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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 OSTI2023

Subtle Molecular Changes Largely Modulate Chiral Helical Assemblies of Achiral Conjugated Polymers by Tuning Solution-State Aggregation

Understanding the solution-state aggregate structure and the consequent hierarchical assembly of conjugated polymers is crucial for controlling multiscale morphologies during solid thin-film deposition and the resultant electronic properties. However, it remains challenging to comprehend detailed solution aggregate structures of conjugated polymers, let alone their chiral assembly due to the complex aggregation behavior. Herein, we present solution-state aggregate structures and their impact on hierarchical chiral helical assembly using an achiral diketopyrrolopyrrole-quaterthiophene (DPP-T4) copolymer and its two close structural analogues wherein the bithiophene is functionalized with methyl groups (DPP-T2M2) or fluorine atoms (DPP-T2F2). Combining in-depth small-angle X-ray scattering analysis with various microscopic solution imaging techniques, we find distinct aggregate in each DPP solution: (i) semicrystalline 1D fiber aggregates of DPP-T2F2 with a strongly bound internal structure, (ii) semicrystalline 1D fiber aggregates of DPP-T2M2 with a weakly bound internal structure, and (iii) highly crystalline 2D sheet aggregates of DPP-T4. These nanoscopic aggregates develop into lyotropic chiral helical liquid crystal (LC) mesophases at high solution concentrations. Intriguingly, the dimensionality of solution aggregates largely modulates hierarchical chiral helical pitches across nanoscopic to micrometer scales, with the more rigid 2D sheet aggregate of DPP-T4 creating much larger pitch length than the more flexible 1D fiber aggregates. Combining relatively small helical pitch with long-range order, the striped twist-bent mesophase of DPP-T2F2 composed of highly ordered, more rigid 1D fiber aggregate exhibits an anisotropic dissymmetry factor (g-factor) as high as 0.09. This study can be a prominent addition to our knowledge on a solution-state hierarchical assembly of conjugated polymers and, in particular, chiral helical assembly of achiral organic semiconductors that can catalyze an emerging field of chiral (opto)electronics.

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

Helical Organic and Inorganic Polymers

Despite being a staple of synthetic plastics and biomolecules, helical polymers are scarcely studied with Gaussian-basis-set ab initio electron-correlated methods on an equal footing with molecules. This article introduces an ab initio second-order many-body Green’s-function [MBGF(2)] method with nondiagonal, frequency-dependent Dyson self-energy for infinite helical polymers using screw-axis-symmetry-adapted Gaussian-spherical-harmonics basis functions. Together with the Gaussian-basis-set density-functional theory for energies, analytical atomic forces, translational-period force, and helical-angle force, it can compute correlated energy, quasiparticle energy bands, structures, and vibrational frequencies of an infinite helical polymer, which smoothly converge at the corresponding oligomer results. These methods can handle incommensurable structures, which have an infinite translational period and are hard to characterize by any other method, just as efficiently as commensurable structures. We apply them to polyethylene (2/1 helix), polyacetylene (Peierls’ system), and polytetrafluoroethylene (13/6 helix) to establish the quantitative accuracy of MBGF(2)/cc-pVDZ in simulating their (angle-resolved) ultraviolet photoelectron spectra, and of B3LYP/cc-pVDZ or 6-31G** in reproducing their structures, infrared and Raman band positions, phonon dispersions, and (coherent and incoherent) inelastic neutron scattering spectra. We then predict the same properties for infinitely catenated chains of nitrogen or oxygen and discuss their possible metastable existence under ambient conditions. They include planar zigzag polyazene (N2)x (Peierls’ system), 11/3-helical isotactic polyazane (NH)x, 9/4-helical isotactic polyfluoroazane (NF)x, and 7/2-helical polyoxane (O)x as potential high-energy-density materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

A three-dimensional finite-element thermal/mechanical analytical technique for high-performance traveling wave tubes

