Search NASA⌕ Search

SEARCH · Search NASA

Results for “helicity”

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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The carboxylation status of osteocalcin has important consequences for its structure and dynamics

The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.

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

Molecular weaving of chicken-wire covalent organic frameworks

Molecular weaving is the interlacing of covalently linked threads to make extended structures. Although weaving based on 3D networks has been reported, the 2D forms remain largely unexplored. Reticular chemistry uses mutually embracing tetrahedral metal complexes as crossing points, which, when linked, typically lead to 3D woven structures. Realizing 2D weaving patterns requires crossing points with an overall planar geometry. We show that polynuclear helicates composed of multiple metal-complex units, and therefore multiple turns, are well suited in this regard. By reticulating helicate units, we successfully obtained 2D weaving structures based on the familiar chicken-wire pattern.

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

Ordered hexagonal columnar liquid crystalline self-assembly of mesogen-free sulfonylated side-chain chiral polyethers and their high dielectric property

To achieve large spontaneous polarization for ferroelectric liquid crystalline polymers, we have designed a series of mesogen-free isotactic polyethers with sulfonylated side chains. Different from prior studies using linear alkyl side chains, in this work a methyl branch was implemented in the alkyl side chains of the chiral polyethers. As a result of the continuous twist from the methyl branches and strong dipole-dipole interactions among neighboring sulfonyl groups, a helical chain conformation with tilted side chains was achieved. When the branched side chains were short (e.g., C5) and double chirality existed in both the main chain and side chains, a crystalline structure was obtained. When the branched side chains were long (e.g., ≥ C8) and single chirality existed in the main chain, an ordered hexagonal columnar liquid crystalline phase was induced. Their high-field dielectric property was studied by electric displacement-electric field (D-E) loop tests; however, no ferroelectric behavior was observed up to 200 MV/m. It was considered that the dipole-dipole interaction among neighboring sulfonyl groups in the helical chains was too strong to allow easy ferroelectric flipping.

36 MATERIALS SCIENCE↗
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 OSTI2024

Structure preserving transport stabilized compatible finite element methods for magnetohydrodynamics

Here, we present compatible finite element space discretizations for the ideal compressible magnetohydrodynamic equations. The magnetic field is considered both in div- and curl-conforming spaces, leading to a strongly or weakly preserved zero-divergence condition, respectively. The equations are discretized in space such that transfers between the kinetic, internal, and magnetic energies are consistent, leading to a preserved total energy. We also discuss further adjustments to the discretization required to additionally achieve magnetic helicity preservation. Finally, we describe new transport stabilization methods for the magnetic field equation which maintain the zero-divergence and energy conservation properties, including one method which also preserves magnetic helicity. The methods' preservation and improved stability properties are confirmed numerically using a steady state and a magnetic dynamo test case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T m ) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [ (-6) MPro H41A and (-6*) MPro H41A , respectively], and its corresponding mature MPro H41A were systematically examined. While the H41A mutation exerts negligible effect on T m and dimer dissociation constant (K dimer ) of MPro H41A , relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in T m and > 85-fold increase in K dimer as compared to MPro H41A . The K d for the binding of the covalent inhibitor GC373 to (-6*) MPro H41A increases ~12-fold, relative to MPro H41A , concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Finally, disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Chirality transfer and chiral turbulence in gauge theories

Chirality transfer between fermions and gauge fields plays a crucial role for understanding the dynamics of anomalous transport phenomena such as the Chiral Magnetic Effect. In this proceeding we present a first principles study of these processes based on classical-statistical real-time lattice simulations of strongly coupled QED (e 2 N f = 64). Furthermore, our simulations demonstrate that a chirality imbalance in the fermion sector triggers chiral plasma instabilities in the gaugefield sector, which ultimately lead to the generation of long range helical magnetic fields via an self-similar turbulent cascade of the magnetic helicity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Spin-orbit entanglement in the Color Glass Condensate

