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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 1,603 records · Page 89
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Native point defects in HgCdTe infrared detector material: Identifying deep centers from first principles

We investigate the native point defects in the long-wavelength infrared (LWIR) detector material Hg0.75Cd0.25Te using a dielectric-dependent hybrid density functional combined with spin–orbit coupling. Characterizing these point defects is essential as they are responsible for intrinsic doping and nonradiative recombination centers in the detector material. The dielectric-dependent hybrid functional allows for an accurate description of the bandgap (Eg) for Hg1−xCdxTe (MCT) over the entire compositional range, a level of accuracy challenging with standard hybrid functionals. Our comprehensive examination of the native point defects confirms that cation vacancies VHg(Cd) are the primary sources of p-type conductivity in the LWIR material given their low defect formation energies and the presence of a shallow acceptor level (−/0) near the valence-band maximum. In addition to the shallow acceptor level, the cation vacancies exhibit a deep charge transition level (2−/−) situated near the midgap, characteristic of nonradiative recombination centers. Our results indicate that Hg interstitial could also be a deep center in the LWIR MCT through a metastable configuration under the Hg-rich growth conditions. While an isolated Te antisite does not show deep levels, the formation of VHg–TeHg defect complex introduces a deep acceptor level within the bandgap.

Physics↗
DOE OSTI2024

Photo-induced electron paramagnetic resonance: A means to identify defects and the defect level throughout the bandgap of ultrawide bandgap semiconductors

Ultrawide bandgap semiconductors (UWBGs) provide great promise for optical devices operating in the near to deep ultraviolet, and recently they have become a viable semiconducting material for high power electronics. From the power grid to electronic vehicles, the intention is to replace massively awkward components with the convenience of a solid state electronic “chip.” Unfortunately, the challenges faced by wide bandgap electronic materials, such as GaN and SiC, increase as the bandgap increases. A point defect, for example, can take on more charge states and energy configurations. This perspective describes a method to investigate the many charge states and their associated transitions—photo-induced electron paramagnetic resonance (photo-EPR) spectroscopy. Although not new to the study of defects in semiconductors, photo-EPR studies can probe the entire ultrawide bandgap given the appropriate light source for excitation. Examples provided here cover specific defects in UWBGs, AlN, and Ga2O3. The discussion also reminds us how the rapid pace of discovery surrounding this newest class of semiconductors is due, in part, to fundamental research studies of the past, some as far back as a century ago and some based on very different materials systems.

Physics↗
DOE OSTI2024

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Identifying environmentally induced calibration changes in cryogenic RF axion detector systems using deep neural networks

The axion is a compelling hypothetical particle that could account for the dark matter in our universe while simultaneously solving the strong CP problem in quantum chromodynamics. The most sensitive axion detection technique demonstrated so far makes use of a high Q cavity immersed in a strong magnetic field, where axions are converted to microwave photons. This is called an axion haloscope and has primarily targeted the 1–10 GHz range. As searches scan up in axion mass, toward the parameter space favored by theoretical predictions, individual cavity sizes decrease in order to achieve higher frequencies. This shrinking cavity volume translates directly to a loss in signal-to-noise, motivating the plan to replace individual cavity detectors with arrays of cavities. When the transition from one to (N) multiple cavities occurs, haloscope searches are anticipated to become much more complicated to operate, requiring N times as many measurements but also the new requirement that N detectors operate in unison, which can be achieved by locking them to a common frequency. To offset this anticipated increase in detector complexity, we aim to develop new tools for diagnosing experiments using neural networks. Current experiments monitor scattering parameters of their receiver for periodically measuring cavity quality factor and coupling. However, off-resonant data remain relatively useless. In this paper, we ask if it is possible that off-resonant information contained in vector network analyzer scans could be used to diagnose equipment failures/anomalies and measure physical conditions (e.g., temperatures and ambient magnetic field). We demonstrate a proof-of-concept that AI techniques can help manage the complexity of an axion haloscope search for operators.

Engel, Andrew W. [Pacific Northwest National Labor↗
DOE OSTI2013

Identifying external influences on global precipitation

Changes in global (ocean and land) precipitation are among the most important and least well-understood consequences of climate change. Increasing greenhouse gas concentrations are thought to affect the zonal-mean distribution of precipitation through two basic mechanisms. First, increasing temperatures will lead to an intensification of the hydrological cycle (“thermodynamic” changes). Second, changes in atmospheric circulation patterns will lead to poleward displacement of the storm tracks and subtropical dry zones and to a widening of the tropical belt (“dynamic” changes). We demonstrate that both these changes are occurring simultaneously in global precipitation, that this behavior cannot be explained by internal variability alone, and that external influences are responsible for the observed precipitation changes. Whereas existing model experiments are not of sufficient length to differentiate between natural and anthropogenic forcing terms at the 95% confidence level, we present evidence that the observed trends result from human activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. Furthermore, the data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor

The polycomb repressive complex 2 (PRC2) histone methyltransferase plays a central role in epigenetic regulation in development and in cancer, and hence to interrogate its role in a specific developmental transition, methods are needed for disrupting function of the complex with high temporal and spatial precision. The catalytic and substrate recognition functions of PRC2 are coupled by binding of the N-terminal helix of the Ezh2 methylase to an extended groove on the EED trimethyl lysine binding subunit. Disrupting PRC2 function can in principle be achieved by blocking this single interaction, but there are few approaches for blocking specific protein–protein interactions in living cells and organisms. Here, in this work, we describe the computational design of proteins that bind to the EZH2 interaction site on EED with subnanomolar affinity in vitro and form tight and specific complexes with EED in living cells. Induction of the EED binding proteins abolishes H3K27 methylation in human embryonic stem cells (hESCs) and at all but the earliest stage blocks self-renewal, pinpointing the first critical repressive H3K27me3 marks in development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Alternative Binding Modes Identified for Growth and Differentiation Factor-associated Serum Protein (GASP) Family Antagonism of Myostatin

Myostatin, a member of the TGF-β family of ligands, is a strong negative regulator of muscle growth. As such, it is a prime therapeutic target for muscle wasting disorders. Similar to other TGF-β family ligands, myostatin is neutralized by binding one of a number of structurally diverse antagonists. Included are the antagonists GASP-1 and GASP-2, which are unique in that they specifically antagonize myostatin. However, little is known from a structural standpoint describing the interactions of GASP antagonists with myostatin. In this paper, we present the First low resolution solution structure of myostatin-free and myostatin-bound states of GASP-1 and GASP-2. Our studies have revealed GASP-1, which is 100 times more potent than GASP-2, preferentially binds myostatin in an asymmetrical 1:1 complex, whereas GASP-2 binds in a symmetrical 2:1 complex. Additionally, C-terminal truncations of GASP-1 result in less potent myostatin inhibitors that form a 2:1 complex, suggesting that the C-terminal domains of GASP-1 are the primary mediators for asymmetric complex formation. Overall, this study provides a new perspective on TGF-β antagonism, where closely related antagonists can utilize different ligand-binding strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structure of Human B 12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases

In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. Here, the striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)

Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156

59 BASIC BIOLOGICAL SCIENCES↗