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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser

We apply ultrashort x-ray laser pulses to track optically excited structural dynamics of [Ir 2 (dimen) 4 ] 2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered x-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir 2 (dimen) 4 ] 2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir 2 (dimen) 4 ] 2+ with a larger Ir–Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. In conclusion, the proposed x-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.

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

Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the “Active” state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the “Active” state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Influence of Surface and Structural Variations in Donor–Acceptor–Donor Sensitizers on Photoelectrocatalytic Water Splitting

Conjugated organic chromophores composed of linked donor (D) and acceptor (A) moieties have attracted considerable attention for photoelectrochemical applications. In this work, we compare the optoelectronic properties and photoelectrochemical performance of two D–A–D structural isomers with thiophene-X-carboxylic acid (X denotes 3 and 2 positions) derivatives and 2,1,3-benzothiadiazole as the D and A moieties, respectively. 5,5′-(Benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-3-carboxylic acid), BTD1, and 5,5′-(benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-2-carboxylic acid), BTD2, were employed in the study to understand how structural isomers affect surface attachments within chromophore–catalyst assemblies and their influence on charge-transfer dynamics. Crystal structures revealed that varying the position of the −COOH anchoring group causes the molecules to either contort out of a plane (BTD1) or adopt a near-perfect planar conformation (BTD2). BTD1 and BTD2 were co-loaded with either a water oxidation catalyst, [Ru(2,6-bis(1-methylbenzimidazol-2-yl)pyridine)-(4,4′-((HO) 2 OPCH 2 )2-2,2′-bipyridine)(OH 2 )] 2 , RuCt 2+ , or proton reduction catalyst [Ni(P 2 Ph N 2 C 6 H 4 CH 2 PO 3 H 2 ) 2 ] 2+ , NiCt 2+ , on oxide electrodes to facilitate photodriven water splitting reactions. Emission quenching measurements indicate that both BTD1 and BTD2 inject electrons into n-type SnO 2 |TiO 2 electrodes and holes into p-type NiO semiconductors from their respective excited states at high efficiencies >60%. Photocurrent densities of chromophore–catalyst assemblies obtained using linear sweep voltammetry (LSV) show that BTD2-sensitized photoanodes generate significantly more photocurrent than BTD1-sensitized electrodes; however, both exhibit similar performances at the photocathode. Photoelectrocatyltic measurements demonstrate that both BTD1 and BTD2 performed similarly, generating Faradaic efficiencies of 39 and 38% at the anode or 61 and 79% at the cathode. Transient absorption measurements suggest that the differences between the LSV and photoelectrocatalytic measurements result from the differences in quantum yields of the photogenerated redox equivalents, which is also a reflection of the varying metal oxide surface conformation. Our findings suggest that BTD2 should be investigated further in photocathodic studies since it has the structural advantage of being incorporated into diverse types of chromophore–catalyst assemblies.

Chromophores↗
DOE OSTI2024

Ca-dimers, solvent layering, and dominant electrochemically active species in Ca(BH4)2 in THF

Abstract Divalent ions (Mg, Ca, and Zn) are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry, but present challenges for stable cycling due to undesirable interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH 4 ) 2 ∣THF using molecular dynamics coupled with a continuum model of bulk and interfacial speciation. Free-energy analysis and unsupervised learning indicate a majority population of neutral Ca dimers and monomers with diverse molecular conformations and an order of magnitude lower concentration of the primary electroactive charged species – the monocation, $${\rm{CaBH}}_{4}^{+}$$ CaBH 4 + – produced via disproportionation of neutral complexes. Dense layering of THF molecules within ~1 nm of the electrode surface strongly modulates local electrolyte species populations. A dramatic increase in monocation population in this interfacial zone is induced at negative bias. We see no evidence for electrochemical activity of fully-solvated Ca 2+ . The consequences for performance are discussed in light of this molecular-scale insight.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Evolution of Chain Dynamics and Oxidation States with Increasing Chain Length for a Donor–Acceptor-Conjugated Oligomer Series

