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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation

Human immunodeficiency virus-1 (HIV-1), the causative agent of AIDS, impacts millions of people. Entry into target cells is mediated by the HIV-1 envelope (Env) glycoprotein interacting with host receptor CD4, which triggers conformational changes allowing binding to a coreceptor and subsequent membrane fusion. Small molecule or peptide CD4-mimetic drugs mimic CD4’s Phe43 interaction with Env by inserting into the conserved Phe43 pocket on Env subunit gp120. Here, we present single-particle cryo-EM structures of CD4-mimetics BNM-III-170 and M48U1 bound to a BG505 native-like Env trimer plus the CD4-induced antibody 17b at 3.7 Å and 3.9 Å resolution, respectively. CD4-mimetic-bound BG505 exhibits canonical CD4-induced conformational changes including trimer opening, formation of the 4-stranded gp120 bridging sheet, displacement of the V1V2 loop, and formation of a compact and elongated gp41 HR1C helical bundle. We conclude that CD4-induced structural changes on both gp120 and gp41 Env subunits are induced by binding to the gp120 Phe43 pocket.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Geometric Transformations Afforded by Rotational Freedom in Aramid Amphiphile Nanostructures

Molecular self-assembly in water leads to nanostructure geometries that can be tuned owing to the highly dynamic nature of amphiphiles. There is growing interest in strongly interacting amphiphiles with suppressed dynamics, as they exhibit ultrastability in extreme environments. However, such amphiphiles tend to assume a limited range of geometries upon self-assembly due to the specific spatial packing induced by their strong intermolecular interactions. To overcome this limitation while maintaining structural robustness, we incorporate rotational freedom into the aramid amphiphile molecular design by introducing a diacetylene moiety between two aramid units, resulting in diacetylene aramid amphiphiles (D-AAs). This design strategy enables rotations along the carbon–carbon sp hybridized bonds of an otherwise fixed aramid domain. We show that varying concentrations and equilibration temperatures of D-AA in water lead to self-assembly into four different nanoribbon geometries: short, extended, helical, and twisted nanoribbons, all while maintaining robust structure with thermodynamic stability. In conclusion, we use advanced microscopy, X-ray scattering, spectroscopic techniques, and two-dimensional (2D) NMR to understand the relationship between conformational freedom within strongly interacting amphiphiles and their self-assembly pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Engineering tertiary chirality in helical biopolymers

Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.

Science & Technology - Other Topics↗
DOE OSTI2025

EuAuSb: An odd-parity helical variation of altermagnetism

EuAuSb is a triangular-lattice Dirac semimetal in which a topological Hall effect has been observed to develop in association with a magnetically ordered phase. Our single-crystal neutron diffraction measurements have identified an incommensurate helical order in which individual ferromagnetic Eu 2+ layers rotate in-plane by ∼ 120° from one layer to the next. An in-plane magnetic field distorts the incommensurate order, eventually leading to a first order transition to a state that is approximately commensurate and that is continuously polarized as the bulk magnetization approaches saturation. From an analysis of the magnetic diffraction intensities versus field, we find evidence for a dip in the ordered in-plane moment at the same field where the topological Hall effect is a maximum, and we propose that this is due to field-induced quantum spin fluctuations. Our electronic structure calculations yield exchange constants compatible with the helical order and show that the bands near the Fermi level lose their spin degeneracy via a mechanism similar to that in the collinear altermagnets. In conclusion, we find that, unlike the even symmetry seen in the altermagnets, the spin splitting in EuAuSb has odd-wave symmetry similar to that recently found in a number of coplanar magnetic materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

High-speed feedback control of an oscillating magnetic helicity injector using a graphics processing unit

A real-time control system has been developed to control the amplitude, phase, and offset of bulk plasma parameters inside an oscillating magnetic helicity injector. Control software running entirely on an Nvidia Tesla P40 graphical processing unit is able to receive digitizer inputs and send response patterns to a Pulse Width Modulation (PWM) controller with a minimum control loop period of 12.8μs. With an input digitization rate of 10 MS/s, a three-parameter proportional integral differential controller is shown to be sufficient to inform the PWM controller to drive the desired oscillating plasma waveform with a frequency of 16.6 kHz that is located near the resonance of a coupled RLC circuit. In particular, the temporal phase of the injector waveform is held within 10 degrees of the target value. Control is demonstrated over the toroidal modal structure of the imposed magnetic perturbations of the helicity injection system, allowing a new class of discharges to be studied.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Proton Spin Structure from Simultaneous Monte Carlo Global QCD Analysis

