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Results for “conformance analysis”

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 OSTI2022

Scalar modular bootstrap and zeros of the Riemann zeta function

Using the technology of harmonic analysis, we derive a crossing equation that acts only on the scalar primary operators of any two-dimensional conformal field theory with U(1) c symmetry. From this crossing equation, we derive bounds on the scalar gap of all such theories. Rather remarkably, our crossing equation contains information about all nontrivial zeros of the Riemann zeta function. As a result, we rephrase the Riemann hypothesis purely as a statement about the asymptotic density of scalar operators in certain two-dimensional conformal field theories. We discuss generalizations to theories with only Virasoro symmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Flexible atomic layer deposition system for coating porous materials

In this paper, we describe an atomic layer deposition (ALD) system that is optimized for the growth of thin films on high-surface-area, porous materials. The system incorporates a moveable dual-zone furnace allowing for rapid transfer of a powder substrate between heating zones whose temperatures are optimized for precursor adsorption and oxidative removal of the precursor ligands. The reactor can both be evacuated, eliminating the need for a carrier gas during precursor exposure, and rotated, to enhance contact between a powder support and the gas phase, both of which help us to minimize mass transfer limitations in the pores during film growth. The capabilities of the ALD system were demonstrated by growing La 2 O 3 , Fe 2 O 3 , and LaFeO 3 films on a 120 m 2 g -1 MgAl 2 O 4 powder. Analysis of these films using scanning transmission electron microscopy and temperature-programmed desorption of 2-propanol confirmed the conformal nature of the oxide films.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The molecular mechanism of sialic acid transport mediated by Sialin

Malfunction of the sialic acid transporter caused by various genetic mutations in the SLC17A5 gene encoding Sialin leads to a spectrum of neurodegenerative conditions called free sialic acid storage disorders. Unfortunately, how Sialin transports sialic acid/proton (H + ) and how pathogenic mutations impair its function are poorly defined. Here, we present the structure of human Sialin in an inward-facing partially open conformation determined by cryo–electron microscopy, representing the first high-resolution structure of any human SLC17 member. Our analysis reveals two unique features in Sialin: (i) The H + coupling/sensing requires two highly conserved Glu residues (E171 and E175) instead of one (E175) as implied in previous studies; and (ii) the normal function of Sialin requires the stabilization of a cytosolic helix, which has not been noticed in the literature. By mapping known pathogenic mutations, we provide mechanistic explanations for corresponding functional defects. We propose a structure-based mechanism for sialic acid transport mediated by Sialin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural Polymorphism of Chitin and Chitosan in Fungal Cell Walls From Solid-State NMR and Principal Component Analysis

Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13 C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity to the model structures of α- and γ-allomorphs; therefore, chitin structure is not significantly affected by interactions with other cell wall components. Addition of antifungal drugs and salts did not significantly perturb the chemical shifts, revealing the structural resistance of chitin to external stress. In addition, the structure of the deacetylated form, chitosan, was found to resemble a relaxed two-fold helix conformation. This study provides high-resolution information on the structure of chitin and chitosan in their cellular contexts. The method is applicable to the analysis of other complex carbohydrates and polymer composites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Celestial IR divergences and the effective action of supertranslation modes

Infrared divergences in perturbative gravitational scattering amplitudes have been recently argued to be governed by the two-point function of the supertranslation Goldstone mode on the celestial sphere. We show that the form of this celestial two-point function simply derives from an effective action that also controls infrared divergences in the symplectic structure of General Relativity with asymptotically flat boundary conditions. This effective action finds its natural place in a path integral formulation of a celestial conformal field theory, as we illustrate by re-deriving the infrared soft factors in terms of celestial correlators. Our analysis relies on a well-posed action principle close to spatial infinity introduced by Compère and Dehouck.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Rigidochromism of tetranuclear Cu( I )–pyrazolate macrocycles: steric crowding with trifluoromethyl groups

Macrocyclic Cu(I)–pyrazolate tetramers (Cu 4 pz 4 ) can fold into compact structures with luminescent Cu 4 cores whose emission wavelengths are sensitive to steric effects along the periphery of the macrocycle. Introducing CF 3 at the C 4 position of 3,5-di- t Bu-pyrazolate increases steric crowding that modifies the conformational behavior of the Cu 4 pz 4 complex, highlighted by a low-temperature martensitic transition. Variable-temperature analysis of solid-state luminescence reveal an unexpected blueshifting of emission with rising temperature.

Rajagopal, Shinaj K.↗
DOE OSTI2023

Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein

Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR’s ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR’s ligand-binding pocket and reduce their safety liability due to PXR binding.

