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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues

This study employed structural information from cocrystals of rufomycin 4 (1a) and caseinolytic protein C1 (ClpC1)-NTD-wt to guide design and semisynthesis of rufomycin analogues, evaluate their antituberculosis (TB) biological profiles, and establish structure–activity relationships (SAR). Covering three regions of interest (ROIs, A–C) as modification sites, 14 of the 30 semisynthetic analogues (2–31) showed similar or improved MICs relative to the main natural precursors, rufomycins 4/6 (1a/b). Compounds 5 and 27 exhibited up to 10-fold enhanced potency against Mycobacterium tuberculosis (Mtb) in vitro, with MIC values of 1.9 and 1.4 nM, respectively. Evaluation of ClpC1-binding properties used existing ClpC1-NTD complexes with rufomycin 4 (PDB: 6cn8) and ecumicin (PDB: 6pbs) as references. The newly reported X-ray ClpC1-NTD cocrystal structure of 11 (syn. But4-Cl) revealed significant conformational effects involving the side chains of certain amino acids of the heptapeptide and confirmed the importance of ROIs A–C for medicinal chemistry efforts. Observed interactions of the N-terminal tail of ClpC1 with the rufomycin analogues vs ecumicin explains their different modes of inactivating the ClpC1/P1/P2 homeostatic machinery. Collectively, the observations inform further SAR optimization strategies for the rufomycin class of antibiotics and complement our understanding of their mode of action.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

From primordial clocks to circadian oscillators

Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides , which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Voltage-Current Behavior of a Superconducting STAR ® Wire in a 6-Around-1 Cable Configuration

A 6-around-1 transposed cable using superconducting STAR® wires can be useful for future circular collider applications. We made three cable samples using single STAR® wires with a diameter of 1.3 mm. The first two samples, made with a cabling machine, used STAR® wires consisting of a 0.7 mm diameter Nb-Ti core. The third cable sample was manually wound and used a STAR® wire made with a 0.81 mm diameter Cu core. The first sample showed severe degradation after the cable was bent to a 75 mm radius. The current-carrying capability of the innermost and outermost REBCO tapes in the STAR® wire degraded by 42% to 98% and the middle REBCO tapes remained intact. This was also the case for the second and straight cable sample. After fabrication of the third cable sample, we observed only about 5% reduction in the current along the wire, measured at different locations inside the terminations. Finally, the results indicate that the differences in architecture or fabrication of the STAR® wires could have caused differences in critical current retention after cabling.

6-around-1 cable↗
DOE OSTI2021

System and method for implementing a zero-sequence current filter for a three-phase power system

In a three-phase, four-wire electrical distribution system, a zig-zag transformer and at least one Cascade Multilevel Modular Inverter (CMMI) is coupled between the distribution system and the neutral. A controller modulates the states of the H-bridges in the CMMI to build an AC waveform. The voltage is chosen by the controller in order to control an equivalent impedance that draws an appropriate neutral current through the transformer. This neutral current is generally chosen to cancel the neutral current sensed in the line. The chosen neutral current may be based on a remotely sensed imbalance, rather than on a local value, determined by the power utility as a critical load point in the system. The desired injection current is then translated by the controller into a desired zero-sequence reactive impedance, based on measurement of the local terminal voltage, allowing the controller to regulate the current without generating or consuming real power.

Benavides, Nicholas↗
DOE OSTI2026

Weak-lensing Detection of Intercluster Filaments in Three Nearby Cluster Systems

Abstract Direct detection of intercluster filaments is challenging due to their low surface density, resulting in a weak deflection field. We present weak-lensing detections of intercluster filaments using wide-field Dark Energy Camera observations from the Local Volume Complete Cluster Survey. A matched-filter method was applied to identify filamentary structures in three nearby ( z < 0.1) systems centered on A401, A2029, and A3558. We discover two filaments (>3 σ ) in each system, with the strongest detections (5.2 σ –5.8 σ ) around A401 and A2029. In particular, we report the first robust weak-lensing detections (≳5 σ ) of the intercluster bridges connecting the cluster pairs A401/399, A2029/2033, A2029/SIG, and A3558/3556. Adopting a filament convergence model motivated by numerical simulations, we infer the maximum convergence ( κ 0 ) and characteristic width ( h c ) for all six filaments, yielding κ 0 ∼ 0.016–0.040 and h c ∼ 0.23–0.43 Mpc. The performance of the matched-filter technique is validated using mock shear catalogs and further tested on a null field around A2351. We explore the potential of using the B-mode lensing signal of filaments to suppress cluster-induced shear contamination. We also quantify the biasing effect of closely separated terminal clusters to the filament signal. These results demonstrate the feasibility of directly mapping dark matter filaments with current and future wide-field weak-lensing datasets.

