the information models.

14 SOLAR ENERGY↗

DOE OSTI2023

Universal Utility Data Exchange (UUDEX): Information Exchange Models for Solar DER

42 ENGINEERING↗

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 OSTI2015

SU-E-J-129: Atlas Development for Cardiac Automatic Contouring Using Multi-Atlas Segmentation

Purpose: To develop a set of atlases for automatic contouring of cardiac structures to determine heart radiation dose and the associated toxicity. Methods: Six thoracic cancer patients with both contrast and non-contrast CT images were acquired for this study. Eight radiation oncologists manually and independently delineated cardiac contours on the non-contrast CT by referring to the fused contrast CT and following the RTOG 1106 atlas contouring guideline. Fifteen regions of interest (ROIs) were delineated, including heart, four chambers, four coronary arteries, pulmonary artery and vein, inferior and superior vena cava, and ascending and descending aorta. Individual expert contours were fused using the simultaneous truth and performance level estimation (STAPLE) algorithm for each ROI and each patient. The fused contours became atlases for an in-house multi-atlas segmentation. Using leave-one-out test, we generated auto-segmented contours for each ROI and each patient. The auto-segmented contours were compared with the fused contours using the Dice similarity coefficient (DSC) and the mean surface distance (MSD). Results: Inter-observer variability was not obvious for heart, chambers, and aorta but was large for other structures that were not clearly distinguishable on CT image. The average DSC between individual expert contours and the fused contours were less than 50% for coronary arteries and pulmonary vein, and the average MSD were greater than 4.0 mm. The largest MSD of expert contours deviating from the fused contours was 2.5 cm. The mean DSC and MSD of auto-segmented contours were within one standard deviation of expert contouring variability except the right coronary artery. The coronary arteries, vena cava, and pulmonary vein had DSC<70% and MSD>3.0 mm. Conclusion: A set of cardiac atlases was created for cardiac automatic contouring, the accuracy of which was comparable to the variability in expert contouring. However, substantial modification may need for auto-segmented contours of indistinguishable small structures.

60 APPLIED LIFE SCIENCES↗

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 OSTI2017

IR-IR Conformation Specific Spectroscopy of Na + (Glucose) Adducts

Here in this paper we report an IR-IR double resonance study of the structural landscape present in the Na + (glucose) complex. Our experimental approach involves minimal modifications to a typical IR predissociation setup, and can be carried out via ion-dip or isomer-burning methods, providing additional flexibility to suit different experimental needs. In the current study, the single-laser IR predissociation spectrum of Na + (glucose), which clearly indicates contributions from multiple structures, was experimentally disentangled to reveal the presence of three α-conformers and five β-conformers. Comparisons with calculations show that these eight conformations correspond to the lowest energy gas-phase structures with distinctive Na+ coordination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Three-dimensional carbon allotropes comprising phenyl rings and acetylenic chains in sp + sp 2 hybrid networks

Here, we here identify by ab initio calculations a new type of three-dimensional (3D) carbon allotropes that consist of phenyl rings connected by linear acetylenic chains in sp + sp 2 bonding networks. These structures are constructed by inserting acetylenic or diacetylenic bonds into an all sp 2 -hybridized rhombohedral polybenzene lattice, and the resulting 3D phenylacetylene and phenyldiacetylene nets comprise a 12-atom and 18-atom rhombohedral primitive unit cells R - 3 m symmetry, which are characterized as the 3D chiral crystalline modification of 2D graphyne and graphdiyne, respectively. Simulated phonon spectra reveal that these structures are dynamically stable. Electronic band calculations indicate that phenylacetylene is metallic, while phenyldiacetylene is a semiconductor with an indirect band gap of 0.58 eV. The present results establish a new type of carbon phases and offer insights into their outstanding structural and electronic properties.

36 MATERIALS SCIENCE↗

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 OSTI2017

Activation of Nrf2 attenuates carbonyl stress induced by methylglyoxal in human neuroblastoma cells: Increase in GSH levels is a critical event for the detoxification mechanism

The present study focused on the methylglyoxal (MG) detoxification mechanism in neuroblastoma cells. The involvement of nuclear factor erythroid 2-related factor 2 (Nrf2)/Kelch-like ECH-associated protein 1 (Keap1) pathway as a defense response against the formation of MG-modified proteins, which is well-known evidence of carbonyl stress, was also examined. We found that MG treatment resulted in accumulation of modified proteins bearing the structure of advanced glycation end products (AGEs) derived from MG in SH-SY5Y cells. This accumulation was suppressed by activation of the Nrf2 pathway prior to MG exposure via pre-treatment with an Nrf2 activator, carnosic acid and CDDO-Im, confirming the involvement of the Nrf2 pathway in MG detoxification. Although pre-treatment with the Nrf2 activator did not affect mRNA levels of GLO1, AKR1B1, and AKR7A2, the expressions of GCL and xCT mRNA, involved in GSH synthesis, were induced prior to increase in GSH levels. Furthermore, we demonstrated that a GSH synthesis inhibitor eliminated the MG detoxification effect derived from pretreatment with the Nrf2 activator. These results indicated that increase in GSH levels, induced by pre-treatment with carnosic acid, promoted the formation of the GLO1 substrate, hemithioacetal, thereby accelerating MG metabolism via the glyoxalase system and suppressing its toxicity. It was, therefore, determined that promotion of GSH synthesis via the Nrf2/Keap1pathway is important in the MG detoxification mechanism against neuronal MG-induced carbonyl stress, and Nrf2 activators contribute to reduction in the accumulation and toxic expression of carbonyl proteins. - Highlights: • Nrf2 activator prevents methylglyoxal-induced cytotoxicity and protein modifications. • MG treatment resulted in accumulation of modified proteins bearing the structure of CEL and MG-H1. • The promotion of GSH synthesis by activation of Nrf2 is a key response to MG detoxification.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. In this report, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine–tryptophan cross-link, which is installed by the radical S -adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon–carbon cross-link in the streptide family of natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Magnetic modification at sub-surface of FeRh bulk by energetic ion beam irradiation

Ferromagnetic layered structure has been made at sub-surface of the antiferromagnetic FeRh bulk samples by high energy He ion beam irradiation. In accordance with the Transport of Ions in Matter simulation, such ion beam can effectively deposit the elastic collision energy in several μm regions in the depth from the surface. Measurement with a superconducting quantum interference device reveals the irradiated samples to be ferromagnetic. Assuming that only the part the energy deposited can be modified to be ferromagnetic, the corresponding irradiation induced magnetization is consistent with the data that we previously reported. On the other hand, the X-ray magnetic circular dichroism (XMCD) spectra for the irradiated samples are totally unchanged as those for the unirradiated samples. Since XMCD signal in total emission yield method is considered to be surface sensitive with a typical probing depth of several nm, the surface magnetic state is maintained to be antiferromagnetic. By utilizing these phenomena, three-dimensional magnetic patterning of FeRh can be realized, which may potentially be used for future magnetic exchange device application such as nano-scale sensors and memories.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