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Results for “higher-order assembly”

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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories

Abstract The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Galaxy-multiplet clustering from DESI DR2

We present an efficient estimator for higher-order galaxy clustering using small groups of nearby galaxies, or multiplets. Using the Luminous Red Galaxy (LRG) sample from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2, we identify galaxy multiplets as discrete objects and measure their cross-correlations with the general galaxy field. Our results show that the multiplets exhibit stronger clustering bias as they trace more massive dark matter halos than individual galaxies. When comparing the observed clustering statistics with the mock catalogs generated from the N-body simulation AbacusSummit, we find that the mocks underpredict multiplet clustering despite reproducing the galaxy two-point auto-correlation reasonably well. This discrepancy indicates that the standard Halo Occupation Distribution (HOD) model is insufficient to describe the properties of galaxy multiplets, revealing the greater constraining power of this higher-order statistic on galaxy-halo connection and the possibility that multiplets are specific to additional assembly bias. We demonstrate that incorporating secondary biases into the HOD model improves agreement with the observed multiplet statistics, specifically by allowing galaxies to preferentially occupy halos in denser environments. Our results highlight the potential of utilizing multiplet clustering, beyond traditional two-point correlation measurements, to break degeneracies in models describing the galaxy-dark matter connection.

cosmology↗
DOE OSTI2025

CpoS-Inc interactions facilitate host cell modulation during Chlamydia trachomatis infection

ABSTRACT Chlamydia trachomatis ( C.t .), the leading bacterial cause of sexually transmitted infections, replicates within a unique intracellular compartment called the inclusion, which is modified by secreted proteins known as inclusion membrane (Inc) proteins. Here, we further characterize CpoS, an Inc protein previously shown to be critical for bacterial replication and inclusion development. We demonstrate that CpoS directly binds multiple coiled-coil region-containing Incs and engages Rab GTPases at a separate site. Notably, CpoS-InaC interactions facilitate the recruitment of select Arf GTPases to the inclusion membrane, while Rab recruitment occurs independently of these interactions. Biochemical and biophysical analyses revealed that Incs self-oligomerize to form higher-ordered structures, with CpoS adopting a tetrameric conformation resembling that of eukaryotic SNARE proteins. We propose that these assemblies serve as scaffolds to orchestrate vesicle docking, tethering, and fusion. Our findings highlight the intricate interplay between bacterial and host factors, revealing how C.t . leverages both Inc-Inc interactions and host protein engagement to manipulate vesicular trafficking and sustain infection.

Tijerina, Xavier [Department of Microbiology and I↗
NASA NTRS2023

The First Extragalactic Detection of Higher-Order Hydrogen Recombination Lines

The Large Magellanic Cloud (LMC) is the nearest (~50 kpc) star-forming galaxy characterized by a low metallicity (Z~0.3-0.5 Z⨀) similar to galaxies during the early phases of their assembly. As a result, star formation studies in the LMC provide a stepping stone to understanding star formation at earlier epochs of the universe where these processes cannot be directly observed. N113 is one of the most prominent star-forming regions in the LMC hosting one of the most massive giant molecular clouds. N113 is small enough to be imaged in its entirety, but large enough to showcase many important phenomena such as multiple generations of stars, stellar feedback, and different environments. We present our findings from an investigation of the early stages of star formation in the N113 region using the Atacama Large Millimeter/submillimeter Array (ALMA) molecular line data probing a wide density range: 12CO, 13CO, and C18O (2-1), 13CO and C18O (1-0), HCN (1-0), HCO+ (1-0), H13CN (1-0) and (3-2), H13CO+ (1-0) and (3-2), CS (2-1) and (5-4), as well as 1.3 mm and 3 mm continuum. We used the Python package quickclump to identify molecular clumps. We utilized the multiline non-LTE fitting tool based on models from RADEX developed by Finn et al. (2021, ApJ, 917, 106) to construct the CO, HCN, HCO+, and CS temperature and column density, and the H2 density maps of N113. We constructed a catalog of molecular clumps including their physical properties, chemical abundances, sizes, velocities, and velocity dispersions. To establish the evolutionary status of the clumps, their positions were compared with previously identified young stellar objects (YSOs) from the Spitzer/SAGE and Herschel/HERITAGE surveys, as well as water and OH masers. We compared the properties of the clumps in N113 to those in the Galaxy and other regions in the LMC to assess the impact of the environment (e.g., metallicity, stellar feedback) on the star formation process.

Marta M Sewilo↗
DOE OSTI2024

Higher-order tails and RG flows due to scattering of gravitational radiation from binary inspirals

Abstract We establish and develop a novel methodology to treat higher-order non-linear effects of gravitational radiation that is scattered from binary inspirals, which employs modern scattering-amplitudes methods on the effective picture of the binary as a composite particle. We spell out our procedure to study such effects: assembling tree amplitudes via generalized-unitarity methods and employing the closed-time-path formalism to derive the causal effective actions, which encompass the full conservative and dissipative dynamics. We push through to a new state of the art for these higher-order effects, up to the third subleading tail effect, at order$$ {G}_N^5 $$ G N 5 and the 5-loop level, which corresponds to the 8.5PN order. We formulate the consequent dissipated energy for these higher-order corrections, and carry out a renormalization analysis, where we uncover new subleading RG flow of the quadrupole coupling. For all higher-order tail effects we find perfect agreement with partial observable results in PN and self-force theories, where available.

