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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
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 OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

TOI-1231 b: A Temperate, Neptune-sized Planet Transiting the Nearby M3 Dwarf NLTT 24399

We report the discovery of a transiting, temperate, Neptune-sized exoplanet orbiting the nearby (d = 27.5 pc), M3V star TOI-1231 (NLTT 24399, L 248-27, 2MASS J10265947-5228099). The planet was detected using photometric data from the Transiting Exoplanet Survey Satellite and followed up with observations from the Las Cumbres Observatory and the Antarctica Search for Transiting ExoPlanets program. Combining the photometric data sets, we find that the newly discovered planet has a radius of 3.65{sub −0.15}{sup +0.16} R{sub ⊕} and an orbital period of 24.246 days. Radial velocity measurements obtained with the Planet Finder Spectrograph on the Magellan Clay telescope confirm the existence of the planet and lead to a mass measurement of 15.5 ± 3.3 M {sub ⊕}. With an equilibrium temperature of just 330 K, TOI-1231 b is one of the coolest small planets accessible for atmospheric studies thus far, and its host star’s bright near-infrared brightness (J = 8.88, K {sub s} = 8.07) makes it an exciting target for the Hubble Space Telescope and the James Webb Space Telescope. Future atmospheric observations would enable the first comparative planetology efforts in the 250–350 K temperature regime via comparisons with K2-18 b. Furthermore, TOI-1231's high systemic radial velocity (70.5 km s{sup −1}) may allow for the detection of low-velocity hydrogen atoms escaping the planet by Doppler, shifting the H i Lyα stellar emission away from the geocoronal and interstellar medium absorption features.

47 OTHER INSTRUMENTATION↗
NASA NTRS2004

Central Stars of Planetary Nebulae in the SMC

In FUSE cycle 3's program C056 we studied four Central Stars of Planetary Nebulae (CSPN) in the Small Magellanic Could. All FUSE observations have been successfully completed and have been reduced and analyzed. The observation of one object (SMP SMC 5) appeared to be off-target and no useful stellar flux was gathered. For another observation (SMP SMC 1) the voltage problems resulted in the loss of data from one of the SiC detectors, but we were still able to analyze the remaining data. The analysis and the results are summarized below. The FUSE data were reduced using the latest available version of the FUSE calibration pipeline (CALFUSE v2.4). The flux of these SMC post-AGB objects is at the threshold of FUSE S sensitivity, and the targets required many orbit-long exposures, each of which typically had low (target) count-rates. The background subtraction required special care during the reduction, and was done in a similar manner to our FUSE cycle 2 BOO1 objects. The resulting calibrated data from the different channels were compared in the overlapping regions for consistency. The final combined, extracted spectra of each target was then modeled to determine the stellar and nebular parameters. The FUSE spectra, combined with archival HST spectra, have been analyzed using stellar atmospheres codes such as TLUSTY and CMFGEN to derive photospheric and wind parameters of the central stars, and with ISM models to determine the amount and temperature of the surrounding atomic and molecular hydrogen. We have combined these results with those of our cycle 4 (D034) program (CSPN of the LMC) in Herald & Bianchi 2004a (paper in preparation, will be submitted to ApJ in June 2004). Two of the three SMC objects analyzed were found to have significantly lower stellar temperatures than had been predicted using nebular photoionization models, indicating either a hotter ionizing companion or the existence of strong shocks in the nebular environment. The analysis also revealed that some objects are surrounded by significant quantities of hot (e.g., 1000- 2000 K) molecular H2, similar to what we found for some LMC and Galactic CSPN (Herald & Bianchi 2002, 2003a, b, 2004b, c, d).

Bianchi, Luciana↗
NASA NTRS2017

Volatile Concentrations and H-Isotope Composition of Unequilibrated Eucrites

Eucrites are among the oldest and best studied asteroidal basalts (1). They represent magmatism that occurred on their parent asteroid, likely 4-Vesta, starting at ~ 4563 Ma and continuing for approx. 30 Myr. Two hypotheses are debated for the genesis of eucrites, a magma ocean model (2), and a mantle partial melting model. In general, volatiles (H, C, F, Cl) have been ignored for eucrites and 4-Vesta, but solubility of wt% levels of H2O are possible at Vestan interior PT conditions. Targeted measurements on samples could aid our understanding considerably. Recent studies have found evidence of volatile elements in eucrites, but quantifying the abundance of volatiles remains problematic (6). Volatile elements have a disproportionately large effect on melt properties and phase stability, relative to their low abundance. The source of volatile elements can be elucidated by examining the hydrogen isotope ratio (D/H), as different H reservoirs have drastically different H isotope compositions. Recent studies of apatite in eucrites have shown that the D/H of 4-Vesta matches that of Earth and carbonaceous chondrites, however, the D/H of apatites may not represent the D/H of a primitive 4-Vesta melt due to the possibility of degassing prior to the crystallization of apatite. Therefore, the D/H of early crystallizing phases must be measured to determine if the D/H of 4-Vesta is equal to that of the Earth and carbonaceous chondrites.

