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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators

LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor–activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Photonic Bandgaps in Photonic Molecules

This talk will focus on photonic bandgaps that arise due to nearly free photon and tight-binding effects in coupled microparticle and ring-resonator systems. The Mie formulation for homogeneous spheres is generalized to handle core/shell systems and multiple concentric layers in a manner that exploits an analogy with stratified planar systems, thereby allowing concentric multi-layered structures to be treated as photonic bandgap (PBG) materials. Representative results from a Mie code employing this analogy demonstrate that photonic bands arising from nearly free photon effects are easily observed in the backscattering, asymmetry parameter, and albedo for periodic quarter-wave concentric layers, though are not readily apparent in extinction spectra. Rather, the periodicity simply alters the scattering profile, enhancing the ratio of backscattering to forward scattering inside the bandgap, in direct analogy with planar quarter-wave multilayers. PBGs arising from tight-binding may also be observed when the layers (or rings) are designed such that the coupling between them is weak. We demonstrate that for a structure consisting of N coupled micro-resonators, the morphology dependent resonances split into N higher-Q modes, in direct analogy with other types of oscillators, and that this splitting ultimately results in PBGs which can lead to enhanced nonlinear optical effects.

Smith, David D.↗
DOE OSTI2023

Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin‐Deubiquitylating Enzyme Interactions

Abstract Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C‐terminal electrophiles (Ub−E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub−Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p‐benzoyl‐L‐phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub‐based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine‐based chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Probing the influence of dielectric environment on excitons in monolayer WSe 2 : Insight from high magnetic fields

Excitons in atomically thin semiconductors necessarily lie close to a surface, and therefore their properties are expected to be strongly influenced by the surrounding dielectric environment. However, systematic studies exploring this role are challenging, in part because the most readily accessible exciton parameter—the exciton’s optical transition energy—is largely unaffected by the surrounding medium. Here we show that the role of the dielectric environment is revealed through its systematic influence on the size of the exciton, which can be directly measured via the diamagnetic shift of the exciton transition in high magnetic fields. Using exfoliated WSe 2 monolayers affixed to single-mode optical fibers, we tune the surrounding dielectric environment by encapsulating the flakes with different materials and perform polarized low-temperature magneto-absorption studies to 65 T. The systematic increase of the exciton’s size with dielectric screening, and concurrent reduction in binding energy (also inferred from these measurements), is quantitatively compared with leading theoretical models. Furthermore, these results demonstrate how exciton properties can be tuned in future 2D optoelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Nicotine-Inspired, De Novo-Designed SARS-CoV-2 Main Protease Inhibitors Reveal Unique Chemistry for Covalently Conjugating Both Cysteine and Histidine Residues in the Catalytic Dyad

Anecdotal reports about smokers with low SARS-CoV-2 infection rates prompted a search for nicotine and its pyrolysis products as SARS-CoV-2 main protease (M Pro ) inhibitors. From this search, 3-vinylpyridine was discovered as a weak binder for the M Pro S1 subsite and was used subsequently as a de novo starting point for covalent inhibitor design that quickly yielded a highly potent inhibitor, SR-A-174, with an IC 50 value of 60 nM. Representing a novel class of M Pro inhibitors, SR-A-174 features an N,N -diaryl-α,α-dichloroacetamide scaffold that facilitated rapid exploration of alternative covalent warheads and various N-substituents, leading to the identification of multiple inhibitors with potent antiviral activity. Eight such M Pro inhibitor structures were determined, all demonstrating covalent binding to catalytic Cys145 of M Pro . In six determined structures, binding is dominated by the covalent bond plus van der Waals contacts, which contrasts with the extensive hydrogen bond networks formed with peptidomimetic inhibitors such as nirmatrelvir. Strikingly, two N,N -diaryl-α,α-dichloroacetamide inhibitors exhibit an unprecedented dual covalent modification mode of the catalytic dyad, forming bonds to both Cys145 and His41 with a concomitant loss of both chlorides and displacing the inhibitors from the S1 subsite. This dyad-targeting reactivity suggests a novel route for bioconjugation of both cysteine and histidine.