Physics↗
NASA NTRS2001

Simulation of Peptides at Aqueous Interfaces

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Pohorille, Andrew↗
DOE OSTI2025

Interpreting scattered neutron spectra on omega cryogenic implosions with measured backgrounds and higher-order scattering

Measurements of the areal density (⁠ρR⁠) of inertially confined implosions are critical to evaluate their performance. On OMEGA, ρR is inferred from measurements of the scattered neutron spectrum via neutron-time-of-flight (nTOF) and magnetic recoil spectrometer detectors. The nTOF measurements, in particular, have the ability to measure a wide range of neutron energies and thus scattering angles, with high precision. However, the neutrons that are backscattered into the detector must transit through the entire dense fuel assembly, and as a result are subject to rescattering effects, which have been heretofore neglected in the interpretation of OMEGA neutron spectra. At the backscatter edge, neglecting rescattering on OMEGA can lead to a ~10 to 20% reduction of the apparent areal density and therefore must be included in the analysis. The low ρR s on OMEGA also mean that backgrounds from non-target physics effects, such as scattering in the target chamber or slow scintillator decays, can significantly alter the measured signal. Here, we discuss how the Monte Carlo neutron spectrum postprocessor IRIS is used to include second-order scattering effects in the interpretation of the scattered neutron spectrum in OMEGA implosion experiments, and how dedicated implosion experiments are used to measure nTOF backgrounds in order to infer backscattered areal densities on OMEGA.

Deuterium↗
DOE OSTI2024

Investigations on the multiple-sector hard-copper X-band accelerating structures

The development of advanced, high gradient accelerating structures is one of the leading activity of the particle accelerator community. In the technological research of new construction methods for these devices, high-power testing is a critical step for the verification of their viability. Recent experiments showed that accelerating cavities made out of hard copper, fabricated without high-temperature processes, can achieve better performance as compared with soft copper ones. Recently, we have built cavities using Tungsten Inert Gas welding and the high-power experiments confirmed that this joining process is a robust and low-cost alternative to brazing or diffusion bonding. This is a good solution for high-gradient operation, with a gradient of about 150 MV/m in X-band, at a breakdown rate of 10 -3 /pulse/meter using a shaped RF pulse with a 150 ns flat part. We continue the design, construction and high power tests of three-cells standing-wave X-band accelerating cavities fabricated with a split-open geometry, made of hard copper and vacuum-sealed by welding. Our aim is the fabrication of accelerating structures made out of hard copper alloys by using innovative cost-effective technologies. Moreover, our method of multiple-sector structures opens the way to new technological approaches and design methods, for example providing the possibility of placing dampers of the parasitic higher-order modes. Such structures with dampers allow for acceleration of multi-bunch beams, both in standing and in travelling-wave accelerating modality. Here, this paper describes the design of two cavities made of multiple sectors that were fabricated at the Italian Institute for Nuclear Physics in Frascati, Italy (INFN-LNF), assembled by means of clamping and then joined with the Tungsten Inert Gas welding in order to preserve the hardness of the metal. These are three-cell standing-wave X-band accelerating cavities, to be operated in the π-mode. We report the low-power RF tests of the first one, made of two halves, and the RF design of the second one, made of four quadrants. Both structures were built for high-gradient tests at SLAC National Accelerator Laboratory.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Capacitor Design for Self-Resonant Coils for Long-Distance Wireless Power Transfer System

In this paper, an integrated capacitor design is proposed for higher-order resonant tank topologies for self-resonant coils, such as series, parallel, LCC, LLC, etc. The capacitor is one of the large, lossy, and thermally vulnerable components of a high-frequency resonant tank, and designing a high-voltage, thermally stable resonant capacitor can be highly challenging. Designing the extremely high-voltage capacitor as an integral part of the coil reduces the size and complexity of the coil assembly. This paper proposes a low-loss PCB-based high-voltage capacitor design to achieve that target, which can be implemented as an integral part of the coil. The proposed capacitor designs are simulated using Multiphysics FEA and tested experimentally. A 23 kV, 133 pF capacitor prototype was built and tested as part of a 1 kW long-distance wireless charging system. The test results verify the capacitor’s voltage, current, and thermal resiliency performance.

Mohammad, Mostak [ORNL] (ORCID:0000000256388783)↗
DOE OSTI2024

Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR

Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.

09 BIOMASS FUELS↗
NASA NTRS1985

A 3-component laser-Doppler velocimeter data acquisition and reduction system

A laser doppler velocimeter capable of measuring all three components of velocity simultaneously in low-speed flows is described. All the mean velocities, Reynolds stresses, and higher-order products can be evaluated. The approach followed is to split one of the two colors used in a 2-D system, thus creating a third set of beams which is then focused in the flow from an off-axis direction. The third velocity component is computed from the known geometry of the system. The laser optical hardware and the data acquisition electronics are described in detail. In addition, full operating procedures and listings of the software (written in BASIC and ASSEMBLY languages) are also included. Some typical measurements obtained with this system in a vortex/mixing layer interaction are presented and compared directly to those obtained with a cross-wire system.

