Structural correlation of the chalcogenide Ge40Se60 glass

NASA Astrophysics Data System (ADS)

Moharram, A. H.

2017-01-01

Binary Ge40Se60 glass was prepared using the melt-quench technique. The total structure factors, S( K), are obtained using the X-ray diffraction in the wave vector interval 0.28 ≤ K ≤ 6.5 Å-1. The appearance of the first sharp diffraction peak (FSDP) in the structure factor indicates the presence of the intermediate range order. Radial distribution functions, RDF( r), have been obtained using either the conventional (Fourier) transformation or the Monte Carlo simulation of the experimental X-ray data. The short range order parameters deduced from the Monte Carlo total correlation, T( r), functions are better than those obtained from the conventional (Fourier) T( r) data. Gaussian analyses of the total correlation function show that Ge2(Se1/2)6 molecular units are the basic structural units for the investigated Ge40Se60 glass.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Jingli; Chen, Cun; Wang, Gang

This study explores the temporal scaling behavior induced shear-branching structure in response to variant temperatures and strain rates during plastic deformation of Zr-based bulk metallic glass (BMG). The data analysis based on the compression tests suggests that there are two states of shear-branching structures: the fractal structure with a long-range order at an intermediate temperature of 223 K and a larger strain rate of 2.5 × 10 –2 s –1; the disordered structure dominated at other temperature and strain rate. It can be deduced from the percolation theory that the compressive ductility, ec, can reach the maximum value at themore » intermediate temperature. Furthermore, a dynamical model involving temperature is given for depicting the shear-sliding process, reflecting the plastic deformation has fractal structure at the temperature of 223 K and strain rate of 2.5 × 10 –2 s –1.« less

Local chiral potentials with Δ -intermediate states and the structure of light nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piarulli, M.; Girlanda, L.; Schiavilla, R.

We present fully local versions of the minimally non-local nucleon-nucleon potentials constructed in a previous paper [M. Piarulli et al., Phys. Rev. C 91, 024003 (2015)], and use them in hypersperical-harmonics and quantum Monte Carlo calculations of ground and excited states of 3H, 3He, 4He, 6He, and 6Li nuclei. The long-range part of these local potentials includes oneand two-pion exchange contributions without and with Δ isobars in the intermediate states up to order Q3 (Q denotes generically the low momentum scale) in the chiral expansion, while the short-range part consists of contact interactions up to order Q4. The low-energy constantsmore » multiplying these contact interactions are fitted to the 2013 Granada database in two different ranges of laboratory energies, either 0–125 MeV or 0–200 MeV, and to the deuteron binding energy and nn singlet scattering length. Fits to these data are performed for three models characterized by long- and short-range cutoffs, RL and RS respectively, ranging from (RL,RS) = (1.2, 0.8) fm down to (0.8, 0.6) fm. The long-range (short-range) cutoff regularizes the one- and two-pion exchange (contact) part of the potential.« less

The thermally reversing window in ternary GexPxS1-2x glasses

NASA Astrophysics Data System (ADS)

Vempati, U.; Boolchand, P.

2004-11-01

GexPxS1-2x glasses in the compositional range 0.05 \\le x \\le 0.19 have been synthesized and examined in temperature modulated differential scanning calorimetry (MDSC) and Raman scattering experiments. Trends in the non-reversing enthalpy ΔHnr(x) near Tg show the term to almost vanish in the 0.090(5)0.135. In analogy to previous results on chalcogenide glasses, we identify compositions at x<0.09 to be elastically floppy, those in the 0.0900.135 to be stressed rigid. MDSC results also show that the ΔHnr term ages in the stressed-rigid and floppy phases but not in the intermediate phase. The intermediate phase is viewed to be a self-organized phase of a disordered network. It consists of at least four isostatically rigid local structures: corner-sharing GeS4, edge-sharing GeS2, pyramidal P(S1/2)3 and quasi-tetrahedral S = P(S1/2)3 units for which evidence comes from Raman scattering. The latter method also shows the existence of P4S7 and P4S10 molecules in the glasses segregated from the backbone. These aspects of structure contribute to an intermediate phase that is significantly narrower in width than in the corresponding selenide glasses.

Transition of temporal scaling behavior in percolation assisted shear-branching structure during plastic deformation

DOE PAGES

Ren, Jingli; Chen, Cun; Wang, Gang; ...

2017-03-22

This study explores the temporal scaling behavior induced shear-branching structure in response to variant temperatures and strain rates during plastic deformation of Zr-based bulk metallic glass (BMG). The data analysis based on the compression tests suggests that there are two states of shear-branching structures: the fractal structure with a long-range order at an intermediate temperature of 223 K and a larger strain rate of 2.5 × 10 –2 s –1; the disordered structure dominated at other temperature and strain rate. It can be deduced from the percolation theory that the compressive ductility, ec, can reach the maximum value at themore » intermediate temperature. Furthermore, a dynamical model involving temperature is given for depicting the shear-sliding process, reflecting the plastic deformation has fractal structure at the temperature of 223 K and strain rate of 2.5 × 10 –2 s –1.« less

Orbital ordering-driven ferromagnetism in LaCoO3 nanowires

NASA Astrophysics Data System (ADS)

Wang, Yang; Fan, Hong Jin

2010-09-01

The structure and magnetic properties of LaCoO3 nanowires are investigated as a function of the diameter in the temperature range of 5-300 K. Ferromagnetism below 85 K is observed in these nanowires, in agreement with the recent observations in LaCoO3 epitaxial thin films and nanoparticles. With the diameter of nanowires decreasing, the unit-cell volume increases, while both the global and local structural distortions lessen, accompanied by the gradual enhancement of ferromagnetism. The structure analysis reveals that LaCoO3 nanowires exhibit a monoclinic distorted structure with I2/a space group in the entire investigated temperature range. Different from bulks, there is no clear spin-state transition occurring with temperature in LaCoO3 nanowires. There exists a noticeable Jahn-Teller (JT) distortion in the nanowires even at the lowest temperature, namely, orbital-ordered JT active Co3+ ions with intermediate-spin (IS) state persist at low temperatures, which is not observed in bulk LaCoO3. These results indicate that the ferromagnetism in the nanowires is driven by the orbital ordering of IS Co3+.

Statistical scaling of pore-scale Lagrangian velocities in natural porous media.

PubMed

Siena, M; Guadagnini, A; Riva, M; Bijeljic, B; Pereira Nunes, J P; Blunt, M J

2014-08-01

We investigate the scaling behavior of sample statistics of pore-scale Lagrangian velocities in two different rock samples, Bentheimer sandstone and Estaillades limestone. The samples are imaged using x-ray computer tomography with micron-scale resolution. The scaling analysis relies on the study of the way qth-order sample structure functions (statistical moments of order q of absolute increments) of Lagrangian velocities depend on separation distances, or lags, traveled along the mean flow direction. In the sandstone block, sample structure functions of all orders exhibit a power-law scaling within a clearly identifiable intermediate range of lags. Sample structure functions associated with the limestone block display two diverse power-law regimes, which we infer to be related to two overlapping spatially correlated structures. In both rocks and for all orders q, we observe linear relationships between logarithmic structure functions of successive orders at all lags (a phenomenon that is typically known as extended power scaling, or extended self-similarity). The scaling behavior of Lagrangian velocities is compared with the one exhibited by porosity and specific surface area, which constitute two key pore-scale geometric observables. The statistical scaling of the local velocity field reflects the behavior of these geometric observables, with the occurrence of power-law-scaling regimes within the same range of lags for sample structure functions of Lagrangian velocity, porosity, and specific surface area.

Zigzag antiferromagnetic ground state with anisotropic correlation lengths in the quasi-two-dimensional honeycomb lattice compound N a2C o2Te O6

NASA Astrophysics Data System (ADS)

Bera, A. K.; Yusuf, S. M.; Kumar, Amit; Ritter, C.

2017-03-01

The crystal structure, magnetic ground state, and the temperature-dependent microscopic spin-spin correlations of the frustrated honeycomb lattice antiferromagnet N a2C o2Te O6 have been investigated by powder neutron diffraction. A long-range antiferromagnetic (AFM) ordering has been found below TN˜24.8 K . The magnetic ground state, determined to be zigzag antiferromagnetic and characterized by a propagation vector k =(1 /2 0 0 ) , occurs due to the competing exchange interactions up to third-nearest neighbors within the honeycomb lattice. The exceptional existence of a limited magnetic correlation length along the c axis (perpendicular to the honeycomb layers in the a b planes) has been found even at 1.8 K, well below the TN˜24.8 K . The observed limited correlation along the c axis is explained by the disorder distribution of the Na ions within the intermediate layers between honeycomb planes. The reduced ordered moments mCo (1 )=2.77 (3 ) μB/C o2 + and mCo (2 )=2.45 (2 ) μB/C o2 + at 1.8 K reflect the persistence of spin fluctuations in the ordered state. Above TN˜24.8 K , the presence of short-range magnetic correlations, manifested by broad diffuse magnetic peaks in the diffraction patterns, has been found. Reverse Monte Carlo analysis of the experimental diffuse magnetic scattering data reveals that the spin correlations are mainly confined within the two-dimensional honeycomb layers (a b plane) with a correlation length of ˜12 Å at 25 K. The nature of the spin arrangements is found to be similar in both the short-range and long-range ordered magnetic states. This implies that the short-range correlation grows with decreasing temperature and leads to the zigzag AFM ordering at T ≤TN . The present study provides a comprehensive picture of the magnetic correlations over the temperature range above and below the TN and their relation to the crystal structure. The role of intermediate soft Na layers on the magnetic coupling between honeycomb planes is discussed.

Local chiral potentials with Δ -intermediate states and the structure of light nuclei

DOE PAGES

Piarulli, M.; Girlanda, L.; Schiavilla, R.; ...

2016-11-28

In this paper, we present fully local versions of the minimally nonlocal nucleon-nucleon potentials constructed in a previous paper [Piarulli et al., Phys. Rev. C 91, 024003 (2015)], and use them in hypersperical harmonics and quantum Monte Carlo calculations of ground and excited states ofmore » $^3$H, $^3$He, $^4$He, $^6$He, and $^6$Li nuclei. The long-range part of these local potentials includes one- and two-pion exchange contributions without and with $$\\Delta$$-isobars in the intermediate states up to order $Q^3$ ($Q$ denotes generically the low momentum scale) in the chiral expansion, while the short-range part consists of contact interactions up to order $Q^4$. The low-energy constants multiplying these contact interactions are fitted to the 2013 Granada database in two different ranges of laboratory energies, either 0–125 MeV or 0–200 MeV, and to the deuteron binding energy and $nn$ singlet scattering length. Fits to these data are performed for three models characterized by long- and short-range cutoffs, $$R_{\\rm L}$$ and $$R_{\\rm S}$$, respectively, ranging from $$(R_{\\rm L},R_{\\rm S})=(1.2,0.8)$$ fm down to $(0.8,0.6)$ fm. Finally, the long-range (short-range) cutoff regularizes the one- and two-pion exchange (contact) part of the potential.« less

Local chiral potentials with Δ -intermediate states and the structure of light nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piarulli, M.; Girlanda, L.; Schiavilla, R.

In this paper, we present fully local versions of the minimally nonlocal nucleon-nucleon potentials constructed in a previous paper [Piarulli et al., Phys. Rev. C 91, 024003 (2015)], and use them in hypersperical harmonics and quantum Monte Carlo calculations of ground and excited states ofmore » $^3$H, $^3$He, $^4$He, $^6$He, and $^6$Li nuclei. The long-range part of these local potentials includes one- and two-pion exchange contributions without and with $$\\Delta$$-isobars in the intermediate states up to order $Q^3$ ($Q$ denotes generically the low momentum scale) in the chiral expansion, while the short-range part consists of contact interactions up to order $Q^4$. The low-energy constants multiplying these contact interactions are fitted to the 2013 Granada database in two different ranges of laboratory energies, either 0–125 MeV or 0–200 MeV, and to the deuteron binding energy and $nn$ singlet scattering length. Fits to these data are performed for three models characterized by long- and short-range cutoffs, $$R_{\\rm L}$$ and $$R_{\\rm S}$$, respectively, ranging from $$(R_{\\rm L},R_{\\rm S})=(1.2,0.8)$$ fm down to $(0.8,0.6)$ fm. Finally, the long-range (short-range) cutoff regularizes the one- and two-pion exchange (contact) part of the potential.« less

Damped spin waves in the intermediate ordered phases in Ni 3V 2O 8

DOE PAGES

Ehlers, Georg; Podlesnyak, Andrey A.; Frontzek, Matthias D.; ...

2015-06-09

Here, spin dynamics in the intermediate ordered phases (between 4 and 9 K) in Ni 3V 2O 8 have been studied with inelastic neutron scattering. It is found that the spin waves are very diffuse, indicative of short lived correlations and the coexistence of paramagnetic moments with the long-range ordered state.