Despite the great effort and achievements made towards understanding proton spin structure in the past few decades, a complete picture is still elusive. Parton distribution functions (PDFs), which in quantum chromodynamics (QCD) encode the momentum and helicity distributions of quarks and gluons inside a proton, provide the means by which to quantify the proton structure information. Being inherently nonperturbative, PDFs have to be extracted from unpolarized and polarized lepton-hadron and hadron-hadron scattering data. In particular, experiments that measure unpolarized and polarized jet observables can provide insight into the momentum and helicity distributions of gluons, which have generally been more difficult to determine reliably than those of quarks. In the past, extraction of the spin-averaged and spin-dependent (or helicity) PDFs has been performed in separate analyses. In this thesis, we perform the first simultaneous extraction of both types of quantities from deep-inelastic scattering (DIS), Drell-Yan and single jet observables, within the Monte Carlo global QCD analysis framework developed by the Jefferson Lab Angular Momentum (JAM) Collaboration. The results from this work indicate that the gluon helicity distributions depend rather strongly on the theory assumptions on which the global analysis is based, which calls for the need of measurements with higher precision. As an application of the new simultaneous JAM analysis, we perform an impact study for future Electron-Ion Collider (EIC) data with parity-conserving and parity-violating polarization asymmetries on quark and gluon helicity distributions in the proton. The extrapolation of structure functions from the current data is studied for the first time in the context of the impact study. Theory assumptions, such as SU(2) and SU(3) flavor symmetries, are also studied to give a more thorough understanding of the impact of EIC pseudodata on proton spin structure.

Zhou, Yiyu↗
DOE OSTI2022

Supramolecular meso -Trick: Ambidextrous Mirror Symmetry Breaking in a Liquid Crystalline Network with Tetragonal Symmetry

Bicontinuous and multicontinuous network phases are among nature's most complex structures in soft matter systems. Here, a chiral bicontinuous tetragonal phase is reported as a new stable liquid crystalline intermediate phase at the transition between two cubic phases, the achiral double gyroid and the chiral triple network cubic phase with an I 23 space group, both formed by dynamic networks of helices. The mirror symmetry of the double gyroid, representing a meso -structure of two enantiomorphic networks, is broken at the transition to this tetragonal phase by retaining uniform helicity only along one network while losing it along the other one. This leads to a conglomerate of enantiomorphic tetragonal space groups, P 4 1 2 1 2 and P 4 3 2 1 2. Phase structures and chirality were analyzed by small-angle X-ray scattering (SAXS), grazing-incidence small-angle X-ray scattering (GISAXS), resonant soft X-ray scattering (RSoXS) at the carbon K-edge, and model-dependent SAXS/RSoXS simulation. In conclusion, our findings not only lead to a new bicontinuous network-type three-dimensional mesophase but also reveal a mechanism of mirror symmetry breaking in soft matter by partial meso -structure racemization at the transition from enantiophilic to enantiophobic interhelical self-assembly.

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

De novo design of high-affinity binders of bioactive helical peptides

Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity to structured proteins. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Unraveling the Molecular Origin of Prey-Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR

Prey wrapping spider silk's unique mechanical properties are investigated confirming the silk's high degree of extensibility and superior toughness compared to other types of spider silk. For the first time, the pre-spinning dope phase is studied in isotope-enriched intact aciniform (AC) silk glands using solution NMR that reveals a combination of α-helical domains linked by disordered random coil chains consistent with previously proposed “beads-on-a-string” models. The model is further refined through the AlphaFold2 protein structure prediction tool. Finally, extensive magic angle spinning (MAS) solid-state (SS) NMR data for isotopically-enriched fibers is used to refine the structural model for AC silk from two species, A. aurantia and A. argentata. The SSNMR data shows that the AC silk fibers are highly α-helical, coiled-coil in structure but, also exhibit significant β-sheet components that can be traced back to the Gly-rich disordered linker regions in the pre-spinning dope phase that are converted to β-sheet structures during fiber formation. This combination of mechanical and structural characterization enhances the understanding of AC silk's liquid-to-solid transition and structure-mechanics relationship. In conclusion, these prey wrap silk results and models will provide the basis for the design of biomimetic materials inspired by the AC spider silk system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Dependence of thick filament structure in relaxed mammalian skeletal muscle on temperature and interfilament spacing