Shinde, Rahul [Brown University] (ORCID:0000000273↗
DOE OSTI2024

Plutonium and Cerium Perrhenate/Pertechnetate Coordination Polymers and Frameworks

Spent nuclear fuel (SNF) contains transuranic and lanthanide species, which are sometimes recovered and repurposed. One particularly problematic fission product, 99 TcO 4 – , hampers this recovery via coextraction with high valence metals, perhaps by complexation during aqueous reprocessing of SNF. There is limited molecular-level knowledge concerning the coordination chemistry between TcO 4 – or its well-known surrogate ReO 4 – and transuranic/lanthanide species. In the current study, we investigated the coordination of ReO 4 – /TcO 4 – with plutonium and cerium cations by structural and chemical characterization of a series of isolated extended solids. In this study, Ce represents both trivalent lanthanides and is considered a surrogate for Pu, respectively, in its common trivalent and tetravalent oxidation states. The structural elucidation of the seven isolated crystalline solids revealed that ReO 4 – /TcO 4 – directly connects to Pu IV , Pu VI O 2 2 + , Ce III , and Ce IV in the terminal and bridging coordination modes, leading to 1-, 2-, and 3-dimensional frameworks. For example, ReO 4 – coordination to Pu(IV) formed a 1D chain or 2D framework, isostructural with previously isolated Th(IV) compounds. However, Pu VI O 2 2 + alternating with ReO 4 – led to a unique 1D chain, different from the prior-reported U(VI)/Np(VI)-ReO 4 – /TcO 4 – structures. Coordination of ReO 4 – /TcO 4 – with Ce(III) promotes the assembly of 3D frameworks. Finally, attempted synthesis of a Ce(IV)-ReO 4 – compound resulted in a 2D framework with a mixed-valence Ce III/IV . The highly acidic reaction conditions supported the reduction of both Ce IV and Tc VII , challenging isolation of compounds featuring these species. Only one TcO 4 -containing structure was obtained in this study (Ce III –TcO 4 3D framework), vs the six total Ce/Pu-ReO 4 compounds. Furthermore, our three Pu-ReO 4 crystal structures are the first reported and translated to atomic-level information about Pu-TcO 4 coordination in nuclear fuel reprocessing scenarios, in addition to broadening our knowledge of bonding trends in the early, high-valence actinides.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

The Escherichia coli MFS-type transporter genes yhjE, ydiM, and yfcJ are required to produce an active bo3 quinol oxidase

Heme-copper oxygen reductases are membrane-bound oligomeric complexes that are integral to prokaryotic and eukaryotic aerobic respiratory chains. Biogenesis of these enzymes is complex and requires coordinated assembly of the subunits and their cofactors. Some of the components are involved in the acquisition and integration of different heme and copper (Cu) cofactors into these terminal oxygen reductases. As such, MFS-type transporters of the CalT family ( e . g ., CcoA) are required for Cu import and heme-Cu B center biogenesis of the cbb 3 -type cytochrome c oxidases ( cbb 3 -Cox). However, functionally homologous Cu transporters for similar heme-Cu containing bo 3 -type quinol oxidases ( bo 3 -Qox) are unknown. Despite the occurrence of multiple MFS-type transporters, orthologs of CcoA are absent in bacteria like Escherichia coli that contain bo 3 -Qox. In this work, we identified a subset of uncharacterized MFS transporters, based on the presence of putative metal-binding residues, as likely candidates for the missing Cu transporter. Using a genetic approach, we tested whether these transporters are involved in the biogenesis of E . coli bo 3 -Qox. When respiratory growth is dependent on bo 3 -Qox, because of deletion of the bd -type Qox enzymes, three candidate genes, yhjE , ydiM , and yfcJ , were found to be critical for E . coli growth. Radioactive metal uptake assays showed that Δ ydiM has a slower 64 Cu uptake, whereas Δ yhjE accumulates reduced 55 Fe in the cell, while no similar uptake defect is associated with Δ ycfJ . Phylogenomic analyses suggest plausible roles for the YhjE, YdiM, and YfcJ transporters, and overall findings illustrate the diverse roles that the MFS-type transporters play in cellular metal homeostasis and production of active heme-Cu oxygen reductases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Polyhydrido Copper Nanoclusters with a Hollow Icosahedral Core: [Cu 30 H 18 {E 2 P(OR) 2 } 12 ] (E=S or Se; R= n Pr, i Pr or i Bu)