Magnetic Ordering of Erbium and Uranium NICKEL(2) SILICON(2) by Neutron Scattering

NASA Astrophysics Data System (ADS)

Lin, Hong

The magnetic ordering has been studied in UNi _2Si_2 and erbium single crystals by elastic neutron scattering. Abundant results are given regarding the magnetic structure, magnetic phase transitions, and the effect of a magnetic field on these properties. Three ordered phases are observed in UNi _2Si_2. They have been determined to be an incommensurate longitudinal spin density wave with a magnetic wave vector around q = 0.74c ^* in the high temperature phase, a simple body-centred antiferromagnet in the intermediate temperature phase, and a square wave in the low temperature phase. This square wave can be viewed equivalently as a longitudinal spin density wave with q = 2/3c ^* superimposed on a ferromagnetic component. Hysteresis and sample dependence are observed in the low-temperature phase transition. The two lower temperature phase transitions are both first order. The transition to paramagnetism is second order with a critical exponent beta = 0.35 +/- 0.03. When a magnetic field is applied along the c axis, the intermediate temperature phase is destabilised and disappears above a field of 3.5T. Although there is no new phase induced by the field, there exists a reentrant point where the three ordered phases can coexist. Erbium has three distinct ordered phases: the cone phase at low temperatures, the c-axis modulated (CAM) phase at higher temperatures, and the intermediate phase with moments modulated both along c and perpendicular to c. Within these phases the modulation of the moments may lock in to the lattice. The observed weak harmonics of the wave vector q in the basal plane for the cone phase and the q = 1/4c^* structure in the intermediate phase can be explained by a basal-plane spin slip model. The effect of magnetic field along the c axis on the magnetic structure is to stabilise the cone phase and to destabilise the intermediate phase. A new lock-in structure with q = 1/4c^* in the cone phase is induced by fields above 1.8T. The presence of the field also stabilises the lock-in structure with q = 2/7c^* in both the intermediate and the CAM phases.

Magnetic specific heat and structural phase transitions in (CH3)4NMnCl3 (TMMC) and TMMC:Cu2+ studied by crystal optics

NASA Astrophysics Data System (ADS)

Levola, T.; Kleemann, W.

1985-10-01

High-resolution refractive index (RI) and linear birefringence (LB) measurements are performed on the one-dimensional antiferromagnet tetramethyl ammonium manganese trichloride (TMMC) in order to reveal the temperature dependence of the magnetic short-range order. In agreement with values obtained by other methods an exchange constant J/kB=-7.3 K is reliably extracted. Anomalies of the in-plane LB and of the ordinary RI at the hexagonal-to-monoclinic structural phase transition (Tc=126 K) are successfully described with the use of linear elasto-optic response theory and the Landau approximation, which accounts for symmetry-adapted coupling between the components of the order parameter and of the spontaneous strain. Cu2+ ions, substituting Mn2+ ions of TMMC at a rate exceeding x=1.5%, are shown to stabilize an intermediate, possibly incommensurate phase. Its stability range is marked by very drastic decreases &=145 K and &=55 K for x=4.5%, respectively.

Self-assembly and structural relaxation in a model ionomer melt

DOE PAGES

Goswami, Monojoy; Borreguero, Jose M.; Sumpter, Bobby G.

2015-02-26

Molecular dynamics simulations are used to understand the self-assembly and structural relaxation in ionomer melts containing less than 10% degree of ionization on the backbone. We study the self-assembly of charged sites and counterions that show structural ordering and agglomeration with a range of structures that can be achieved by changing the dielectric constant of the medium. The intermediate scattering function shows a decoupling of charge and counterion relaxation at longer length scales for only high dielectric constant and at shorter length scales for all dielectric constants. Finally, the slow structural decay of counterions in the strongly correlated ionomer systemmore » closely resembles transport properties of semi-flexible polymers.« less

Changes in the Coherent Dynamics of Nanoconfined Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Vallejo, Kevin; Cano, Melissa; Li, Song; Rotner, Gernot; Faraone, Antonio; Banuelos, Jose

Confinement and temperature effects on the coherent dynamics of the room temperature ionic liquid (RTIL) [C10MPy+] [Tf2N-] were investigated using neutron spin-echo (NSE) in two silica matrices with different pore size. Several intermolecular forces give rise to the bulk molecular structure between anions and cations. NSE provided dynamics (via the coherent intermediate scattering function) in the time range of 0.004 to 10 ns, and at Q-values corresponding to intermediate range ordering and inter- and intra-molecular length scales of the RTIL. Pore wall effects were delineated by comparing bulk RTIL dynamics with those of the confined fluid in 2.8 nm and 8 nm pores. Analytical models were applied to the experimental data to extract decay times and amplitudes of each component. We find a fast relaxation outside the experiment time window, a primary relaxation, and slow, surface-induced dynamics, which all speed up with increased temperature, however, the temperature dependence differs between bulk and confinement. This study sheds light on the structure and dynamics of RTILs and is relevant to the optimization of RTILs for green technologies and applications.

Observing in space and time the ephemeral nucleation of liquid-to-crystal phase transitions.

PubMed

Yoo, Byung-Kuk; Kwon, Oh-Hoon; Liu, Haihua; Tang, Jau; Zewail, Ahmed H

2015-10-19

The phase transition of crystalline ordering is a general phenomenon, but its evolution in space and time requires microscopic probes for visualization. Here we report direct imaging of the transformation of amorphous titanium dioxide nanofilm, from the liquid state, passing through the nucleation step and finally to the ordered crystal phase. Single-pulse transient diffraction profiles at different times provide the structural transformation and the specific degree of crystallinity (η) in the evolution process. It is found that the temporal behaviour of η exhibits unique 'two-step' dynamics, with a robust 'plateau' that extends over a microsecond; the rate constants vary by two orders of magnitude. Such behaviour reflects the presence of intermediate structure(s) that are the precursor of the ordered crystal state. Theoretically, we extend the well-known Johnson-Mehl-Avrami-Kolmogorov equation, which describes the isothermal process with a stretched-exponential function, but here over the range of times covering the melt-to-crystal transformation.

Investigations into the Structure and Dynamics of Chalcogenide Glasses using High-Resolution Nuclear Magnetic Resonance Spectroscopy

NASA Astrophysics Data System (ADS)

Kaseman, Derrick Charles

Chalcogenide glasses constitute an important class of materials that are sulfides, selenides or tellurides of group IV and/or V elements, namely Ge, As, P and Si with minor concentrations of other elements such as Ga, Sb, In. Because of their infrared transparency that can be tuned by changing chemistry and can be actively altered by exposure to band gap irradiation, chalcogenide glasses find use in passive and active optical devices for applications in the areas of photonics, remote sensing and memory technology. Therefore, it is important to establish predictive models of structure-property relationships for these materials for optimization of their physical properties for various applications. Structural elucidation of chalcogenide glasses is experimentally challenging and in order to make predictive structural models, structural units at both short and intermediate -range length scales must be identified and quantified. Nuclear Magnetic Resonance (NMR) spectroscopy is an element-specific structural probe that is uniquely suited for this task, but resolution and sensitivity issues have severely limited the applications of such techniques in the past. The recent development of multi-dimensional solid-state NMR techniques, such as Phase Adjusted Spinning Sidebands (PASS) and Magic Angle Turning (MAT) can potentially alleviate such issues. In this study novel two-dimensional, high-resolution 77Se and 125Te MATPASS NMR spectroscopic techniques are utilized to elucidate quantitatively the compositional evolution of the short- and intermediate- range atomic structure in three binary chalcogenide glass-forming systems, namely: GexSe100-x, AsxSe100-x , and AsxTe100-x. The spectroscopic results provide unambiguous site speciation and quantification for short- and intermediate-range structural motifs present in these glasses. In turn, for all systems, robust structural models and the corresponding structure-property relationships are successfully established as a function of composition. The results indicate that the physical properties are intimately tied to the topology and chemical order present in each system. Finally, a dynamic version of the two-dimensional 31P PASS NMR spectroscopy is used to study the molecular motion in a supercooled chalcogenide liquid of composition P5Se3. The results clearly display the presence of isotropic rotational reorientation of the constituent molecules at timescales significantly decoupled from that of the structural relaxation near and above Tg. This behavior is atypical of conventional molecular glasses in organic systems in which rotational and translational dynamics remain coupled near Tg. When taken together with previous reports on the dynamics of other globular inorganic molecules, the results support the existence of a "plastic glass" phase where the molecules perform rapid rotation without significant translation.

The weaker effects of First-order mean motion resonances in intermediate inclinations

NASA Astrophysics Data System (ADS)

Chen, YuanYuan; Quillen, Alice C.; Ma, Yuehua; Chinese Scholar Council, the National Natural Science Foundation of China, the Natural Science Foundation of Jiangsu Province, the Minor Planet Foundation of the Purple Mountain Observatory

2017-10-01

During planetary migration, a planet or planetesimal can be captured into a low-order mean motion resonance with another planet. Using a second-order expansion of the disturbing function in eccentricity and inclination, we explore the sensitivity of the capture probability of first-order mean motion resonances to orbital inclination. We find that second-order inclination contributions affect the resonance strengths, reducing them at intermediate inclinations of around 10-40° for major first-order resonances. We also integrated the Hamilton's equations with arbitrary initial arguments, and provided the varying tendencies of resonance capture probabilities versus orbital inclinations for different resonances and different particle or planetary eccentricities. Resonance-weaker ranges in inclinations generally appear at the places where resonance strengths are low, around 10-40° in general. The weaker ranges disappear with a higher particle eccentricity (≳0.05) or planetary eccentricity (≳0.05). These resonance-weaker ranges in inclinations implies that intermediate-inclination objects are less likely to be disturbed or captured into the first-order resonances, which would make them entering into the chaotic area around Neptune with a larger fraction than those with low inclinations, during the epoch of Neptune's outward migration. The privilege of high-inclination particles leave them to be more likely captured into Neptune Trojans, which might be responsible for the unexpected high fraction of high-inclination Neptune Trojans.

Influence of Magnesium Content on the Local Structure of Amorphous Calcium Carbonate (ACC): Real Time Determination by In Situ PDF Analysis

NASA Astrophysics Data System (ADS)

Mergelsberg, S. T.; Ulrich, R. N.; Michel, F. M.; Dove, P. M.

2016-12-01

Calcium carbonate minerals are an essential component in the exoskeletons of crustaceans and mollusks. The onset of exoskeleton mineralization includes the precipitation of amorphous calcium carbonate (ACC) as a reactive intermediate that later transforms to produce diverse structures. Despite the importance of ACC as a critical phase during skeleton formation, the chemical and physical properties are not well characterized at conditions that approximate biological environments. Of particular interest are the solubility of ACC, the short-range structure at the time of formation, and the evolution of ACC structure to final products. Recent advances showing the widespread occurrence of multistep pathways to mineralization in biological and geological settings (De Yoreo et al., 2015) underline the importance of understanding amorphous intermediates. Using quantitative laboratory techniques developed by our research group (Blue et al., 2013; Blue and Dove, 2015; Blue et al., in press), this experimental study quantifies the solubility of ACC in parallel with the physical characterization of the corresponding structure. We measured ACC solubility at specific time points during the precipitation and during its subsequent evolution under the mild pH conditions that approximate biological and environmental conditions. In parallel experiments, structural data were collected from in situ pair distribution function (PDF) analyses were conducted to follow the evolution of individual samples from initial precipitation to final product. The measurements are leading to a quantitative solubility function for ACC with variable Mg contents and an x-ray based understanding of ACC structure in the same particles. We are also finding temporal changes in the short-range order of ACC after precipitation and this order is dependent upon Mg content. Moreover, the data show Mg distribution through the ACC particles is dependent upon total alkalinity. Insights from this study hold promise for better understanding the nature of the initial ACC that forms and factors that influence its structural evolution to final products.

A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

PubMed

Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

2006-06-02

The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important.

Micro-structure and motion of two-dimensional dense short spherocylinder liquids

NASA Astrophysics Data System (ADS)

Wang, Wen; Lin, Jyun-Ting; Su, Yen-Shuo; I, Lin

2018-03-01

We numerically investigate the micro-structure and motion of 2D liquids composed of dense short spherocylinders, by reducing the shape aspect ratio from 3. It is found that reducing shape aspect ratio from 3 causes a smooth transition from heterogeneous structures composed of crystalline ordered domains with good tetratic alignment order to those with good hexagonal bond-orientational order at an aspect ratio equaling 1.35. In the intermediate regime, both structural orders are strongly deteriorated, and the translational hopping rate reaches a maximum due to the poor particle interlocking of the disordered structure. Shortening rod length allows easier rotation, induces monotonic increase of rotational hopping rates, and resumes the separation of rotational and translational hopping time scales at the small aspect ratio end, after the crossover of their rates in the intermediate regime. At the large shape aspect ratio end, the poor local tetratic order has the same positive effects on facilitating local rotational and translational hopping. In contrast, at the small shape aspect ratio end, the poor local bond orientational order has the opposite effects on facilitating local rotational and translational hopping.

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Short, intermediate and mesoscopic range order in sulfur-rich binary glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bychkov, E.; Miloshova, M.; Price, D.L.

2008-09-29

Pulsed neutron and high-energy X-ray diffraction, small-angle neutron scattering, Raman spectroscopy and DSC were used to study structural changes on the short, intermediate and mesoscopic range scale for sulfur-rich AsS{sub x} (x {ge} 1.5) and GeS{sub x} (x {ge} 2) glasses. Two structural regions were found in the both systems. (1) Between stoichiometric (As{sub 2}S{sub 3} and GeS{sub 2}) and 'saturated' (AsS{sub 2.2} and GeS{sub 2.7}) compositions, excessive sulfur atoms form sulfur dimers and/or short chains, replacing bridging sulfur in corner-sharing AsS{sub 3/2} and GeS{sub 4/2} units. (2) Above the 'saturated' compositions at [As] < 30.5 at.% and [Ge]

Transformation of BCC and B2 High Temperature Phases to HCP and Orthorhombic Structures in the Ti-Al-Nb System. Part II: Experimental TEM Study of Microstructures

PubMed Central

Bendersky, L. A.; Boettinger, W. J.