Contraction of skeletal muscle is regulated by structural changes in both actin-containing thin filaments and myosin-containing thick filaments, but myosin-based regulation is unlikely to be preserved after thick filament isolation, and its structural basis remains poorly characterized. Here, we describe the periodic features of the thick filament structure in situ by high-resolution small-angle x-ray diffraction and interference. We used both relaxed demembranated fibers and resting intact muscle preparations to assess whether thick filament regulation is preserved in demembranated fibers, which have been widely used for previous studies. We show that the thick filaments in both preparations exhibit two closely spaced axial periodicities, 43.1 nm and 45.5 nm, at near-physiological temperature. The shorter periodicity matches that of the myosin helix, and x-ray interference between the two arrays of myosin in the bipolar filament shows that all zones of the filament follow this periodicity. The 45.5-nm repeat has no helical component and originates from myosin layers closer to the filament midpoint associated with the titin super-repeat in that region. Cooling relaxed or resting muscle, which partially mimics the effects of calcium activation on thick filament structure, disrupts the helical order of the myosin motors, and they move out from the filament backbone. Compression of the filament lattice of demembranated fibers by 5% Dextran, which restores interfilament spacing to that in intact muscle, stabilizes the higher-temperature structure. The axial periodicity of the filament backbone increases on cooling, but in lattice-compressed fibers the periodicity of the myosin heads does not follow the extension of the backbone. Thick filament structure in lattice-compressed demembranated fibers at near-physiological temperature is similar to that in intact resting muscle, suggesting that the native structure of the thick filament is largely preserved after demembranation in these conditions, although not in the conditions used for most previous studies with this preparation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lattice QCD Benchmark of Proton Helicity and Flavor-Dependent Unpolarized Transverse Momentum-Dependent Parton Distribution Functions at Physical Quark Masses

We present the first lattice QCD calculations of the isovector helicity transverse momentum-dependent parton distribution function (TMDPDF) and the flavor-dependent unpolarized TMDPDFs for up and down quarks in the proton. Our computations utilize domain-wall fermion discretization with physical quark masses. Employing Coulomb-gauge-fixed quark correlation functions within the large-momentum effective theory framework, we access nonperturbative transverse quark separations 𝑏 𝑇 up to approximately 1 fm, corresponding to transverse momenta as low as 200 MeV. Based on the quasi-TMD factorization theorem, we construct renormalization-group–invariant ratios that are equal to the corresponding light-cone TMDPDF ratios. At moderate 𝑥, our results reveal that the isovector helicity and unpolarized TMDPDFs exhibit nearly identical transverse structure up to a normalization factor, and the unpolarized distributions display only mild flavor dependence. These findings not only support key trends observed in recent global analyses but also provide robust, nonperturbative constraints that can distinguish between different parameterizations. This Letter establishes a first-principles benchmark for TMDPDFs, offering valuable input for ongoing and future experimental efforts to map the proton’s three-dimensional structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

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

De novo designed ice-binding proteins from twist-constrained helices

Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure–activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure–activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

Science & Technology - Other Topics↗
DOE OSTI2020

Characterizing magnetized plasmas with dynamic mode decomposition

Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear and computationally intensive and can be difficult to interpret, while often only approximating the true dynamics. In this work, data-driven techniques recently developed in the field of fluid dynamics are leveraged to develop interpretable reduced-order models of plasmas that strike a balance between accuracy and efficiency. In particular, dynamic mode decomposition (DMD) is used to extract spatio-temporal magnetic coherent structures from the experimental and simulation datasets of the helicity injected torus with steady inductive (HIT-SI) experiment. Three-dimensional magnetic surface probes from the HIT-SI experiment are analyzed, along with companion simulations with synthetic internal magnetic probes. A number of leading variants of the DMD algorithm are compared, including the sparsity-promoting and optimized DMD. Optimized DMD results in the highest overall prediction accuracy, while sparsity-promoting DMD yields physically interpretable models that avoid overfitting. These DMD algorithms uncover several coherent magnetic modes that provide new physical insights into the inner plasma structure. These modes were subsequently used to discover a previously unobserved three-dimensional structure in the simulation, rotating at the second injector harmonic. Finally, using data from probes at experimentally accessible locations, DMD identifies a resistive kink mode, a ubiquitous instability seen in magnetized plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Helical magnetic order and Fermi surface nesting in noncentrosymmetric ScFeGe