SARS-CoV-2↗
DOE OSTI2019

Hydrogen bond dynamics and conformational flexibility in antipsychotics

Effective treatment of disorders of the central nervous system can often be achieved using bioactive molecules of similar moieties to those known to be tolerable. A better understanding of the solid-state characteristics of such molecules could thereby create new opportunities for research on pharmaceutical preparations and drug prescriptions, while information about their rich intramolecular dynamics may well add an important aspect in the field of in silico drug discovery. As such, we have investigated three different antipsychotic drugs: haloperidol (C 21 H 23 ClFNO 2 , HAL), aripiprazole (C 23 H 27 Cl 2 N 3 O 2 , APZ) and quetiapine hemifumarate (C 21 H 25 N 3 O 2 S·0.5C 4 H 4 O 4 , QTP) based on similarities either in their structures, hydrophobic and hydrophilic moieties, or in their modes of action, typical or atypical. Our aim was to test the structural and molecular stability of these three different antipsychotics. To this end, we compared the molecular vibrations observed by inelastic neutron spectroscopy of these systems with those from theoretical periodic calculations of the crystalline antipsychotics using the Vienna ab initio simulation package (VASP). While most of the observed features in the lattice region were reasonably well represented by the calculations, the overall spectra were relatively complex, and hence traditional assignment procedures for the approximately 600 normal modes in the unit cell were not possible. These results indicate that in the search for new drug candidates, not only analysis of the flexibility of the receptor, but also the dynamics of the active molecules play a role in improving the prediction of binding affinities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ A 4 ) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ A 4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σ A 4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σ A 4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σ A 4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a

CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Ac. species Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cell editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Momentum-exchange interactions in a Bragg atom interferometer suppress Doppler dephasing

Large ensembles of laser-cooled atoms interacting through infinite-range photon-mediated interactions are powerful platforms for quantum simulation and sensing. Here we realize momentum-exchange interactions in which pairs of atoms exchange their momentum states by collective emission and absorption of photons from a common cavity mode, a process equivalent to a spin-exchange or XX collective Heisenberg interaction. The momentum-exchange interaction leads to an observed all-to-all Ising-like interaction in a matter-wave interferometer. A many-body energy gap also emerges, effectively binding interferometer matter-wave packets together to suppress Doppler dephasing in analogy to Mössbauer spectroscopy. The tunable momentum-exchange interaction expands the capabilities of quantum interaction–enhanced matter-wave interferometry and may enable the realization of exotic behaviors, including simulations of superconductors and dynamical gauge fields.

Science & Technology - Other Topics↗
DOE OSTI2022

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating the specific residues that compose the interface of protein complexes. In recent years, new machine learning and other algorithmic approaches have been proposed to solve this problem. However, little effort has been made in finding better training datasets to improve the performance of these methods. With the aim of vindicating the importance of the training set compilation procedure, in this work we present BIPSPI+, a new version of our original server trained on carefully curated datasets that outperforms our original predictor. We show how prediction performance can be improved by selecting specific datasets that better describe particular types of protein interactions and interfaces (e.g. homo/hetero). In addition, our upgraded web server offers a new set of functionalities such as the sequence-structure prediction mode, hetero- or homo-complex specialization and the guided docking tool that allows to compute 3D quaternary structure poses using the predicted interfaces. BIPSPI+ is freely available at https://bipspi.cnb.csic.es.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Syntheses of Colloidal F:In 2 O 3 Cubes: Fluorine-Induced Faceting and Infrared Plasmonic Response

Cube-shaped nanocrystals (NCs) of conventional metals like gold and silver generally exhibit localized surface plasmon resonance (LSPR) in the visible region with spectral modes determined by their faceted shapes. Yet, faceted NCs exhibiting LSPR response in the infrared (IR) region are relatively rare. Here, we describe the colloidal synthesis of nanoscale fluorine-doped indium oxide (F:In 2 O 3 ) cubes with LSPR response in the IR region, wherein fluorine was discovered to both direct the cubic morphology and act as an aliovalent dopant. Single-crystalline 160 nm F:In 2 O 3 cubes terminated by (100) facets and concave cubes were synthesized using a colloidal heat-up method. The presence of fluorine was found to impart higher stabilization to the (100) facets through density functional theory calculations that evaluated the energetics of F-substitution at surface oxygen sites. These calculations suggest that the cubic morphology results from surface binding of F atoms. In addition, fluorine acts as an anionic aliovalent dopant in the cubic bixbyite lattice of In 2 O 3 , introducing a high concentration of free electrons leading to LSPR. We confirmed the presence of lattice fluorine dopants in these cubes using solid-state 19 F and 115 In nuclear magnetic resonance spectroscopy. The cubes exhibit narrow, shape-dependent multimodal LSPR extinction peaks due to corner- and edge-centered modes. The spatial origin of these different contributions to the spectral response is directly visualized by electron energy loss spectroscopy in a scanning transmission electron microscope.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structural basis of superinfection exclusion by bacteriophage T4 Spackle