Current research in high-efficiency, high-performance traveling wave tubes (TWT's) has led to the development of novel thermal/ mechanical computer models for use with helical slow-wave structures. A three-dimensional, finite element computer model and analytical technique used to study the structural integrity and thermal operation of a high-efficiency, diamond-rod, K-band TWT designed for use in advanced space communications systems. This analysis focused on the slow-wave circuit in the radiofrequency section of the TWT, where an inherent localized heating problem existed and where failures were observed during earlier cold compression, or 'coining' fabrication technique that shows great potential for future TWT development efforts. For this analysis, a three-dimensional, finite element model was used along with MARC, a commercially available finite element code, to simulate the fabrication of a diamond-rod TWT. This analysis was conducted by using component and material specifications consistent with actual TWT fabrication and was verified against empirical data. The analysis is nonlinear owing to material plasticity introduced by the forming process and also to geometric nonlinearities presented by the component assembly configuration. The computer model was developed by using the high efficiency, K-band TWT design but is general enough to permit similar analyses to be performed on a wide variety of TWT designs and styles. The results of the TWT operating condition and structural failure mode analysis, as well as a comparison of analytical results to test data are presented.

Bartos, Karen F.↗
NASA NTRS1992

A three-dimensional finite-element thermal/mechanical analytical technique for high-performance traveling wave tubes

Current research in high-efficiency, high-performance traveling wave tubes (TWT's) has led to the development of novel thermal/mechanical computer models for use with helical slow-wave structures. A three-dimensional, finite element computer model and analytical technique used to study the structural integrity and thermal operation of a high-efficiency, diamond-rod, K-band TWT designed for use in advanced space communications systems. This analysis focused on the slow-wave circuit in the radiofrequency section of the TWT, where an inherent localized heating problem existed and where failures were observed during earlier cold compression, or 'coining' fabrication technique that shows great potential for future TWT development efforts. For this analysis, a three-dimensional, finite element model was used along with MARC, a commercially available finite element code, to simulate the fabrication of a diamond-rod TWT. This analysis was conducted by using component and material specifications consistent with actual TWT fabrication and was verified against empirical data. The analysis is nonlinear owing to material plasticity introduced by the forming process and also to geometric nonlinearities presented by the component assembly configuration. The computer model was developed by using the high efficiency, K-band TWT design but is general enough to permit similar analyses to be performed on a wide variety of TWT designs and styles. The results of the TWT operating condition and structural failure mode analysis, as well as a comparison of analytical results to test data are presented.

Shalkhauser, Kurt A.↗
NASA NTRS1990

Magnetic flux ropes in the ionosphere of Venus

The Pioneer Venus Orbiter has shown that the ionosphere of Venus is often filled with filamentary magnetic fields. These magnetic flux tubes apparently are created at the ionopause in the subsolar region and sink to low altitudes. As they sink they twist and compress, maintaining about the same magnetic flux, 2 to 3 Webers, until they sink below 175 km. Ropes also appear to become kink unstable at about 200 km generating spatial helices. These 3-dimensional structures can lead to increased interaction between flux ropes.

Russell, C. T.↗
NASA NTRS1998

New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces. Measuring these units was not attempted before and most studies have assumed that the growth unit consisted of individual protein molecules. The linescan mode of AFM instruments allows the crystal surface to be scanned along a single line. By scanning across a growth step an image showing the motion of the step is obtained. Normally such an image shows a straight line for continuous and constant step velocity. In this study by increasing the scan rate and by decreasing the step velocity (by decreasing the supersaturation), we were able to capture images of individual growth events, shown by jump discontinuities in the step line. By suitable integration of the image the growth unit dimension in the scanned direction can be obtained. Since multiple units can be involved in the growth process it is necessary to collect a statistically relevant sample before drawing conclusions about the growth mechanism. This technique was successfully employed to obtain the dimensions of growth units for the (110) face, showing that they consisted of various aggregates corresponding to the 43 helices in the crystal structure.

