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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CFTs blueshift tensor fluctuations universally

The strong constraints of conformal symmetry cause any nearly-conformal sector to blueshift tensor fluctuations in cosmology. Hidden sectors with approximate conformal symmetry, which may be quite large, are a well-motivated extension of physics beyond the Standard Models of particle physics and cosmology. They can therefore lead to a detectable shift in the tensor tilt for next-generation CMB and gravitational wave experiments. Here, we compute the leading-order contribution to the in-in graviton two-point function from virtual loops in such sectors to demonstrate this universal effect. In units where a single conformally-coupled scalar is 1, limits from Stage-IV CMB experiments could bound the size of this extra sector to be smaller than ~10 15 , under a plausible calculational assumption backed by a simple power counting argument. This would be sufficient to rule out N-Naturalness as a complete resolution of the hierarchy problem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli .

protofilaments↗
DOE OSTI2022

Antibody Recognition of CD4-Induced Open HIV-1 Env Trimers

Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Accelerating GNNs on GPU Sparse Tensor Cores through N:M Sparsity-Oriented Graph Reordering

Recent advancements in GPU hardware support have introduced the capability to leverage N:M sparse patterns for substantial performance gains. Graphs in Graph Neural Networks (GNNs) are typically sparse, but the sparsity is often irregular, not conforming to such sparse patterns. In this paper, we propose a novel graph reordering algorithm, the first of its kind, to reshape irregular graph data into the N:M structured sparse pattern at the tile level, allowing linear-algebra-based graph operations in GNNs to benefit from the N:M sparse hardware. The optimization is lossless, maintaining the accuracy of GNN. It can remove 98-100\% violations of the N:M sparse patterns at the vector level, and increase the proportion of conforming graphs in SuiteSparse collection from 5-9\% to 88.7-93.5\%. On A100 GPUs, the optimization accelerates Sparse Matrix Matrix (SpMM) by up to 43X (2.3X -- 7.5X on average) and speeds up the key graph operations in GNNs on real graphs by as much as 8.6X (3.5X on average).

artificial intelligence, graph neural networks↗
DOE OSTI2020

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BP SS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BP SS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BP SS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BP SS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R 0 ) and fluorophore orientation factor (κ 2 ) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Satellite Enveloped with STITCHED Engineering Sensors for Detection of Approaching Objects

Today as well as tomorrows spaceborne assets impact almost all areas of national and nuclear security. Spaceborne assets can not only collect and disseminate valuable data, well beyond just the visual, but also track terrestrial-based mobile assets in real-time, and active spaceborne platforms potentially pose serious risk to vulnerable earth-based systems and infrastructures. The capability to defend national spaceborne assets from attack/interference is critical for security interests. This effort supports this mission through the cost-effective preeminent detection of approaching threats to our nation’s vital resources, in order to help secure and trust these high-value assets against the threats of tomorrow. This project develops novel fabrication techniques for conformal, low-profile and lightweight leakywave antenna (LWA) detection/imaging systems, which fuses technical embroidery (TE) and laser ablation (LA) processes with LWA design. Technical embroidery is an emerging field in additive textile manufacturing where flexible materials and functionalized fabrics are created for a wide variety of uses and purposes, while laser ablation is the process of removing material from a solid surface by irradiating it with a laser beam. Here, thin, conformal antenna designs are designed, modeled and fabricated using both TE and LA, to create lightweight, flexible and conformal object detection and imaging radars. This novel development ensures our nation’s ability to field advanced lightweight and conformal technologies to protect spaceborne assets.