Rodman, L. C.↗
DOE OSTI2024

Opto-twistronic Hall effect in a three-dimensional spiral lattice

Studies of moire systems have elucidated the exquisite effect of quantum geometry on the electronic bands and their properties, leading to the discovery of new correlated phases. However, most experimental studies have been confined to a few layers in the 2D limit. The extension of twistronics to its 3D limit, where the twist is extended into the third dimension between adjacent layers, remains underexplored due to the challenges in precisely stacking layers. Here, in this study, we focus on 3D twistronics on a platform of self-assembled spiral superlattice of multilayered WS 2 . Our findings reveal an opto-twistronic Hall effect in the spiral superlattice. This mesoscopic response is an experimental manifestation of the noncommutative geometry that arises when translational symmetry is replaced by a non-symmorphic screw operation. We also discover signatures of altered laws of optical excitation, manifested as an unconventional photon momentum-lattice interaction owing to moire of moire modulations in the 3D twistronic system. Crucially, our findings mark the initial identification of higher-order quantum geometrical tensors in light-matter interactions. This breakthrough opens new avenues for designing quantum materials-based optical lattices with large nonlinearities, paving the way for the development of advanced quantum nanophotonic devices.

Ji, Zhurun↗
NASA NTRS1986

A 3-component laser-Doppler velocimeter data acquisition and reduction system

This report describes a laser Doppler velocimeter capable of measuring all three components of velocity simultaneously in low-speed flows. All the mean velocities, Reynolds stresses, and higher-order products can then be evaluated. The approach followed is to split one of the colors used in a 2-D system, thus creating a third set of beams which is then focused in the flow from an off-axis direction. The third velocity component is computed from the known geometry of the system. In this report, the laser optical hardware and the data acquisition electronics are described in detail. In addition, full operating procedures and listings of the software (written in BASIC and assembly languages) are also included. Some typical measurements obtained with this system in a vortex/mixing layer interaction are presented and compared directly to those obtained with a cross-wire system.

Rodman, L. C.↗
DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗
DOE OSTI2024

Effects of N -glycans on the structure of human IgA2

The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and structural characterization of recombinant monomeric human IgA2, which varies in the amount/locations of attached glycans. Monomeric IgA2 antibodies were produced by removing the N-linked glycans in the CH1 and CH2 domains. The impact of glycans on oligomer formation, thermal stability, and receptor binding was evaluated. In addition, we performed a structural analysis of recombinant IgA2 in solution using Small Angle X-Ray Scattering (SAXS) to examine the effect of glycans on protein structure and flexibility. Our results indicate that the absence of glycans in the Fc tail region leads to higher-order aggregates. SAXS, combined with atomistic modeling, showed that the lack of glycans in the CH2 domain results in increased flexibility between the Fab and Fc domains and a different distribution of open and closed conformations in solution. When binding with the Fcα-receptor, the dissociation constant remains unaltered in the absence of glycans in the CH1 or CH2 domain, compared to the fully glycosylated protein. These results provide insights into N-glycans’ function on IgA2, which could have important implications for developing more effective IgA-based therapeutics in the future.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

Ka-Band Wide-Bandgap Solid-State Power Amplifier: Prototype Combiner Spurious Mode Suppression and Power Constraints

Results of prototype hardware activities related to a 120-W, 32-GHz (Ka-band) solid-state power amplifier (SSPA) architecture study are presented. Spurious mode suppression and the power-handling capability of a prototype 24-way radial combiner and a prototype 2-way septum binary combiner were investigated. Experimental data indicate that a commercial absorptive filter, designed to pass the circular TE01 mode, effectively suppressed the higher-order modes generated by a narrowband, flower-petal-type mode transducer. However, the same filter was not effective in suppressing higher-order modes generated by the broadband Marie mode transducer that is used in the prototype waveguide radial combiner. Should greater filtering be required by a particular SSPA application, a broadband mode filter that can suppress specifically those higher-order modes that are generated by the Marie transducer will need to be developed. A back-to-back configuration of the prototype radial combiner was tested with drive power up to approximately 50 W. No anomalous behavior was observed. Power measurements of the septum combiner indicate that up to 10-W radio frequency (RF) can be dissipated in the integrated resistive element before a permanent performance shift is observed. Thus, a given adder (a single-stage, 2-way combiner) can safely combine two 20-W sources, and the adder will not be damaged in the event of a source failure. This result is used to calculate the maximum source power that can be safely combined as a function of the number of sources combined and the number of source failures allowed in a multi-stage combiner. The analysis shows that SSPA power >140 W can be generated by power combining 16 sources producing 10 W each. In this configuration, up to three sources could fail with the guarantee that the combiner would not be damaged. Finally, a modified prototype septum combiner design was verified. The improved design reduced the assembly time from over 2 hours to about 15 minutes per adder.

Khan, P.↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