1993-01-01

Possible transformation paths that involve no long range diffusion and their corresponding microstructural details were predicted by Bendersky, Roytburd, and Boettinger [J. Res. Natl. Inst. Stand. Technol. 98, 561 (1993)] for Ti-Al-Nb alloys cooled from the high temperature BCC/B2 phase field into close-packed orthorhombic or hexagonal phase fields. These predictions were based on structural and symmetry relations between the known phases. In the present paper experimental TEM results show that two of the predicted transformation paths are indeed followed for different alloy compositions. For Ti-25Al-12.5Nb (at%), the path includes the formation of intermediate hexagonal phases, A3 and DO19, and subsequent formation of a metastable domain structure of the low-temperature O phase. For alloys close to Ti-25Al-25Nb (at%), the path involves an intermediate B19 structure and subsequent formation of a translational domain structure of the O phase. The path selection depends on whether B2 order forms in the high temperature cubic phase prior to transformation to the close-packed structure. The paper also analyzes the formation of a two-phase modulated microstructure during long term annealing at 700 °C. The structure forms by congruent ordering of the DO19 phase to the O phase, and then reprecipitation of the DO19 phase, possibly by a spinodal mechanism. The thermodynamics underlying the path selection and the two-phase formation are also discussed. PMID:28053488

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

Resonance-Raman spectro-electrochemistry of intermediates in molecular artificial photosynthesis of bimetallic complexes.

PubMed

Zedler, Linda; Guthmuller, Julien; Rabelo de Moraes, Inês; Kupfer, Stephan; Krieck, Sven; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-05-25

The sequential order of photoinduced charge transfer processes and accompanying structure changes were analyzed by UV-vis and resonance-Raman spectroscopy of intermediates of a Ru(ii) based photocatalytic hydrogen evolving system obtained by electrochemical reduction.

P-T phase diagram and structural transformations of molten P2O5 under pressure

NASA Astrophysics Data System (ADS)

Brazhkin, V. V.; Katayama, Y.; Lyapin, A. G.; Saitoh, H.

2014-03-01

The P2O5 compound is an archetypical glass-forming oxide with a record high hygroscopicity, which makes its study extremely difficult. We present the in situ x-ray diffraction study of the pressure-temperature phase diagram of P2O5 and, particularly, of the liquid P2O5 structure under high pressure up to 10 GPa. Additionally, quenching from the melt has been used to extend the melting curve up to 15 GPa. We found that structural transformation in the liquid P2O5 under pressure is unique and includes three stages: first, the disappearance of the intermediate range order of the melt together with a slow increase in the average first-coordination number (P-O and O-P neighbors) up to 4 GPa; second, the "normal" compression almost without structural modification at higher pressures up to 8-9 GPa; and, finally, the abrupt change of the short-range order structure of the liquid with the jumplike increase at 9-10 GPa. The last stage correlates with the melting curve maximum (≈1250 °C) at ≈10 GPa and can be interpreted as a transformation to the liquid phase with entirely fivefold-coordinated phosphorus and twofold-coordinated oxygen atoms.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

The origin of and conditions for clustering in fluids with competing interactions

NASA Astrophysics Data System (ADS)

Jadrich, Ryan; Bollinger, Jonathan; Truskett, Thomas

2015-03-01

Fluids with competing short-range attractions and long-range repulsions exhibit a rich phase behavior characterized by intermediate range order (IRO), as quantified via the static structure factor. This phase behavior includes cluster formation depending upon density-controlled packing effects and the magnitude and range of the attractive and repulsive interactions. Such model systems mimic (to zeroth order) screened, charge-stabilized, aqueous colloidal dispersions of, e.g., proteins. We employ molecular dynamics simulations and integral equation theory to elucidate a more fundamental microscopic explanation for IRO-driven clustering. A simple criterion is identified that indicates when dynamic, amorphous clustering emerges in a polydisperse system, namely when the Ornstein-Zernike thermal correlation length in the system exceeds the repulsive potential tail range. Remarkably, this criterion also appears tightly correlated to crystalline cluster formation in a monodisperse system. Our new gauge is compared to another phenomenological condition for clustering which is when the IRO peak magnitude exceeds ~ 2.7. Ramifications of crystalline versus amorphous clustering are discussed and potential ways of using our new measure in experiment are put forward.

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the course of this study, we refine knowledge of intermediate range order structural configurations and the bistabilities related to these configurations. The importance of the lone-pair orbital interactions in the chalcogenide glassy network is underscored.

Neutron diffraction study of aqueous Laponite suspensions at the NIMROD diffractometer.

PubMed

Tudisca, V; Bruni, F; Scoppola, E; Angelini, R; Ruzicka, B; Zulian, L; Soper, A K; Ricci, M A

2014-09-01

The process of dynamical arrest, leading to formation of different arrested states such as glasses and gels, along with the closely related process of aging, is central for both basic research and technology. Here we report on a study of the time-dependent structural evolution of two aqueous Laponite clay suspensions at different weight concentrations. Neutron diffraction experiments have been performed with the near and intermediate range order diffractometer (NIMROD) that allows studies of the structure of liquids and disordered materials over a continuous length scale ranging from 1 to 300 Å, i.e., from the atomistic to the mesoscopic scales. NIMROD is presently a unique diffractometer, bridging the length scales traditionally investigated by small angle neutron scattering or small angle x-ray scattering with that accessible by traditional diffractometers for liquids. Interestingly, we have unveiled a signature of aging of both suspensions in the length scale region of NIMROD. This phenomenon, ascribed to sporadic contacts between Laponite platelets at long times, has been observed with the sample arrested as gel or as repulsive glass. Moreover, water molecules within the layers closest to Laponite platelets surface show orientational and translational order, which maps into the crystalline structure of Laponite.

Reversibility and intermediate steps as key tools for the growth of extended ordered polymers via on-surface synthesis

NASA Astrophysics Data System (ADS)

Di Giovannantonio, Marco; Contini, Giorgio

2018-03-01

Surface-confined polymerization is a bottom-up strategy to create one- and two-dimensional covalent organic nanostructures with a π-conjugated backbone, which are suitable to be employed in real-life electronic devices, due to their high mechanical resistance and electronic charge transport efficiency. This strategy makes it possible to change the properties of the final nanostructures by a careful choice of the monomer architecture (i.e. of its constituent atoms and their spatial arrangement). Several chemical reactions have been proven to form low-dimensional polymers on surfaces, exploiting a variety of precursors in combination with metal (e.g. Cu, Ag, Au) and insulating (e.g. NaCl, CaCO3) surfaces. One of the main challenges of such an approach is to obtain nanostructures with long-range order, to boost the conductance performances of these materials. Most of the exploited chemical reactions use irreversible coupling between the monomers and, as a consequence, the resulting structures often suffer from poor order and high defect density. This review focuses on the state-of-the-art surface-confined polymerization reactions, with particular attention paid to reversible coupling pathways and irreversible processes including intermediate states, which are key aspects to control to increase the order of the final nanostructure.

Classical and quantum filaments in the ground state of trapped dipolar Bose gases

NASA Astrophysics Data System (ADS)

Cinti, Fabio; Boninsegni, Massimo

2017-07-01

We study, by quantum Monte Carlo simulations, the ground state of a harmonically confined dipolar Bose gas with aligned dipole moments and with the inclusion of a repulsive two-body potential of varying range. Two different limits can clearly be identified, namely, a classical one in which the attractive part of the dipolar interaction dominates and the system forms an ordered array of parallel filaments and a quantum-mechanical one, wherein filaments are destabilized by zero-point motion, and eventually the ground state becomes a uniform cloud. The physical character of the system smoothly evolves from classical to quantum mechanical as the range of the repulsive two-body potential increases. An intermediate regime is observed in which ordered filaments are still present, albeit forming different structures from the ones predicted classically; quantum-mechanical exchanges of indistinguishable particles across different filaments allow phase coherence to be established, underlying a global superfluid response.

Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides

NASA Astrophysics Data System (ADS)

Todorova, Nevena; Bentvelzen, Alan; English, Niall J.; Yarovsky, Irene

2016-02-01

Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.

Exploring between the extremes: conversion-dependent kinetics of phosphite-modified hydroformylation catalysis.

PubMed

Kubis, Christoph; Selent, Detlef; Sawall, Mathias; Ludwig, Ralf; Neymeyr, Klaus; Baumann, Wolfgang; Franke, Robert; Börner, Armin

2012-07-09

The kinetics of the hydroformylation of 3,3-dimethyl-1-butene with a rhodium monophosphite catalyst has been studied in detail. Time-dependent concentration profiles covering the entire olefin conversion range were derived from in situ high-pressure FTIR spectroscopic data for both, pure organic components and catalytic intermediates. These profiles fit to Michaelis-Menten-type kinetics with competitive and uncompetitive side reactions involved. The characteristics found for the influence of the hydrogen concentration verify that the pre-equilibrium towards the catalyst substrate complex is not established. It has been proven experimentally that the hydrogenolysis of the intermediate acyl complex remains rate limiting even at high conversions when the rhodium hydride is the predominant resting state and the reaction is nearly of first order with respect to the olefin. Results from in situ FTIR and high-pressure (HP) NMR spectroscopy and from DFT calculations support the coordination of only one phosphite ligand in the dominating intermediates and a preferred axial position of the phosphite in the electronically saturated, trigonal bipyramidal (tbp)-structured acyl rhodium complex. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interfacial Metal-Oxide Interactions in Resistive Switching Memories.

PubMed

Cho, Deok-Yong; Luebben, Michael; Wiefels, Stefan; Lee, Kug-Seung; Valov, Ilia

2017-06-07

Metal oxides are commonly used as electrolytes for redox-based resistive switching memories. In most cases, non-noble metals are directly deposited as ohmic electrodes. We demonstrate that irrespective of bulk thermodynamics predictions an intermediate oxide film a few nanometers in thickness is always formed at the metal/insulator interface, and this layer significantly contributes to the development of reliable switching characteristics. We have tested metal electrodes and metal oxides mostly used for memristive devices, that is, Ta, Hf, and Ti and Ta 2 O 5 , HfO 2 , and SiO 2 . Intermediate oxide layers are always formed at the interfaces, whereas only the rate of the electrode oxidation depends on the oxygen affinity of the metal and the chemical stability of the oxide matrix. Device failure is associated with complete transition of short-range order to a more disordered main matrix structure.

Mass production of shaped particles through vortex ring freezing

NASA Astrophysics Data System (ADS)

An, Duo; Warning, Alex; Yancey, Kenneth G.; Chang, Chun-Ti; Kern, Vanessa R.; Datta, Ashim K.; Steen, Paul H.; Luo, Dan; Ma, Minglin

2016-08-01

A vortex ring is a torus-shaped fluidic vortex. During its formation, the fluid experiences a rich variety of intriguing geometrical intermediates from spherical to toroidal. Here we show that these constantly changing intermediates can be `frozen' at controlled time points into particles with various unusual and unprecedented shapes. These novel vortex ring-derived particles, are mass-produced by employing a simple and inexpensive electrospraying technique, with their sizes well controlled from hundreds of microns to millimetres. Guided further by theoretical analyses and a laminar multiphase fluid flow simulation, we show that this freezing approach is applicable to a broad range of materials from organic polysaccharides to inorganic nanoparticles. We demonstrate the unique advantages of these vortex ring-derived particles in several applications including cell encapsulation, three-dimensional cell culture, and cell-free protein production. Moreover, compartmentalization and ordered-structures composed of these novel particles are all achieved, creating opportunities to engineer more sophisticated hierarchical materials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shephard, Jacob J.; Vickers, Martin; Salzmann, Christoph G., E-mail: c.salzmann@ucl.ac.uk

Low-density amorphous (LDA) ice is involved in critical cosmological processes and has gained prominence as one of the at least two distinct amorphous forms of ice. Despite these accolades, we still have an incomplete understanding of the structural diversity that is encompassed within the LDA state and the dynamic processes that take place upon heating LDA. Heating the high-pressure ice VIII phase at ambient pressure is a remarkable example of temperature-induced amorphisation yielding LDA. We investigate this process in detail using X-ray diffraction and Raman spectroscopy and show that the LDA obtained from ice VIII is structurally different from themore » more “traditional” states of LDA which are approached upon thermal annealing. This new structural relaxation pathway involves an increase of structural order on the intermediate range length scale. In contrast with other LDA materials the local structure is more ordered initially and becomes slightly more disordered upon annealing. We also show that the cascade of phase transitions upon heating ice VIII at ambient pressure includes the formation of ice IX which may be connected with the structural peculiarities of LDA from ice VIII. Overall, this study shows that LDA is a structurally more diverse material than previously appreciated.« less

Boson peak, heterogeneity and intermediate-range order in binary SiO2-Al2O3 glasses.

PubMed

Ando, Mariana F; Benzine, Omar; Pan, Zhiwen; Garden, Jean-Luc; Wondraczek, Katrin; Grimm, Stephan; Schuster, Kay; Wondraczek, Lothar

2018-03-29

In binary aluminosilicate liquids and glasses, heterogeneity on intermediate length scale is a crucial factor for optical fiber performance, determining the lower limit of optical attenuation and Rayleigh scattering, but also clustering and precipitation of optically active dopants, for example, in the fabrication of high-power laser gain media. Here, we consider the low-frequency vibrational modes of such materials for assessing structural heterogeneity on molecular scale. We determine the vibrational density of states VDoS g(ω) using low-temperature heat capacity data. From correlation with low-frequency Raman spectroscopy, we obtain the Raman coupling coefficient. Both experiments allow for the extraction of the average dynamic correlation length as a function of alumina content. We find that this value decreases from about 3.9 nm to 3.3 nm when mildly increasing the alumina content from zero (vitreous silica) to 7 mol%. At the same time, the average inter-particle distance increases slightly due to the presence of oxygen tricluster species. In accordance with Loewensteinian dynamics, this proves that mild alumina doping increases structural homogeneity on molecular scale.

Maskelynite formation via solid-state transformation: Evidence of infrared and x-ray anisotropy

DOE PAGES

Jaret, Steven J.; Ehm, Lars; Woerner, William R.; ...

2015-03-24

We present optical microscopy, micro-Raman spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, high-energy X-ray total scattering experiments, and micro-Fourier transform infrared (micro-FTIR) spectroscopy on shocked labradorite from the Lonar Crater, India. We show that maskelynite of shock class 2 is structurally more similar to fused glass than to crystalline plagioclase. However, there are slight but significant differences – preservation of original pre-impact igneous zoning, anisotropy at Infrared wavelengths, X-ray anisotropy, and preservation of some intermediate range order – which are all consistent with a solid-state transformation formation of maskelynite.