Here, an investigation of the structural, magnetic, thermodynamic, and charge transport properties of noncentrosymmetric hexagonal ScFeGe reveals it to be an anisotropic metal with a transition to a weak itinerant incommensurate helimagnetic state below T N =36 K. Neutron diffraction measurements discovered a temperature and field independent helical wave vector k = (0 0 0.193) with magnetic moments of 0.53 μ B per Fe confined to the ab-plane. Density functional theory calculations are consistent with these measurements and find several bands that cross the Fermi level along the c-axis with a nearly degenerate set of flat bands just above the Fermi energy. The anisotropy found in the electrical transport is reflected in the calculated Fermi surface, which consists of several warped flat sheets along the c-axis with two regions of significant nesting, one of which has a wave vector that closely matches that found in the neutron diffraction. The electronic structure calculations, along with a strong anomaly in the c-axis conductivity at TN, signal a Fermi surface driven magnetic transition, similar to that found in spin density wave materials. Magnetic fields applied in the ab-plane result in a metamagnetic transition with a threshold field of ≈ 6.7 T along with a sharp, strongly temperature dependent discontinuity and a change in sign of the magnetoresistance for in-plane currents. Thus, ScFeGe is an ideal system to investigate the effect of in-plane magnetic fields on a helimagnet with a c-axis propagation vector, where the relative strength of the magnetic interactions and anisotropies determine the topology and magnetic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

X-ray Crystal Structure of Thorium Tetrahydroborate, Th(BH 4 ) 4 , and Computational Studies of An(BH 4 ) 4 (An = Th, U)

Here the crystal structure of Th(BH 4 ) 4 is described. Two of the four BH 4 – ions are terminal and tridentate (κ 3 ), whereas the other two bridge between neighboring Th IV centers in a κ 2 ,κ 2 (i.e., bis-bidentate) fashion. Thus, each thorium center is bound to six BH 4 – groups by 14 Th–H bonds. The six boron atoms describe a distorted octahedron in which the κ 3 -BH 4 – ions are mutually cis; the 14 ligating hydrogen atoms define a highly distorted bicapped hexagonal antiprism. The thorium centers are linked into a polymer consisting of interconnected helical chains wound about 4-fold screw axes. The structures of An(BH 4 ) 4 (An = Th, U) were also investigated by DFT. The geometries of [An(BH 4 ) 6 ] 2– , [An3(BH 4 ) 16 ] 4– , and [An 5 (BH 4 ) 26 ] 6– fragments of the polymeric structures were optimized at the B3LYP and/or PBE levels. Most calculated geometries are 14-coordinate and agree with the experimental structures, but isolated [Th(BH 4 ) 6 ] 2– units are predicted to feature 16-coordinate Th IV centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Large-eddy simulations of turbulent wake flows behind helical- and straight-bladed vertical axis wind turbines rotating at low tip speed ratios

Turbulent wake flows behind helical- and straight-bladed vertical axis wind turbines (VAWTs) rotating at low tip speed ratios (TSRs) are studied numerically. The turbulent flows are simulated using the large-eddy simulation (LES) model, and the rotating turbine blades are modeled using the actuator line method. The helical VAWT has identical key parameters as the straight VAWT except for the 135° helical twist of the blades over the 0.3m vertical span. A set of LES runs are performed for two TSRs, 0.6 and 0.4, and the results are reported and analyzed. At these low TSRs, the wake behind the straight-bladed VAWT exhibits two-dimensional dominant flow motions (in the horizontal plane perpendicular to the straight blades) in the near-wake region that cause considerable spanwise expansion of the wake as it extends downstream. In contrast, the helical-bladed VAWT generates highly three-dimensional (3D) wake flow structures and upward/downward mean flow motions within the wake that cause the wake to expand mainly in the vertical direction. Turbulence statistical analyses also show that the 3D wake flow features induced by the helical blades accelerate the wake transition to turbulence and enhance the small-scale turbulent dissipation (as shown by the subgrid-scale turbulent dissipation in the LES), which leads to a more rapid decay of the wake turbulence intensity than that in the straight-bladed VAWT case at the same TSR. Finally, compared with the straight-bladed VAWT, the helical-bladed VAWT also exhibits much smaller temporal variations for the torque and power coefficients during the rotation cycle, which can be beneficial for wind power generation.

17 WIND ENERGY↗