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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
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 OSTI2011

ExploreNEOs. V. AVERAGE ALBEDO BY TAXONOMIC COMPLEX IN THE NEAR-EARTH ASTEROID POPULATION

Examining the albedo distribution of the near-Earth object (NEO) population allows for a better understanding of the relationship between absolute (H) magnitude and size, which impacts calculations of the size frequency distribution and impact hazards. Examining NEO albedos also sheds light on the differences between the NEO and Main Belt populations. We combine albedo results from the ExploreNEOs Warm Spitzer Exploration Science program with taxonomic classifications from the literature, publicly available data sets, and new observations from our concurrent spectral survey to derive the average albedos for C-, D-, Q-, S-, V-, and X-complex NEOs. Using a sample size of 118 NEOs, we calculate average albedos of 0.29{sup +0.05}{sub -0.04}, 0.26{sup +0.04}{sub -0.03}, and 0.42{sup +0.13}{sub -0.11} for the Q-, S-, and V-complexes, respectively. The averages for the C- and D-complexes are 0.13{sup +0.06}{sub -0.05} and 0.02{sup +0.02}{sub -0.01}, but these averages are based on a small number of objects (five and two, respectively) and will improve with additional observations. We use albedos to assign X-complex asteroids to one of the E-, M-, or P-types. Our results demonstrate that the average albedos for the C-, S-, V-, and X-complexes are higher for NEOs than the corresponding averages observed in the Main Belt.

79 ASTRONOMY AND ASTROPHYSICS↗
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 OSTI2011

Subunit organization in the Dam1 kinetochore complex and its ring around microtubules

All eukaryotic cells must segregate their chromosomes equally between two daughter cells at each division. This process needs to be robust, as errors in the form of loss or gain of genetic material have catastrophic effects on viability. Chromosomes are captured, aligned, and segregated to daughter cells via interaction with spindle microtubules mediated by the kinetochore. In Saccharomyces cerevisiae one microtubule attaches to each kinetochore, requiring extreme processivity from this single connection. The yeast Dam1 complex, an essential component of the outer kinetochore, forms rings around microtubules and in vitro recapitulates much of the functionality of a kinetochore–microtubule attachment. To understand the mechanism of the Dam1 complex at the kinetochore, we must know how it binds to microtubules, how it assembles into rings, and how assembly is regulated. We used electron microscopy to map several subunits within the structure of the Dam1 complex and identify the organization of Dam1 complexes within the ring. Of importance, new data strongly support a more passive role for the microtubule in Dam1 ring formation. Integrating this information with previously published data, we generated a structural model for the Dam1 complex assembly that advances our understanding of its function and will direct future experiments.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2011

Calculation of complex DNA damage induced by ions

This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms may not be sufficiently effective. We study the flux of secondary electrons through the surface of nucleosomes and calculate the radial dose and the distribution of clustered damage around the ion's path. The calculated radial dose distribution is compared to simulations. The radial distribution of the complex damage is found to be different from that of the dose. A comparison with experiments may solve the question of what is more lethal for the cell, damage complexity or absorbed energy. We suggest a way to calculate the probability of cell death based on the complexity of the damage. This work is done within the framework of the phenomenon-based multiscale approach to radiation damage by ions.

61 RADIATION PROTECTION AND DOSIMETRY↗
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↗
DOE OSTI2016

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power.In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation.The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware.This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.

97 MATHEMATICS AND COMPUTING↗