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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Symmetric Mass Generation with Four SU(2) Doublet Fermions

We study a single exactly massless staggered fermion in the fundamental representation of an SU(2) gauge group. We utilize an nHYP-smeared fermion action supplemented with additional heavy Pauli-Villars fields that serve to decrease lattice artifacts. The phase diagram exhibits a clear two-phase structure with a conformal phase at weak coupling and a novel new phase, the symmetric mass generation (SMG) phase, appearing at strong coupling. The SMG phase is confining with all states gapped and chiral symmetry unbroken. Our finite size scaling analysis provides strong evidence that the phase transition between these two phases is continuous, which would allow for the existence of a continuum SMG phase. Furthermore, the renormalization group flows are consistent with a 𝛽 function that vanishes quadratically at the new fixed point, suggesting that the 𝑁 𝑓 = 4 flavor SU(2) gauge theory lies at the opening of the conformal window.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

How Do Ionic Liquids “Fold” Ionenes? Computational and Experimental Analysis of Imidazolium Polymers Based on Ether and Alkyl Chain Variations Dissolved in an Ionic Liquid

Molecular dynamics (MD) simulations and complementary experiments are used here to understand the inter- and intramolecular structure and conformational properties of ionenes (i.e., cationic polymers formed from condensation reactions) dissolved in an ionic liquid (IL), 1-ethyl-3-methylimidazolium bistriflimide [C 2 mim + ][Tf 2 N - ]. The simulated structural properties are benchmarked against experimental analyses of these same polymers, mainly using dynamic light scattering (DLS) experiments. Four different imidazolium ionenes are considered, corresponding to variations in the chemistry and structure of the repeat units including: (1) poly (decylimidazolium) (PD 10 ); (2) poly (tetraethyleneglycolimidazolium) (PE 10 ); (3) alternating copolymer (P(ED) 5 ); and (4) a block copolymer (PE 5 D 5 ). Detailed computational analyses of the polymer structure and conformational properties were performed, including the radius of gyration, end-to-end distance, torsional distributions, and site-site and spatial distribution functions. Overall, there is a competition between intramolecular associations between the imidazolium groups and the ether sites in the polymers versus the intermolecular interactions of the polymer imidazolium groups with the surrounding anion molecules. The polymer with only ether linkages (PE 10 ) results in the most intramolecular interactions, leading to significant coiling behavior and chain contraction. These strong interactions reduce chain flexibility, but they also result in much more linear chain configurations and alignment of the imidazolium groups. The polymer structure is strongly affected as the concentration of alkyl groups is increased, and we find that the polymer architecture (alternating versus block copolymer) also has an important influence. Furthermore, these detailed observations are important for understanding the connection between the molecular design of imidazolium polymers and their emergent structural properties, which could lead to unique opportunities for creating polymer composites.

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

A one-loop test of the near-AdS 2 /near-CFT 1 correspondence

We analyze quantum fluctuations around black hole solutions to the Jackiw-Teitelboim model. We use harmonic analysis on Euclidean AdS 2 to show that the logarithmic corrections to the partition function are determined entirely by quadratic holomorphic differentials, even when conformal symmetry is broken and harmonic modes are no longer true zero modes. Our quantum-corrected partition function agrees precisely with the SYK result. We argue that our effective quantum field theory methods and results generalize to other theories of two-dimensional dilaton gravity.

2D Gravity↗
DOE OSTI2025

Structural determinants for pH-dependent activation of a plant metacaspase

Arabidopsis thaliana metacaspase 9 (AtMC9) plays roles in clearing dead cells, forming xylem vessels, and regulating immunity and programmed cell death in plants. The protease's activation is controlled by pH levels, but the exact structural mechanism behind this has not been elucidated. In this work, high-resolution crystal structures for AtMC9 at active (pH 5.5 and pH 4.2) and inactive (pH 7.5) conditions are reported. The three structures are similar except for local conformations where their hydrogen bonding interactions with solvents are mediated through the protonation of specific titratable amino acid residues' side chains. By combining structural analysis, molecular dynamics simulations under constant pHs, and biochemical assays coupled with site-directed mutagenesis, we show that the regulation of AtMC9 activation involves multiple titratable glutamate and histidine residues across the three domains of p20, linker, and p10. Specifically, deprotonated Glu112, His193, and His208 can suppress AtMC9 proteolytic activity, while protonation of Glu255 and His307 at acidic pH may promote it. This study provides valuable insights into the pH-dependent activation of AtMC9 and could potentially lead to improving crops with enhanced immunity and controlled cell death, ultimately increasing agricultural productivity.

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 OSTI2025

Sensitive detection of structural dynamics using a statistical framework for comparative crystallography

Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differences that are subtle or arise in only a subset of molecules. Direct comparison of crystallographic datasets is, in principle, more powerful, but systematic errors (“scales”) often mask changes in the crystallographic observables (“structure factors”). Machine learning algorithms that jointly estimate scales and structure factors can address this limitation. Here, we augment this approach with multivariate, structured priors derived from crystallographic theory, implemented in the variational deep learning framework Careless. Doing so strongly improves the detection of protein dynamics, element-specific anomalous signals, and the binding of drug candidates, offering a robust approach to comparative crystallography and, potentially, to detection of protein dynamics by other structure determination methods.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗
DOE OSTI2023

Boosting Piezoelectricity by 3D Printing PVDF‐MoS 2 Composite as a Conformal and High‐Sensitivity Piezoelectric Sensor

Abstract Additively manufactured flexible and high‐performance piezoelectric devices are highly desirable for sensing and energy harvesting of 3D conformal structures. Herein, the study reports a significantly enhanced piezoelectricity in polyvinylidene fluoride (PVDF) achieved through the in situ dipole alignment of PVDF within PVDF‐2D molybdenum disulfide (2D MoS 2 ) composite by 3D printing. The shear stress‐induced dipole poling of PVDF and 2D MoS 2 alignment are harnessed during 3D printing to boost piezoelectricity without requiring a post‐poling process. The results show a remarkable, more than the eight‐fold increment in the piezoelectric coefficient ( d 33 ) for 3D printed PVDF‐8wt.% MoS 2 composite over cast neat PVDF. The underlying mechanism of piezoelectric property enhancement is attributed to the increased volume fraction of β phase in PVDF, filler fraction, heterogeneous strain distribution around PVDF‐MoS 2 interfaces, and strain transfer to the nanofillers as confirmed by microstructural analysis and finite element simulation. These results provide a promising route to design and fabricate high‐performance 3D piezoelectric devices via 3D printing for next‐generation sensors and mechanical–electronic conformal devices.