We compute the spin-orbit correlations of quarks and gluons at small-x and show that the helicity and the orbital angular momentum of individual partons are strongly anti-aligned even in unpolarized or spinless hadrons and nuclei. Combined with the fact that gluons in the Color Glass Condensate are linearly polarized, our finding indicates that the helicity and the orbital angular momentum of single gluons are maximally entangled in a quantum mechanical sense.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

First polarisation measurement of coherently photoproduced J/ ψ in ultra-peripheral Pb–Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

The first measurement of the polarisation of coherently photoproduced J/ψ mesons in ultra-peripheral Pb–Pb collisions, using data at $\sqrt{s_{NN}}$ = 5.02 TeV, is presented. The J/ψ meson is measured via its dimuon decay channel in the forward rapidity interval –4.0 < y < –2.5 using the ALICE detector at the CERN LHC. An event sample corresponding to an integrated luminosity of 750 μb –1 ± 5% (syst) is analysed. Hadronic activity is highly suppressed since the interaction is mediated by a photon. The polar and azimuthal angle distributions of the decay muons are measured, and the polarisation parameters λ θ , λ φ , λ θφ , are extracted. The analysis is carried out in the helicity frame. The results are found to be consistent with a transversely polarised J/ψ. These values are compared with previous measurements by the H1 and ZEUS experiments. The polarisation parameters of coherent J/ψ photoproduction in Pb–Pb collisions are found to be consistent with the s-channel helicity conservation hypothesis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Mid-century climate change impacts on tornado-producing tropical cyclones

Tornadoes are a co-occurring extreme that can be produced by landfalling tropical cyclones (TCs). These tornadoes can exacerbate the loss of life and property damage caused by the TC from which they were spawned. It is uncertain how the severe weather environments of landfalling TCs may change in a future climate and how this could impact tornado activity from TCs. In this study, we investigated four TCs that made landfall in the U.S. and produced large tornado outbreaks. We performed four-member ensembles of convective-allowing (4-km resolution) regional climate model simulations representing each TC in the historical climate and a mid-twenty-first century future climate. To identify potentially tornadic storms, or TC-tornado (TCT) surrogates, we used thresholds for three-hourly maximum updraft helicity and radar reflectivity, as tornadoes are not resolved in the model. We found that the ensemble-mean number of TCT-surrogates increased substantially (56–299%) in the future, supported by increases in most-unstable convective available potential energy, surface-to-700-hPa bulk wind shear, and 0–1-km storm-relative helicity in the tornado-producing region of the TCs. On the other hand, future changes in most-unstable convective inhibition had minimal influence on future TCT-surrogates. This provides robust evidence that tornado activity from TCs may increase in the future. Furthermore, TCT-surrogate frequency between 00Z and 09Z increased for three of the four cases, suggesting enhanced tornado activity at night, when people are asleep and more likely to miss warnings. All of these factors indicate that TC-tornadoes may become more frequent and a greater hazard in the future, compounding impacts from future increases in TC winds and precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Estimation of cutting tool wear using an elastomeric tactile sensor

Machining performance of cutting tools and part quality are affected by the geometric condition of the cutting edge, which is influenced by thermomechanical loads experienced during the process. Tool condition monitoring (TCM) systems provide insight for timely replacement of cutting tools. However, existing TCM systems are expensive and require specialized equipment or sensors, hindering widespread adoption. A novel TCM system is developed herein using an elastomeric tactile sensor. Sensor images of the cutting edge are used to quantify wear using two distinct algorithms. In the first algorithm, the unworn and worn edges are identified based on Canny edge detect. In the second, the unworn edge is identified using edge detection while the region of wear is identified using a relative intensity method. In both cases, the maximum wear width is calculated based on an experimentally determined pixel to-physical distance scale. The TCM system is first used to estimate flank wear on a solid carbide helical end mill before evaluating its robustness by employing it to estimate insert wear of an indexable helical end mill. Measurements are also performed manually using an optical microscope and a high-resolution focus variation microscope for verification. The novel technique estimates flank wear in the solid carbide tool with a high accuracy of 98%. Larger discrepancies are observed for the inserts, however, with overlapping uncertainties. In conclusion, the technique shows promise in adaptability, automation, and closed loop control of machine tools.

