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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4

Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. Finally, by identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.

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

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. Here, in this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.

Hamiltonians↗
DOE OSTI2020

Mapping the Temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage

We explore the kinetic processes that sustain equilibrium in a microscopic, finite system. This is accomplished by monitoring the spontaneous, time-dependent frequency evolution (the frequency autocorrelation) of a single OH oscillator, embedded in a water cluster held in a temperature-controlled ion trap. The measurements are carried out by applying two-color, IR-IR photodissociation mass spectrometry to the D3O+?(HDO)(D2O)19 isotopologue of the “magic number” protonated water cluster, H+?(H2O)21. The OH group can occupy any one of the five spectroscopically distinct sites in the distorted pentagonal dodecahedron cage structure. The OH frequency is observed to evolve over tens of milliseconds in the temperature range (90-120 K). Starting at 100 K, large “jumps” are observed between two OH frequencies separated by ~300 cm-1 indicating migration of the OH group from the bound OH site at 3350 cm-1 to the free position at 3686 cm-1. Increasing the temperature to 110 K leads to partial interconversion among many sites. All sites are observed to interconvert at 120 K such that the distribution of the unique OH group among them adopts the form one would expect for a canonical ensemble. The spectral dynamics displayed by the clusters thus offer an unprecedented view into the molecular-level processes that drive spectral diffusion in an extended network of water molecules.

Yang, Nan↗
DOE OSTI2021

Subaru Hyper Suprime-Cam revisits the large-scale environmental dependence on galaxy morphology over 360 deg2 at z = 0.3–0.6

This study investigates the role of large-scale environments on the fraction of spiral galaxies at z = 0.3–0.6 sliced to three redshift bins of Δz = 0.1. Here, we sample 276220 massive galaxies in a limited stellar mass of 5 × 1010 solar mass (~M*) over 360 deg2, as obtained from the Second Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). By combining projected two-dimensional density information (Shimakawa et al. 2021, MNRAS, 503, 3896) and the CAMIRA cluster catalog (Oguri et al. 2018, PASJ, 70, S20), we investigate the spiral fraction across large-scale overdensities and in the vicinity of red sequence clusters. We adopt transfer learning to reduce the cost of labeling spiral galaxies significantly and then perform stacking analysis across the entire field to overcome the limitations of sample size. Here we employ a morphological classification catalog by the Galaxy Zoo Hubble (Willett et al., 2017, MNRAS, 464, 4176) to train the deep learning model. Based on 74103 sources classified as spirals, we find moderate morphology–density relations on a 10 comoving Mpc scale, thanks to the wide-field coverage of HSC-SSP. Clear deficits of spiral galaxies have also been confirmed, in and around 1136 red sequence clusters. Furthermore, we verify whether there is a large-scale environmental dependence on rest-frame u - r colors of spiral galaxies; such a tendency was not observed in our sample.

Astronomy & Astrophysics↗
DOE OSTI2023

Band Energy Dependence of Defect Formation in the Topological Semimetal Cd3As2

Cadmium Arsenide (Cd3As2) is a prototypical Dirac semimetal that manifests topological properties in a 3D bulk material. In defect-free Cd3As2, the Fermi level lies at a minimum in the density of states at the Dirac point, but experimentally it forms with excess electron carriers and an elevated EF, thereby masking the topological features. To computationally study the self-doping of Cd3As2, we combine density functional theory (DFT) calculations for defect formation energies with quasi-particle self-consistent GW (QSGW) electronic structure calculations. We demonstrate an innate dependence of the point defect formation energies on carrier concentrations and use the QSGW calculated density of states to extrapolate formation energies to arbitrary electron concentrations. This approach allows the quantitative modeling of thermodynamic defect equilibria in topological semimetals and is used to predict how Cd3As2 growth conditions affect the position of EF relative to the Dirac point.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗
DOE OSTI2021

Hydraulic architecture explains species moisture dependency but not mortality rates across a tropical rainfall gradient