Sarafian, Adam R.↗
NASA NTRS2024

Solar System Science With the Single Aperture Large Telescope for Universe Studies Space Observatory

Single Aperture Large Telescope for Universe Studies (SALTUS) is a NASA Astrophysics Probe Explorer (APEX)-class mission concept employing a robust far-infrared pointed space observatory. SALTUS comprises a 14-m inflatable reflector that provides 16× the sensitivity and 4× the angular resolution of Herschel, with a sunshield that radiatively cools the primary to 45 K, along with cryogenic detectors that collectively span the 34 to 660 μm far-infrared spectral range at high and moderate spectral resolutions. The high sensitivity and high spectral resolving power of the SALTUS heterodyne receivers enable both submillimeter and far-infrared observations of trace compounds comprising water and its isotopologues, hydrogen deuteride (HD), and a plethora of molecular species containing carbon, hydrogen, nitrogen, oxygen, phosphorus, or sulfur (CHNOPS), all of which are obscured by the Earth’s atmosphere. The high sensitivity and broadband spectral coverage of the SALTUS far-infrared grating spectrometer enables far-infrared observations of the lattice vibrational spectral signatures of ices and mineral grains contained within a wide variety of solar system targets, including comets, planetary atmospheres, near Enceladus’ plumes, and on the surfaces of icy moons, Jupiter trojans, centaurs, and Kuiper Belt objects. A key objective of SALTUS is to measure HDO∕H 2 O in both Jupiter family and Oort cloud comets. Additional observations will allow us to characterize the water torus around Saturn generated by its icy moon Enceladus, determine the source of stratospheric water in the giant planets, ascertain the time evolution of water on Venus, and search for H 2 O plumes on Europa, Ganymede, and Callisto. SALTUS will measure HD∕H 2 in all four giant planets to constrain models of their origin. SALTUS can also measure the abundance of CHNOPS-containing molecules and halides in the atmosphere of Venus and in the comae of comets. We review the extensive amount of solar system science achievable with SALTUS for both the Guaranteed Time Observation and the Guest Observer APEX mission observing programs.

Carrie M. Anderson↗
DOE OSTI2020

Conversion, Stability, and Selectivity Improvements Through Catalyst Development for the Reductive Etherification Reaction

Economical pathways from lignocellulosic non-food biomass feedstocks to biofuels with appropriate fuel properties are necessary for displacing fossil-fuel derived diesel use in medium-/heavy duty vehicles. Oxygenated compounds have recently shown promise due to low sooting tendencies and autoignition properties and molecules with sufficiently high carbon numbers can meet the requisite standards for water solubility and flash point. Coupling waste biomass derived small molecules into bioblendstock targets through the reductive etherification reaction shows potential for increasing molecular weight without losing the advantages of oxygenates. However, the transition to industrial viability for this process is limited by strong catalyst deactivation in typical flow reactor systems. Strong acid resins such as Amberlyst-15 (A-15) show excellent activity in batch reactions but are limited to low temperatures and are poisoned by the side-product, water. In this talk, I will describe our recent work in catalyst synthesis and testing to select superior options with improved aqueous and thermal stability in reductive etherification flow reactions. Water-tolerant solid acid catalysts have potential to improve the conversion and selectivity to the ether target at temperatures above the degradation point of A-15. Analysis techniques such as physisorption, chemisorption, x-ray diffraction and transmission electron microscopy are being used to characterize the active sites. These techniques are also being used to evaluate degradation of the catalyst after extensive flow reactions in addition to comparative efficiency testing with standardized cyclohexene hydrogenation reactions. Finally, I will discuss a demonstration of the full pathway from bio-derived butyric acid to the performance-advantaged ether product and the additional obstacles from side-products and purification limitations in the preliminary upgrading reactions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Cathodic Protection Modeling for Hanford Underground Double-Shell Tank Farms

