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DOE OSTI2013

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering

Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. Thus far, crystallographic structures of integrin components are solved only separately, and for some integrin types. Also, the sequence of interactions that leads to signal transduction remains ambiguous. Particularly, it remains controversial whether the homo-dimerization of integrin transmembrane domains occurs following the integrin activation (i.e. when integrin ectodomain is stretched out) or if it regulates integrin clustering. This study employs molecular dynamics modeling approaches to address these questions in molecular details and sheds light on the crucial effect of the plasma membrane. Conducting a normal mode analysis of the intact αllbβ3 integrin, it is demonstrated that the ectodomain and transmembrane-cytoplasmic domains are connected via a membrane-proximal hinge region, thus merely transmembrane cytoplasmic domains are modeled. By measuring the free energy change and force required to form integrin homo-oligomers, this study suggests that the β-subunit homo-oligomerization potentially regulates integrin clustering, as opposed to α-subunit, which appears to be a poor regulator for the clustering process. If α-subunits are to regulate the clustering they should overcome a high-energy barrier formed by a stable lipid pack around them. Finally, an outside-in activation-clustering scenario is speculated, explaining how further loading the already-active integrin affects its homo-oligomerization so that focal adhesions grow in size.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

A computational study of yttria-stabilized zirconia: I. Using crystal chemistry to search for the ground state on a glassy energy landscape

Yttria-stabilized zirconia (YSZ), a ZrO 2 -Y 2 O 3 solid solution that contains a large population of oxygen vacancies, is widely used in energy and industrial applications. Past computational studies correctly predicted the anion diffusivity but not the cation diffusivity, which is important for material processing and stability. One of the challenges lies in identifying a plausible configuration akin to the ground state in a glassy landscape. This is unlikely to come from random sampling of even a very large sample space, but the odds are much improved by incorporating packing preferences revealed by a modest sized configurational library established from empirical potential calculations. Ab initio calculations corroborated these preferences, which prove remarkably robust extending to the fifth cation-oxygen shell about 8 Å away. Yet because of frustration there are still rampant violations of packing preferences and charge neutrality in the ground state, and the approach toward it bears a close analogy to glass relaxations. Fast relaxations proceed by fast oxygen movement around cations, while slow relaxations require slow cation diffusion. The latter is necessarily cooperative because of strong coupling imposed by the long-range packing preferences.

36 MATERIALS SCIENCE↗

DOE OSTI2018

A neutron tomography study: probing the spontaneous crystallization of randomly packed granular assemblies

We study the spontaneous crystallization of an assembly of highly monodisperse steel spheres under shaking, as it evolves from localized icosahedral ordering towards a packing reaching crystalline ordering. Towards this end, real space neutron tomography measurements on the granular assembly are carried out, as it is systematically subjected to a variation of frequency and amplitude. As expected, we see a presence of localized icosahedral ordering in the disordered initial state (packing fraction ≈ 0.62). As the frequency is increased for both the shaking amplitudes (0.2 and 0.6 mm) studied here, there is a rise in packing fraction, accompanied by an evolution to crystallinity. The extent of crystallinity is found to depend on both the amplitude and frequency of shaking. We find that the icosahedral ordering remains localized and its extent does not grow significantly, while the crystalline ordering grows rapidly as an ordering transition point is approached. In the ordered state, crystalline clusters of both face centered cubic (FCC) and hexagonal close packed (HCP) types are identified, the latter of which grows from stacking faults. Our study shows that an earlier domination of FCC gives way to HCP ordering at higher shaking frequencies, suggesting that despite their coexistence, there is a subtle dynamical competition at play. This competition depends on both shaking amplitude and frequency, as our results as well as those of earlier theoretical simulations demonstrate. It is likely that this involves the very small free energy difference between the two structures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

