Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structure Interactions”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2024

Integrated experimental studies of pore structure and fluid uptake in the Bossier Shale in eastern Texas, USA

Within the Haynesville-Bossier Shale complex, the Bossier Shale has not been extensively studied by either industry and academia, despite it being an unconventional gas reservoir and a potential caprock for carbon storage in the underlaying Haynesville Shale. The lack of knowledge of the complex pore structures and fluid-rock interactions hinders the effective extraction of gas and the characterization of fluid reservoirs and sealing capacity. Integrated experimental studies of pore structure and fluid-rock interactions were conducted in seven Bossier Shale core samples collected in eastern Texas. Petrographic, geochemical, and petrophysical properties such as mineral composition, organic richness, thermal maturity, porosity, pore/pore throat diameter distribution, water-accessible pores, liquid water imbibition, and water vapor adsorption were characterized using complementary approaches of thin-section petrography, scanning electron microscopy, X-ray diffraction, total organic matter, pyrolysis, mercury intrusion porosimetry, nuclear magnetic resonance, (Ultra-) small angle X-rays scattering as well as small angle neutron scattering with deuterated liquids and contrast variation. Further, the results show that the thermally mature Bossier Shales are composed of mixed argillaceous mudstone, mixed mudstone, and mixed carbonate mudstone. The shale contains both organic and inorganic pores, with porosities of 3.24-9.37 %, pore-to-throat ratios of 1.65 to 19.4, and water-accessible pores accounting for 28.7-72.6 % of total pores. Approaches of liquid water imbibition and water vapor adsorption, with and without direct contact of water with shale samples, indicate that liquid water first enters the nano-sized pores under high capillary pressures, and water vapor adsorption is mainly controlled by both clay minerals and pores with diameters less than 10 nm. These findings contribute to a better understanding of pore structures and water-shale interactions and their controlling factors in the Bossier Shale.

58 GEOSCIENCES↗
DOE OSTI2025

Multiphysics simulation of recent experiments on alkali‐silica reaction expansion in reinforced concrete members

Alkali‐silica reaction (ASR) is an important degradation process that causes volumetric expansion and damage in concrete, and is affected significantly by the local temperature, moisture and stress conditions that often vary across the regions of a structure. Numerical simulation is essential to predict the progression and effects of ASR on the performance of structures. Because of the interactions between thermal and moisture transport and mechanical deformation, it is important for numerical models to represent all these physical phenomena and the coupling between them. Simulations of ASR in reinforced concrete (RC) structures are further complicated by the need to capture interactions between concrete and embedded reinforcing bars. Here, this paper describes the implementation of a scalable, coupled‐physics ASR model for simulating RC structures and assesses the ability of that model to predict ASR‐induced expansion in recent laboratory tests on RC block and beam specimens. These laboratory tests and the simulation approach were selected because of their applicability to RC structural‐scale simulations. This validation study helps builds confidence the ability of this approach to model ASR expansion in large, complex RC structures, which is a current high‐priority need.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Dynamic realization of emergent high-dimensional optical vortices

The dimensionality of vortical structures has recently been extended beyond two dimensions, providing additional topological complexity and robustness for high-capacity information processing and turbulence control. The generation of high-dimensional vortical structures has mostly been demonstrated in classical systems through the complex interference of fluidic, acoustic, or electromagnetic waves. However, natural materials rarely support three- or higher-dimensional vortical structures and their physical interactions. Here, we experimentally demonstrate a high-dimensional gradient thickness optical cavity (GTOC) in which the optical coupling of planar metal-dielectric multilayers implements topological interactions across multiple dimensions. At non-trivial topological phases, high-dimensional GTOC induces high-dimensional vortical structures in generalized parameter space in three, four dimensions, and beyond. These emergent high-dimensional vortical structures are observed under electro-optic tomography as optical vortex dynamics in two-dimensional real-space, employing the optical thicknesses of dielectric layers as synthetic dimensions. Our findings hold significant promise for emulating high-dimensional physics and developing active topological photonic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ionic-content-driven restructuring of spirobisindane ionene networks: implications for mechanics, self-healing, and gas transport