42 ENGINEERING↗
DOE OSTI2024

Adaptive Protection and Validated Models to Enable Deployment of High Penetrations of Solar PV (PV-MOD)

The availability and validation of various PV models in commercial tools differ, with some models not yet thoroughly validated for advanced inverter functionalities and reliable performance under weak system conditions. Many existing models do not fully incorporate new inverter control functions, which can affect system stability. The increasing deployment of solar PV and other inverter-based resources (IBRs), including distributed energy resources (DERs), is influencing the reliable operation of protection schemes in distribution systems and microgrids. Emerging adaptive protection schemes (APS) offer new opportunities for protecting these systems during varying configurations and DER operating conditions, though their demonstration and validation remain limited. Adaptive protection schemes face similar challenges, as they are typically designed for specific configurations. There is a growing need for tools and methodologies to streamline the deployment of adaptive protection for safe and reliable DER integration. The project main objective was to develop and validate high-fidelity generic models of solar PV facilities for stability, protection, EMT, and QSTS analyses. This objective was achieved, and these models can now be integrated into commercial software tools, enabling utilities, vendors, and developers to study high-penetration PV systems more confidently. The project also demonstrated advanced applications of these models, including the design and deployment of adaptive protection schemes in high-penetration field applications and microgrids, supporting grid safety and reliability. Several milestones were reached by the end of the project. A sophisticated inverter test plan was developed, and inverters representative of the North American marketplace were selected. EPRI and NREL tested various inverters, conforming to IEEE standards. Improvements were made to existing generic models of IBR units, IBR plants, and aggregated feeders for various analyses. The first generic electromagnetic transient (EMT) model for a solar PV plant was developed, conforming to IEEE Std 2800™-2022 and validated against laboratory measurements of a 2.2 MVA large-scale battery energy storage system (BESS) inverter. That model was then used to produce reference responses illustrating examples of validated and verified IBR plant models that pass or fail tests for technical minimum capability and performance as specified in the IEEE standard. The developed, tested, and validated generic models can be used for transmission planning, stability assessments, expansion planning, and evaluating potential future IBR interconnection requirements. They can also support interconnection screens and conformity assessments of IBR plants, including solar PV. The project significantly contributed to the ongoing standardization and model-based representation and verification of IBR responses. The project further addressed challenges of common distribution protection schemes with increasing deployment of DER by developing, validating, and demonstrating adaptive protection schemes (APS) that can improve the reliable and safe integration of DER into distribution systems. New APS were designed using improved DER models for three common distribution systems: a radial feeder, a meshed network, and a microgrid. Modeling and hardware-in-the-loop (HIL) testing of the APS were conducted, successfully showing their effectiveness and selectivity. Proof-of-concept field demonstration was achieved for two APS, i.e., one on a radial feeder and another one in a microgrid. Field demonstration could not be achieved for the APS on a meshed network, primarily due apprehension of one utility partner and also due to limited access to the protective algorithms in the network protectors. Guidelines developed from the lessons learned in the project lay out the general process followed in the design, installation, and commissioning of APS for various distribution systems. Distribution utility partners’ apprehension about field demonstration of the new APS were addressed—with varying success—by taking a stepped risk-management approach of modeling of a wide range of sensitivities first, performing in-depth proof-of-concept testing in the laboratory including HIL next, and finally deliberately implementing and commissioning the actual protection equipment and algorithms into parts of—or in parallel operation to—the three real distribution systems. Future work should include pilot projects that further show the acceptable performance of the developed APS before these schemes be rolled out more widely. Inclusion of both utility and original equipment manufacturers (OEMs) in future projects could increase chances of successful field demonstration. Despite challenges in achieving the field demonstration goal of the project for all three APS, the research significantly contributed to the innovation of adaptive protection solutions for scalable and reliable DER integration into distribution systems. This project significantly enhances the understanding of the impact of using appropriate inverter models on distribution and transmission (T&D) systems. By addressing the limitations of existing generic models, the project introduces high-fidelity models for stability, protection, electromagnetic transient (EMT), and quasi-static time series (QSTS) analyses. These models, integrated into commercial software tools, enable utilities, vendors, and developers to confidently study high-penetration PV systems. The project also demonstrates advanced applications, including adaptive protection schemes (APS) for distribution systems and microgrids, ensuring grid safety and reliability. The technical effectiveness and economic feasibility of the methods are evident through the development and validation of sophisticated inverter test plans and the selection of representative inverters. Testing by EPRI and NREL on retail, commercial, and utility-scale inverters, conforming to IEEE standards, underscores the robustness of the models. Improvements to existing generic models for various analyses further enhance their validity and applicability. The project also identifies gaps in common distribution protection schemes and designed new APS using improved DER models, demonstrating their effectiveness through modeling and hardware-in-the-loop (HIL) testing. The project’s benefits to the public are manifold. By advancing the standardization and model-based representation of IBR response, it supports transmission planning, stability assessments, and future IBR interconnection requirements. The generic models can facilitate better communication between transmission planners and developers, supporting expected IBR plant capability and performance. Additionally, the development of APS for radial feeders, meshed networks, and microgrids supports the integration of distributed energy resources (DERs) into distribution systems, enhancing grid reliability and safety. The project’s emphasis on thorough testing and simplicity in design ensures practical and scalable solutions for DER integration.

