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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

On the effect of flux-surface shaping on trapped-electron modes in quasi-helically symmetric stellarators

Using a novel optimization procedure, it has been shown that the Helically Symmetric eXperiment stellarator can be optimized for reduced trapped-electron-mode (TEM) instability [Gerard et al., Nucl. Fusion 63, (2023) 056004]. Presently, with a set of 563 experimental candidate configurations, gyrokinetic simulations are performed to investigate the efficacy of available energy EA, quasi-helical symmetry, and flux-surface shaping parameters as metrics for TEM stabilization. It is found that lower values of EA correlate with reduced growth rates, but only when separate flux-surface shaping regimes are considered. Moreover, configurations with improved quasi-helical symmetry demonstrate a similar reduction in growth rates and less scatter compared to EA. Regarding flux-surface shaping, a set of helical shaping parameters is introduced that show increased elongation is strongly correlated with reduced TEM growth rates, however, only when the quasi-helical symmetry is preserved. Using a newly derived velocity-space-averaged TEM resonance operator, these trends are analyzed to provide insights into the physical mechanism of the observed stabilization. For elongation, stabilization is attributed to geometric effects that reduce the destabilizing particle drifts across the magnetic field. Regarding quasi-helical symmetry, the TEM resonance in the maximally resonant trapping well is shown to increase as the quasi-helical symmetry is broken, and breaking quasi-helical symmetry increases the prevalence of highly resonant trapping wells. While these results demonstrate the limitations of using any single metric as a linear TEM proxy, it is shown that quasi-helical symmetry and plasma elongation are highly effective metrics for reducing TEM growth rates in helical equilibria.

Physics↗
DOE OSTI2024

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Chemistry↗
DOE OSTI2024

Verification of electromagnetic simulation capabilities in global gyrokinetic particle-in-cell code GTS

Recently, the numerical scheme presented by Mishchenko et al. enabled explicit gyrokinetic simulations of low-frequency electromagnetic instabilities in tokamaks at experimentally relevant values of plasma β⁠. This scheme resolved the long-standing cancellation problem that previously hindered gyrokinetic particle-in-cell code simulations of magnetohydrodynamic phenomena with inherently small parallel electric fields. Moreover, the scheme did not employ approximations that eliminate critical tearing-type instabilities. Here, we report on the implementation of this numerical scheme in the global gyrokinetic particle-in-cell code GTS. This implementation allows for a more complete and accurate picture of interaction between small scale turbulence and MHD modes in tokamaks. Additionally, we present a comprehensive set of verification simulations of numerous electromagnetic instabilities relevant to present-day tokamaks. These simulations encompass the kinetic ballooning mode, the internal kink mode, the tearing mode, the micro-tearing mode, and the toroidal Alfven eigenmode destabilized by energetic ions, which are all instrumental in understanding tokamak physics. We will also showcase the preliminary nonlinear simulations of kinetic ballooning instabilities and (2,1) island formation due to tearing mode instability. These simulations validate the accuracy of the scheme implementation and pave the way for studying how these instabilities affect plasma confinement and performance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Eigenmode twist by energy flux during fast-ion driven instabilities

Twisting of the spatial structure of eigenmodes by energy fluxes generated due to the spatial channeling (SC)—the fast-ion energy and momentum transfer across the magnetic field by destabilized modes—is considered. It is revealed that there is a correlation between the direction of the radial wave energy flux, orientation of the mode twist (MT), and the direction of mode rotation. The mode twist parameter is introduced and relations connecting it with the energy flux are established. It is shown the energy flux transforms zeros of the radial profile of the mode amplitude into minima (i.e., zeros disappear). It is found that the radial group velocity and phase velocity of reversed shear Alfvén eigenmodes (RSAEs) have opposite directions. These findings can be used for diagnostics of the energy fluxes during fast-ion driven instabilities and understanding whether the SC degrades or improves plasma performance. Specific calculations are carried out for fast magnetoacoustic modes, FMMs (known also as compressional Alfvén eigenmodes, CAEs), and Alfvén eigenmodes, AEs. A DIII-D experiment where RSAEs were observed is considered. It is concluded that an outward SC took place in this experiment. Peculiarities of various modes are discussed, which may explain why twisting of AEs, but not of FMMs, was observed experimentally in the DIII-D and NSTX tokamaks.

