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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping

Single-molecule fluorescence spectroscopy allows direct, real-time observation of dynamic photophysical changes in light harvesting complexes. The Anti-Brownian ELectrokinetic (ABEL) trap is one such single-molecule method with useful advantages. This approach is particularly well-suited to make detailed spectroscopic measurements of pigment-protein complexes in solution phase because it enables extended-duration single-molecule observation by counteracting Brownian motion. This Perspective summarizes recent contributions by the authors and others that have utilized the unique capabilities of the ABEL trap to advance our understanding of phycobiliproteins and the phycobilisome complex, the primary light-harvesting apparatus of cyanobacteria. Monitoring the rich spectroscopic data from these measurements, which include brightness, fluorescence lifetime, polarization, and emission spectra, among other measurable parameters, has provided direct characterization of pigments and energy transfer pathways in the phycobilisome, spanning scales from single pigments and monomeric phycobiliproteins to higher order oligomers and protein-protein interactions of the phycobilisome complex. Importantly, new photophysical states and photodynamics were observed to modulate the flow of energy through the phycobilisome and suggest a previously unknown complexity in phycobilisome light harvesting and energy transport with a possible link to photoadaptive or photoprotective functions in cyanobacteria. Here, beyond deepening our collective understanding of natural light-harvesting systems, these and future discoveries may serve as inspiration for engineering improved artificial light-harvesting technologies.

14 SOLAR ENERGY↗
DOE OSTI2026

Complexity analysis of a CT injection experiment on BRB

In this work, we use Jensen–Shannon complexity and permutation entropy to analyze the magnetic field fluctuations of an astrophysically scaled plasma experiment. The experiment was intended to emulate an interplanetary coronal mass ejection event in the lab, recreating the major sections seen in satellite data. We also use a technique called “delay,” in which we use select elements, skipping one or more data points at a time, in our time series data to obtain Jensen–Shannon complexity as a function of frequency and investigate the frequency of maximized complexity. We then compare the delay frequencies to other frequencies in the plasma. We found that the frequencies for maximum complexity do not correspond to the frequencies investigated, implying that other physical mechanisms lead to an increase in complexity at these frequencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Ultrafast energy relaxation in single light-harvesting complexes

Significance The excitation energy transfer in light-harvesting complexes is usually studied either by ultrafast bulk spectroscopy or by single-molecule spectroscopy. These methods are to a high degree complementary: Bulk spectroscopy measures ultrafast processes averaged over thousands of complexes, whereas single-molecule spectroscopy observes much slower dynamics in individual complexes. In this work, we combine these approaches using a recently developed ultrafast single-molecule spectroscopy technique. This enables us, for the first time (to our knowledge), to observe ultrafast energy relaxation with a rate around 100 fs in individual light-harvesting complexes. We determine the distribution of the relaxation times, observe changes of the relaxation time in one complex, and find how the relaxation depends on excitation wavelength.

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

Redox conditions correlated with vibronic coupling modulate quantum beats in photosynthetic pigment–protein complexes

Significance Photosynthetic organisms evolved their light-harvesting antenna complexes to optimize energy transfer. It was recently shown that the redox environment can tune the mixing of electronic and vibrational states to steer energy through different pathways of a pigment–protein complex. Quantum beating signals in the spectra of pigment–protein complexes have been used to probe the excited-state dynamics within the complexes, but the microscopic dynamics that generate these signals and their role in promoting energy transfer are not fully understood. Here, we show that the redox environment that tunes energy transfer similarly tunes the quantum beating signals in the same complex. We find that the beats report on excited-state vibrations that maintain coherence through the vibronically enhanced energy transfer process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes

Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η 5 -pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η 4 -pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2′-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)] + , an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)] + . Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.