Structural analysis of zwitterionic liquids vs. homologous ionic liquids

NASA Astrophysics Data System (ADS)

Wu, Boning; Kuroda, Kosuke; Takahashi, Kenji; Castner, Edward W.

2018-05-01

Zwitterionic liquids (Zw-ILs) have been developed that are homologous to monovalent ionic liquids (ILs) and show great promise for controlled dissolution of cellulosic biomass. Using both high energy X-ray scattering and atomistic molecular simulations, this article compares the bulk liquid structural properties for novel Zw-ILs with their homologous ILs. It is shown that the significant localization of the charges on Zw-ILs leads to charge ordering similar to that observed for conventional ionic liquids with monovalent anions and cations. A low-intensity first sharp diffraction peak in the liquid structure factor S(q) is observed for both the Zw-IL and the IL. This is unexpected since both the Zw-IL and IL have a 2-(2-methoxyethoxy)ethyl (diether) functional group on the cationic imidazolium ring and ether functional groups are known to suppress this peak. Detailed analyses show that this intermediate range order in the liquid structure arises for slightly different reasons in the Zw-IL vs. the IL. For the Zw-IL, the ether tails in the liquid are shown to aggregate into nanoscale domains.

Partially Disordered Phase in Frustrated Triangular Lattice Antiferromagnet CuFeO 2

NASA Astrophysics Data System (ADS)

Mitsuda, Setsuo; Kasahara, Noriaki; Uno, Takahiro; Mase, Motoshi

1998-12-01

We reinvestigated successive magnetic phase transitions (T N1˜14.0 K, T N2˜10.5 K) in a frustrated triangular lattice antiferromagnet (TLA) CuFeO2 by neutron diffraction measurements using single crystals. The magnetic structure of the intermediate-temperature phase between T N1 and T N2 is found to be a quasi-long range ordered sinusoidally amplitude-modulated structure with a temperature dependent propagation wave vector (q q 0). These features of successive phase transitions are well explained by reinvestigated Monte-Carlo simulation of a 2D Ising TLA with competing exchange interactions up to 3rd neighbors, in spite of the Heisenberg spin character of orbital singlet Fe3+ magnetic ions.

High-lying intermediate excitations in the nuclear effective interaction with a super-soft-core potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goode, P.R.; Barrett, B.R.; Portilho, O.

1979-02-01

The earlier calculations of Goode and Barrett are repeated using the super-soft-core potential of Gogny, Pires, and de Tourreil. The particular third-order folded diagram which they calculated now converges in its intermediate-state energy summation, because of the suppression of the strong short-range repulsive effects present in earlier calculations.

X-ray absorption spectroscopy with time-tagged photon counting: application to study the structure of a Co(i) intermediate of H2 evolving photo-catalyst.

PubMed

Smolentsev, Grigory; Guda, Alexander A; Janousch, Markus; Frieh, Cristophe; Jud, Gaudenz; Zamponi, Flavio; Chavarot-Kerlidou, Murielle; Artero, Vincent; van Bokhoven, Jeroen A; Nachtegaal, Maarten

2014-01-01

In order to probe the structure of reaction intermediates of photochemical reactions a new setup for laser-initiated time-resolved X-ray absorption (XAS) measurements has been developed. With this approach the arrival time of each photon in respect to the laser pulse is measured and therefore full kinetic information is obtained. All X-rays that reach the detector are used to measure this kinetic information and therefore the detection efficiency of this method is high. The newly developed setup is optimized for time-resolved experiments in the microsecond range for samples with relatively low metal concentration (∼1mM). This setup has been applied to study a multicomponent photocatalytic system with a Co(dmgBF(2))(2) catalyst (dmg(2-) = dimethylglyoximato dianion), [Ru(bpy)(3)](2+) chromophore (bpy = 2,2'-bipyridine) and methyl viologen as the electron relay. On the basis of the analysis of hundreds of Co K-edge XAS spectra corresponding to different delay times after the laser excitation of the chromophore, the presence of a Co(i) intermediate is confirmed. The calculated X-ray transient signal for a model of Co(i) state with a 0.14 Å displacement of Co out of the dmg ligand plane and with the closest solvent molecule at a distance of 2.06 Å gives reasonable agreement with the experimental data.

Inverted micellar intermediates and the transitions between lamellar, cubic, and inverted hexagonal lipid phases. II. Implications for membrane-membrane interactions and membrane fusion.

PubMed Central

Siegel, D P

1986-01-01

Results of a kinetic model of thermotropic L alpha----HII phase transitions are used to predict the types and order-of-magnitude rates of interactions between unilamellar vesicles that can occur by intermediates in the L alpha----HII phase transition. These interactions are: outer monolayer lipid exchange between vesicles; vesicle leakage subsequent to aggregation; and (only in systems with ratios of L alpha and HII phase structural dimensions in a certain range or with unusually large bilayer lateral compressibilities) vesicle fusion with retention of contents. It was previously proposed that inverted micellar structures mediate membrane fusion. These inverted micellar structures are thought to form in all systems with such transitions. However, I show that membrane fusion probably occurs via structures that form from these inverted micellar intermediates, and that fusion should occur in only a sub-set of lipid systems that can adopt the HII phase. For single-component phosphatidylethanolamine (PE) systems with thermotropic L alpha----HII transitions, lipid exchange should be observed starting at temperatures several degrees below TH and at all higher temperatures, where TH is the L alpha----HII transition temperature. At temperatures above TH, the HII phase forms between apposed vesicles, and eventually ruptures them (leakage). In most single-component PE systems, fusion via L alpha----HII transition intermediates should not occur. This is the behavior observed by Bentz, Ellens, Lai, Szoka, et al. in PE vesicle systems. Fusion is likely to occur under circumstances in which multilamellar samples of lipid form the so-called "inverted cubic" or "isotropic" phase. This is as observed in the mono-methyl DOPE system (Ellens, H., J. Bentz, and F. C. Szoka. 1986. Fusion of phosphatidylethanolamine containing liposomes and the mechanism of the L alpha-HII phase transition. Biochemistry. In press.) In lipid systems with L alpha----HII transitions driven by cation binding (e.g., Ca2+-cardiolipin), fusion should be more frequent than in thermotropic systems. PMID:3719075

Characterization of the intermediate-range order in new superionic conducting AgI-Ag2S-AgPO3 glasses by neutron diffraction

NASA Astrophysics Data System (ADS)

Kartini, E.; Kennedy, S. J.; Itoh, K.; Fukunaga, T.; Suminta, S.; Kamiyama, T.

Superionic conducting glasses are of considerable technological interest because of their use in batteries, sensors, and displays. We have investigated the new ternary systems AgI-Ag2S-AgPO3 where the ratio AgI:Ag2S is 1:1. The system (AgI)x(Ag2S)x(AgPO3)1-2x, for a AgI+Ag2S fraction less than 82mol%, yields glasses. We have used a neutron-diffraction technique to obtain the total scattering structure factor S(Q) of this system at room temperature by using the HIT spectrometer at the High Energy Accelerator (KEK), Tsukuba, Japan. As for AgI-AgPO3 glasses, S(Q) shows a peak at anomalously low Q in the range from 0.6 to 0.9 Å-1. This peak is not observed in the corresponding glass Ag2S-AgPO3 or pure AgPO3. The peak depends strongly on the dopant salt. Its intensity increases as the amount of (AgI+Ag2S) increases and its position shifts to lower Q, while the number density of the glasses decreases with x. This peak can be associated with an intermediate structure of particles lying inside a continuous host with the characteristic length between 5 and 10 Å [1].

Cleave and couple: toward fully sustainable catalytic conversion of lignocellulose to value added building blocks and fuels.

PubMed

Sun, Zhuohua; Barta, Katalin

2018-06-21

The structural complexity of lignocellulose offers unique opportunities for the development of entirely new, energy efficient and waste-free pathways in order to obtain valuable bio-based building blocks. Such sustainable catalytic methods - specifically tailored to address the efficient conversion of abundant renewable starting materials - are necessary to successfully compete, in the future, with fossil-based multi-step processes. In this contribution we give a summary of recent developments in this field and describe our "cleave and couple" strategy, where "cleave" refers to the catalytic deconstruction of lignocellulose to aromatic and aliphatic alcohol intermediates, and "couple" involves the development of novel, sustainable transformations for the formation of C-C and C-N bonds in order to obtain a range of attractive products from lignocellulose.

A medium range order structural connection to the configurational heat capacity of borate-silicate mixed glasses.

PubMed

Liu, Hao; Smedskjaer, Morten M; Tao, Haizheng; Jensen, Lars R; Zhao, Xiujian; Yue, Yuanzheng

2016-04-28

It has been reported that the configurational heat capacity (C(p,conf)) first increases and then becomes saturated with increasing B2O3/SiO2 ratio in borate-silicate mixed glasses. Through Raman spectroscopy measurements, we have, in this work, found an implication for the intermediate range order (IRO) structural connection to the composition dependence of the C(p,conf) of borate-silicate mixed glasses. In the silica-rich compositions, the C(p,conf) rapidly increases with increasing B2O3 content. This is attributed to the increase of the content of the B-O-Si network units ([B2Si2O8](2-)) and 6-membered borate rings with 1 or 2 B(4). In the boron-rich compositions, the C(p,conf) is almost constant, independent of the increase in the B2O3/SiO2 ratio. This is likely attributed to the counteraction between the decrease of the fraction of two types of metaborate groups and the increase of the fraction of other borate superstructural units (particularly 6-membered borate rings). The overall results suggest that the glasses containing more types of superstructural units have a larger C(p,conf).

Suppression of the Hall number due to charge density wave order in high-Tc cuprates

NASA Astrophysics Data System (ADS)

Sharma, Girish; Nandy, S.; Taraphder, A.; Tewari, Sumanta

2018-05-01

Understanding the pseudogap phase in hole-doped high-temperature cuprate superconductors remains a central challenge in condensed-matter physics. From a host of recent experiments there is now compelling evidence of translational-symmetry-breaking charge density wave (CDW) order in a wide range of doping inside this phase. Two distinct types of incommensurate charge order, bidirectional at zero or low magnetic fields and unidirectional at high magnetic fields close to the upper critical field Hc 2, have been reported so far in approximately the same doping range between p ≃0.08 and p ≃0.16 . In concurrent developments, recent high-field Hall experiments have also revealed two indirect but striking signatures of Fermi surface reconstruction in the pseudogap phase, namely, a sign change of the Hall coefficient to negative values at low temperatures in the intermediate range of hole doping and a rapid suppression of the positive Hall number without a change in sign near optimal doping p ˜0.19 . We show that the assumption of a unidirectional incommensurate CDW (with or without a coexisting weak bidirectional order) at high magnetic fields near optimal doping and the coexistence of both types of orders of approximately equal magnitude at high magnetic fields in the intermediate range of doping may help explain the striking behavior of the low-temperature Hall effect in the entire pseudogap phase.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

Giant phonon anomaly associated with superconducting fluctuations in the pseudogap phase of cuprates

DOE PAGES

Liu, Ye-Hua; Konik, Robert M.; Rice, T. M.; ...

2016-01-20

The pseudogap in underdoped cuprates leads to significant changes in the electronic structure, and was later found to be accompanied by anomalous fluctuations of superconductivity and certain lattice phonons. Here we propose that the Fermi surface breakup due to the pseudogap, leads to a breakup of the pairing order into two weakly coupled sub-band amplitudes, and a concomitant low energy Leggett mode due to phase fluctuations between them. This increases the temperature range of superconducting fluctuations containing an overdamped Leggett mode. In this range inter-sub-band phonons show strong damping due to resonant scattering into an intermediate state with a pairmore » of overdamped Leggett modes. In the ordered state, the Leggett mode develops a finite energy, changing the anomalous phonon damping into an anomaly in the dispersion. Finally, this proposal explains the intrinsic connection between the anomalous pseudogap phase, enhanced superconducting fluctuations and giant anomalies in the phonon spectra.« less

Pressure-induced structural modifications of rare-earth hafnate pyrochlore

NASA Astrophysics Data System (ADS)

Turner, Katlyn M.; Rittman, Dylan R.; Heymach, Rachel A.; Tracy, Cameron L.; Turner, Madison L.; Fuentes, Antonio F.; Mao, Wendy L.; Ewing, Rodney C.

2017-06-01

Complex oxides with the pyrochlore (A2B2O7) and defect-fluorite ((A,B)4O7) structure-types undergo structural transformations under high-pressure. Rare-earth hafnates (A2Hf2O7) form the pyrochlore structure for A  =  La-Tb and the defect-fluorite structure for A  =  Dy-Lu. High-pressure transformations in A2Hf2O7 pyrochlore (A  =  Sm, Eu, Gd) and defect-fluorite (A  =  Dy, Y, Yb) were investigated up to ~50 GPa and characterized by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Raman spectra at ambient pressure revealed that all compositions, including the defect-fluorites, have some pyrochlore-type short-range order. In situ high-pressure synchrotron XRD showed that all of the rare earth hafnates investigated undergo a pressure-induced phase transition to a cotunnite-like (orthorhombic) structure that begins between 18 and 25 GPa. The phase transition to the cotunnite-like structure is not complete at 50 GPa, and upon release of pressure, the hafnates transform to defect-fluorite with an amorphous component. For all compositions, in situ Raman spectroscopy showed that disordering occurs gradually with increasing pressure. Pyrochlore-structured hafnates retain their short-range order to a higher pressure (30 GPa vs.  <10 GPa) than defect-fluorite-structured hafnates. Rare earth hafnates quenched from 50 GPa show Raman spectra consistent with weberite-type structures, as also reported for irradiated rare-earth stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of ~250 GPa for hafnates with the pyrochlore structure, and ~400 GPa for hafnates with the defect-fluorite structure. Dy2Hf2O7 is intermediate in its response, with some pyrochlore-type ordering, based on Raman spectroscopy and the equation of state, with a bulk modulus of ~300 GPa. As predicted based on the similar ionic radius of Zr4+ and Hf4+, rare-earth hafnates show similar behavior to that reported for rare earth zirconates at high pressure.