Although atomically precise polyhydrido copper nanoclusters are of prime interest for a variety of applications, they have so far remained scarce. Here, we describe the synthesis of a dithiophosphate-protected copper(I) hydride-rich nanocluster (NC), [Cu 30 H 18 {S 2 P(O n Pr) 2 } 12 ] ( 1 H ), fully characterized by various spectroscopic methods and single-crystal X-ray diffraction. The X-ray structure of 1 H reveals an unprecedented central Cu 12 hollow icosahedron. Six faces of this icosahedron are capped by Cu 3 triangles, the whole Cu 30 core being wrapped by twelve dithiophosphate ligands and the whole cluster has ideal S 6 symmetry. The locations of the 18 hydrides in 1 H were ascertained by a single-crystal neutron diffraction study. They are composed of three types: capping μ 3 -H, interstitial μ 4 -H (seesaw) and μ 5 -H ligands (square pyramidal), in good agreement with the DFT simulations. The numbers of hydrides and ligand resonances in the 1 H NMR spectrum of 1 H are in line with their coordination environment in the solid state, retaining the S 6 symmetry in solution. Furthermore, two new Se-protected polyhydrido copper nanoclusters, [Cu 30 H 18 {Se 2 P(OR) 2 } 12 ] ( 2 H : R= i Pr 3 H : R= i Bu) were synthesized from their sulfur relative 1 H via ligand displacement reaction and their X-ray structures feature the exceptional case where both the NC shape and size are fully conserved during the course of ligand exchange. DFT and TD-DFT calculations allow understanding the bonding and optical properties of clusters 1 H – 3 H . In addition, the reaction of 1 H with [Pd(PPh 3 ) 2 Cl 2 ] in the presence of terminal alkynes led to the formation of new bimetallic Cu–Pd alloy clusters [PdCu 14 H 2 {S 2 P(O n Pr) 2 } 6 (C≡CR) 6 ] ( 4 : R=Ph; 5 : R = C 6 H 4 F).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Probing Electron Correlations in 1D Electronic Materials Using Single Quantum Channels (Final Technical Report)

This research focuses on the investigation of strong electron correlations in quasi-one-dimensional oxide nanostructures. The archetypical system consisting of heterostructures formed from an ultrathin layer of LaAlO 3 and TiO 2 -terminated SrTiO 3 offers a unique laboratory for probing strong correlations due to intrinsic richness of the physical system and its ability to be modulated at extreme nanoscale dimensions. Under suitable conditions, SrTiO 3 is known to exhibit a variety of important properties associated with strong electronic correlations, especially superconductivity, magnetism. Understanding the nature of these electronic correlations at fundamental scales, and in reduced spatial dimensions, will provide the scientific basis for new energy technologies, information technologies, and materials. The research program is motivated by recent discoveries and technical advances in the PIs' lab, specifically, (1) pioneering work to create conductive nanostructures to be created in LaAlO 3 /SrTiO 3 heterointerfaces with 2 nm spatial resolution, (2) the discovery of a novel correlated electronic phases in which electrons pair without forming a superconductor, and (3) the demonstrated ability to form high-quality quantum point contacts (QPCs) and achieve ballistic electron transport over micrometer-scales in LaAlO 3 /SrTiO 3 nanowires. The program has three major components. First, we have press forward to develop a full microscopic understanding of the mechanism for electron pairing in LaAlO 3 /SrTiO 3 nanostructures. Understanding the “glue” that leads to pairing and superconductivity in a doped semiconductor will help to form a scientific basis for the correlated oxide nanoelectronics platform being developed. Second, we have used their ability to create well-defined quantum channels in nanowires allows to allow novel “scattering” experiments to be performed that probe fundamentally new quasiparticle excitations using an unprecedented combination of experimental methodologies. Experiments already underway with artificially defined superlattices (5 nm period) demonstrate the feasibility of this approach. Third, we have investigated 1D correlations in proximally coupled nanowires, which are predicted exhibit Majorana-like zero modes in the absence of superconductivity or spin-orbit coupling. These studies provide insight not only into new and emergent phenomena in the rich class of complex oxides, but also fundamental mechanisms of superconductivity and magnetism. Thematically, the research aims to combine some of the most important and interesting challenges in the physics of semiconductor nanostructures and correlated electronic materials. The increased understanding of electron correlations can pave the way to the development of new materials with outstanding or novel properties, which could be relevant for energy-related technologies such as low-power high performance computing, quantum computation, or the development of novel materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large–scale in silico and in vivo analyses

Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C-terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large-scale and in-depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low-frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated in vivo. Follow-up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a ‘basic-nonpolar-basic’ pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons

Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.

Genetics & Heredity↗
DOE OSTI2021

Impact of solar geoengineering on temperatures over the Indonesian Maritime Continent

Climate change has been projected to increase the intensity and magnitude of extreme temperature in Indonesia. Solar radiation management (SRM) has been proposed as a strategy to temporarily combat global warming, buying time for negative emissions. Though the global impacts of SRM have been extensively studied in recent years, regional impacts, especially in the tropics, have received much less attention. This paper investigates the potential stratospheric sulfate aerosol geoengineering to modify mean and extreme temperature, as well as the relative humidity and wet bulb temperature (WBT) change over Indonesian Maritime Continent (IMC) based on simulations from three different earth system models. We applied statistical downscaling and corrected the bias of model output to reproduce historical temperatures and relative humidity over IMC. We compared SRM as specified by the Geoengineering Model Intercomparison Project (GeoMIP) G4 experiment – 5 Tg of SO 2 into the lower stratosphere between 2020 and 2069 – concurrent with the RCP4.5 emissions scenario. SRM is able to significantly reduce the temperature means and extremes, and although differences in magnitude of response and spatial pattern occur, there is a generally consistent response. Additionally, the spatial response of changes forced by RCP4.5 scenario and SRM impact is notably heterogeneous in the archipelago, highlighting uncertainties that would be critical in assessing socio-economic consequences of both doing, and not doing SRM. In general, SRM has bigger impacts in reducing temperatures over land than oceans, and the southern monsoon region shows more variability. SRM is also effective at reducing the likelihood of WBT > 27OC events compared to RCP4.5 after some years of SRM deployment as well as during the post-termination period of SRM. Regional downscaling may be an effective tool in obtaining policy-relevant information about local effects of different future scenarios involving SRM.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

An Open-source Llm Enhanced-tool Specialized In Helping Moose Related Problems And Tasks

MOOSEenger is an open-source, terminal-first chat application for the MOOSE ecosystem that couples specialized parsing of MOOSE documentation and “.i” input files with retrieval-augmented generation to deliver grounded answers about multiphysics modeling and workflows. It includes dedicated readers for MOOSE-style HTML and a pyhit-based parser that uses the MOOSE syntax tree to preserve block structure and attach retrieval metadata. A data-ingestion pipeline performs semantic chunking into atomic facts and stores them hierarchically in a local Chroma vector database that maintains parent–child relationships across documents; the system can ingest directories, individual files, and single-page web content, and it provides CRUD operations (insert, update, delete) to manage the corpus. At query time, relevant chunks are embedded, retrieved, and fused into the model context, with interactive features such as token streaming, persistent chat history, and dynamic RAG (retrieval triggered by user input or intermediate model output). Deployment is flexible: MOOSEenger runs with local Ollama models or remote Hugging Face/OpenAI backends—typically coordinating generation, lightweight tagging/summarization, and embeddings across three models—and it also supports a server mode and integration with the VS Code Continue interface.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗
DOE OSTI2020

The carboxylation status of osteocalcin has important consequences for its structure and dynamics

The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Optimisation of the Kaplan hydropower system via PID 2 and digital twin