Aim Intensified droughts are affecting tropical forests across the globe. However, the underlying mechanisms of tree drought response and mortality are poorly understood. Hydraulic traits and especially hydraulic safety margins (HSMs), i.e. the extent to which plants buffer themselves from thresholds of water stress, provide insights into species-specific drought vulnerability. Methods We investigated hydraulic traits during an intense drought triggered by the 2015-2016 El Niño on 27 canopy trees across three tropical forest sites with differing precipitation. We capitalized on the drought event as a time when plant water status might approach or exceed thresholds of water stress. We investigated the degree to which these traits varied across the rainfall gradient, as well as relationships amongst hydraulic traits and species-specific optimal moisture and mortality rates. Results There were no differences among sites for any measured trait. There was strong coordination among traits, with a network analysis revealing two major groups of coordinated traits. In one group there were water potentials, turgor loss point, sapwood capacitance and density, HSMs, and mortality rate. In the second group there was leaf mass per area, leaf dry matter content, hydraulic architecture (leaf area to sapwood area ratio), and species-specific optimal moisture. Conclusion These results demonstrated that while species with greater safety from turgor loss had lower mortality rates, hydraulic architecture was the only trait that explained species’ moisture dependency. Species with a greater leaf area to sapwood area ratio were associated with drier sites and reduced their transpirational demand during the dry season via deciduousness.

Hydraulic Saftey Margins, drought, tropical forest↗
DOE OSTI2021

Potential Dependent Mn Oxidation and Its Role in Passivation of Ni 38 Fe 20 Cr 22 Mn 10 Co 10 Multi-Principal Element Alloy Using Multi-Element Resolved Atomic Emission Spectroelectrochemistry

The identity of passivating oxides on multi-principal element alloys is of great interest as their optimization offers the potential for exceptional corrosion resistance in aqueous solutions over a broad range of potential and pH. This study focuses on a non-equiatomic Ni 38 Fe 20 Cr 22 Mn 10 Co 10 solid solution alloy and tracks the fate of each alloying element during linear sweep voltammetry, low and intermediate potential holds in the passive potential domain as well as during open circuit relaxation after anodic polarization in slightly acidified Cl − solution. Ni dissolves at all potentials investigated in this work, Fe and Co are incorporated into oxides or hydroxides in low concentrations whilst Cr and Mn are enriched at passive potentials. At low passivating potentials, Mn(II) dissolves and is incorporated in minor amounts in oxides containing large concentrations of Cr(III). Considerable enrichment in Mn(II)-species occurs relative to Cr(III) in the oxide at 0.1 V vs SCE. Electrochemical impedance spectroscopy suggests the presence of layered oxides with marginal passivation at high Mn(II) levels. The formation of these oxides depends on a combination of thermodynamic and kinetic factors as well as the sequence of passivation.

Han, Junsoo (ORCID:0000000192952954)↗
DOE OSTI2022

Report on Depth-Dependent Q from Frequency-Dependent Lg Q

As a phase that travels through the crustal waveguide, Lg samples the velocity and attenuation structure of the crust. We have developed methods (Pasyanos et al., 2009a; Pasyanos et al., 2009b) to estimate Qp and Qs of the crust and upper mantle from the amplitudes of regional phases, and have applied it to a number of regions around the world, and over a broad frequency band (0.5 - 10 Hz). In prior attenuation modeling, Lg phase amplitudes are able to effectively distinguish the high Q (low attenuation) of old stable cratonic crust from the low Q (high attenuation) of more recently active tectonic regions. For a variety of purposes (e.g. waveform modeling, seismic hazard, etc.), it is useful to have more information on the depth-dependence of the Q structure in the crust. One obvious candidate for doing this is using the frequency-dependence information of Lg Q, in the manner of surface waves. Unfortunately, however, Lg samples the whole of the crust without much differentiation with respect to frequency that is characteristic of fundamental mode surface waves. Lg is generally thought to be the sum of supercritically reflected S-waves trapped in the crustal waveguide (e.g. Xie and Lay, 1994). The phase can also be modeled as a superposition of surface waves. At lower frequencies, it is primarily composed of fundamental and low-order surface waves, while at higher frequencies, it is comprised purely of many high-order surface waves. The low-order surface waves that comprise Lg in low frequency bands (< 1 Hz) are preferentially sensitive to shallow earth structure, such as sedimentary basins and upper crust, while high-order surface waves have a more homogenized sensitivity to the whole crust. Furthermore, at the lower frequencies, we might expect to see some differentiation in the sensitivity between early Lg (herein referred to as Lg1) and late Lg (referred to as Lg2) where the latter is comprised of lower-order surface waves and, hence, shallower structure. Therefore, we might expect to see the signature of shallow features, primarily the lower Q of sediments as compared to crystalline crust, at lower frequencies and in later arriving Lg amplitudes.