Li, Huayu↗
DOE OSTI2022

Flow structures of the cross-flow over a five-layer helically coiled steam generator geometry

The helically-coiled heat exchanger (HCSG) offers advantages over straight tubes such as compactness in geometry, increased heat transfer coefficients, and capability to absorb thermal expansion. In this study, the time-resolved velocity field data of shell-side crossflow over a five-layer helically coiled steam generator geometry was obtained using Particle Image Velocimetry (PIV) between adjacent rods in four regions with up to 5000 frames per second (5 kHz) at approximately Re u = 3600. The slant rod bundle created different flow patterns in different regions. Proper Orthogonal Decomposition (POD) revealed high-energy-mode flow structures. Due to the confined flow channel geometry, the large flow structures were not advected resulting in no strong POD mode paring. Continuous Wavelet Transform (CWT) visualized the characteristics of flow fluctuation in time and frequency domain simultaneously, which ranged in Strouhal number, S u , between 0.03 and 1.17. In the wake regions of the rods, flows changed in both pattern and magnitude over time. Once a pattern formed, it continued for relatively shorter than straight tube arrays, before changing the pattern again. The histograms of the POD time coefficients presented this multimodal flow characteristics. The current study focuses more on whole flow field analyses in the selected regions rather than local point-wise analyses. Finally, this study revealed that various Strouhal numbers can exist in the helically coiled heat exchanger geometry, which was not observed in straight tube arrays. In particular, Strouhal numbers smaller than 0.1 do not seem to be caused by vortex shedding but seem to be the result of the combination of complex geometry and possible multimodal trends. Based on the current observation, further works would involve intensive instantaneous point-wise analyses on the interactions between important locations such as separation points, stagnation points, shear layers, etc.

42 ENGINEERING↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Triel-Defined Helicity in One-Dimensional III–VI–VII van der Waals Crystals

Inorganic extended lattice solids that bear complex helical motifs manifest unusual physical and quantum states that arise due to their noncentrosymmetric or chiral nature. However, the systematic understanding of how elemental composition influences the structure and physical properties in helical inorganic crystals has been precluded by the rarity of these materials and the lack of modular phases that display such motifs. Here, we report the synthesis of AlSeI single crystals, the first aluminum-containing helical crystal in the III-VI-VII 1D van der Waals class. AlSeI completes the experimentally accessible triel series in the helical selene iodides alongside InSeI and GaSeI. Using the Al, Ga, and In triel series in this selene iodide class, we experimentally demonstrate the evolution of the local quasi-tetrahedral building unit geometry, chain packing, helical parameters, and band gaps based primarily on the identity of the triel atom. Our results underscore the chemical modularity of these phases, the broad range of helical parameters, and the spectrum of electronic states from the visible to the ultraviolet range in this emergent class of 1D, exfoliable, and helical extended lattice solids.

Chemical structure↗
NASA NTRS1998

Observation and Modeling of Single Wall Carbon Nanotube Bend Junctions

Single wall carbon nanotube (SWNT) bends, with diameters from approx. 1.0 to 2.5 nm and bend angles from 18 deg. to 34 deg., are observed in catalytic decomposition of hydrocarbons at 600 - 1200 C. An algorithm using molecular dynamics simulation (MD) techniques is developed to model these structures that are considered to be SWNT junctions formed by topological defects (i.e. pentagon-heptagon pairs). The algorithm is used to predict the tube helicities and defect configurations for bend junctions using the observed tube diameters and bend angles. The number and arrangement of the defects at the junction interfaces are found to depend on the tube helicities and bend angle. The structural and energetic calculations using the Brenner potential show a number of stable junction configurations for each bend angle with the 34 deg. bends being more stable than the others. Tight binding calculations for local density of state (LDOS) and transmission coefficients are carried out to investigate electrical properties of the bend junctions.