Hanford stores millions of gallons of radioactive and chemically hazardous waste from the production of weapon materials in tank farms consisting of underground carbon-steel storage tanks surrounded by reinforced concrete. Six of these Hanford tank farms use double-shell storage tanks (DSTs). The DST farms were constructed from 1968 to 1986 with a planned 40–50 year design life, so some are already operating beyond their initial life expectancy. Ultrasonic testing (UT) has indicated significant thinning on the bottom of the secondary (outer) liner of these tanks, believed to arise from groundwater intrusion driving concrete side corrosion. There is no direct access to the steel/concrete interface between the tank and the concrete pad, making it difficult to apply a chemical-based mitigation strategy or to conduct repairs, but cathodic protection (CP) is a possible method to inhibit further concrete-side corrosion. Hanford already uses CP to protect below grade steel piping within the tank farms and connected to the tanks, but this system was not designed to protect the tank bottoms. CP design must account for the structures surrounding the DSTs, including the steel reinforcing bars (rebar) within the concrete pad and vault, various process lines, and the existing CP system. In this study, finite element analysis (FEA) modeling was carried out to simulate CP protection of 1) a single tank and CP anode to develop options for modeling the rebar and to compare to a simpler circuit model and 2) the entire Hanford AN tank farm as a representative example consisting of seven tanks, associated piping, and both existing and new CP anodes. Both circuit and FEA models predict that significant protective current could be delivered to the bottoms of the tanks with the addition of tank-protection anodes below the depth of the tanks. Simulations with only the existing pipe-protection anodes active confirmed that only a very small current to the tank bottoms is predicted under present conditions. Multiple simplified representations of the dome and wall rebar were tested to reduce the computational complexity of the tank-farm simulations, resulting in modeling the rebar as edge elements with a prescribed effective circumference that matches the real rebar surface area. The geometry of the rebar is also simplified into horizontal hoops around the tank walls and radial rebar over the dome with increased effective circumference to retain the target surface area. This simplification was found to greatly reduce the complexity and solution time of the models without large changes in current distributions, especially to the tank bottom. A range of values were tested for model parameters such as soil and concrete resistivities and polarization resistance to investigate their impact on the current and electric potential distributions. Depending on the parameters used, FEA simulations predict some risk of overprotection, particularly on the piping system; since overprotection can also lead to surface damage associated with hydrogen gas generation at the interface (e.g. hydrogen embrittlement or damage to coatings), this needs to be considered when refining the design of the new CP system. Comparison between the FEA models and the circuit model representation demonstrated that the circuit model could not match the predicted FEA current distribution, even when using the exact same surface areas. This discrepancy appeared to be at least partly attributable to the impact of the relative positions of the tank components and anodes to each other and to the ground surface. The FEA model accounts for the relative positions since it solves the governing equations in three dimensions, but the circuit model cannot account for the positioning. In particular, the circuit model underpredicts the current to the tank bottom and overpredicts the current to the dome compared to FEA for the baseline geometry. The FEA models omitted the electrically isolated rebar in the bottom concrete slab. However, a circuit based stray current model estimated that only 2.1% of the total current through the slab would stray into the rebar, corresponding to ~0.21 A for a target current density of 2 mA/ft2 to the tank bottom. The estimated corrosion driven by this amount of stray current is predicted to yield a lifetime of >400 years for the minimum rebar diameter, assuming an acceptable cross-section area loss of 10%.

d'Entremont, Anna [Savannah River National Laborat↗
DOE OSTI2026

Automated and High-Throughput Phase Separation Control for Supramolecular Polymer Blends Enabled by Machine Learning

Supramolecular polymer blends (SPBs) offer tunable morphologies that dictate their macroscopic properties, yet their rational design is limited by the absence of predictive structure−morphology models. Here, we introduce a data-driven highthroughput workflow that integrates modular polymer synthesis, robotic formulation, automated morphology characterization, and machine learning (ML) for accelerated SPB discovery. Using a plug-and-play synthetic strategy, 33 hydrogen-bonding endfunctional homopolymers were prepared and orthogonally combined to generate 260 SPBs in 1 day. A fully automated atomic force microscopy (AFM) pipeline enabled systematic imaging, producing 2340 morphology data sets with minimal human intervention. Domain spacings were extracted through complementary imageprocessing methods and used to train ML models. A support vector regression (SVR) model accurately predicted target phase-separation sizes (50, 100, and 150 nm), which were experimentally validated. This work demonstrates the power of coupling high-throughput experimentation with ML to accelerate morphology discovery and provides one of the first large-scale experimental data sets for supramolecular polymer systems.