Machining↗
DOE OSTI2021

Kinetic-ballooning-mode turbulence in low-average-magnetic-shear equilibria

In this work, kinetic-ballooning-mode (KBM) turbulence is studied via gyrokinetic flux-tube simulations in three magnetic equilibria that exhibit small average magnetic shear: the Helically Symmetric eXperiment (HSX), the helical-axis Heliotron-J and a circular tokamak geometry. For HSX, the onset of KBM being the dominant instability at low wavenumber occurs at a critical value of normalized plasma pressure $\beta ^{\rm KBM}_{\rm crit}$ that is an order of magnitude smaller than the magnetohydrodynamic (MHD) ballooning limit $\beta ^{\rm MHD}_{\rm crit}$ when a strong ion temperature gradient (ITG) is present. However, $\beta ^{\rm KBM}_{\rm crit}$ increases and approaches the MHD ballooning limit as the ITG tends to zero. For these configurations, $\beta ^{\rm KBM}_{\rm crit}$ also increases as the magnitude of the average magnetic shear increases, regardless of the sign of the normalized magnetic shear. Simulations of Heliotron-J and a circular axisymmetric geometry display behaviour similar to HSX with respect to $\beta ^{\rm KBM}_{\rm crit}$ . Despite large KBM growth rates at long wavelengths in HSX, saturation of KBM turbulence with $\beta > \beta _{\rm crit}^{\rm KBM}$ is achievable in HSX and results in lower heat transport relative to the electrostatic limit by a factor of roughly five. Nonlinear simulations also show that KBM transport dominates the dynamics when KBMs are destabilized linearly, even if KBM growth rates are subdominant to ITG growth rates.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Mapping the space of quasisymmetric stellarators using optimized near-axis expansion

A method is demonstrated to rapidly calculate the shapes and properties of quasi-axisymmetric and quasi-helically symmetric stellarators. In this approach, optimization is applied to the equations of magnetohydrodynamic equilibrium and quasisymmetry, expanded in the small distance from the magnetic axis, as formulated by Garren & Boozer [ Phys. Fluids B, vol. 3, 1991, p. 2805]. Due to the reduction of the equations by the expansion, the computational cost is significantly reduced, to times of the order of 1 cpu second, enabling wide and high-resolution scans over parameter space. In contrast to traditional stellarator optimization, here, the cost function serves to maximize the volume in which the expansion is accurate. A key term in the cost function is $\| \boldsymbol {\nabla }\boldsymbol B \|$ , the norm of the magnetic field gradient, to maximize scale lengths in the field. Using this method, a database of $5\times 10^5$ optimized configurations is calculated and presented. Quasisymmetric configurations are observed to exist in continuous bands, varying in the ratio of the magnetic axis length to average major radius. Several qualitatively new types of configuration are found, including quasi-helically symmetric fields in which the number of field periods is two or more than six.

Landreman, Matt (ORCID:000000027233577X)↗
DOE OSTI2025

Collisionless zonal-flow dynamics in quasisymmetric stellarators

The linear collisionless plasma response to a zonal-density perturbation in quasisymmetric stellarators is studied, including the geodesic-acoustic-mode oscillations and the Rosenbluth–Hinton residual flow. While the geodesic-acoustic-mode oscillations in quasiaxisymmetric configurations are similar to tokamaks, they become non-existent in quasi-helically symmetric configurations when the effective safety factor in helical-angle coordinates is small. Compared with concentric-circular tokamaks, the Rosenbluth–Hinton residual is also found to be multiplied by a geometric factor $\mathcal {C}$ that arises from the flux-surface-averaged classical polarization. Using the near-axis-expansion framework, we derive an analytic expression for $\mathcal {C}$ , which varies significantly among different configurations. These analytic results are compared with numerical simulation results from the global gyrokinetic particle-in-cell code GTC, and good agreement with the theoretical Rosenbluth–Hinton residual level is achieved when the quasisymmetry error is small enough.

Zhu, Hongxuan (ORCID:0000000198446972)↗
DOE OSTI2022

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

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

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