Kolesnichenko, Ya. I. (ORCID:0000000323219681)↗
DOE OSTI2025

Analysis of the HAE activity in the TJ-II stellarator using a Landau closure model

The aim of this study is to analyze the stability of helical Alfvén eigenmodes (HAEs) in TJ-II discharges and the stabilizing effect of the energetic particles generated by the neutral beam injector (NBI) on pressure gradient-driven modes (PGDMs). HAE and PGDM stability is studied using the linear version of the gyro-fluid code FAR3d and the continuous structure by the STELLGAP code. First, Alfvén eigenmode (AE) and PGDM activity observed in the experiments is reproduced by the simulations, identifying unstable m/n = 4/7 − 2/3 and 7/12 − 5/8 HAEs triggered around ρ = 0.66 showing a frequency of 209 and 204 kHz, respectively, as well as 5/3 PGDM. Next, a parametric study is performed with respect to the thermal ion density and iota profile in the middle-outer plasma region to verify the robustness of the simulation results with respect to the uncertainty of experimental profiles. The analysis confirms that experimental uncertainty does not cause large deviations in the simulation results, showing the destabilization of the same HAEs for all the configurations tested. The simulations also indicate the decay of the 5/3 PGDM growth rate as the energetic particle (EP) population in the plasma increases, consistent with the experiment. Stability analysis of the n = 3, 7, 11, n = 5, 9, 13, n = 6, 10, 14, and n = 8, 12 helical families is performed with respect to the NBI operational regime for different EP energies, β as well as deposition profiles. The most unstable configuration is the radially localized on-axis NBI operation (stiff EP density profile gradients nearby the magnetic axis). Using the simulation model that reproduces the observed Alfvén activity, we extend the study to analyze NBI performance within a theoretical framework. It shows that increasing NBI voltage (which raises EP energy) leads to a degradation in NBI performance for a given power (related to EP β and their density). To achieve better NBI operation, higher voltage must be balanced with lower injection power, ensuring stable AEs while keeping the same EP β.

Plasma confinement↗
DOE OSTI2025

Carboxylic acid induced restructuring of the Fe 3 O 4 (001) surface

The redox properties of Fe 3 O 4 surfaces are central to many catalytic processes and enable dynamic, reduction-induced morphological restructuring during reactions. Here, we investigate the structural changes of the Fe 3 O 4 (001) surface during the decomposition of formic and acetic acids using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations. Both acids readily deprotonate, forming ordered carboxylate overlayers on the surface. Product formation pathways involve the removal of lattice oxygen, resulting in extensive surface restructuring. For formic acid, only a modest level of surface oxygen removal (∼3%) is observed, resulting in elongated pits along the octahedral Fe rows and exhibiting an aspect ratio of ∼3. In contrast, acetic acid induces more extensive reduction, with the removal of ∼20% of surface oxygen, yielding significantly larger pits while maintaining a similar aspect ratio. Repeated exposure to acetic acid further enlarges the pits, indicating preferential etching at step edges. DFT calculations reveal a mechanistic sequence in which lattice oxygen removal destabilizes adjacent Fe atoms, promoting their migration into the bulk and subsequent pit propagation and step edge formation. Together, these findings provide atomistic insights into the coupling between carboxylic acid conversion and oxide surface restructuring, underscoring the strong interplay between redox chemistry and morphological changes on catalytically active Fe 3 O 4 surfaces.

Ortiz-Garcia, José J. [Pacific Northwest National ↗
DOE OSTI2025

Peeling-ballooning modes in spherical tokamaks: Multi-branch instabilities and effects beyond ideal MHD

A number of important physics effects on the stability of relatively high-n (n is the toroidal mode number) peeling-ballooning modes (PBMs) are investigated based on an equilibrium reconstructed from a NSTX discharge, utilizing extended magnetohydrodynamic (MHD) eigenvalue solvers. For a given toroidal mode number n, multiple branches of instabilities are computed, with the total number of unstable branches roughly linearly scaling with n. Most of the unstable branches are located in the plasma core region, but edge-localized branches, i.e., PBMs, are also identified at higher n-numbers. For the single-fluid-wise most unstable PBM with n = 19⁠, stabilizing/destabilizing effects due to various physics beyond ideal MHD are systematically investigated. Plasma toroidal flow is found to be weakly stabilizing. Local flow shear is generally stabilizing as well, with the degree of stabilization depending on the initial growth rate (without flow shear) of the mode. The plasma resistivity can strongly destabilize the PBM within the single-fluid framework. Anisotropic thermal transport, strong parallel sound wave damping, as well as two-fluid effects are all stabilizing to the mode. In particular, diamagnetic stabilization (within the two-fluid model) is found to be very strong for this mode.