Comproportionation reactions of rare-earth metal trihalides (RX{sub 3}) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ((T{sub 3}R{sub 11})X{sub 15}-type, P6{sub 3}/m), tetramers ((T{sub 4}R{sub 16})X{sub 28}(R{sub 4}) (P-43m), (T{sub 4}R{sub 16})X{sub 20} (P4{sub 2}/nnm), (T{sub 4}R{sub 16})X{sub 24}(RX{sub 3}){sub 4} (I4{sub 1}/a) and (T{sub 4}R{sub 16})X{sub 23} (C2/m) types of structure) and pentamers ((Ru{sub 5}La{sub 14}){sub 2}Br{sub 39}, Cc) of (TR{sub r}){sub n} (n=2–5) clusters. These oligomers are further enveloped by inner (X{sup i}) as well as outer (X{sup a}) halido ligands, which possess diverse functionalities and interconnect like oligomers through i–i, i–a and/or a–i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of (TR{sub 6}) octahedra via common edges are more frequent than trimers and pentamers, in which the (TR{sub r}) clusters share common faces. - Graphical abstract: Rare earth-metal cluster complexes with endohedral transition metal atoms (TR{sub 6}) may connect via common edges or faces to form dimers, trimers, tetramers and pentamers of which the tetramers are the most prolific. Packing effects and electron counts play an important role. - Highlights: • Rare-earth metal cluster complexes encapsulate transition metal atoms. • Oligomers are built via connection of octahedral clusters via common edges or faces. • Dimers through pentamers with closed structures are known. • Tetramers including a tetrahedron of endohedral atoms are the most prolific.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Sluggish atomic dynamics in a Y-Sc-Co-Al high entropy bulk metallic glass

We present how 20 at% Sc addition affects the atomic packing and dynamics in a Y-Co-Al metallic glass (MG) and find that it greatly suppresses the dynamics of Co atoms by reducing the atomic packing difference in their surroundings. The Co atoms tending to be mobile or static depend on their nearest neighbors, i.e., possessing more Y/Y+Sc atoms but fewer Co atoms or vice versa. The X-ray absorption fine structure results confirm that Sc addition mainly changes the local environment around Co atoms, forming more Co-Co and Co-Sc pairs but significantly fewer Co-Y pairs than in the ternary counterpart, which can seriously slow the atomic dynamics and stabilize the competing phases. Our findings shed new light on the understanding of strong glass forming ability of the Sc-added Y-based high entropy MG from its local structure and dynamics and will be helpful in developing new bulk MGs.

36 MATERIALS SCIENCE↗

DOE OSTI2017

BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy: BECN2 CCD Structure and Interaction with ATG14

ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Fabrication of Pop-up Detector Arrays on Si Wafers

High sensitivity is a basic requirement for a new generation of thermal detectors. To meet the requirement, close-packed, two-dimensional silicon detector arrays have been developed in NASA Goddard Space Flight Center. The goal of the task is to fabricate detector arrays configured with thermal detectors such as infrared bolometers and x-ray calorimeters to use in space fliGht missions. This paper focuses on the fabrication and the mechanical testing of detector arrays in a 0.2 mm pixel size, the smallest pop-up detectors being developed so far. These array structures, nicknamed "PUDS" for "Pop-Up Detectors", are fabricated on I pm thick, single-crystal, silicon membranes. Their designs have been refined so we can utilize the flexibility of thin silicon films by actually folding the silicon membranes to 90 degrees in order to obtain close-packed two-dimensional arrays. The PUD elements consist of a detector platform and two legs for mechanical support while also serving as electrical and thermal paths. Torsion bars and cantilevers connecting the detector platform to the legs provide additional flexures for strain relief. Using micro-electromechanical structure (MEMS) fabrication techniques, including photolithography, anisotropic chemical etching, reactive-ion etching, and laser dicing, we have fabricated PLTD detector arrays of fourteen designs with a variation of four parameters including cantilever length, torsion bar length and width, and leg length. Folding tests were conducted to test mechanical stress distribution for the array structures. We obtained folding yields and selected optimum design parameters to reach minimal stress levels. Computer simulation was also employed to verify mechanical behaviors of PUDs in the folding process. In addition, scanning electron microscopy was utilized to examine the flatness of detectors and the alignment of detector pixels in arrays. The fabrication of thermistors and heaters on the pop-up detectors is under way, preparing us for the next step of the experiment, the thermal test.