Polymers of intrinsic microporosity (PIMs) offer exceptional gas permeability but remain brittle and susceptible to physical aging, limiting their durability in separation applications. Here, we introduce a reconfigurable microporous polymer network that uniquely integrates permanent PIM microporosity with autonomous, intrinsic self-healing driven by imidazolium-based ionic motifs. Spirobisindane units generate the intrinsic free-volume architecture, while an imidazolium-containing polyamide ionene supplies dynamic ionic and hydrogen-bonding interactions that reorganize under mild activation. Incorporation of imidazolium-based ionic liquids further tunes cohesion, mobility, and densification, enabling the network to relax, re-associate, and retain microporosity without structural collapse. Through a comprehensive multiscale approach combining spectroscopy, scattering, thermal and mechanical characterization with all-atom molecular dynamics and density functional theory calculations, we elucidate how ionic content, as a single control parameter that reshapes free-volume distributions, modulates local coordination environments, and governs relaxation and healing kinetics. At intermediate ionic loadings, the networks achieve rapid, repeatable self-healing while maintaining CO$_2$ selectivity, demonstrating an optimal balance between segmental mobility and structural integrity. By establishing how hierarchical ionic interactions couple structure, dynamics, and transport in microporous ionene networks, this work provides generalizable design rules for adaptive soft-matter systems that require simultaneous mechanical resilience, reconfigurability, and selective gas transport.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structural Analysis of 23S rRNA Methylating Enzyme Cfr Reveals RNA-Binding Determinants for Methylation Regiospecificity and Antibiotic Resistance

The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.

AlphaFold↗
DOE OSTI2024

Topological edge conduction induced by strong anisotropic exchange interactions

Here, we predict that an interplay between isotropic and anisotropic exchange interactions in a honeycomb lattice structure can lead to topological edge conduction when the anisotropic interaction is at least twice the strength of the isotropic interaction. For materials like Na 2 ⁢IrO 3 , such a strong anisotropic exchange interaction simultaneously induces a zigzag type of antiferromagnetic order that breaks the time-reversal symmetry of the topological edge conductor. We show that the electronic transport in such topological conductors will exhibit a quantized Hall conductance without any external magnetic field when the Fermi energy lies within a particular energy range.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structural Analysis of a Serpentine Superconducting Magnet for the Interaction Region of the Electron Ion Collider

The electron ion collider (EIC) is under design to collide the high energy and highly polarized hadron with electron beams with luminosities up to 10 34 cm −2 s −1 . The superconducting magnet designs at the interaction region (IR) are quite challenging due to the close proximity of the hadron and electron beams. Several serpentine types of superconducting magnets have been designed due to the space restrictions at the IR. Here, to validate the designs in terms of the mechanical strength, structural integrity, as well as the allowed deformations, a detailed structural mechanical analysis for a 12-layer superconducting quadrupole serpentine magnet (Q1BpR) in the rear side hadron beams has been carried out using the finite element method (FEM) considering the pretension stress, shrinking due to cool down, and the electromagnetic force on the conductors. Anisotropy material properties and individual roving tension have been considered. The electro-magnetic (EM) simulations were performed using COMSOL, confirmed with RAT, the structural mechanical analysis were performed using COMSOL by considering the contact elements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Extended interaction length laser-driven acceleration in a tunable dielectric structure

The development of long, tunable structures is critical to increasing energy gain in laser-driven dielectric accelerators (DLAs). Here we combine pulse-front-tilt illumination with slab-geometry structures assembled by precisely aligning off-the-shelf 4 mm long transmission gratings to achieve up to 200 keV energy modulation for 6 MeV injected electrons. The effective interaction length is longer than 1 mm, limited by the dephasing of the accelerated particles in the structure. The piezo-based independent mounting system for the gratings allows tuning of the gap and field distribution inside the structure. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Electrosome assembly: Structural insights from high voltage-activated calcium channel (CaV)–chaperone interactions

Ion channels are multicomponent complexes (termed here as“electrosomes”) that conduct the bioelectrical signals required for life. It has been appreciated for decades that assembly is critical for proper channel function, but knowledge of the factors that undergird this important process has been lacking. Although there are now exemplar structures of representatives of most major ion channel classes, there has been no direct structural information to inform how these complicated, multipart complexes are put together or whether they interact with chaperone proteins that aid in their assembly. Recent structural characterization of a complex of the endoplasmic membrane protein complex (EMC) chaperone and a voltage-gated calcium channel (CaV) assembly intermediate comprising the pore-forming CaVα1 and cytoplasmic CaVβ subunits offers the first structural view into the assembly of a member of the largest ion channel class, the voltagegated ion channel (VGIC) superfamily. The structure shows how the EMC remodels the CaVα1/CaVβ complex through a set of rigid body movements for handoff to the extracellular CaVα2δ subunit to complete channel assembly in a process that involves intersubunit coordination of a divalent cation and ordering of CaVα1 elements. These findings set a new framework for deciphering the structural underpinnings of ion channel biogenesis that has implications for understanding channel function, how drugs and disease mutations act, and for investigating how other membrane proteins may engage the ubiquitous EMC chaperone.