ML-guided polymer design↗
DOE OSTI2026

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

Drago, Victoria N. [Oak Ridge National Laboratory ↗
NASA NTRS1993

Removal of carbonaceous contaminants from silica aerogel

Capture of micrometeorite material from low Earth orbit or dust grains around active comets for return to terrestrial laboratories, capable of practicing the most up to date techniques of chemical isotopic and mineralogical analysis, will greatly enhance our knowledge of primitive material in the solar system. The next generation of space launched cosmic dust collectors will undoubtedly include extremely low density target materials such as silica aerogel as the decelerating and arresting medium. This material has been found to be clean from the point of view of inorganic elements and is thus acceptable for the purpose of harvesting grains to be studied by, for example PIXE, INAA, or SXRF. However, the process used in making aerogel leaves substantial carbon and hydrogen containing residues which would negate their suitability for collection and subsequent investigation of the very important CHON particles. Attempts to precondition aerogel by solvent extraction or heating at 500 C and 750 C in air for 24 hours or under a vacuum of 2(7)(exp -7) torr at 260 C were largely ineffective except that pyrolysis did reduce volatile species. In this investigation we have examined the use of supercritical fluids for the purpose of extracting organic residues. The logic of the new approach is that beyond the supercritical point a substance has the solvating properties of a liquid but the viscosity characteristics of a gas. For example carbon dioxide becomes supercritical at a pressure of 73 atmospheres and a temperature of 31 C; in consequence it can transform to a very powerful and ultraclean solvent. It can dissolve organic matter from low molecular weight up to molecules containing 90 carbon atoms. On release of pressure the fluid reverts to a gas which can easily be pumped away and removed from the substrate being extracted.

Huang, Hui-Ping↗
DOE OSTI2023

From Well Log to Formation Model: A Novel Laboratory Calibrated Methodology with Demonstration

This work demonstrates how the characterization and modeling of both elastic and creep properties are essential to describe zones in layered rock formations as either low-stress targets for stimulation or high-stress barriers to fracture growth. Prediction of fracture height is critical for designing stimulation operations in oil and gas wells. Ideally, fractures are placed in target zones which will produce hydrocarbons and should not propagate into zones expected to be unproductive or to produce unwanted fluids such as water which in turn must be treated and/or disposed. The essential task in designing stimulation plans is predicting which zones have low horizontal stresses and which will be high-stress barriers to fracture growth. Despite this importance, there are gaps in current knowledge and a complete workflow from laboratory characterization to a finite element model which includes time dependent rock deformation is required. While the research and methodology presented here also have application to CO 2or hydrogen storage, wastewater injection, and geothermal applications, the focus will be on hydrocarbon extraction. This thesis presents the results of a characterization-to-prediction workflow for the Caney shale, which is an emerging hydrocarbon resource in Oklahoma, USA. It begins with an investigation to enable critical evaluation of the Caney zonation into nominally “brittle” and “ductile” zones based on properties observed from well logs. It shows none of the zones are consistently “brittle” or “ductile” mechanical behavior based on the variety of definitions of these terms. However, the nominally ductile zones are weaker and more prone to creep. A laboratory investigation of samples including strength, elastic, and creep properties, is then used in a finite element model of stress evolution. The model includes both elastic deformation and viscoplastic creep. Results predict the least creep-prone layers to have the lowest horizontal stresses, therefore comprising hydraulic fracturing targets. The most creep-prone layers attain a horizontal stress similar to the vertical stress and therefore are predicted to be high stress barriers to hydraulic fracture stimulation. In addition to defining stimulation target intervals, the model shows how as tectonic strain rate increases, there is a transition from creep-dominated stresses to stresses dominated by elasticity.

Benge, Margaret↗
NASA NTRS1972

Developable images produced by x-rays using the nickel-hypophosphite system. 2: Exposure and development parameters for sodium hypophosphite

Crystalline sodium hypophosphite was X-irradiated and then treated with an ammoniacal nickel hypophosphite solution. Treatment resulted in the precipitation of nickel metal. The yield of nickel metal varied directly with particle size, sample weight, X-ray voltage, target current, exposure time, and development time. These findings show the process to be potentially useful in X-ray type photography. The half-life for the latent image species was found to be relatively short; but this is not critical in most X-ray photography applications. Furthermore, the work can be interpreted on the basis that a hydrogen atom is involved in the mechanism and indicates that the autocatalytic development step may be self-poisoning.