Here, this paper proposes a proportional–integral-double–derivative (PID 2 ) optimisation method for the Kaplan hydropower system by building a digital twin. The study first uses one multilayer perceptron (MLP) to model the hydroturbine dynamic and then adopts three connected MLPs to model the generator dynamic, both in an open-loop fashion. Inspired by stochastic distribution control (SDC) theory, we regard the training of the turbine's neural network model as a process control problem, and we propose minimising entropy loss to update the network parameters. The next step is to build the digital twin by connecting the neural network models with a PID 2 controller and a lead-lag exciter and run the whole model in a closed-loop fashion. After that, a binary search approach is applied to optimise the PID 2 parameters based on the obtained digital twin model. The simulation results show that the proposed method can reduce the mean square tracking error by more than 90%. Furthermore, the method is extended to jointly optimise the PID 2 controller and excitation system gains through multiobjective optimisation, leveraging Pareto frontier analysis to balance active power and voltage tracking performance. Simulation results confirm the effectiveness of the proposed method, achieving a 83.46% reduction in relative mean square error of active power, a 47.13% reduction in terminal voltage tracking error, and an 82.78% improvement in the overall scalarized objective.

Hydropower system↗
DOE OSTI2021

Scaling of atomic layer etching of SiO 2 in fluorocarbon plasmas: Transient etching and surface roughness

Fabricating sub-10 nm microelectronics places plasma processing precision at atomic dimensions. Atomic layer etching (ALE) is a cyclic plasma process used in semiconductor fabrication that has the potential to remove a single layer of atoms during each cycle. In self-limiting ideal ALE, a single monolayer of a material is consistently removed in each cycle, typically expressed as EPC (etch per cycle). In plasma ALE of dielectrics, such as SiO 2 and Si 3 N 4 , using fluorocarbon gas mixtures, etching proceeds through deposition of a thin polymer layer and the process is not strictly self-terminating. As a result, EPC is highly process dependent and particularly sensitive to the thickness of the polymer layer. In this paper, results are discussed from a computational investigation of the ALE of SiO 2 on flat surfaces and in short trenches using capacitively coupled plasmas consisting of a deposition step (fluorocarbon plasma) and an etch step (argon plasma). We found that ALE performance is a delicate balance between deposition of polymer during the first half cycle and etching (with polymer removal) during the second half cycle. In the absence of complete removal of the overlying polymer in each cycle, ALE may be transient as the polymer thickness grows with each cycle with a reduction in EPC until the thickness is too large to enable further etching. Small and statistical amounts of polymer left from a previous cycle can produce statistical variation in polymer thickness on the next cycle, which in turn can lead to a spatially dependent EPC and ALE roughness. Based on synergy between T i (sputtering time) and T p (passivation time), dielectric ALE can be described as having three modes: deposition, roughening surface (transitioning to etch-stop), and smooth surface with steady-state EPC.

Materials Science↗
DOE OSTI2024

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Increasing Power Generation at the Patua Nevada Geothermal Field through Targeted and Adaptive EGS

In 2020, Patua Acquisition Company LLC, submitted the proposal “Increasing Power Generation at the Patua Nevada Geothermal Field through Targeted and Adaptive EGS”, in response to the DOE’s Geothermal Wells of Opportunity Funding Opportunity Announcement. The primary goal of the project was to convert an idle well, Patua 16-29, to an active producer and generate at least an additional 5 MWe at the Patua plant. The project was intended to provide an example of a reproducible methodology for well stimulation in Enhanced Geothermal Systems The project was proposed to be performed in three phases over a period of performance of four years. A first project go/no-go decision was made at the end of Phase 1 based on feasibility of the wellbore, site, and ability to realize a 5 MWe benefit from the project. Several factors were recognized that led to a no-go decision at this phase: • Electrical needs for placing the stimulated well on production were not considered in the initial scoping. Costs of pipeline costs were also underestimated in the original cost share. Easements and rights-of-way to establish a geothermal pipeline underneath or across an interstate highway were also found to be intractable on the time scale of the project. • The plant is injection limited, and no design or cost estimate was in place to handle the additional production needed to realize a 5 Mwe benefit. A new injection well would need to be drilled in addition to the other facility improvements to bring in the stimulated well. Patau Acquisition Company attempted to locate additional wells of opportunity that could realize the SOPOs goals, but was unsuccessful. As a result, this project is being terminated at the end of Phase 1.

15 GEOTHERMAL ENERGY↗