Li, Mary J.↗

DOE OSTI2014

Indentation size effect and the plastic compressibility of glass

Oxide glasses exhibit significant densification under an applied isostatic pressure at the glass transition temperature. The glass compressibility is correlated with the chemical composition and atomic packing density, e.g., borate glasses with planar triangular BO{sub 3} units are more disposed for densification than silicate glasses with tetrahedral units. We here show that there is a direct relation between the plastic compressibility following hot isostatic compression and the extent of the indentation size effect (ISE), which is the decrease of hardness with indentation load exhibited by most materials. This could suggest that the ISE is correlated with indentation-induced shear bands, which should form in greater density when the glass network is more adaptable to volume changes through structural and topological rearrangements under an applied pressure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Metasurface-assisted phase-matching-free second harmonic generation in lithium niobate waveguides

The phase-matching condition is a key aspect in nonlinear wavelength conversion processes, which requires the momenta of the photons involved in the processes to be conserved. Conventionally, nonlinear phase matching is achieved using either birefringent or periodically poled nonlinear crystals, which requires careful dispersion engineering and is usually narrowband. In recent years, metasurfaces consisting of densely packed arrays of optical antennas have been demonstrated to provide an effective optical momentum to bend light in arbitrary ways. Here, we demonstrate that gradient metasurface structures consisting of phased array antennas are able to circumvent the phase-matching requirement in on-chip nonlinear wavelength conversion. We experimentally demonstrate phase-matching-free second harmonic generation over many coherent lengths in thin film lithium niobate waveguides patterned with the gradient metasurfaces. Efficient second harmonic generation in the metasurface-based devices is observed over a wide range of pump wavelengths (λ = 1580–1650 nm).

42 ENGINEERING↗

DOE OSTI2024

Two-dimensional-lattice-confined single-molecule-like aggregates

Intermolecular distance largely determines the optoelectronic properties of organic matter. Conventional organic luminescent molecules are commonly used either as aggregates or as single molecules that are diluted in a foreigner matrix. They have garnered great research interest in recent decades for a variety of applications, including light-emitting diodes, lasers and quantum technologies, among others. However, there is still a knowledge gap on how these molecules behave between the aggregation and dilution states. Here we report an unprecedented phase of molecular aggregate that forms in a two-dimensional hybrid perovskite superlattice with a near-equilibrium distance, which we refer to as a single-molecule-like aggregate (SMA). By implementing two-dimensional superlattices, the organic emitters are held in proximity, but, surprisingly, remain electronically isolated, thereby resulting in a near-unity photoluminescence quantum yield, akin to that of single molecules. Moreover, the emitters within the perovskite superlattices demonstrate strong alignment and dense packing resembling aggregates, allowing for the observation of robust directional emission, substantially enhanced radiative recombination and efficient lasing. Molecular dynamics simulations together with single-crystal structure analysis emphasize the critical role of the internal rotational and vibrational degrees of freedom of the molecules in the two-dimensional lattice for creating the exclusive SMA phase. Furthermore, this two-dimensional superlattice unifies the paradoxical properties of single molecules and aggregates, thus offering exciting possibilities for advanced spectroscopic and photonic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Tailoring plasmon resonances in the deep-ultraviolet by size-tunable fabrication of aluminum nanostructures