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

Conformal correlators on the Lorentzian torus

The general form of a 2D conformal field theory (CFT) correlator on a Euclidean Riemann surface, Lorentzian plane or Lorentzian cylinder is well known. This paper describes the general form of 2- and 3-point CFT correlators on the Lorentzian torus LT 2 which arises as the conformal boundary of the group manifold SL ( 2 , R ) ≃ AdS 3 / Z . We consider only generic points, thereby omitting an analysis of contact terms, which already exhibits a surprisingly rich structure. The results are relevant to celestial holography, for which the LT 2 at the boundary of Klein space is the home of the putative celestial CFT. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2020

FiXR : a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid β fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid β fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Formation and detection of metastable formic acid in a supersonic expansion: High resolution infrared spectroscopy of the jet-cooled cis -HCOOH conformer

High-resolution direct absorption infrared spectra of metastable cis-formic acid (HCOOH) trapped in a cis-well resonance behind a 15 kcal/mol barrier are reported for the first time, with the energetically unstable conformer produced in a supersonic slit plasma expansion of trans-formic acid/H 2 mixtures. We present a detailed high-resolution rovibrational analysis for cis-formic acid species in the OH stretch (ν 1 ) fundamental, providing first precision vibrational band origin, rotational constants, and term values, which in conjunction with ab initio calculations at the couple-cluster with single, double, and perturbative triple [CCSD(T)]/ANOn (n = 0, 1, 2) level support the experimental assignments and establish critical points on the potential energy surface for internal rotor trans-to-cis isomerization. Relative intensities for a- and b-type transitions observed in the spectra permit the transition dipole moment components to be determined in the body fixed frame and prove to be in good agreement with ab initio CCSD(T) theoretical estimates but in poor agreement with simple bond-dipole predictions. As a result, the observed signal dependence on H 2 in the discharge suggests the presence of a novel H atom radical chemical mechanism for strongly endothermic “up-hill” internal rotor isomerization between trans- and cis-formic acid conformers.

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

A Constrained Data Assimilation Algorithm Based on GSI Hybrid 3D-EnVar and Its Application

Abstract Data assimilation (DA) at mesoscales is important for severe weather forecasts, yet the techniques of data assimilation at this scale remain a challenge. This study introduces dynamical constraints in the Gridpoint Statistical Interpolation (GSI) three-dimensional ensemble variational (3D-EnVar) data assimilation algorithm to enable the use of high-resolution surface observations of precipitation to improve atmospheric analysis at mesoscales. The constraints use the conservations of mass and moisture. Mass constraint suppresses the unphysical high-frequency oscillation, while moisture conservation constrains the atmospheric states to conform with the observed high-resolution precipitation. We show that the constrained data assimilation (CDA) algorithm significantly reduced the spurious residuals of the mass and moisture budgets compared to the original data assimilation (ODA). A case study is presented for a squall line over the Southern Great Plains on 20 May 2011 during Midlatitude Continental Convective Clouds Experiment (MC3E) of the Atmospheric Radiation Measurement (ARM) program by using ODA or CDA analysis as initial condition of forecasts. The state variables, and the location and intensity of the squall line are better simulated in the CDA experiment. Results show how surface observation of precipitation can be used to improve atmospheric analysis through data assimilation by using the dynamical constraints of mass and moisture conservations.

Wang, Jia↗
DOE OSTI2023

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
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 OSTI2026

Link statistics of dislocation network during strain hardening

Dislocations are line defects in crystals that multiply and self-organize into a complex network during strain hardening. The length of dislocation links, connecting neighboring nodes within this network, contains crucial information about the evolving dislocation microstructure. By analyzing data from Discrete Dislocation Dynamics (DDD) simulations in face-centered cubic (fcc) Cu, we characterize the statistical distribution of link lengths of dislocation networks during strain hardening on individual slip systems. Here, our analysis reveals that link lengths on active slip systems follow a double-exponential distribution, while those on inactive slip systems conform to a single-exponential distribution. The distinctive long tail observed in the double-exponential distribution is attributed to the stress-induced bowing out of long links on active slip systems, a feature that disappears upon removal of the applied stress. We further demonstrate that both observed link length distributions can be explained by extending a one-dimensional Poisson process to include different growth functions. Specifically, the double-exponential distribution emerges when the growth rate for links exceeding a critical length becomes super-linear, which aligns with the physical phenomenon of long links bowing out under stress. This work advances our understanding of dislocation microstructure evolution during strain hardening and elucidates the underlying physical mechanisms governing its formation.

Crystal plasticity↗
DOE OSTI2020

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Grampositive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the D-Ala-D-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (V D ) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue V D to L-Lys-D-Ala-D-Ala and L-Lys-D-Ala-D-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of V D , which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the D-Ala-D-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycinresistant S. aureus.

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

Excitation spectra of quantum matter without quasiparticles. I. Sachdev-Ye-Kitaev models

Here, we study the low-frequency spectra of complex Sachdev-Ye-Kitaev models at general densities. The analysis applies also to SU(M) magnets with random exchange at large M. The spectral densities are computed by numerical analysis of the saddle-point equations on the real frequency ω axis at zero temperature T. The asymptotic low-ω behaviors are found to be in excellent agreement with the scaling dimensions of irrelevant operators which perturb the conformally invariant critical states. Of possible experimental interest is our computation of the universal spin spectral weight of the SU(M) magnets at low ω and T; this includes a contribution from the time reparametrization mode, which is the boundary graviton of the holographic dual. This analysis is extended to a random t-J model in the following paper [M. Tikhanovskaya et al., following paper, Phys. Rev. B 103, 075142 (2021)].

36 MATERIALS SCIENCE↗
DOE OSTI2021

Universal relations for holographic interfaces

We study the entanglement entropy in 1+1 dimensional conformal field theories in the presence of interfaces from a holographic perspective. Compared with the well-known case of boundary conformal field theories, interfaces allow for several interesting new observables. Depending on how the interface is located within the entangling region, the entanglement entropies differ and exhibit surprising new patterns and universal relations. While our analysis is performed within the framework of holography, we expect our results to hold more generally.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