Biochemistry & Molecular Biology↗
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 OSTI2026

Extreme confinement of hydrogen gas within fullerenelike nanoporous carbon

Nanoporous carbons and carbon nanostructures can store hydrogen at cryogenic temperatures but lack the volumetric and gravimetric capacity to be industrially significant. Recent inelastic neutron scattering experiments suggest a highly dense phase of hydrogen at temperatures well above the melting point of solid hydrogen. However, it remains unclear how pore geometry and intermolecular interactions enable these dense phases to exist, with dispersion (van der Waals) or electrostatic/induction suggested to be the key effects in slit and curved pores but their relative contributions have yet to be quantified. In this paper, we perform benchmark electronic structure calculations allowing the interactions between planar and curved aromatic molecules with hydrogen to be accurately determined. Dispersion was found to dominate over electrostatic and inductive effects with some many-body charge transfer (Dobson type-A) effects needed to capture the most highly curved structures. Density functional methods that include type-A many-body effects were found to accurately describe the intermolecular interactions at a fraction of the cost of coupled-cluster simulations and these approaches were used to calculate the energies inside large carbon bowl and slit pores. The interaction energies inside the bowl pores were found to depend on the orientation of the hydrogen molecule. This rotational barrier, modeled as a quantum hindered rotor, could reproduce the peak splitting observed in inelastic neutron scattering experiments, with weak splitting arising from bowl-like fullerene pores and strong splitting from highly confining nanotubelike pores. Increasing the fraction of such curved pores in nanoporous carbons may therefore offer a pathway to enhance their hydrogen-storage capacity. Moreover, the preferential adsorption of ortho hydrogen on nanotubelike pores could enable the storage of high-density hydrogen without the need to remove heat produced during the ortho-para hydrogen conversion.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Coupling between collective modes in the deformed 98 Zr nucleus: Insights from consistent HFB + QRPA calculations with the Gogny interaction

The zirconium isotopes exhibit structural properties that present multiple challenges to nuclear theory. Investigations of the coupling present within isoscalar modes and within isovector modes are scarce but important for advancing our understanding of the microscopic picture of nuclei. To explore some of these underlying coupling features, and to test the predictive power of a state-of-the-art nuclear structure approach, we provide a detailed analysis of the properties of 90,96,98 Zr . This region includes a benchmarking case and offers insights into nuclear deformation phenomena. Here, to investigate the coupling between collective modes in deformed nuclei, we focused our analysis on the ground and excited-state properties of these isotopes, employing a consistent approach with the axially symmetric deformed Hartree-Fock-Bogoliubov (HFB) and the quasiparticle random phase approximation (QRPA) framework, both using the Gogny D1M force. This approach effectively describes both low-lying and giant-resonance states. We devoted special attention to the deformed 98 Zr nucleus, where we confirm the existence of coupling between monopole and quadrupole excitations through the 𝐾 𝜋 = 0 + QRPA components and demonstrate an analogous dipole-octupole coupling through the 𝐾 𝜋 = 0 − and 𝐾 𝜋 = 1 − components. Intrinsic transition densities and associated radial projections illustrate the coupling. Our work complements and extends earlier studies carried out using density-functional-based methods and notably, we included the complete Coulomb interaction also in the pairing fields, i.e., we treat terms exactly that are approximated in typical calculations that use the Gogny D1 and D2 interaction families.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Structural Characterization of Linker Shielding in ADC Site-Specific Conjugates

Background/Objectives: Antibody–Drug Conjugates (ADCs) have rapidly evolved from early, rudimentary conjugates to highly targeted and precisely engineered molecules. Despite notable clinical successes, ADCs continue to face significant challenges, including aggregation and high hydrophobicity driven by high drug-to-antibody ratios (DARs), premature payload release, dose-limiting toxicities, and suboptimal pharmacokinetics. While site-specific linker–payload conjugation has improved ADC homogeneity and stability, the structural basis of antibody–linker interactions at specific sites remains underexplored. Methods: In this work, we present the crystal structures of trastuzumab Fab and Fc domains site-specifically conjugated with a cleavable linker–payload. Results: Our findings suggest that pockets within both Fab and Fc regions may interact with and shield the linker portion of the conjugate. Conclusions: These insights highlight the previously underappreciated potential of structure-based design to drive the optimization of ADC linker chemistry and facilitate the co-design of bespoke linker–payloads tailored to individual antibody conjugation sites.