14 SOLAR ENERGY↗
DOE OSTI2021

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparative Study of High-Resolution LysB29(Nε-myristoyl) des(B30) Insulin Structures Display Novel Dynamic Causal Interrelations in Monomeric-Dimeric Motions

The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic β-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with type 1 diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here, we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 Å resolution at cryogenic temperature. We computationally further investigated our crystal structure’s monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ), obtained at elevated pH, provides electrostatically triggered minor movements in the equilibrium between alternate conformational substates compared to the previous structure, suggesting it might induce an intermediate state in the dissociation pathway of the insulin detemir’s hexamer:dihexamer equilibrium. Supplemented with orientational cross-correlation analysis by a Gaussian network model (GNM), this alternate oligomeric conformation offers the distinct cooperative motions originated by loose coupling of distant conformational substates of a protracted insulin analog that has not been previously observed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation

While drug resistance mutations can often be attributed to the loss of direct or solvent-mediated protein−ligand interactions in the drug-mutant complex, in this study we show that a resistance mutation for the picomolar HIV-1 capsid (CA)-targeting antiviral (GS-6207) is mainly due to the free energy cost of the drug-induced protein side chain reorganization in the mutant protein. Among several mutations, M66I causes the most suppression of the GS-6207 antiviral activity (up to ~84,000-fold), and only 83- and 68-fold reductions for PF74 and ZW-1261, respectively. To understand the molecular basis of this drug resistance, we conducted molecular dynamics free energy simulations to study the structures, energetics, and conformational free energy landscapes involved in the inhibitors binding at the interface of two CA monomers. To minimize the protein−ligand steric clash, the I66 side chain in the M66I−GS-6207 complex switches to a higher free energy conformation from the one adopted in the apo M66I. In contrast, the binding of GS-6207 to the wild-type CA does not lead to any significant M66 conformational change. Based on an analysis that decomposes the absolute binding free energy into contributions from two receptor conformational states, it appears that it is the free energy cost of side chain reorganization rather than the reduced protein−ligand interaction that is largely responsible for the drug resistance against GS-6207.

Sun, Qinfang (ORCID:0000000173621543)↗
DOE OSTI2020

Chemical and structural investigation of the paroxetine-human serotonin transporter complex

Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation, leading to questions about relationships of these structures to the bonafide conformation and inhibitor binding poses of wild-type transporter. To address these concerns, we determined the structures of ΔN72/ΔC13 and ts2-inactive SERT bound to paroxetine analogues using single-particle cryo-EM and x-ray crystallography, respectively. We synthesized enantiopure analogues of paroxetine containing either bromine or iodine instead of fluorine. We exploited the anomalous scattering of bromine and iodine to define the pose of these inhibitors and investigated inhibitor binding to Asn177 mutants of ts2-active SERT. These studies provide mutually consistent insights into how paroxetine and its analogues bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1975

Raman spectra of gases. XVIII - Internal rotational motions in ethylamine and ethylamine-d2