A bacterial cell infected with T4 phage rapidly establishes resistance against further infections by the same or closely related T-even-type bacteriophages – a phenomenon called superinfection exclusion. Here we show that one of the T4 early gene products and a periplasmic protein, Spackle, forms a stoichiometric complex with the lysozyme domain of T4 tail spike protein gp5 and potently inhibits its activity. Crystal structure of the Spackle-gp5 lysozyme complex shows that Spackle binds to a horseshoe-shaped basic patch surrounding the oligosaccharide-binding cleft and induces an allosteric conformational change of the active site. In contrast, Spackle does not appreciably inhibit the lysozyme activity of cytoplasmic T4 endolysin responsible for cell lysis to release progeny phage particles at the final step of the lytic cycle. Our work reveals a unique mode of inhibition for lysozymes, a widespread class of enzymes in biology, and provides a mechanistic understanding of the T4 bacteriophage superinfection exclusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Excited-state vibronic coherences and intramolecular charge transfer dynamics of the photoinactive cyanobacteriochrome NpF2164g5

We have characterized the excited-state structural dynamics that follow optical excitation of the photoinactive cyanobacteriochrome (CBCR) NpF2164g5 to determine the first events along the photoisomerization reaction coordinate of the phycocyanobilin (PCB) chromophore in red-to-green photoactive CBCRs. Within 25 fs of photoexcitation to the first excited singlet state, S1, a cross peak begins to develop below the diagonal of the broadband two-dimensional electronic spectrum (2DES) owing to the formation of a twisted conformation of the PCB chromophore with an enhanced intramolecular charge-transfer (ICT) character. Excited-state coherent wavepacket motions, including a torsion of the methine bridge between rings C and D and the carbon–hydrogen out-of-plane (HOOP) wagging vibration, are rapidly damped as the cross peak forms. This finding supports an assignment of the torsional and HOOP modes to the reaction coordinate of a coherent nonadiabatic mechanism. The ICT process is accompanied by an ultrafast Stokes shift and rapidly damped oscillations at the torsional mode’s frequency, which are sensed by measurements of the energy gap of the cross peak using its first moment with respect to the detection frequency axis of the 2DES spectrum. Furthermore, these results have the further implication that polar side chains of nearby amino acid residues in the binding site of the PCB chromophore can manipulate the barrier height for photoisomerization in red-to-green photoactive CBCRs and in phytochromes by redistributing the π-electron density along the methine bridge between the C and D rings.

Charge transfer↗
DOE OSTI2019

Spectroscopically Resolved Binding Sites for the Adsorption of Sarin Gas in a Metal–Organic Framework: Insights beyond Lewis Acidity

Here we report molecular level details regarding the adsorption of sarin (GB) gas in a prototypical zirconium-based metal–organic framework (MOF, UiO-66). By combining predictive modeling and experimental spectroscopic techniques, we unambiguously identify several unique bindings sites within the MOF, using the P=O stretch frequency of GB as a probe. Remarkable agreement between predicted and experimental IR spectrum is demonstrated. As previously hypothesized, the undercoordinated Lewis acid metal site is the most favorable binding site. Yet multiple sites participate in the adsorption process; specifically, the Zr-chelated hydroxyl groups form hydrogen bonds with the GB molecule, and GB weakly interacts with fully coordinated metals. Importantly, this work highlights that subtle orientational effects of bound GB are observable via shifts in characteristic vibrational modes; this finding has large implications for degradation rates and opens a new route for future materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Effect of alloying elements on defect evolution in Ni-20X binary alloys