Jaime-Garza, Maru [Discovery Chemistry, Merck & Co↗
DOE OSTI2024

Nucleon Structure Studies at Jefferson Lab and the Electron Ion Collider

The research programs of Thomas Jefferson Laboratory (JLab) and the future Electron- Ion Collider (EIC) focus on one of the main goals of strong interaction studies : understanding the structure of nucleons in terms of the quarks and gluons composing them. Their structure is encoded in functions such as Generalized Parton Distributions (GPDs), which describe how quarks and gluons’ transverse position and longitudinal momentum are distributed inside nucleons. GPDs allow to obtain three-dimensional pictures of nucleons and to understand some of their fundamental properties, such as their internal pressure or the emergence of their spin from the dynamics of the partons composing them. At JLab and the EIC, electron beams are used to probe nucleons. Measurement of reactions such as Deeply Virtual Compton Scattering (DVCS) allows access to GPDs. The first longitudinally polarized-target experiment of the CLAS12 program at Jlab took place in 2022-2023. Combining polarized electron beams and nucleon targets, this experiment offers unique access to observables that allow the measurement of different types of GPDs. In particular, the DVCS beam- and target-spin asymmetries for protons and neutrons in deuterium will be measured for the first time. They give access to kinds of GPDs that are still poorly known, and the comparison between proton and neutron data will allow the extraction of the flavor dependence of the structure of nucleons. Specific analysis methods have been implemented to work with a polarized nuclear target and are presented in this thesis. These methods allow to obtain preliminary results for the asymmetries, waiting for the complete statistics to be available. In the long term, the experimental program for the EIC has been established with a strong emphasis on the measurement of the structure of nucleons at high energy. Measurements of reactions such as DVCS impose strict requirements on the electromagnetic calorimeter that will allow to measure the energy of the scattered electrons and photons. This calorimeter, which is under development, will be based on scintillating crystals read by Silicon Photomultipliers (SiPMs). A new type of glass-based scintillating material was tested, evaluating the possibilities to meet the technical requirements concerning their light yield and resistance to radiation damage in particular. Several models of SiPMs have been characterized, demonstrating they can operate over the vast energy range necessary to address the physics case at the EIC and providing guidelines for developing their readout electronics.

Pilleux, Noemie↗
DOE OSTI2025

Single-Molecule Vibrational Characterization of Binding Geometry Effects on Isocyanide–Metal Interactions

Isocyanide−metal binding is governed by σ-donation and π-back-bonding, which affects the isocyanide stretching energy, a characteristic probe for ligand−metal interactions. While extensive correlations exist between structure and spectroscopy in molecular isocyanide−metal systems, interactions of isocyanide with crystalline metallic surfaces, where ligands often bind in various geometries, remain underexplored. Conventional vibrational spectroscopies such as infrared and Raman spectroscopies lack the molecular-scale resolution to distinguish this binding inhomogeneity. In contrast, inelastic electron tunneling spectroscopy with scanning tunneling microscopy (STM-IETS) directly visualizes ligand adsorption geometries and their vibrational signatures. Using STM-IETS, we investigate a metal-adsorbed m -terphenyl isocyanide ligand and find that the adsorption geometry on Cu(100) induces a significant shift in isocyanide stretching frequency, more prominent than replacing Cu(100) with Ag(111). Density functional theory confirms that this shift arises from atomic-scale variations in coordination environments. This study elucidates how precise binding influences the vibrational fingerprints of isocyanide ligands, an often-overlooked factor in understanding the isocyanide−metal interplay.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Coupling between collective modes in the deformed 98 Zr nucleus: Insights from consistent HFB+QRPA calculations with the Gogny interaction

The Zirconium isotopes exhibit structural properties that present multiple challenges to nuclear theory. Investigations of the coupling present within isoscalar modes and within isovector modes are scarce but important for advancing our understanding of the microscopic picture of nuclei. To explore some of these underlying coupling features, and to test the predictive power of a state-of the-art nuclear structure approach, we provide a detailed analysis of the properties of 90,96,98Zr. This region includes a benchmarking case and offers insights into nuclear deformation phenomena. To investigate the coupling between collective modes in deformed nuclei, we focused our analysis on the ground and excited-state properties of these isotopes, employing a consistent approach with the axially-symmetric deformed Hartree-Fock-Bogoliubov (HFB) and the Quasiparticle Random Phase Approximation (QRPA) framework, both using the Gogny D1M force. This approach effectively describes both low-lying and giant-resonance states. We devoted special attention to the deformed 98Zr nucleus, where we confirm the existence of coupling between monopole and quadrupole excitations through the K π = 0 + QRPA components and demonstrate an analogous dipole-octupole coupling through the K π = 0 − and K π = 1 − components. Intrinsic transition densities and associ ated radial projections illustrate the coupling. Our work complements and extends earlier studies carried out using density-functional-based methods and notably, we included the complete Coulomb interaction also in the pairing fields, i.e. we treat terms exactly that are approximated in typical calculations that use the Gogny D1 and D2 interaction families.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