While it is known that the chain length strongly affects the properties of π-conjugated polymers, the effects of chain length on the molecular structure, chain conformation, and oxidation state properties in donor–acceptor-type conjugated structures remain unclear. This limits our understanding of how the polymer molecular weight impacts material properties. Here, a discrete and monodisperse oligomer series (n = 3, 5, 7, 9, 15, and 21) and polymers (nPB), composed of the donor 3,4-propylenedioxythiophene (ProDOT), the acceptor benzothiadiazole (BTD), and methylthio end-capping groups, are synthesized by C–H-activated cross-coupling. The molecular structure, molecular weight, and dispersity of each oligomer/polymer are thoroughly characterized by nuclear magnetic resonance spectroscopy, mass spectrometry, and gel permeation chromatography. This series reveals a rod-to-coil transition at n = 15 and coil formation at polymer length scales of ~28 units via solution small-angle neutron scattering characterization. The oxidation states are deciphered via cyclic voltammetry, differential pulse voltammetry, spectroelectrochemistry, and density functional theory calculations. Oligomers 3–9 undergo successive one-electron oxidation steps, while 15 and higher undergo multielectron oxidations per step in CH 2 Cl 2 –TBAPF6 at a Pt ultramicroelectrode. The electronic transition of each oxidation state (1+, 2+, 3+, etc.) is tracked by absorption spectroscopy, revealing a “bipolaron to di-polaron” transition at n = 7 at which shorter oligomers prefer bipolaron formation and longer oligomers prefer di-polaron formation in their dication states. Furthermore, oxidized 15 has a lower electronic transition energy compared to its polymer homologue, as shown by spectroelectrochemistry, revealing a synergy between the chain length and the oxidation state properties. This study proves that the convergence limit between small molecule and polymer behavior occurs at approximately 15 units and highlights the property transitions that occur as a function of chain length for a donor–acceptor class of conjugated organic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2

Allosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg 2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain—the αX I-domain—corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg 2+ -binding site establish long-range couplings, leading to both pH- and Mg 2+ -occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg 2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH- and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Carbohydrate-aromatic interface and molecular architecture of lignocellulose

Abstract Plant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase

TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Probing single-chain conformation and its impact on the optoelectronic properties of donor–accepter conjugated polymers

The chain conformation of donor–acceptor conjugated polymers (D–A CPs) is critical to their optical and electronic properties. However, probing the conformation of D–A CPs (e.g., persistence length and contour length) at a single-chain level is challenging due to the formation of aggregates in dilute solution, even in a good solvent. In this work, we studied the chain conformation and corresponding optical spectra for high-performance D–A CPs in the single-chain state by multimodal variable-temperature scattering and spectroscopy techniques, as well as by molecular dynamics simulations. Here we found a critical role of the side-chain length and branch point in the persistence length and optical absorption due to steric effects. Hence, it is important to consider both the chain rigidity and coplanarity of the polymer backbone to achieve desirable optoelectronic properties. Our findings bridge the fundamental knowledge gaps to design new CPs with desired optoelectronic properties via molecular engineering for next-generation electronic devices.

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

C-terminal conformational changes in SCF-D3/MAX2 ubiquitin ligase are required for KAI2-mediated signaling

Karrikins (KARs) are bioactive molecules derived from burning vegetation. Plants perceive KARs through the hydrolase KARRIKIN INSENSITIVE 2 (KAI2) that interacts with the F-box protein ubiquitin ligase MORE AXILLARY GROWTH 2 (MAX2). MAX2 also plays a role in the perception and signal activation by Strigolactone (SL), a phytohormone controlling various developmental processes in plants. SL also acts as a rhizosphere signal to activate arbuscular mycorrhiza fungi that can be exploited by parasitic plants. kai2 knockouts exhibit distinct developmental defects and therefore KAI2 is hypothesized to perceive an unidentified endogenous ligand provisionally termed KAI2-Ligand (KL). Upon KAR/KL perception, the protein complex of KAI2-MAX2 targets SUPPRESSOR OF MAX2-1/2 (SMAX1)/SMXL2 for proteasomal degradation. Despite the identification of the key components KAI2, MAX2, and SMAX1 in KAR/KL signaling, their mode of interaction and regulation remains elusive. Recently, the regulatory function of the conformational switch of MAX2 C-terminal helix (CTH) in SL signaling has been demonstrated however its role in KAR/KL signaling remained unknown. Here we address the function of MAX2-CTH dynamics both in vitro and in planta and show that the central role of CTH is conserved between SL and KAR/KL signaling pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗
NASA NTRS1993

Actuated forebody strake controls for the F-18 high alpha research vehicle

A series of ground-based studies have been conducted to develop actuated forebody strake controls for flight test evaluations using the NASA F-18 High-Alpha Research Vehicle. The actuated forebody strake concept has been designed to provide increased levels of yaw control at high angles of attack where conventional rudders become ineffective. Results are presented from tests conducted with the flight-test strake design, including static and dynamic wind-tunnel tests, transonic wind-tunnel tests, full-scale wind-tunnel tests, pressure surveys, and flow visualization tests. Results from these studies show that a pair of conformal actuated forebody strakes applied to the F-18 HARV can provide a powerful and precise yaw control device at high angles of attack. The preparations for flight testing are described, including the fabrication of flight hardware and the development of aircraft flight control laws. The primary objectives of the flight tests are to provide flight validation of the groundbased studies and to evaluate the use of this type of control to enhance fighter aircraft maneuverability.