The effect of alloying elements on radiation-induced microstructural evolution in Ni and Ni-20X (X = Fe, Cr, Mn and Pd) binary alloys was investigated using ion irradiation and cross-sectional transmission electron microscopy. The three-dimensional migration mode is identified to be the dominating migration mechanism for interstitial clusters in these binary alloys, contrary to the one-dimensional mode that dominates in the well-studied dilute alloys. The results reveal that: (1) the average size of defect clusters decreases as the solute atomic volume size factor increases. Smaller void size in Ni-20Cr is attributed to faster vacancy mobility in the near surface region, and weaker vacancy binding energy beyond the irradiation peak than Ni-20Fe. The smaller voids observed in Ni-20Mn and Ni-20Pd beyond the damage peak are due to the stronger Mn/Pd-vacancy binding effect of largely oversized solute atoms. (2) Oversized solutes can act as strong trapping sites for interstitials. The larger the solute atomic volume factor, the stronger the trapping force. This leads to a more significantly sluggish interstitial migration and smaller dislocation loop size. The average dislocation loop size in Ni-20Fe was four times larger than Ni-20Pd (atomic volume factor being 10.6% and 41.3%) but an order of magnitude lower in density. The smaller dislocation loop size in Ni-20Cr is attributed to stronger interstitial binding of Cr-Ni. In conclusion, overall, the alloying effect on defects is more significant in concentrated binary alloys than in dilute binary alloys, due to the concentration difference of alloying atoms and the interstitial dominant migration mechanisms in the main irradiated region.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Estimation of the Electron–Phonon Coupling Constants for Graphene and Metallic and Nonmetallic Substrates

Two modes of graphene–substrate interaction have been considered: a weak van der Waals bond and a strong covalent bond. The Lennard–Jones potential and Harrison bond-orbital method are used in the former and latter cases, respectively. Analytical expressions for the electron–phonon interaction constants, which contain only two parameters (binding energy E{sub B} for graphene and a substrate and distance d between them) have been obtained. The constants have been calculated for metallic, semiconductor, and dielectric substrates.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

The energetics and dynamics of confinement in flexible frameworks and molecular confinement

Porous frameworks form the chemical and structural basis for critical technologies in separations, catalysis, nuclear waste containment and biomedical applications. Hundreds of zeolites and metal organic frameworks (MOFs) have been synthesized, and their ability to separate and store hydrogen, methane and carbon dioxide has been investigated both experimentally and theoretically. Nevertheless, a fundamental and systematic molecular-level understanding of the thermodynamic and structural factors governing the stability and guest-host interactions in these materials lags behind focused studies of specific systems. Because the guest molecules interact with each other and with the host framework, molecular confinement is a finely balanced and complex phenomenon. The ability of the guest molecules to bind and diffuse through the pores is determined by the nature of the host framework which, in turn, responds to the nature and concentration of guest molecules and to pressure and temperature. The work explores how framework flexibility, tailored by structure, composition, temperature and pressure, is a general phenomenon, similar in nature but variable in extent, in both zeolites and MOFs and is part of a free energy landscape in which framework-guest interactions, pressure, and temperature result in changes in framework geometry and, in some cases, phase transitions. These subtle and/or pronounced changes in lattice geometry, energetics, and dynamics can play a decisive role in confinement and in differentiating the binding of molecules of similar size. The free energy landscape created by these structural changes links polymorphism, amorphization, “breathing,” “gate opening” and confinement. Specifically, the generality of such behavior arises from commonalities in lattice dynamics and energetics of frameworks containing a combination of strong rigid bonds and weaker more flexible deformation modes. Identifying and describing these common and collective phenomena is the focus of the research on a selected group of zeolites and MOFs. Structural studies using X-ray and neutron diffraction explore the mechanical functionality of these important materials, specifically how framework materials respond to changes in temperature, pressure and guest loading. These structural studies are combined with calorimetric measurements, using techniques uniquely developed in the participating laboratories, of heats of formation, heat capacities and entropies, and guest-host interactions. The experimental thermodynamic studies are complemented by inelastic neutron scattering studies of the lattice dynamics related both to framework vibrations and to guest-host interactions. The report below summarizes the work done at UC Davis, which is complemented by work done at BYU (Woodfield) and Virginia Tech (Ross).

36 MATERIALS SCIENCE↗