Linear stability analysis↗
DOE OSTI2015

Origins of stereoselectivity in evolved ketoreductases

Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo - and NADP + -bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. Our method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Free-energy landscape of a hyperstable RNA tetraloop

In this paper, we report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Finally, our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

E3 ubiquitin ligase SP1 regulates peroxisome biogenesis in Arabidopsis

Peroxisomes are ubiquitous eukaryotic organelles that play pivotal roles in a suite of metabolic processes and often act coordinately with other organelles, such as chloroplasts and mitochondria. Peroxisomes import proteins to the peroxisome matrix by peroxins (PEX proteins), but how the function of the PEX proteins is regulated is poorly understood. In this study, we identified the Arabidopsis RING (really interesting new gene) type E3 ubiquitin ligase SP1 [suppressor of plastid protein import locus 1 (ppi1) 1] as a peroxisome membrane protein with a regulatory role in peroxisome protein import. SP1 interacts physically with the two components of the peroxisome protein docking complex PEX13–PEX14 and the (RING)-finger peroxin PEX2. Loss of SP1 function suppresses defects of the pex14-2 and pex13-1 mutants, and SP1 is involved in the degradation of PEX13 and possibly PEX14 and all three RING peroxins. An in vivo ubiquitination assay showed that SP1 has the ability to promote PEX13 ubiquitination. Our study has revealed that, in addition to its previously reported function in chloroplast biogenesis, SP1 plays a role in peroxisome biogenesis. The same E3 ubiquitin ligase promotes the destabilization of components of two distinct protein-import machineries, indicating that degradation of organelle biogenesis factors by the ubiquitin–proteasome system may constitute an important regulatory mechanism in coordinating the biogenesis of metabolically linked organelles in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Deciphering the super relaxed state of human β-cardiac myosin and the mode of action of mavacamten from myosin molecules to muscle fibers

Mutations in β-cardiac myosin, the predominant motor protein for human heart contraction, can alter power output and cause cardiomyopathy. However, measurements of the intrinsic force, velocity, and ATPase activity of myosin have not provided a consistent mechanism to link mutations to muscle pathology. An alternative model posits that mutations in myosin affect the stability of a sequestered, super relaxed state (SRX) of the protein with very slow ATP hydrolysis and thereby change the number of myosin heads accessible to actin. Here we show that purified human β-cardiac myosin exists partly in an SRX and may in part correspond to a folded-back conformation of myosin heads observed in muscle fibers around the thick filament backbone. Mutations that cause hypertrophic cardiomyopathy destabilize this state, while the small molecule mavacamten promotes it. These findings provide a biochemical and structural link between the genetics and physiology of cardiomyopathy with implications for therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning

The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing Gaucher disease, an autosomal recessive disorder that displays profound genotype–phenotype nonconcordance. More than 250 disease-causing mutations in GBA1 , the gene encoding GCase, have been discovered, although only one of these, N370S, causes 70% of disease. In this work, we have used a knowledge-based docking protocol that considers experimental data of protein–protein binding to generate a complex between GCase and its known facilitator protein saposin C (SAPC). Multiscale molecular-dynamics simulations were used to study lipid self-assembly, membrane insertion, and the dynamics of the interactions between different components of the complex. Deep learning was applied to propose a model that explains the mechanism of GCase activation, which requires SAPC. Notably, we find that conformational changes in the loops at the entrance of the substrate-binding site are stabilized by direct interactions with SAPC and that the loss of such interactions induced by N370S and another common mutation, L444P, result in destabilization of the complex and reduced GCase activation. Our results provide an atomistic-level explanation for GCase activation and the precise mechanism through which N370S and L444P cause Gaucher disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species

Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. In this work, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases. We show that this oxygen-binding di-iron protein (ODP) acts as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td) . The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable μ-peroxo adduct. Crystal structures of ODP from Td and the thermophile Thermotoga maritima (Tm) in the Fe[III] 2- O 2 2– , Zn[II], and apo states display differences in subunit association, conformation, and metal coordination that indicate potential mechanisms for sensing. In reconstituted systems, iron-peroxo ODP destabilizes the phosphorylated form of the receptor-coupled histidine kinase CheA, thereby providing a biochemical link between oxygen sensing and chemotaxis in diverse prokaryotes, including anaerobes of ancient origin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Allosteric regulation of thioesterase superfamily member 1 by lipid sensor domain binding fatty acids and lysophosphatidylcholine

Nonshivering thermogenesis occurs in brown adipose tissue to generate heat in response to cold ambient temperatures. Thioesterase superfamily member 1 (Them1) is transcriptionally up-regulated in brown adipose tissue upon exposure to the cold and suppresses thermogenesis in order to conserve energy reserves. It hydrolyzes long-chain fatty acyl-CoAs that are derived from lipid droplets, preventing their use as fuel for thermogenesis. In addition to its enzymatic domains, Them1 contains a C-terminal StAR-related lipid transfer (START) domain with unknown ligand or function. By complementary biophysical approaches, we show that the START domain binds to long-chain fatty acids, products of Them1’s enzymatic reaction, as well as lysophosphatidylcholine (LPC), lipids shown to activate thermogenesis in brown adipocytes. Certain fatty acids stabilize the START domain and allosterically enhance Them1 catalysis of acyl-CoA, whereas 18:1 LPC destabilizes and inhibits activity, which we verify in cell culture. Additionally, we demonstrate that the START domain functions to localize Them1 near lipid droplets. Overall, these findings define the role of the START domain as a lipid sensor that allosterically regulates Them1 activity and spatially localizes it in proximity to the lipid droplet.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem-loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. In this work, we solved structures of the bacterial ribosome containing either wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ or tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ containing a reversed 32–38 pair on cognate and near-cognate codons. Structures of wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ bound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon-anticodon interaction is cognate or near cognate. Further, the 32–38 pair is destabilized in the context of a near-cognate codon-anticodon pair. Reversal of the pairing in tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ ablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32–38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electronic structure and photophysics of a supermolecular iron complex having a long MLCT-state lifetime and panchromatic absorption

Exploiting earth-abundant iron-based metal complexes as high-performance photosensitizers demands long-lived electronically excited metal-to-ligand charge-transfer (MLCT) states, but these species suffer typically from femtosecond timescale charge-transfer (CT)-state quenching by low-lying nonreactive metal-centered (MC) states. Here, we engineer supermolecular Fe(II) chromophores based on the bis(tridentate-ligand)metal(II)-ethyne-(porphinato)zinc(II) conjugated framework, previously shown to give rise to highly delocalized low-lying 3 MLCT states for other Group VIII metal (Ru, Os) complexes. Electronic spectral, potentiometric, and ultrafast pump–probe transient dynamical data demonstrate that a combination of a strong σ-donating tridentate ligand and a (porphinato)zinc(II) moiety with low-lying π*-energy levels, sufficiently destabilize MC states and stabilize supermolecular MLCT states to realize Fe(II) complexes that express 3 MLCT state photophysics reminiscent of their heavy-metal analogs. The resulting Fe(II) chromophore archetype, FeNHCPZn, features a highly polarized CT state having a profoundly extended 3MLCT lifetime (160 ps), 3 MLCT phosphorescence, and ambient environment stability. Density functional and domain-based local pair natural orbital coupled cluster [DLPNO-CCSD(T)] theory reveal triplet-state wavefunction spatial distributions consistent with electronic spectroscopic and excited-state dynamical data, further underscoring the dramatic Fe metal-to-extended ligand CT character of electronically excited FeNHCPZn. This design further prompts intense panchromatic absorptivity via redistributing high-energy absorptive oscillator strength throughout the visible spectral domain, while maintaining a substantial excited-state oxidation potential for wide-ranging photochemistry––highlighted by the ability of FeNHCPZn to photoinject charges into a SnO 2 /FTO electrode in a dye-sensitized solar cell (DSSC) architecture. Concepts enumerated herein afford opportunities for replacing traditional rare-metal–based emitters for solar-energy conversion and photoluminescence applications.

74 ATOMIC AND MOLECULAR PHYSICS↗