Murri, Daniel G.↗
NASA NTRS2017

Trajectory Specification for Terminal Air Traffic: Pairwise Conflict Detection and Resolution

Trajectory specification is the explicit bounding and control of aircraft trajectories such that the position at each point in time is constrained to a precisely defined volume of space. The bounding space is defined by cross-track, along-track, and vertical tolerances relative to a reference trajectory that specifies position as a function of time. The tolerances are dynamic and will be based on the aircraft navigation capabilities and the current traffic situation. A standard language will be developed to represent these specifications and to communicate them by datalink. Assuming conformance, trajectory specification can guarantee safe separation for an arbitrary period of time even in the event of an air traffic control (ATC) system or datalink failure, hence it can help to achieve the high level of safety and reliability needed for ATC automation. As a more proactive form of ATC, it can also maximize airspace capacity and reduce the reliance on tactical backup systems during normal operation. It applies to both enroute airspace and the terminal area around airports, but this paper focuses on the terminal area and presents algorithms and software for spacing arrivals and deconflicting both arrivals and departures.

air traffic control↗
DOE OSTI2025

Conformal collider physics meets LHC data

The remarkably high energies of the Large Hadron Collider (LHC) have allowed for the first measurements of the shapes and scalings of multipoint correlators of energy flow operators, ⟨ Ψ | E ( n → 1 ) E ( n → 2 ) ⋯ E ( n → k ) | Ψ ⟩ , providing new insights into the Lorentzian dynamics of quantum chromodynamics (QCD). In this letter, we use recent advances in effective field theory to derive a rigorous factorization theorem for the light-ray density matrix, ρ = | Ψ ⟩ ⟨ Ψ | , inside high transverse momentum jets at the LHC. Using the light-ray operator product expansion, the scaling behavior of multipoint correlators can be computed from the expectation value of the twist-2 spin- J light-ray operators, O [ J ] , in this state, Tr [ ρ O [ J ] ] . We compute the light-ray density matrix at next-to-leading order, and combine this with results for the next-to-leading logarithmic scaling behavior of the correlators up to six-points, comparing with CMS open data. This theoretical accuracy allows us to resolve the quantum scaling dimensions of QCD light-ray operators inside jets at the LHC. Our factorization theorem for the light-ray density matrix at the LHC completes the link between recent developments in the study of energy correlators and LHC phenomenology, opening the door to a wide variety of precision jet substructure studies. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1977

Dynamic spares provisioning for the DSN

A method is proposed to maintain cost-effective spares stockpiles for an entire DSN station or complex as new modules or subsystems are continuously added. Levels of spares are calculated individually for each new module type so as to conform to an established standard for the entire spares pool. Finding the spares levels is computationally simplified and in many cases is reduced to consulting a Down-Time Ratio Chart. A simple modification permits taking into account a criticality factor.

Eisenberger, I.↗
DOE OSTI2023

Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity

DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

An adaptive scalable fully implicit algorithm based on stabilized finite element for reduced visco-resistive MHD

The magnetohydrodynamics (MHD) equations are continuum models used in the study of a wide range of plasma physics systems, including the evolution of complex plasma dynamics in tokamak disruptions. However, efficient numerical solution methods for MHD are extremely challenging due to disparate time and length scales, strong hyperbolic phenomena, and nonlinearity. Additionally, therefore the development of scalable, implicit MHD algorithms and high-resolution adaptive mesh refinement strategies is of considerable importance. In this work, we develop a high-order stabilized finite-element algorithm for the reduced visco-resistive MHD equations based on the MFEM finite element library (mfem.org). The scheme is fully implicit, solved with the Jacobian-free Newton-Krylov (JFNK) method with a physics-based preconditioning strategy. Our preconditioning strategy is a generalization of the physics-based preconditioning methods in Chacón et al. (2002) to adaptive, stabilized finite elements. Algebraic multigrid methods are used to invert sub-block operators to achieve scalability. A parallel adaptive mesh refinement scheme with dynamic load-balancing is implemented to efficiently resolve the multi-scale spatial features of the system. Our implementation uses the MFEM framework, which provides arbitrary-order polynomials and flexible adaptive conforming and non-conforming meshes capabilities. Results demonstrate the accuracy, efficiency, and scalability of the implicit scheme in the presence of large scale disparity. The potential of the AMR approach is demonstrated on an island coalescence problem in the high Lundquist-number regime (≥ 10 7 ) with the successful resolution of plasmoid instabilities and thin current sheets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