Pressure-induced structural modifications of rare-earth hafnate pyrochlore.

PubMed

Turner, Katlyn M; Rittman, Dylan R; Heymach, Rachel A; Tracy, Cameron L; Turner, Madison L; Fuentes, Antonio F; Mao, Wendy L; Ewing, Rodney C

2017-06-28

Complex oxides with the pyrochlore (A 2 B 2 O 7 ) and defect-fluorite ((A,B) 4 O 7 ) structure-types undergo structural transformations under high-pressure. Rare-earth hafnates (A 2 Hf 2 O 7 ) form the pyrochlore structure for A  =  La-Tb and the defect-fluorite structure for A  =  Dy-Lu. High-pressure transformations in A 2 Hf 2 O 7 pyrochlore (A  =  Sm, Eu, Gd) and defect-fluorite (A  =  Dy, Y, Yb) were investigated up to ~50 GPa and characterized by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Raman spectra at ambient pressure revealed that all compositions, including the defect-fluorites, have some pyrochlore-type short-range order. In situ high-pressure synchrotron XRD showed that all of the rare earth hafnates investigated undergo a pressure-induced phase transition to a cotunnite-like (orthorhombic) structure that begins between 18 and 25 GPa. The phase transition to the cotunnite-like structure is not complete at 50 GPa, and upon release of pressure, the hafnates transform to defect-fluorite with an amorphous component. For all compositions, in situ Raman spectroscopy showed that disordering occurs gradually with increasing pressure. Pyrochlore-structured hafnates retain their short-range order to a higher pressure (30 GPa vs.  <10 GPa) than defect-fluorite-structured hafnates. Rare earth hafnates quenched from 50 GPa show Raman spectra consistent with weberite-type structures, as also reported for irradiated rare-earth stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of ~250 GPa for hafnates with the pyrochlore structure, and ~400 GPa for hafnates with the defect-fluorite structure. Dy 2 Hf 2 O 7 is intermediate in its response, with some pyrochlore-type ordering, based on Raman spectroscopy and the equation of state, with a bulk modulus of ~300 GPa. As predicted based on the similar ionic radius of Zr 4+ and Hf 4+ , rare-earth hafnates show similar behavior to that reported for rare earth zirconates at high pressure.

Determination of the Effects of Magnesium on the Structural Order of Amorphous Calcium Phosphate

NASA Astrophysics Data System (ADS)

Hoeher, A.; Michel, F. M.; Rakovan, J. F.; Borkiewicz, O.; Klysubun, W.

2016-12-01

Determining the pathways and mechanisms of calcium phosphate formation is important for understanding bone mineralization and advancing potential biological applications such as coatings on internal prosthetics. Studies show that amorphous calcium phosphate (ACP) is a precursor phase in the low temperature crystallization of hydroxylapatite, the primary mineral component found in bone and teeth of most modern vertebrates. ACP has been shown to have a structural order out to about 1 nm. Our recent extended x-ray absorption fine structure (EXAFS) spectroscopy analysis of synthetic ACP showed that the local structure of calcium in ACP differed from that in hydroxylapatite. Phosphorus EXAFS, however, indicated that the local structure in ACP is similar to hydroxylapatite (i.e., tetrahedrally coordinated with oxygen). EXAFS results were limited to only the first and second nearest neighbors in these samples, so the intermediate range order in ACP is yet unexplored. Furthermore, it remains unclear how ACP structure varies as a function of initial solution chemistry, how common impurities such as Mg are incorporated, and what role they play in determining the structural and physical characteristics of the final crystalline solid. We are using synchrotron x-ray total scattering for pair distribution function (PDF) analysis to investigate the influence of initial solution chemistry and Mg content on the structure of ACP. Magnesium is commonly used to stabilize the amorphous nature of the material, preventing crystallization. Ex situ samples synthesized at pH 10, with Ca:Mg ratios of 2:1, and freeze-dried are structurally similar to hydroxylapatite. Samples synthesized in identical conditions without Mg are structurally similar to another calcium phosphate mineral, brushite. In situ PDF measurements done at similar conditions in a custom mixed-flow reactor reveal that the short range order of ACP after 10 minutes of reacting is structurally different from ACP formed ex situ in the laboratory. Future analysis is aimed at quantifying the influence of these differences and to determine the validity of competing structural models proposed for ACP. This information is essential to further develop our understanding of the ACP transformation process into hydroxylapatite.

Characterization of a transient +2 sulfur oxidation state intermediate from the oxidation of aqueous sulfide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vairavmurthy, M.A.; Zhou, Weiqing

1995-04-01

The oxidation H{sub 2}S to sulfate involves a net transfer of eight electrons and occurs through the formation of several partially oxidized intermediates with oxidation states ranging from {minus}1 to +5. Known intermediates include elemental sulfur (oxidation state 0), polysulfides (outer sulfur: {minus}1, inner sulfur: 0), sulfite (+4) and thiosulfate (outer sulfur: {minus}1, inner sulfur: +5). A noticeable gap in this series of intermediates is that of a +2 sulfur oxidation state oxoacid/oxoanion species, which was never detected experimentally. Here, we present evidence of the transient existence of +2 oxidation state intermediate in the Ni(II)-catalyzed oxidation of aqueous sulfide. X-raymore » absorption near-edge structure (XANES) spectroscopy and Fourier-transform-infrared (FT-IR) spectroscopy were used to characterize this species; they suggest that it has a sulfoxylate ion (SO{sub 2}{sup 2{minus}}) structure.« less

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

PubMed

Junker; Reif; Steinhagen; Junker; Felli; Reggelin; Griesinger

2000-09-01

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.

Structure of naturally hydrated ferrihydrite revealed through neutron diffraction and first-principles modeling

NASA Astrophysics Data System (ADS)

Chappell, Helen F.; Thom, William; Bowron, Daniel T.; Faria, Nuno; Hasnip, Philip J.; Powell, Jonathan J.

2017-08-01

Ferrihydrite, with a ``two-line'' x-ray diffraction pattern (2L-Fh), is the most amorphous of the iron oxides and is ubiquitous in both terrestrial and aquatic environments. It also plays a central role in the regulation and metabolism of iron in bacteria, algae, higher plants, and animals, including humans. In this study, we present a single-phase model for ferrihydrite that unifies existing analytical data while adhering to fundamental chemical principles. The primary particle is small (20-50 Å) and has a dynamic and variably hydrated surface, which negates long-range order; collectively, these features have hampered complete characterization and frustrated our understanding of the mineral's reactivity and chemical/biochemical function. Near and intermediate range neutron diffraction (NIMROD) and first-principles density functional theory (DFT) were employed in this study to generate and interpret high-resolution data of naturally hydrated, synthetic 2L-Fh at standard temperature. The structural optimization overcomes transgressions of coordination chemistry inherent within previously proposed structures, to produce a robust and unambiguous single-phase model.

Atomic and electronic structures of an extremely fragile liquid.

PubMed

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-18

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Atomic and electronic structures of an extremely fragile liquid

PubMed Central

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Mass production of shaped particles through vortex ring freezing

PubMed Central

An, Duo; Warning, Alex; Yancey, Kenneth G.; Chang, Chun-Ti; Kern, Vanessa R.; Datta, Ashim K.; Steen, Paul H.; Luo, Dan; Ma, Minglin

2016-01-01

A vortex ring is a torus-shaped fluidic vortex. During its formation, the fluid experiences a rich variety of intriguing geometrical intermediates from spherical to toroidal. Here we show that these constantly changing intermediates can be ‘frozen' at controlled time points into particles with various unusual and unprecedented shapes. These novel vortex ring-derived particles, are mass-produced by employing a simple and inexpensive electrospraying technique, with their sizes well controlled from hundreds of microns to millimetres. Guided further by theoretical analyses and a laminar multiphase fluid flow simulation, we show that this freezing approach is applicable to a broad range of materials from organic polysaccharides to inorganic nanoparticles. We demonstrate the unique advantages of these vortex ring-derived particles in several applications including cell encapsulation, three-dimensional cell culture, and cell-free protein production. Moreover, compartmentalization and ordered-structures composed of these novel particles are all achieved, creating opportunities to engineer more sophisticated hierarchical materials. PMID:27488831

Molecular Dynamics Analysis of Lysozyme Protein in Ethanol-Water Mixed Solvent Environment

NASA Astrophysics Data System (ADS)

Ochije, Henry Ikechukwu

Effect of protein-solvent interaction on the protein structure is widely studied using both experimental and computational techniques. Despite such extensive studies molecular level understanding of proteins and some simple solvents is still not fully understood. This work focuses on detailed molecular dynamics simulations to study of solvent effect on lysozyme protein, using water, alcohol and different concentrations of water-alcohol mixtures as solvents. The lysozyme protein structure in water, alcohol and alcohol-water mixture (0-12% alcohol) was studied using GROMACS molecular dynamics simulation code. Compared to water environment, the lysozome structure showed remarkable changes in solvents with increasing alcohol concentration. In particular, significant changes were observed in the protein secondary structure involving alpha helices. The influence of alcohol on the lysozyme protein was investigated by studying thermodynamic and structural properties. With increasing ethanol concentration we observed a systematic increase in total energy, enthalpy, root mean square deviation (RMSD), and radius of gyration. a polynomial interpolation approach. Using the resulting polynomial equation, we could determine above quantities for any intermediate alcohol percentage. In order to validate this approach, we selected an intermediate ethanol percentage and carried out full MD simulation. The results from MD simulation were in reasonably good agreement with that obtained using polynomial approach. Hence, the polynomial approach based method proposed here eliminates the need for computationally intensive full MD analysis for the concentrations within the range (0-12%) studied in this work.

An epistemology on the nature of polymers.

PubMed

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity.

An Epistemology on the Nature of Polymers

PubMed Central

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity. PMID:25329440

X-ray absorption spectroscopy with time-tagged photon counting: Application to study the structure of Co(I) intermediate of H2 evolving photo-catalyst

PubMed Central

Smolentsev, Grigory; Guda, Alexander; Janousch, Markus; Frieh, Cristophe; Jud, Gaudenz; Zamponi, Flavio; Chavarot-Kerlidou, Murielle; Artero, Vincent; van Bokhoven, Jeroen A.; Nachtegaal, Maarten

2015-01-01

In order to probe the structure of reaction intermediates of photochemical reactions a new setup for laser-initiated time-resolved X-ray absorption (XAS) measurements has been developed. With this approach the arrival time of each photon in respect to the laser pulse is measured and therefore full kinetic information is obtained. All X-rays that reach the detector are used to measure this kinetic information and therefore the detection efficiency of this method is high. The newly developed setup is optimized for time-resolved experiments in the microsecond range for samples with relatively low metal concentration (~1mM). This setup has been applied to study a multicomponent photocatalytic system with a Co(dmgBF2)2 catalyst (dmg2− = dimethylglyoximato dianion), [Ru(bpy)3]2+ chromophore (bpy=2,2′-bipyridine) and methyl viologen as the electron relay. On the basis of analysis of hundreds of Co K-edge XAS spectra corresponding to different delay times after the laser excitation of the chromophore, the presence of a Co(I) intermediate is confirmed. The calculated X-ray transient signal for a model of Co(I) state with a 0.14 Å displacement of Co out of the dmg ligand plane and with the closest solvent molecule at a distance of 2.06 Å gives reasonable agreement with the experimental data. PMID:25415460

Cooperative magnetic behaviour in the new valence fluctuating compound Ce2Rh3Ge

NASA Astrophysics Data System (ADS)

Falkowski, M.; Strydom, A. M.

2015-10-01

In this study we report the physical properties of the new ternary compound Ce2Rh3Ge that crystallizes in the rhombohedral, triple hexagonal MgCu2-type of structure. The electronic ground state properties of Ce2Rh3Ge were characterized by magnetic susceptibility, specific heat, electrical resistivity and thermal transport measurements. The results indicate the presence of short range magnetic interaction, probably of ferromagnetic origin below T C  =  4 K. The shape of χ -1(T) deviates from the Curie-Weiss behavior with a broad minimum at about T\\min{{χ-1}}   =  450 K reminiscent of valence fluctuating cerium systems. At T  =  10 K, the magnetic part of the resistivity ρ 4 f (T) exhibits a shallow minimum followed by increase of resistivity ρ(T) \\propto   -lnT, which hints at a substantial Kondo screening effect. Ce2Rh3Ge belongs to a small group of strongly correlated cerium compounds in which the two competing effects of Kondo and RKKY interactions produce long-range magnetic order from strongly hybridized and intermediate-valent 4 f spins. At sufficiently low temperatures Ce2Rh3Ge scales well with the Kadowaki-Woods ratio A/γ 2 and the value of the Wilson ratio χ(T  →  0)/γ found for this compound classifies it as a mixed-valence compound. The presence of valence fluctuation and magnetic order it is rare for these attributes to be found simultaneously in same compound, in same temperature range. In our opinion a novelty of presented results of Ce2Rh3Ge is that this compound adds a new member to a small but growing class of systems bearing a strongly mixed- or intermediate-valent 4 f magnetic moment, but in which the lattice of spins nevertheless end up finding it possible to order magnetically.

Protein vivisection reveals elusive intermediates in folding

PubMed Central

Zheng, Zhongzhou; Sosnick, Tobin R.