58 GEOSCIENCES↗
NASA NTRS1992

The simulated features of heliospheric cosmic-ray modulation with a time-dependent drift model. III - General energy dependence

The time-dependent cosmic-ray transport equation is solved numerically in an axially symmetric heliosphere. Gradient and curvature drifts are incorporated, together with an emulated wavy neutral sheet. This model is used to simulate heliospheric cosmic-ray modulation for the period 1985-1989 during which drifts are considered to be important. The general energy dependence of the modulation of Galactic protons is studied as predicted by the model for the energy range 1 MeV to 10 GeV. The corresponding instantaneous radial and latitudinal gradients are calculated, and it is found that, whereas the latitudinal gradients follow the trends in the waviness of the neutral sheet to a large extent for all energies, the radial gradients below about 200 MeV deviate from this general pattern. In particular, these gradients increase when the waviness decreases for the simulated period 1985-1987.3, after which they again follow the neutral sheet by increasing rapidly.

Potgieter, M. S.↗
NASA NTRS1992

Time-dependent three dimensional compressible convection with depth-dependent properties

Using a spectral code, we have studied the time-dependent regime of three-dimensional anelastic compressible convection with depth-dependent thermal expansivity, viscosity and thermal conductivity in a wide box of size 5 x 5 x 1. Surface Rayleigh numbers up to 5 x 10 exp 6 have been considered. Very few cylindrical plumes are developed at the bottom but they join up collectively to form strong upwellings, which pulsate chaotically. Major descending flows occur in sheets which form rectangular planform at the top. The thermal and flow fields are dominated by large-scale features. The bottom 20 percent of the convecting layer is found to be superadiabatic.

Balachandar, S.↗
DOE OSTI2023

Curing the Divergence in Time-Dependent Density Functional Quadratic Response Theory

While time-dependent density functional theory has emerged as a method of choice for computing electronic spectra and response of molecules and materials, its reliability is hindered by the adiabatic approximation that is commonly made. In this work, we address one problematic aspect that arises from this approximation: an incorrect pole structure in the quadratic response function, leading to unphysical divergences in excited state-to-state transition probabilities and hyperpolarizabilties. We find the form of the exact quadratic response kernel and derive a practical and accurate approximation that cures the divergence. Here, we demonstrate our results on excited state-to-state transition probabilities of a model system and of the LiH molecule.

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

Temperature dependence of irradiation-induced nanocrystallization in amorphous silicon carbide

Ion irradiation induced nucleation and growth in amorphous SiC at elevated temperatures are investigated in this study. Both as-deposited amorphous and Kr ion irradiation-amorphized SiC films are used for the investigation. Similar behavior of particle precipitation in the two types of the films is observed. It is found that the threshold temperature for nucleation is between 550 and 700 K, which is considerably higher than the critical temperature for full amorphization in SiC irradiated with Kr ions. There is a temperature regime up to at least 900 K, where the growth rates are only weakly dependent of the irradiation temperature. This temperature regime is potentially useful to tailor the size and density of nanocrystalline SiC precipitates by optimizing the ion irradiation conditions.

Ion irradiation, Nucleation and Growth, Silicon Ca↗
DOE OSTI2023

Measuring Relative Energies of Ligand Binding Conformations on Nanocluster Surfaces with Temperature-Dependent FTIR Spectroscopy

We present a method to measure relative energies between binding conformations of carboxylate ligands on InP magic-sized clusters in solution. Using Markov chain Monte Carlo global fitting analysis on temperature-dependent vibrational spectra of cluster-bound ligands, we observe significantly different relative energies between various bidentate and monodentate binding motifs. Relative to the monodentate motif, the chelating conformation is 0.7 ± 0.3 kcal/mol more stable and the syn–syn bridging conformation is 1.1 ± 0.5 kcal/mol more stable, but the syn–anti bridging conformation exhibits no significant difference. Our results demonstrate that the relative energy between monodentate-bound carboxylates and unbound carboxylic acids is 4.52 ± 0.05 kcal/mol, or 1582 ± 19 cm –1 , nearly identical to the carboxylate asymmetric stretching frequency. Here, we suggest that the ligand vibrational energy may play a key role in ligand dissociation by compensating for energy differences between bound and dissociated ligand states. This approach gives important experimental insights into ligand binding and can inform future nanocrystal surface engineering.

Conformation↗