Han, Jie↗
DOE OSTI2024

Vortex bursting and associated twist dynamics on helical vortex tubes and vortex rings

The interaction of opposite-signed twist waves on vortex tubes can lead to vortex bursting, a process where the core expands into a double ring-like structure with strong swirling flows. Previous works have studied vortex bursting on rectilinear vortices by axially perturbing the initial core size to generate the twist waves, and observed largely axisymmetric bursting dynamics. In this work, we numerically study bursting on vortical structures with curved centrelines, analysing the interaction between the centreline dynamics, twist wave generation and propagation, and vortex bursting. We focus on axially perturbed helical vortex tubes with small radius-to-pitch ratios up to$0.0625$, as well as vortex rings with a large radius-to-core size ratio$10$, both at a circulation-based Reynolds number$5000$. The results show that though the initial twist wave propagation speeds are relatively unaffected by the curvature and torsion of the centreline, the bursting process is altered significantly compared with rectilinear vortices. The self-induced rotation of the centreline of the helical tube induces a non-axisymmetric distortion of the bursting structure, which rapidly breaks up the vortex core into small-scale helical structures. A similar destabilization of the bursting structure also occurs on vortex rings. The enstrophy increase and accelerated energy decay associated with bursting are predominantly determined by the twist wave strength, rather than the curvature and torsion of the centreline. Combined, our findings imply that bursting could play an important role in transferring and dissipating energy of vortical structures in wakes, and turbulent flows in general.

Mechanics↗
DOE OSTI2023

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag + and Hg 2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, in this study, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

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

The protein structurome of Orthornavirae and its dark matter

Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile-based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed an Orthornavirae “structurome” consisting of already annotated as well as unannotated (“dark matter”) proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either “generic” folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Dynamics of adaptive structures: Design through simulations

The use of a helical bi-morph actuator/sensor concept by mimicking the change of helical waveform in bacterial flagella is perhaps the first application of bacterial motions (living species) to longitudinal deployment of space structures. However, no dynamical considerations were analyzed to explain the waveform change mechanisms. The objective is to review various deployment concepts from the dynamics point of view and introduce the dynamical considerations from the outset as part of design considerations. Specifically, the impact of the incorporation of the combined static mechanisms and dynamic design considerations on the deployment performance during the reconfiguration stage is studied in terms of improved controllability, maneuvering duration, and joint singularity index. It is shown that intermediate configurations during articulations play an important role for improved joint mechanisms design and overall structural deployability.

Park, K. C.↗
DOE OSTI2022

Field study of group effects on the pullout capacity of “deep” helical piles in sand

This paper presents the results of a field load test program used to investigate group effects on the pullout capacity of single-helix “deep” helical piles/anchors in sand. The high tensile capacity and silent installation of helical piles has given them serious consideration as an alternative to conventional deep foundations and anchors for offshore renewable energy structures. New offshore applications may consider the use of groups of helical piles to resist structural loads. Group interaction effects are known to occur in helical piles, but there is a scarcity of field data on groups in sands under tensile loading. This study involved the installation and load testing of single-helix 152mm diameter round shaft piles and pile groups embedded in sand to depths of 12 and 18 helix diameters below the ground surface. The study was designed to explore the effects of close pile spacing, group configuration (i.e., number of piles), and soil strength (i.e., friction angle) as interpreted from cone penetration test (CPT) resistance. The results showed group efficiencies ranging from about 0.6 to 1.0 at a horizontal spacing of 2 to 3 times the helix diameter in sands with friction angles of about 39° to 44°. The data from this study may also be useful for validation of numerical models for analysis of helical pile group interactions.

Engineering↗
DOE OSTI2023

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Abstract Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

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

Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors

Human p97 ATPase is crucial in various cellular processes, making it a target for inhibitors to treat cancers, neurological, and infectious diseases. Triazole allosteric p97 inhibitors have been demonstrated to match the efficacy of CB-5083, an ATP-competitive inhibitor, in cellular models. However, the mechanism is not well understood. This study systematically investigates the structures of new triazole inhibitors bound to both wild-type and disease mutant forms of p97 and measures their effects on function. These inhibitors bind at the interface of the D1 and D2 domains of each p97 subunit, shifting surrounding helices and altering the loop structures near the C-terminal α2 G helix to modulate domain-domain communications. A key structural moiety of the inhibitor affects the rotameric conformations of interacting side chains, indirectly modulating the N-terminal domain conformation in p97 R155H mutant. The differential effects of inhibitor binding to wild-type and mutant p97 provide insights into drug design with enhanced specificity, particularly for oncology applications.

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

Role of backbone strain in de novo design of complex α/β protein structures

Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