2D MoS2↗
DOE OSTI2020

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

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

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Interchangeability of the Assays Used to Assess the Activity of Anti-SARS-CoV-2 Monoclonal Antibodies

The recent global COVID-19 pandemic caused by SARS-CoV-2 lasted for over three years. A key measure in combatting this pandemic involved the measurement of the monoclonal antibody (mAb)-mediated inhibition of binding between the spike receptor-binding domain (RBD) and hACE2 receptor. Potency assessments of therapeutic anti-SARS-CoV-2 mAbs typically include binding or cell-based neutralization assays. We assessed the inhibitory activity of five anti-SARS-CoV-2 mAbs using ELISA, surface plasmon resonance (SPR), and four cell-based neutralization assays using different pseudovirus particles and 293T or A549 cells expressing hACE2 with or without TMPRSS2. We assessed the interchangeability between cell-based and binding assays by applying the Bland–Altman method under certain assumptions. Our data demonstrated that the IC50 [nM] values determined by eight neutralization assays are independent of the cell line, presence of TMPRSS2 enzyme on the cell surface, and pseudovirus backbone used. Moreover, the Bland–Altman analysis showed that the IC50 [nM] and KD [nM] values determined by neutralization/ELISA or by SPR are equivalent and that the anti-spike mAb activity can be attributed to one variable directly related to its tertiary conformational structure conformation, rate dissociation constant Koff. This parameter is independent from the concentrations of the components of the mAb:RBD:hACE2 complexes and can be used for a comparison between the activities of the different mAbs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Mitigating Calendar Aging in Si-NMC Batteries with Advanced Dual-Salt Glyme Electrolytes

In addressing the critical challenge of calendar aging in silicon (Si)-based lithium-ion batteries, this study introduces a groundbreaking strategy utilizing glyme-type dual-salt electrolytes (lithium bis(trifluoromethanesulfonyl)imide [LiTFSI] and lithium difluoro(oxalato)borate [LiDFOB]). These electrolytes are demonstrated to significantly mitigate parasitic reactions and capacity loss in Si-NMC (lithium nickel manganese cobalt oxide) full cells, especially when compared with traditional carbonate-based electrolytes. Further, our exhaustive mechanistic analysis reveals that such electrolytes not only preserve the integrity of the Si anode but also improve the cathode/electrolyte interphases (CEI) through the formation of a conformal coating on the high-voltage cathode surface. This dual-salt approach, enhanced by the addition of a phosphate additive, effectively decelerates calendar aging, marking a substantial advance in the quest for durable and reliable Si-based energy storage technologies. The findings underscore the vital role of electrolyte composition in extending the calendar life of Si batteries, offering an alternative avenue toward maximizing the performance and longevity of next-generation Li-Si batteries.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

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

Semiclassical Trans-Series from the Perturbative Hopf-Algebraic Dyson-Schwinger Equations: $\phi$ 3 QFT in 6 Dimensions

We analyze the asymptotically free massless scalar $\phi$ 3 quantum field theory in 6 dimensions, using resurgent asymptotic analysis to find the trans-series solutions which yield the non-perturbative completion of the divergent perturbative solutions to the Kreimer–Connes Hopf-algebraic Dyson–Schwinger equations for the anomalous dimension. This scalar conformal field theory is asymptotically free and has a real Lipatov instanton. In the Hopf-algebraic approach we find a trans-series having an intricate Borel singularity structure, with three distinct but resonant non-perturbative terms, each repeated in an infinite series. These expansions are in terms of the renormalized coupling. The resonant structure leads to powers of logarithmic terms at higher levels of the trans-series, analogous to logarithmic terms arising from interactions between instantons and anti-instantons, but arising from a purely perturbative formalism rather than from a semi-classical analysis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Chiral limit of 2d QCD revisited with lightcone conformal truncation

We study the chiral limit of 2d QCD with a single quark flavor at finite Nc using LCT. By modifying the LCT basis according to the quark mass in a manner motivated by ’t Hooft’s analysis, we are able to restore convergence for quark masses much smaller than the QCD strong coupling scale. For such small quark masses, the IR of the theory is expected to be well described by the Sine-Gordon model. We verify that LCT numerics are able to capture in detail the spectrum and correlation functions of the Sine-Gordon model. This opens up the possibility for studying deformations of various integrable CFTs using LCT by considering the chiral limit of QCD like theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention

The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia, gastrointestinal stromal tumor, and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo electron microscopy (cryo-EM) structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the overall symmetric arrangement of the extracellular domain of ligand-occupied KIT dimers contains asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an “Achilles heel” for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. Binding of SCF to this mutant fully restores the conformation of wild-type KIT dimers, including the formation of salt bridges responsible for D4 homotypic contacts and other hallmarks of SCF-induced KIT dimerization. These experiments reveal an unexpected structural plasticity of oncogenic KIT mutants and a therapeutic target in D5.

60 APPLIED LIFE SCIENCES↗