08 HYDROGEN↗
DOE OSTI2012

PRESENT-DAY GALACTIC EVOLUTION: LOW-METALLICITY, WARM, IONIZED GAS INFLOW ASSOCIATED WITH HIGH-VELOCITY CLOUD COMPLEX A

The high-velocity cloud Complex A is a probe of the physical conditions in the Galactic halo. The kinematics, morphology, distance, and metallicity of Complex A indicate that it represents new material that is accreting onto the Galaxy. We present Wisconsin H{alpha} Mapper kinematically resolved observations of Complex A over the velocity range of -250 to -50 km s{sup -1} in the local standard of rest reference frame. These observations include the first full H{alpha} intensity map of Complex A across (l, b) = (124 Degree-Sign , 18 Degree-Sign ) to (171 Degree-Sign , 53 Degree-Sign ) and deep targeted observations in H{alpha}, [S II] {lambda}6716, [N II] {lambda}6584, and [O I] {lambda}6300 toward regions with high H I column densities, background quasars, and stars. The H{alpha} data imply that the masses of neutral and ionized material in the cloud are similar, both being greater than 10{sup 6} M{sub Sun }. We find that the Bland-Hawthorn and Maloney model for the intensity of the ionizing radiation near the Milky Way is consistent with the known distance of the high-latitude part of Complex A and an assumed cloud geometry that puts the lower-latitude parts of the cloud at a distance of 7-8 kpc. This compatibility implies a 5% ionizing photon escape fraction from the Galactic disk. We also provide the nitrogen and sulfur upper abundance solutions for a series of temperatures, metallicities, and cloud configurations for purely photoionized gas; these solutions are consistent with the sub-solar abundances found by previous studies, especially for temperatures above 10{sup 4} K or for gas with a high fraction of singly ionized nitrogen and sulfur.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%, respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Path integrals, complex probabilities and the discrete Weyl representation

Abstract A discrete formulation of the real-time path integral as the expectation value of a functional of paths with respect to a complex probability on a sample space of discrete valued paths is explored. The formulation in terms of complex probabilities is motivated by a recent reinterpretation of the real-time path integral as the expectation value of a potential functional with respect to a complex probability distribution on cylinder sets of paths. The discrete formulation in this work is based on a discrete version of the Weyl algebra that can be applied to any observable with a finite number of outcomes. The origin of the complex probability in this work is the completeness relation. In the discrete formulation the complex probability exactly factors into products of conditional probabilities and exact unitarity is maintained at each level of approximation. The approximation of infinite dimensional quantum systems by discrete systems is discussed. The method is illustrated by applying it to scattering theory and quantum field theory. The implications of these applications for quantum computing is discussed.

Physics↗
DOE OSTI2015

MAGNETIC COMPLEXITY AS AN EXPLANATION FOR BIMODAL ROTATION POPULATIONS AMONG YOUNG STARS

Observations of young open clusters have revealed a bimodal distribution of fast and slower rotation rates that has proven difficult to explain with predictive models of spin down that depend on rotation rates alone. The Metastable Dynamo Model proposed recently by Brown, employing a stochastic transition probability from slow to more rapid spin down regimes, appears to be more successful but lacks a physical basis for such duality. Using detailed 3D MHD wind models computed for idealized multipole magnetic fields, we show that surface magnetic field complexity can provide this basis. Both mass and angular momentum losses decline sharply with increasing field complexity. Combined with observation evidence for complex field morphologies in magnetically active stars, our results support a picture in which young, rapid rotators lose angular momentum in an inefficient way because of field complexity. During this slow spin-down phase, magnetic complexity is eroded, precipitating a rapid transition from weak to strong wind coupling.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗
DOE OSTI2021

Carbon complexes in highly C-doped GaN

We investigate the properties of heavily C-doped GaN grown by hydride vapor phase epitaxy using both optical experiments and hybrid density functional theory calculations. Previous work has established that carbon acceptors (C N ) give rise to a yellow luminescence band near 2.2 eV along with a blue luminescence band near 2.9 eV. Photoluminescence measurements show the yellow band shifting as a function of carbon concentration, suggesting a change in the behavior of carbon species as carbon content increases. With hybrid density functional theory we calculate the electrical and optical behavior of carbon centers containing multiple carbon impurities, which may arise in heavily doped material. We compare the behavior of these complexes to the isolated centers, and find that the dicarbon donor-acceptor (C Ga –C N ) complex is a candidate to explain the shift in the yellow luminescence peak. Tricarbon complexes have high formation energies and modest binding energies, and also give rise to optical transitions that are inconsistent with the observed spectra. We also identify the split dicarbon interstitial on the gallium site as a low-energy species with a large binding energy that may act to compensate carbon acceptors. Here, local vibrational modes are calculated for carbon impurity centers, and we compare these results to recent experiments. Dicarbon and tricarbon complexes involving C Ga and C N exhibit modes that are only slightly higher than the isolated species, while carbon interstitials and related complexes give rise to vibrational modes much higher than C Ga and C N .