The Raman spectra of gaseous CH3CH2NH2 and CH3CH2ND2 have been recorded at wavenumbers from 100 to 600. Both ground and excited states of the methyl and amino torsional modes for the gauche conformer have been observed. The overtone of the methyl torsion has also been observed for the gauche conformer. The methyl barriers in the gauche conformers of the CH3CH2NH2 and CH3CH2ND2 molecules were found to be 3.71 + or - 0.05 and 3.59 + or - 0.05 kcal/mole, respectively. The apparent difference in the barrier heights for these two isotopic species is attributed to a difference in the coupling between the methyl and amino torsions in these two molecules. The potential function for internal rotation around the C-N bond in CH3CH2ND2 was determined. The energy difference between the potential energy minima of the gauche and trans conformations is 0.592 kcal/mole with the trans being the more stable.

Durig, J. R.↗
NASA NTRS1975

Torsional potential function of glyoxal

We have shown, using the fact that glyoxal exists in the trans conformer and the pseudo stable cis conformer that a potential function can be calculated which fits the infrared data of the trans conformer and the microwave intensity data of the cis conformer. This potential function was extended to the d sub 1 and d sub 2 analogs. A study of the potential function of 1,3-butadiene using a different molecular geometry than was previously used was undertaken. Results are presented with different possible vibrational assignments and potential functions which would be consistent with the observed infrared and Raman spectra.

Durig, J. R.↗
NASA NTRS1978

Configurations of base-pair complexes in solutions

A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

Egan, J. T.↗
NASA NTRS1986

Development of a numerical procedure to map a general 3-d body onto a near-circle

Conformal mapping is a classical technique utilized for solving problems in aerodynamics and hydrodynamics. Conformal mapping is utilized in the construction of grids around airfoils, engine inlets and other aircraft configurations. These shapes are transformed onto a near-circle image for which the equations of fluid motion are discretized on the mapped plane and solved numerically by utilizing the appropriate techniques. In comparison to other grid-generation techniques such as algerbraic or differential type, conformal mapping offers an analytical and accurate form even if the grid deformation is large. One of the most appealing features is that the grid can be constrained to remain orthogonal to the body after the transformation. Hence, the grid is suitable for analyzing the supersonic flow past a blunt object. The associated shock as a coordinate surface adjusts its position in the course of computation until convergence is reached. The present work applied conformal mapping to 3-D bodies with no axis of symmetry such as the Aerobraking Flight Experiment (AFE) vehicle, transforming the AFE shape onto a near-circle image. A numerical procedure and code are used to generate grids around the AFE body.

Hommel, M. J.↗
NASA NTRS1990

Photophysics of poly(2,3,4,5,6-pentafluoro styrene) film

The temperature-dependent steady-state emission, emission polarization anisotropy, and fluorescence-kinetics of poly(2,3,4,5,6-pentafluoro styrene) film are reported. Two interconverting excited-state conformations of the chromophore have been identified. The fluorescence of the higher energy conformation results from excitation on the red edge of the polymer absorption band at temperatures below 180 K. The energy barrier for conversion of the high energy conformer to the lower energy conformer is estimated to be E/hc = 27 + or - 7/cm. Electronic energy migration is not evident in this polymer.

O'Connor, Donald B.↗
NASA NTRS2011

Connector pin and method

An electrical connector and method includes a connector and a conforming element proximate to or in contact with the mating end of the connector so as to prevent distortion of a matable end. The matable end of the connector may be of a female or male type and may be of a post, tube, blade, pin, or other configuration. An element made of conforming material, for example, an elastomer, epoxy or rubber type material, is configured and positioned in contact with the matable end of the connector, providing support during assembly to prevent distortion of the matable end. The conforming element may be rectangular, wedge, cylindrical, conical, annular, or of another configuration as required to provide support to the connector pin. The conforming element may be fastened with an adhesive to the matable end to further prevent distortion.

Davis, Donald R.↗