Localized surface plasmon resonances were controlled at deep-ultraviolet (DUV) wavelengths by fabricating aluminum (Al) nanostructures in a size-controllable manner. Plasmon resonances were obtained at wavelengths from near-UV down to 270 nm (4.6 eV) depending on the fabricated structure size. Such precise size control was realized by the nanosphere lithography technique combined with additional microwave heating to shrink the spaces in a close-packed monolayer of colloidal nanosphere masks. By adjusting the microwave heating time, the sizes of the Al nanostructures could be controlled from 80 nm to 50 nm without the need to use nanosphere beads of different sizes. With the outstanding controllability and versatility of the presented fabrication technique, the fabricated Al nanostructure is promising for use as a DUV plasmonic substrate, a light-harvesting platform for mediating strong light-matter interactions between UV photons and molecules placed near the metal nanostructure.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2015

Structural and magnetic effects of Cd{sub 1-x}In{sub x}Cr{sub 2}Se{sub 4}

Polycrystalline CdCr{sub 2}Se{sub 4} spinels with non-magnetic indium substitution were investigated with an aim to study the influence of non-magnetic substitution at the Cd site on its structural and magnetic properties. We carried out powder XRD and magnetic measurements on three compositions: Cd{sub 1-x}In{sub x}Cr{sub 2}Se{sub 4} (x=0, 0.05, 0.1). The XRD patterns were analyzed by carrying out Rietveld analysis and structural parameters were estimated. Phase purity of the compounds using reitveld refinement technique where confirming the indium distribution at tetrahedral site of the cubic close-packed sublattice formed by the selenium ions. The chemical compositions of these compounds were determined by energy dispersive x-ray analysis. Compared to parent compound, CdCr{sub 2}Se{sub 4}, the ferromagnetic Curie temperature T{sub C} was found to decrease from 130K to 123K and 114K as x varied from 0 to 0.05 and 0.1 respectively, whereas the saturation magnetization increases in Cd{sub 0.95}In{sub 0.05}Cr{sub 2}Se{sub 4} and again decreases in Cd{sub 0.9}In{sub 0.1}Cr{sub 2}Se{sub 4}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.

Horton, J. R.↗

DOE OSTI2015

Performance characterization of high quantum efficiency metal package photomultiplier tubes for time-of-flight and high-resolution PET applications

Purpose: Metal package photomultiplier tubes (PMTs) with a metal channel dynode structure have several advanced features for devising such time-of-flight (TOF) and high spatial resolution positron emission tomography (PET) detectors, thanks to their high packing density, large effective area ratio, fast time response, and position encoding capability. Here, we report on an investigation of new metal package PMTs with high quantum efficiency (QE) for high-resolution PET and TOF PET detector modules. Methods: The latest metal package PMT, the Hamamatsu R11265 series, is served with two kinds of photocathodes that have higher quantum efficiency than normal bialkali (typical QE ≈ 25%), super bialkali (SBA; QE ≈ 35%), and ultra bialkali (UBA; QE ≈ 43%). In this study, the authors evaluated the performance of the new PMTs with SBA and UBA photocathodes as a PET detector by coupling various crystal arrays. They also investigated the performance improvements of high QE, focusing in particular on a block detector coupled with a lutetium-based scintillator. A single 4 × 4 × 10 mm{sup 3} LYSO, a 7 × 7 array of 3 × 3 × 20 mm{sup 3} LGSO, a 9 × 9 array of 1.2 × 1.2 × 10 mm{sup 3} LYSO, and a 6 × 6 array of 1.5 × 1.5 × 7 mm{sup 3} LuYAP were used for evaluation. All coincidence data were acquired with a DRS4 based fast digitizer. Results: This new PMT shows promising crystal positioning accuracy, energy and time discrimination performance for TOF, and high-resolution PET applications. The authors also found that a metal channel PMT with SBA was enough for both TOF and high-resolution application, although UBA gave a minor improvement to time resolution. However, significant performance improvement was observed in relative low light output crystals (LuYAP) coupled with UBA. Conclusions: The results of this study will be of value as a useful reference to select PMTs for high-performance PET detectors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