May, C. E.↗
NASA NTRS1975

Rocket and spacecraft studies of ultraviolet emissions from astrophysical targets

Rocket and spacecraft far-UV spectral measurements of several astrophysical targets are reviewed. These include observations of Ly-alpha emissions from Arcturus, Apollo-17 far-UV spectrometry of eta UMa and five other stars, Apollo-17 observations of the lunar atmosphere and the diffuse UV background, and far-UV spectral studies of Venus, Jupiter, and Comet Kohoutek. The Arcturus observations indicated a chromosphere with neutral atomic-hydrogen and atomic-oxygen emissions as well as a very weak atomic-carbon line. The planetary studies revealed O I and C I emissions in the Venusian spectrum as well as large Ly-alpha emissions and possible molecular-hydrogen emissions in that of Jupiter. The lunar observations demonstrated that solar protons do not produce an atomic-hydrogen atmosphere on the moon.

Fastie, W. G.↗
NASA NTRS1985

Electrostatic ion cyclotron waves in a plasma with an ion beam and counterstreaming bulk electrons - Waves in the zero-frequency band

A common feature of the auroral plasma in the region above field-aligned (parallel) potential drops are electrostatic hydrogen cyclotron (EHC) waves. The present paper has the objective to show that wave excitation in the zero-frequency band can occur when the ion beams and the current-carrying bulk electrons counterstream. The instability mechanism involves the Landau interaction of the slow (negative energy) ion-beam-cyclotron waves with the drifting electrons and also with the target (background) ions. Only the latter resonant interaction between the beam and the target ions was considered by Okuda and Nishikawa (1984). In this study, it is shown that an electron drift makes an additional unstable contribution to the waves in the zero-frequency band, including those discussed by Okuda and Nishikawa.

Singh, N.↗
NASA NTRSDate not supplied

Plasma-Induced Electron Screening at the Bragg Peak

Over 36 years of laboratory astrophysics experiments employing accelerated hydrogen isotope beams have demonstrated the role of electron screened, enhanced nuclear reactions. The astrophysical role of weak and strong electron screening was first discussed by Saltpeter [1] in 1954 and later by Hagino and Balantekin [2] in 2002. Assenbaum, et al. [3], Czerski, et al. [4], and Schenkel, et al., [5] have used accelerated deuteron beams on various metal targets and observed increased fusion rates over the expected Astrophysical, S(E), and Gamow Factors for bare deuteron-deuteron fusion rates. The Pines calculated both electron screened direct and asymptotic enhancement factors, f(E) [6]. Arguably, electron screening makes LENR possible.

plasma↗
DOE OSTI2020

Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment

Duchenne muscular dystrophy is a genetic disorder that shows chronic and progressive damage to skeletal and cardiac muscle leading to premature death. Antiinflammatory corticosteroids targeting the glucocorticoid receptor (GR) are the current standard of care but drive adverse side effects such as deleterious bone loss. Through subtle modification to a steroidal backbone, a recently developed drug, vamorolone, appears to preserve beneficial efficacy but with significantly reduced side effects. We use combined structural, biophysical, and biochemical approaches to show that loss of a receptor-ligand hydrogen bond drives these remarkable therapeutic effects. Moreover, vamorolone uniformly weakens coactivator associations but not corepressor associations, implicating partial agonism as the main driver of its dissociative properties. Additionally, we identify a critical and evolutionarily conserved intramolecular network connecting the ligand to the coregulator binding surface. Interruption of this allosteric network by vamorolone selectively reduces GR-driven transactivation while leaving transrepression intact. Our results establish a mechanistic understanding of how vamorolone reduces side effects, guiding the future design of partial agonists as selective GR modulators with an improved therapeutic index.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

The COVID-19 pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the “D-form” to the “G-form”) that carried an amino acid substitution D614G in its “Spike” protein. The G-form is more infectious in vitro and associated with increased viral loads. To gain insight into the molecular-level underpinnings of these characteristics, we employed microsecond all-atom simulations. Here we show that changes in the protein energetics favor a higher population of infection-capable (open) states through release of hydrogen bonds of an asymmetry present in the D-form but not the G-form. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies. These results are significant for vaccine design. The Molecular Dynamics Simulations datasets generated in this study, namely that of the soluble form SARS-CoV-2 Spike protein are made available here. Details of the trajectory and supporting files are given in the README.txt file.

59 BASIC BIOLOGICAL SCIENCES↗