36 MATERIALS SCIENCE↗
DOE OSTI2026

Carbon-nitrogen complex as an alternative to the 𝑇 center in Si

A first-principles study of a carbon-nitrogen (CN) impurity complex in silicon is presented as an isoelectronic alternative to the T center [(CCH) Si ]. The latter has been pursued for applications in quantum information science, yet its sensitivity to the presence of hydrogen is still problematic. Our proposed complex has no hydrogen, thereby eliminating this issue. First, we show that the CN complex is stable against decomposition into substitutional and interstitial defects. Next, we show that due to being isoelectronic to the T center, the CN complex has a similar electronic structure, and therefore could be used in similar applications. We assess several low-energy configurations of the CN complex, finding (CN) Si to be stable and have the largest Debye-Waller factor. We predict a zero-phonon line (ZPL) of 828 meV (in the telecom S-band) and a radiative lifetime of 4.2 μs, comparable to the T center. Due to the presence of a bound exciton, choice of the exchange-correlation functional and also supercell-size scaling of the ZPL and transition dipole moment require special scrutiny; we rigorously justify our extrapolation schemes that allow computing values in the dilute limit.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Protein–peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase

A rational surface-engineering approach led to the crystal structure determination of ERK2–docking peptide complexes. Linear motifs normally bind with only medium binding affinity (K{sub d} of ∼0.1–10 µM) to shallow protein-interaction surfaces on their binding partners. The crystallization of proteins in complex with linear motif-containing peptides is often challenging because the energy gained upon crystal packing between symmetry mates in the crystal may be on a par with the binding energy of the protein–peptide complex. Furthermore, for extracellular signal-regulated kinase 2 (ERK2) the protein–peptide docking surface is comprised of a small hydrophobic surface patch that is often engaged in the crystal packing of apo ERK2 crystals. Here, a rational surface-engineering approach is presented that involves mutating protein surface residues that are distant from the peptide-binding ERK2 docking groove to alanines. These ERK2 surface mutations decrease the chance of ‘unwanted’ crystal packing of ERK2 and the approach led to the structure determination of ERK2 in complex with new docking peptides. These findings highlight the importance of negative selection in crystal engineering for weakly binding protein–peptide complexes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Systematic analysis of protein–detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials

Application of in situ dynamic light scattering to solutions of protein–detergent complexes permits characterization of these complexes in samples as small as 2 µl in volume. Detergents are widely used for the isolation and solubilization of membrane proteins to support crystallization and structure determination. Detergents are amphiphilic molecules that form micelles once the characteristic critical micelle concentration (CMC) is achieved and can solubilize membrane proteins by the formation of micelles around them. The results are presented of a study of micelle formation observed by in situ dynamic light-scattering (DLS) analyses performed on selected detergent solutions using a newly designed advanced hardware device. DLS was initially applied in situ to detergent samples with a total volume of approximately 2 µl. When measured with DLS, pure detergents show a monodisperse radial distribution in water at concentrations exceeding the CMC. A series of all-transn-alkyl-β-d-maltopyranosides, from n-hexyl to n-tetradecyl, were used in the investigations. The results obtained verify that the application of DLS in situ is capable of distinguishing differences in the hydrodynamic radii of micelles formed by detergents differing in length by only a single CH{sub 2} group in their aliphatic tails. Subsequently, DLS was applied to investigate the distribution of hydrodynamic radii of membrane proteins and selected water-insoluble proteins in presence of detergent micelles. The results confirm that stable protein–detergent complexes were prepared for (i) bacteriorhodopsin and (ii) FetA in complex with a ligand as examples of transmembrane proteins. A fusion of maltose-binding protein and the Duck hepatitis B virus X protein was added to this investigation as an example of a non-membrane-associated protein with low water solubility. The increased solubility of this protein in the presence of detergent could be monitored, as well as the progress of proteolytic cleavage to separate the fusion partners. This study demonstrates the potential of in situ DLS to optimize solutions of protein–detergent complexes for crystallization applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 m M sodium/potassium phosphate with 100 m M bis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space group P 4 1 2 1 2, with unit-cell parameters a = b = 99.49, c = 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

62 RADIOLOGY AND NUCLEAR MEDICINE↗