2010-01-01

Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu→Glu−) to destabilize and unfold a specific region of the protein. We apply this strategy to Ubiquitin, reversibly trapping a folding intermediate in which the β5 strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high energy states. PMID:20144618

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aromí, G.; Beavers, C. M.; Sánchez Costa, J.

Crystal-to-crystal transformations have been crucial in the understanding of solid-state processes, since these may be studied in detail by means of single crystal X-ray diffraction (SCXRD) techniques. The description of the mechanisms and potential intermediates of those processes remains very challenging. In fact, solid-state transient states have rarely been observed, at least to a sufficient level of detail. We have investigated the process of guest extrusion from the non-porous molecular material [Fe(bpp)(H 2L)](ClO 4) 2·1.5C 3H 6O (bpp = 2,6-bis(pyrazol-3-yl)pyridine; H 2L = 2,6-bis(5-(2-methoxyphenyl)-pyrazol-3-yl)pyridine; C 3H 6O = acetone), which occurs through ordered diffusion of acetone in a crystal-to-crystal manner,more » leading to dramatic structural changes. The slow kinetics of the transition allows thermal trapping of the system at various intermediate stages. The transiting single crystal can be then examined at these points through synchrotron SCXRD, offering a window upon the mechanism of the transformation at the molecular scale. These experiments have unveiled the development of an ordered intermediate phase, distinct from the initial and the final states, coexisting as the process advances with either of these two phases or, at a certain moment with both of them. The new intermediate phase has been structurally characterized in full detail by SCXRD, providing insights into the mechanism of this diffusion triggered solid-state phenomenon. Lastly, the process has been also followed by calorimetry, optical microscopy, local Raman spectroscopy and powder X-ray diffraction. The discovery and description of an intermediate ordered state in a molecular solid-state transformation is of great interest and will help to understand the mechanistic details and reaction pathways underlying these transformations.« less

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP.

PubMed

Colletier, Jacques-Philippe; Sliwa, Michel; Gallat, François-Xavier; Sugahara, Michihiro; Guillon, Virginia; Schirò, Giorgio; Coquelle, Nicolas; Woodhouse, Joyce; Roux, Laure; Gotthard, Guillaume; Royant, Antoine; Uriarte, Lucas Martinez; Ruckebusch, Cyril; Joti, Yasumasa; Byrdin, Martin; Mizohata, Eiichi; Nango, Eriko; Tanaka, Tomoyuki; Tono, Kensuke; Yabashi, Makina; Adam, Virgile; Cammarata, Marco; Schlichting, Ilme; Bourgeois, Dominique; Weik, Martin

2016-03-03

Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

A Multiwavelength Study of POX 52, a Dwarf Seyfert Galaxy with an Intermediate Mass Black Hole

NASA Astrophysics Data System (ADS)

Barth, Aaron

2004-09-01

POX 52 is a Seyfert 1 galaxy with unprecedented properties: its host galaxy is a dwarf elliptical, and its stellar velocity dispersion is only 36 km/s. The stellar velocity dispersion and the broad emission-line widths both suggest a black hole mass of order 10^5 solar masses. We request HST ACS/HRC imaging to perform a definitive measurement of the host galaxy structure; STIS UV and optical spectroscopy to study the nonstellar continuum and the structure of the broad-line region; and Chandra ACIS imaging to investigate the spectral and variability properties of the X-ray emission. The results of this program will give a detailed understanding of the host galaxy and accretion properties of one of the very few known black holes in the mass range around 10^5 solar masses.

Solid-to-solid phase transformations of nanostructured selenium-tin thin films induced by thermal annealing in oxygen atmosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serra, A.; Rossi, M.; Buccolieri, A.

2014-06-19

The structural and morphological evolution of nanostructured thin films obtained from thermal evaporation of polycrystalline Sn-Se starting charge as a function of the subsequent annealing temperature in an oxygen flow has been analysed. High-resolution transmission electron microscopy, small area electron diffraction, digital image processing, x-ray diffraction and Raman spectroscopy have been employed in order to investigate the structure and the morphology of the obtained films. The results evidenced, in the temperature range from RT to 500°C, the transition of the material from a homogeneous mixture of SnSe and SnSe{sub 2} nanocrystals, towards a homogeneous mixture of SnO{sub 2} and SeO{submore » 2} nanocrystals, with an intermediate stage in which only SnSe{sub 2} nanocrystals are present.« less

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deus, R.C.; Cortés, J.A., E-mail: leandrosrr89@gmail.com; Ramirez, M.A.

Highlights: • CeO{sub 2} nanoparticles were obtained by microwave-hydrothermal method. • Rietveld refinement reveals a cubic structure. • KOH mineralizer agent exhibit weak agglomeration at low temperature and shorter time. - Abstract: The structural and photoluminescent properties at room temperature of CeO{sub 2} and La-doped CeO{sub 2} particles were undertaken. The obtained particles were synthesized by a microwave-assisted hydrothermal method (MAH) under different lanthanum contents. X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Fourier transform Raman (FT-Raman), Ultra-violet spectroscopy (UV–vis) and photoluminescence (PL) measurements were carried out. XRD revealed that the powders are free of secondary phases and crystallize in themore » cubic structure. Raman data show that increasing La doping content increase oxygen vacancies due to lattice expansion. The UV/vis absorption spectroscopy suggested the presence of intermediate energy levels in the band gap of structurally ordered powders. Lanthanum addition creates oxygen vacancies and shifts the photoluminescence in the low energy range leading to intense PL emission.« less

The use of HVSR measurements for investigating buried tectonic structures: the Mirandola anticline, Northern Italy, as a case study

NASA Astrophysics Data System (ADS)

Tarabusi, G.; Caputo, R.

2017-01-01

The Mirandola anticline represents a buried fault-propagation fold which has been growing during Quaternary due to the seismogenic activity of a blind segment belonging to the broader Ferrara Arc. The last reactivation occurred during the May 2012 Emilia sequence. In correspondence with this structure, the thickness of the marine and continental deposits of the Po Plain foredeep is particularly reduced. In order to better define the shallow geometry of this tectonic structure, and hence its recent activity, we investigated in a depth range which is intermediate between the surficial morphological observations and seismic profiles information. In particular, we carried out numerous passive seismic measurements (single-station microtremor) for obtaining the horizontal-to-vertical spectral ratio. The results of a combined analysis of the peak frequency and its amplitude nicely fit the available geological information, suggesting that this low-cost geophysical technique could be successfully applied in other sectors of wide morphologically flat alluvial plains to investigate blind and completely buried potential seismogenic structures.

Intermediates and the folding of proteins L and G

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Scott; Head-Gordon, Teresa

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contactsmore » involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.« less

Intermediates and the folding of proteins L and G

PubMed Central

Brown, Scott; Head-Gordon, Teresa

2004-01-01

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted β-1 and β-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third β-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment. PMID:15044729

Microscopic coexistence of magnetism and superconductivity in charge-compensated Ba1-xKx(Fe1-yCoy)2As2

NASA Astrophysics Data System (ADS)

Goltz, Til; Zinth, Veronika; Johrendt, Dirk; Rosner, Helge; Pascua, Gwendolyne; Luetkens, Hubertus; Materne, Philipp; Klauss, Hans-Henning

2014-04-01

We present a detailed investigation of the electronic phase diagram of effectively charge compensated Ba1-xKx(Fe1-yCoy)2As2 with x /2≈y. Our experimental study by means of x-ray diffraction, Mössbauer spectroscopy, muon spin relaxation and ac-susceptibility measurements on polycrystalline samples is complemented by density functional electronic structure calculations. For low substitution levels of x /2≈y≤0.13, the system displays an orthorhombically distorted and antiferromagnetically ordered ground state. The low-temperature structural and magnetic order parameters are successively reduced with increasing substitution level. We observe a linear relationship between the structural and the magnetic order parameter as a function of temperature and substitution level for x /2≈y≤0.13. At intermediate substitution levels in the range between 0.13 and 0.19, we find superconductivity with a maximum Tc of 15 K coexisting with static magnetic order on a microscopic length scale. For higher substitution levels x /2≈y≥0.25, a tetragonal nonmagnetic ground state is observed. Our DFT calculations yield a significant reduction of the Fe 3d density of states at the Fermi energy and a strong suppression of the ordered magnetic moment in excellent agreement with experimental results. The appearance of superconductivity within the antiferromagnetic state can by explained by the introduction of disorder due to nonmagnetic impurities to a system with a constant charge carrier density.

Determination of intermediate perturbed orbits of Near-Earth asteroids from range and range rate measurements at three times

NASA Astrophysics Data System (ADS)

Shefer, V. A.

2014-12-01

Two methods that the author developed earlier for finding the intermediate perturbed orbit of a small celestial body from three pairs of range and range rate observations [1, 2] are applied to the determination of orbits of Near-Earth asteroids. The methods are based on using the superosculating orbits with three- and fourth-order tangency. The degrees of approximation of the real motion by the constructed intermediate orbits near the middle measurement time are two and three orders of magnitude higher than by the Keplerian orbit determined with the help of traditional methods. We calculated the orbits of the asteroids 99942 Apophis, 1566 Icarus, 4179 Toutatis, 2007 DN41 and 2012 DA14. For the sake of brevity, we call the method based on the orbit with third-order tangency as Algorithm A1 and the method based on the orbit with fourth-order tangency -- as Algorithm A2. The results of the calculations are compared with the results of the calculations by the version of the methods mentioned that allows us to construct the unperturbed Keplerian orbit. We call this version of the methods as Algorithm A. The observational data were simulated using the nominal trajectories of the selected asteroids. These trajectories were obtained by the numerical integration of the differential equations of motion subject to the perturbations from the eight major planets, Pluto, and the Moon. The integration was carried out with the help of the 15-order Everhart procedure [3]. The main results of the calculations are the following. When the reference time interval is shortened by half (for small sizes of this interval), the errors in the compared algorithms A, A1, A2 decrease approximately by the factors 4, 16, 64 in coordinates and by the factors 2, 8, 16 in velocities, respectively. Such behavior of the errors is most clearly seen with the asteroids 2007 DN41 and 2012 DA14. This leads to a significant increase in the accuracy of the real motion approximation by the intermediate orbits constructed using the A1 and A2 algorithms (2-4 orders of magnitude in coordinates and 4-7 orders of magnitude in velocities higher) compared to the accuracy of the approximation by Keplerian orbits with decreasing the reference arc of the trajectory. Here, the higher is the efficiency of the algorithms A1 and A2, the smaller are the values of the topocentric distances, i.e., the greater are the perturbations caused by the Earth's gravitation. The advantage of Algorithm A2 over Algorithm A1 in accuracy extends approximately one order of magnitude. The minimal methodic errors of the position vector by using the A1 and A2 algorithms range from several meters in the case of the asteroid Apophis to several millimeters in the case of the asteroid 2012 DA14. Hence, the numerical examples analyzed in this work lead us to conclude that the proposed in [1, 2] methods for determination of an intermediate perturbed orbit from range and range rate measurements at three time points allow for significantly raising the accuracy of the calculation of the initial asteroid orbits in comparison with the algorithm based on the finding the unperturbed Keplerian orbit. The shorter is the orbital arc specified by the extreme time points, the greater is the advantage of the algorithms suggested over the algorithms of the traditional approach in the accuracy. The advantage of the algorithms suggested in the accuracy increases with raising the perturbations too, which is especially important for calculation of the initial trajectories of the space objects detected in the Earth's neighbourhood. The work was supported by the Ministry of Education and Science of the Russian Federation, project no. 2014/223(1567).

Structural properties of medium-range order in CuNiZr alloy

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Hu, Xuechen; Xie, Quan; Li, Yidan; Ren, Lei

2017-10-01

The evolution characteristics of icosahedral clusters during the rapid solidification of Cu50Ni10Zr40 alloy at cooling rate of 1011 K s-1 are investigated based on molecular dynamics simulations. The structural properties of the short-range order and medium-range order of Cu50Ni10Zr40 alloy are analyzed by several structural characterization methods. The results reveal that the icosahedral clusters are the dominant short-range order structure, and that they assemble themselves into medium-range order by interpenetrating connections. The different morphologies of medium-range order are found in the system and include chain, triangle, tetrahedral, and their combination structures. The tetrahedral morphologies of medium-range order have excellent structural stability with decreasing temperature. The Zr atoms are favorable to form longer chains, while the Cu atoms are favorable to form shorter chains in the system. Those chains interlocked with each other to improve the structural stability.

Multiple competing interactions and reentrant ferrimagnetism in Tb 0.8Nd 0.2Mn 6Ge 6

NASA Astrophysics Data System (ADS)

Schobinger-Papamantellos, P.; André, G.; Rodríguez-Carvajal, J.; Duong, N. P.; Buschow, K. H. J.

2001-06-01

The magnetic ordering of the hexagonal compound Tb 0.8Nd 0.2Mn 6Ge 6 has been studied by neutron diffraction and magnetic measurements in the temperature range 1.5-800 K. This compound was found to undergo consecutive magnetic transitions with temperature. The magnetic phase diagram comprises four distinct regions and requires the wave vectors: q1=(0, 0, qz) and q2=0 for its description. The low temperature range (LT): 1.5 K< T< T1=85 K, is characterised by a triple ferrimagnetic conical (spiral) structure with qz=0.128 r.l.u and a net moment along the c direction ( q2=0). The intermediate temperature range displays two transitions: At T1=85 K the conical structure transforms to a simple triple (flat) spiral persisting in range (ITa) 85 K< T< T2≈340 K, with a small thermal variation of the wave vector. Above T2 in range (ITb) T2< T< TS≈390 K the destabilised spiral transforms to a FAN-like structure with a fast decrease of the wave vector length towards zero while a ferrimagnetic planar structure ( q2=0) develops at the cost of the spiral. The planar ferrimagnetic magnetic structure ( q2=0) dominates the high temperature range (HT) 390 K< T< Tc=450 K. The onset of re-entrant ferrimagnetism reflects the interplay of multiple competing inter- and intra- sublattice interactions of the three types of magnetic ions with different crystal field anisotropies. The Nd and Tb sublattices are coupled antiferromagnetically while the Tb-Mn and Nd-Mn interactions are negative and positive, respectively.