Fractals of graphene quantum dots in photoluminescence of shungite

Viewing shungite as loosely packed fractal nets of graphene-based (reduced graphene oxide, rGO) quantum dots (GQDs), we consider photoluminescence of the latter as a convincing proof of the structural concept as well as of the GQD attribution to individual rGO fragments. We study emission from shungite GQDs for colloidal dispersions in water, carbon tetrachloride, and toluene at both room and low temperatures. As expected, the photoluminescence of the GQD aqueous dispersions is quite similar to that of synthetic GQDs of the rGO origin. The morphological study of shungite dispersions shows a steady trend of GQDs to form fractals and to drastically change the colloid fractal structure caused by the solvent exchange. Spectral study reveals a dual character of the emitting centers: individual GQDs are responsible for the spectra position while the fractal structure of GQD colloids ensures high broadening of the spectra due to structural inhomogeneity, thus causing a peculiar dependence of the photoluminescence spectra on the excitation wavelength. For the first time, photoluminescence spectra of individual GQDs were observed in frozen toluene dispersions, which paves the way for a theoretical treatment of the GQD photonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

High-Pressure Electrides: A Quantum Chemical Perspective

It has long been assumed that all matter will adopt simple close-packed lattices and become metallic under pressure, in accordance with the Thomas–Fermi–Dirac (TFD) model. However, this model struggles to explain pressure-driven complex structural transitions that have been observed in elements, including sodium, challenging our conventional understanding of compressed matter. Moreover, in stark contrast to the TFD model, first-principles calculations suggest that various elements and compounds become electrides under pressure. Electrides, characterized by concentrations of charge density at interstitial regions, can be thought of as ionic compounds where electrons behave as the anions. Though ambient-pressure molecular electrides have been extensively studied via experiments and computations, high-pressure electrides (HPEs) are not well-understood. The identification and characterization of HPEs have been, to date, based purely on theory, including topological analysis of the electron density and the electron localization function. Here, we review these theoretical analysis tools and suggest guidelines that can be used to classify systems as electrides. Moreover, we describe models used to rationalize the electronic structure of HPEs, drawing parallels with ambient-pressure molecular systems, and encourage the development of experimental techniques that provide evidence for the theoretically calculated charge localization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

Neuronal RNA granules: a link between RNA localization and stimulation-dependent translation

RNA granules are a macromolecular structure observed in neurons, where they serve as motile units that translocate mRNAs. Isolated RNA granules are highly enriched in Staufen protein and ultrastructurally contain densely packed clusters of ribosomes. With depolarization, many mRNAs, including those involved in plasticity, rapidly shift from the RNA granule fraction to polysomes. Depolarization reorganizes granules and induces a less compact organization of their ribosomes. RNA granules are not translationally competent, as indicated by the failure to incorporate radioactive amino acids and the absence of eIF4E, 4G, and tRNAs. We concluded that RNA granules are a local storage compartment for mRNAs under translational arrest but are poised for release to actively translated pools. Local release of mRNAs and ribosomes from granules may serve as a macromolecular mechanism linking RNA localization to translation and synaptic plasticity.

NASA Discipline Neuroscience↗

NASA NTRS2013

Radiative Transfer Theory Verified by Controlled Laboratory Experiments

We report the results of high-accuracy controlled laboratory measurements of the Stokes reflection matrix for suspensions of submicrometer-sized latex particles in water and compare them with the results of a numerically exact computer solution of the vector radiative transfer equation (VRTE). The quantitative performance of the VRTE is monitored by increasing the volume packing density of the latex particles from 2 to 10. Our results indicate that the VRTE can be applied safely to random particulate media with packing densities up to 2. VRTE results for packing densities of the order of 5 should be taken with caution, whereas the polarized bidirectional reflectivity of suspensions with larger packing densities cannot be accurately predicted. We demonstrate that a simple modification of the phase matrix entering the VRTE based on the so-called static structure factor can be a promising remedy that deserves further examination.

Radiative transfer↗