A new method of intermediate orbit determination based on range and range rate measurements at three times. (Russian Title: Новый метод определения промежуточной орбиты по измерениям дальности и скорости ее изменения в три момента времени)

NASA Astrophysics Data System (ADS)

Shefer, V. A.

2013-12-01

A new method is proposed for computing the preliminary orbit of a small celestial body from three pairs of range and range rate observations. The method is based on using the superosculating intermediate orbit with a fourth-order tangency that we previously constructed. This intermediate orbit allows for most of the perturbations in the motion of the body under study. The methodical error of orbit determination by the proposed method is three orders smaller than the corresponding error of the commonly used approach based on the construction of the unperturbed Keplerian orbit. Using the examples of finding the orbits of artificial Earth satellites, the results obtained by the procedure implementing the traditional approach and the new method are compared. The comparison shows that the new method is a highly efficient means for studying perturbed motion.

Preparation of ordered mesoporous and macroporous thermoplastic polyurethane surfaces for potential medical applications.

PubMed

Chennell, Philip; Feschet-Chassot, Emmanuelle; Sautou, Valérie; Mailhot-Jensen, Bénédicte

2018-05-01

Thermoplastic polyurethanes are widely used in medical devices. In order to limit some of their shortfalls, like microbial attachment, surfaces modifications can be required. In this work, a two-step replication method was used to create ordered macroporous and mesoporous thermoplastic polyurethane surfaces using anodic aluminum oxide as master template. The intermediate mould materials that were tested were polystyrene and a polyacrylate resin with inorganic filler. All obtained surfaces were characterized by scanning electron microscopy. The initial anodic aluminum oxide surfaces possessed macro or mesopores, function of anodization conditions. The intermediate mould structure correctly replicated the pattern, but the polystyrene surface structures (pillars) were less resistant than the polyacrylate resin ones. The thermoplastic polyurethane pattern possessed macropores or mesopores of about 130 nm or 46 nm diameter and of about 300 nm or 99 nm interpore distances, respectively, in accordance with the initial pattern. Thermoplastic polyurethanes pore depth was however less than initial anodic aluminum oxide pore depth, linked to an incomplete replication during intermediate mould preparation (60 to 90% depth replication). The correct replication of the original pattern confirms that this novel fabrication method is a promising route for surface patterning of thermoplastic polyurethanes that could be used for medical applications.

Large structural modulations in the relaxor ferroelectric and intermediate state of strontium rich members (x>0.6) of the Sr{sub x}Ba{sub 1−x}Nb{sub 2}O{sub 6} (sbn) solid solution series

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graetsch, H.A., E-mail: heribert.graetsch@rub.de

The amplitudes of the positional, occupational and adp modulations of sbn mixed crystals are strongly enhanced for high strontium contents. The increase of structural modulations is accompanied by reduced spontaneous electric polarization largely due to smaller off-center shifts of the niobium atoms. Beyond the room temperature ferroelectric – intermediate transition near x=0.77, anomal large U{sub 33} atomic displacement parameters of the niobium atoms indicate static disorder caused by loss of orientational coupling between residual shifts of Nb atoms in neighboring NbO{sub 6} octahedra. Change of satellite intensities show a reduction from two-dimensional to one-dimensional modulation which is not consistent withmore » tetragonal symmetry. The pseudo-tetragonally twinned crystal structure of sbn82 was refined in the orthorhombic super-space group A2mm(½0γ)000. The apparent tetragonal symmetry of the other investigated sbn samples also seems to be due to pseudo tetragonal twinning with equal twin volumes. The modulations mainly consist of cooperatively tilted NbO{sub 6} octahedra and wave-like ordered incomplete occupation of the largest cation sites (Me2a and b) by Ba{sup 2+} and Sr{sup 2+}. Furthermore, the atomic displacement parameters of the Me2 sites are strongly modulated. - Graphical abstract: Satellite reflections and modulation coefficients in the solid solution series Sr{sub x}Ba{sub 1−x}Nb{sub 2}O{sub 6}. - Highlights: • The modulationed structures are refined for the whole composition range of sbn32–sbn82 in tetragonal and orthorhombic setting. • The amplitudes of positional, occupational and adp modulations increase strongly with the strontium content. • Evidence is presented that the sbn crystals are pseudo tetragonally twinned. • The ferroelectric–intermediate paraelectric transition is not accompanied by a change of symmetry. • Anomal adp of intermediate (non-ferroelectric) sbn82 indicate loss of coupling between off-center shifts of neighboring niobium.« less

Theory of intermediate- and high-field mobility in dilute nitride alloys

NASA Astrophysics Data System (ADS)

Seifikar, Masoud; O'Reilly, Eoin P.; Fahy, Stephen

2011-10-01

We have solved the steady-state Boltzmann transport equation in bulk GaAs1-xNx. Two different models of the conduction band structure have been studied to investigate the behavior of electrons with increasing electric field in these alloys: (1) carriers in parabolic Γ and L bands are scattered by resonant nitrogen substitutional defect states, polar optic and acoustic phonons, and intervalley optical phonons; (2) carriers, constrained in the lower band of the band-anticrossing (BAC) model, are scattered by phonons and by nitrogen states. We consider scattering both by isolated N atoms and also by a full distribution of N states. We find that it is necessary to include the full distribution of levels in order to account for the small low-field mobility and the absence of a negative differential velocity regime observed experimentally with increasing x. Model 2 breaks down at intermediate and high field, due to the unphysical constraint of limiting carriers to the lower BAC band. For model 1, carrier scattering into the L bands is reduced at intermediate electric fields but is comparable at high fields to that observed in GaAs, with the calculated high-field mobility and carrier distribution then also being comparable to GaAs. Overall the results account well for a wide range of experimental data.

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Short and Medium-Range Order in Liquid Ternary Al80Co10Ni10, Al72.5Co14.5Ni13, and Al65Co17.5Ni17.5 Alloys

NASA Astrophysics Data System (ADS)

Roik, Oleksandr S.; Samsonnikov, Oleksiy; Kazimirov, Volodymyr; Sokolskii, Volodymyr

2010-01-01

A local short-to-intermediate range order of liquid Al80Co10Ni10, Al72.5Co14.5Ni13, and Al65Co17.5Ni17.5 alloys was examined by X-ray diffraction and the reverse Monte Carlo modelling. The comprehensive analysis of three-dimensional models of the liquid ternary alloys was performed by means of the Voronoi-Delaunay method. The existence of a prepeak on the S(Q) function of the liquid alloys is caused by medium range ordering of 3d-transition metal atoms in dense-packed polytetrahedral clusters at temperatures close to the liquidus. The non-crystalline clusters, represented by aggregates of pentagons that consist of good tetrahedra, and chemical short-range order lead to the formation of the medium range order in the liquid binary Al-Ni, Al-Co and ternary Al-Ni-Co alloys.

Development of pair distribution function analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondreele, R.; Billinge, S.; Kwei, G.

1996-09-01

This is the final report of a 3-year LDRD project at LANL. It has become more and more evident that structural coherence in the CuO{sub 2} planes of high-{Tc} superconducting materials over some intermediate length scale (nm range) is important to superconductivity. In recent years, the pair distribution function (PDF) analysis of powder diffraction data has been developed for extracting structural information on these length scales. This project sought to expand and develop this technique, use it to analyze neutron powder diffraction data, and apply it to problems. In particular, interest is in the area of high-{Tc} superconductors, although wemore » planned to extend the study to the closely related perovskite ferroelectric materials andother materials where the local structure affects the properties where detailed knowledge of the local and intermediate range structure is important. In addition, we planned to carry out single crystal experiments to look for diffuse scattering. This information augments the information from the PDF.« less

Nonlinear dielectric properties of planar structures based on ferroelectric betaine phosphite films

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Svinarev, F. B.; Yurko, E. I.

2014-02-01

Ferroelectric films of partly deuterated betaine phosphite are grown on NdGaO3(001) substrates with an interdigitated system of electrodes on their surfaces by evaporation at room temperature. These films have a high capacitance in the ferroelectric phase transition range. The dielectric nonlinearity of the grown structures is studied in small-signal and strong-signal response modes and in the intermediate region between these two modes by measuring the capacitance in a dc bias field, dielectric hysteresis loops, and the Fourier spectra of an output signal in the Sawyer-Tower circuit. In the phase transition range, the capacitance control ratio at a bias voltage U bias = 40 V is K ≅ 7. The dielectric nonlinearity of the structures in the paraelectric phase is described by the Landau theory of second-order phase transitions. The additional contribution to the nonlinearity in the ferroelectric phase is related to the motion of domain walls and manifests itself when the input signal amplitude is higher than U st ˜ 0.7-1.0 V. The relaxation times of domain walls are determined from an analysis of the frequency dependences of the dielectric hysteresis.

Crystallization of DNA-coated colloids

PubMed Central

Wang, Yu; Wang, Yufeng; Zheng, Xiaolong; Ducrot, Étienne; Yodh, Jeremy S.; Weck, Marcus; Pine, David J.

2015-01-01

DNA-coated colloids hold great promise for self-assembly of programmed heterogeneous microstructures, provided they not only bind when cooled below their melting temperature, but also rearrange so that aggregated particles can anneal into the structure that minimizes the free energy. Unfortunately, DNA-coated colloids generally collide and stick forming kinetically arrested random aggregates when the thickness of the DNA coating is much smaller than the particles. Here we report DNA-coated colloids that can rearrange and anneal, thus enabling the growth of large colloidal crystals from a wide range of micrometre-sized DNA-coated colloids for the first time. The kinetics of aggregation, crystallization and defect formation are followed in real time. The crystallization rate exhibits the familiar maximum for intermediate temperature quenches observed in metallic alloys, but over a temperature range smaller by two orders of magnitude, owing to the highly temperature-sensitive diffusion between aggregated DNA-coated colloids. PMID:26078020

Counter-ions dynamics in highly plastic and conducting compounds of poly(aniline). A quasi-elastic neutron scattering study.

PubMed

Djurado, David; Bée, Marc; Sniechowski, Maciej; Howells, Spencer; Rannou, Patrice; Pron, Adam; Travers, J P; Luzny, Wojciech

2005-03-21

Proton dynamics in films of poly(aniline) "plastdoped" with di-esters of sulfophthalic (or sulfosuccinic) acids have been investigated by using quasi-elastic neutron scattering techniques. A broad time range (10(-13)-10(-9) s) has been explored by using four different spectrometers. In this time range, the dynamics is exclusively due to protons attached to the flexible tails of the counter-ions. A model of limited diffusion in spheres whose radii are distributed in size gives a realistic view of the geometry of molecular motions. However, it is found that the characteristic times of these motions are widely distributed over several orders of magnitude. The time decay of the intermediate scattering function is well described by a time power law. This behaviour is qualitatively discussed in connection with the structure of the systems and by comparison with other so-called complex systems.

Providing effective and preferred care closer to home: a realist review of intermediate care.

PubMed

Pearson, Mark; Hunt, Harriet; Cooper, Chris; Shepperd, Sasha; Pawson, Ray; Anderson, Rob

2015-11-01

Intermediate care is one of the number of service delivery models intended to integrate care and provide enhanced health and social care services closer to home, especially to reduce reliance on acute care hospital beds. In order for health and social care practitioners, service managers and commissioners to make informed decisions, it is vital to understand how to implement the admission avoidance and early supported discharge components of intermediate care within the context of local care systems. This paper reports the findings of a theory-driven (realist) review conducted in 2011-2012. A broad range of evidence contained in 193 sources was used to construct a conceptual framework for intermediate care. This framework forms the basis for exploring factors at service user, professional and organisational levels that should be considered when designing and delivering intermediate care services within a particular local context. Our synthesis found that involving service users and their carers in collaborative decision-making about the objectives of care and the place of care is central to achieving the aims of intermediate care. This pivotal involvement of the service user relies on practitioners, service managers and commissioners being aware of the impact that organisational structures at the local level can have on enabling or inhibiting collaborative decision-making and care co-ordination. Through all interactions with service users and their care networks, health and social care professionals should establish the meaning which alternative care environments have for different service users. Doing so means decisions about the best place of care will be better informed and gives service users choice. This in turn is likely to support psychological and social stability, and the attainment of functional goals. At an organisational level, integrated working can facilitate the delivery of intermediate care, but there is not a straightforward relationship between integrated organisational processes and integrated professional practice. © 2015 John Wiley & Sons Ltd.

4-spin plaquette singlet state in the Shastry-Sutherland compound SrCu2(BO3)2

NASA Astrophysics Data System (ADS)

Zayed, M. E.; Rüegg, Ch.; Larrea J., J.; Läuchli, A. M.; Panagopoulos, C.; Saxena, S. S.; Ellerby, M.; McMorrow, D. F.; Strässle, Th.; Klotz, S.; Hamel, G.; Sadykov, R. A.; Pomjakushin, V.; Boehm, M.; Jiménez-Ruiz, M.; Schneidewind, A.; Pomjakushina, E.; Stingaciu, M.; Conder, K.; Rønnow, H. M.

2017-10-01

The study of interacting spin systems is of fundamental importance for modern condensed-matter physics. On frustrated lattices, magnetic exchange interactions cannot be simultaneously satisfied, and often give rise to competing exotic ground states. The frustrated two-dimensional Shastry-Sutherland lattice realized by SrCu2(BO3)2 (refs ,) is an important test case for our understanding of quantum magnetism. It was constructed to have an exactly solvable 2-spin dimer singlet ground state within a certain range of exchange parameters and frustration. While the exact dimer state and the antiferromagnetic order at both ends of the phase diagram are well known, the ground state and spin correlations in the intermediate frustration range have been widely debated. We report here the first experimental identification of the conjectured plaquette singlet intermediate phase in SrCu2(BO3)2. It is observed by inelastic neutron scattering after pressure tuning to 21.5 kbar. This gapped singlet state leads to a transition to long-range antiferromagnetic order above 40 kbar, consistent with the existence of a deconfined quantum critical point.

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arai, Shigeki; Yonezawa, Yasushi; Ishibashi, Matsujiro

2014-03-01

In order to clarify the structural basis of the halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp. 593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. The structural properties of surface negative charge and core hydrophobicity were shown to be intermediate between those characteristic of halophiles and non-halophiles, and may explain the unique functional adaptation to a wide range of salt concentrations. Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). Inmore » order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (C{sup α} r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior comprising 329 C atoms from completely buried residues, whereas that of VAP comprised 264 C atoms, which may maintain the stability of HaAP under low-salt conditions. These characteristics of HaAP may be responsible for its unique functional adaptation permitting activity over a wide range of salt concentrations.« less

Epithelial structure revealed by chemical dissection and unembedded electron microscopy.

PubMed

Fey, E G; Capco, D G; Krochmalnic, G; Penman, S

1984-07-01

Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton was further fractionated by extraction with (NH4)2SO4, which left a structure enriched in intermediate filaments and desmosomes around the nuclei. A further digestion with nuclease and elution with (NH4)2SO4 removed the chromatin. The stable structure that remained after this procedure retained much of the epithelial morphology and contained essentially all of the cytokeratin filaments and desmosomes and the chromatin-depleted nuclear matrices. This structural network may serve as a scaffold for epithelial organization. The cytoskeleton and the underlying nuclear matrix intermediate filament scaffold, when examined in both conventional embedded thin sections and in unembedded whole mounts and thick sections, showed the retention of many of the detailed morphological aspects of the intact cells, which suggests a structural continuum linking the nuclear matrix, the intermediate filament network, and the intercellular desmosomal junctions. Most importantly, the protein composition of each of the four fractions obtained by this sequential procedure was essentially unique. Thus, the proteins constituting the soluble fraction, the cytoskeleton, the chromatin fraction, and the underlying nuclear matrix-intermediate filament scaffold are biochemically distinct.

Epithelial structure revealed by chemical dissection and unembedded electron microscopy

PubMed Central

Fey, E. G.; Capco, D. G.; Krochmalnic, G.; Penman, S.

1984-01-01

Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton was further fractionated by extraction with (NH4)2SO4, which left a structure enriched in intermediate filaments and desmosomes around the nuclei. A further digestion with nuclease and elution with (NH4)2SO4 removed the chromatin. The stable structure that remained after this procedure retained much of the epithelial morphology and contained essentially all of the cytokeratin filaments and desmosomes and the chromatin-depleted nuclear matrices. This structural network may serve as a scaffold for epithelial organization. The cytoskeleton and the underlying nuclear matrix intermediate filament scaffold, when examined in both conventional embedded thin sections and in unembedded whole mounts and thick sections, showed the retention of many of the detailed morphological aspects of the intact cells, which suggests a structural continuum linking the nuclear matrix, the intermediate filament network, and the intercellular desmosomal junctions. Most importantly, the protein composition of each of the four fractions obtained by this sequential procedure was essentially unique. Thus, the proteins constituting the soluble fraction, the cytoskeleton, the chromatin fraction, and the underlying nuclear matrix-intermediate filament scaffold are biochemically distinct. PMID:6540264

Examination of the Mechanism of Human Brain Aspartoacylase through the Binding of an Intermediate Analogue†‡

PubMed Central

Le Coq, Johanne; Pavlovsky, Alexander; Malik, Radhika; Sanishvili, Ruslan; Xu, Chengfu; Viola, Ronald E.

2009-01-01

Canavan disease is a fatal neurological disorder caused by the malfunctioning of a single metabolic enzyme, aspartoacylase, that catalyzes the deacetylation of N-acetyl-l-aspartate to produce l-aspartate and acetate. The structure of human brain aspartoacylase has been determined in complex with a stable tetrahedral intermediate analogue, N-phosphonomethyl-l-aspartate. This potent inhibitor forms multiple interactions between each of its heteroatoms and the substrate binding groups arrayed within the active site. The binding of the catalytic intermediate analogue induces the conformational ordering of several substrate binding groups, thereby setting up the active site for catalysis. The highly ordered binding of this inhibitor has allowed assignments to be made for substrate binding groups and provides strong support for a carboxypeptidase-type mechanism for the hydrolysis of the amide bond of the substrate, N-acetyl-l-aspartate. PMID:18293939

Examination of the mechanism of human brain aspartoacylase through the binding of an intermediate analogue.

PubMed

Le Coq, Johanne; Pavlovsky, Alexander; Malik, Radhika; Sanishvili, Ruslan; Xu, Chengfu; Viola, Ronald E

2008-03-18

Canavan disease is a fatal neurological disorder caused by the malfunctioning of a single metabolic enzyme, aspartoacylase, that catalyzes the deacetylation of N-acetyl-L-aspartate to produce L-aspartate and acetate. The structure of human brain aspartoacylase has been determined in complex with a stable tetrahedral intermediate analogue, N-phosphonomethyl-L-aspartate. This potent inhibitor forms multiple interactions between each of its heteroatoms and the substrate binding groups arrayed within the active site. The binding of the catalytic intermediate analogue induces the conformational ordering of several substrate binding groups, thereby setting up the active site for catalysis. The highly ordered binding of this inhibitor has allowed assignments to be made for substrate binding groups and provides strong support for a carboxypeptidase-type mechanism for the hydrolysis of the amide bond of the substrate, N-acetyl- l-aspartate.

Curcumin Modulates α-Synuclein Aggregation and Toxicity

PubMed Central

2012-01-01

In human beings, Parkinson’s disease (PD) is associated with the oligomerization and amyloid formation of α-synuclein (α-Syn). The polyphenolic Asian food ingredient curcumin has proven to be effective against a wide range of human diseases including cancers and neurological disorders. While curcumin has been shown to significantly reduce cell toxicity of α-Syn aggregates, its mechanism of action remains unexplored. Here, using a series of biophysical techniques, we demonstrate that curcumin reduces toxicity by binding to preformed oligomers and fibrils and altering their hydrophobic surface exposure. Further, our fluorescence and two-dimensional nuclear magnetic resonance (2D-NMR) data indicate that curcumin does not bind to monomeric α-Syn but binds specifically to oligomeric intermediates. The degree of curcumin binding correlates with the extent of α-Syn oligomerization, suggesting that the ordered structure of protein is required for effective curcumin binding. The acceleration of aggregation by curcumin may decrease the population of toxic oligomeric intermediates of α-Syn. Collectively; our results suggest that curcumin and related polyphenolic compounds can be pursued as candidate drug targets for treatment of PD and other neurological diseases. PMID:23509976

Design principles from multiscale simulations to predict nanostructure in self-assembling ionic liquids

DOE PAGES

Nebgen, Benjamin Tyler; Magurudeniya, Harsha D.; Kwock, Kevin Wen Chi; ...

2017-07-18

Molecular dynamics simulations (up to the nanoscale) were performed on the 3-methyl-1-pentylimidazolium ionic liquid cation paired with three anions; chloride, nitrate, and thiocyanate as aqueous mixtures, using the effective fragment potential (EFP) method, a computationally inexpensive way of modeling intermolecular interactions. The simulations provided insight (preferred geometries, radial distribution functions and theoretical proton NMR resonances) into the interactions within the ionic domain and are validated against 1H NMR spectroscopy and small- and wide-angle X-ray scattering experiments on 1-decyl-3-methylimidazolium. Ionic liquids containing thiocyanate typically resist gelation and form poorly ordered lamellar structures upon mixing with water. Conversely, chloride, a strongly coordinatingmore » anion, normally forms strong physical gels and produces well-ordered nanostructures adopting a variety of structural motifs over a very wide range of water compositions. Nitrate is intermediate in character, whereby upon dispersal in water it displays a range of viscosities and self-assembles into nanostructures with considerable variability in the fidelity of ordering and symmetry, as a function of water content in the binary mixtures. The observed changes in the macro and nanoscale characteristics were directly correlated to ionic domain structures and intermolecular interactions as theoretically predicted by the analysis of MD trajectories and calculated RDFs. Specifically, both chloride and nitrate are positioned in the plane of the cation. Anion to cation proximity is dependent on water content. Thiocyanate is more susceptible to water insertion into the second solvent shell. Experimental 1H NMR chemical shifts monitor the site-specific competition dependence with water content in the binary mixtures. As a result, thiocyanate preferentially sits above and below the aromatic ring plane, a state disallowing interaction with the protons on the imidazolium ring.« less

Design principles from multiscale simulations to predict nanostructure in self-assembling ionic liquids.

PubMed

Nebgen, Benjamin T; Magurudeniya, Harsha D; Kwock, Kevin W C; Ringstrand, Bryan S; Ahmed, Towfiq; Seifert, Sönke; Zhu, Jian-Xin; Tretiak, Sergei; Firestone, Millicent A

2017-12-14

Molecular dynamics simulations (up to the nanoscale) were performed on the 3-methyl-1-pentylimidazolium ionic liquid cation paired with three anions; chloride, nitrate, and thiocyanate as aqueous mixtures, using the effective fragment potential (EFP) method, a computationally inexpensive way of modeling intermolecular interactions. The simulations provided insight (preferred geometries, radial distribution functions and theoretical proton NMR resonances) into the interactions within the ionic domain and are validated against 1 H NMR spectroscopy and small- and wide-angle X-ray scattering experiments on 1-decyl-3-methylimidazolium. Ionic liquids containing thiocyanate typically resist gelation and form poorly ordered lamellar structures upon mixing with water. Conversely, chloride, a strongly coordinating anion, normally forms strong physical gels and produces well-ordered nanostructures adopting a variety of structural motifs over a very wide range of water compositions. Nitrate is intermediate in character, whereby upon dispersal in water it displays a range of viscosities and self-assembles into nanostructures with considerable variability in the fidelity of ordering and symmetry, as a function of water content in the binary mixtures. The observed changes in the macro and nanoscale characteristics were directly correlated to ionic domain structures and intermolecular interactions as theoretically predicted by the analysis of MD trajectories and calculated RDFs. Specifically, both chloride and nitrate are positioned in the plane of the cation. Anion to cation proximity is dependent on water content. Thiocyanate is more susceptible to water insertion into the second solvent shell. Experimental 1 H NMR chemical shifts monitor the site-specific competition dependence with water content in the binary mixtures. Thiocyanate preferentially sits above and below the aromatic ring plane, a state disallowing interaction with the protons on the imidazolium ring.

Long-Range Near-Side Angular Correlations in Proton-Proton Interactions in CMS.

ScienceCinema

None

2017-12-09

The CMS Collaboration Results on two-particle angular correlations for charged particles emitted in proton-proton collisions at center of mass energies of 0.9, 2.36 and 7TeV over a broad range of pseudorapidity (?) and azimuthal angle (f) are presented using data collected with the CMS detector at the LHC. Short-range correlations in ??, which are studied in minimum bias events, are characterized using a simple independent cluster parameterization in order to quantify their strength (cluster size) and their extent in ? (cluster decay width). Long-range azimuthal correlations are studied more differentially as a function of charged particle multiplicity and particle transverse momentum using a 980nb-1 data set at 7TeV. In high multiplicity events, a pronounced structure emerges in the two-dimensional correlation function for particles in intermediate pT’s of 1-3GeV/c, 2.0< |??|<4.8 and ?f˜0. This is the ?rst observation of such a ridge-like feature in two-particle correlation functions in pp or p-pbar collisions. EVO Universe, password "seminar"; Phone Bridge ID: 2330444 Password: 5142

Phase Transitions of Thermoelectric TAGS-85.

PubMed

Kumar, Anil; Vermeulen, Paul A; Kooi, Bart J; Rao, Jiancun; van Eijck, Lambert; Schwarzmüller, Stefan; Oeckler, Oliver; Blake, Graeme R

2017-12-18

The alloys (GeTe) x (AgSbTe 2 ) 100-x , commonly known as TAGS-x, are among the best performing p-type thermoelectric materials for the composition range 80 ≤ x ≤ 90 and in the temperature range 200-500 °C. They adopt a rhombohedrally distorted rocksalt structure at room temperature and are reported to undergo a reversible phase transition to a cubic structure at ∼250 °C. However, we show that, for the optimal x = 85 composition (TAGS-85), both the structural and thermoelectric properties are highly sensitive to the initial synthesis method employed. Single-phase rhombohedral samples exhibit the best thermoelectric properties but can only be obtained after an annealing step at 600 °C during initial cooling from the melt. Under faster cooling conditions, the samples obtained are inhomogeneous, containing multiple rhombohedral phases with a range of lattice parameters and exhibiting inferior thermoelectric properties. We also find that when the room-temperature rhombohedral phase is heated, an intermediate trigonal structure containing ordered cation vacancy layers is formed at ∼200 °C, driven by the spontaneous precipitation of argyrodite-type Ag 8 GeTe 6 which alters the stoichiometry of the TAGS-85 matrix. The rhombohedral and trigonal phases of TAGS-85 coexist up to 380 °C, above which a single cubic phase is obtained and the Ag 8 GeTe 6 precipitates redissolve into the matrix. On subsequent cooling a mixture of rhombohedral, trigonal, and Ag 8 GeTe 6 phases is again obtained. Initially single-phase samples exhibit thermoelectric power factors of up to 0.0035 W m -1 K -2 at 500 °C, a value that is maintained on subsequent thermal cycling and which represents the highest power factor yet reported for undoped TAGS-85. Therefore, control over the structural homogeneity of TAGS-85 as demonstrated here is essential in order to optimize the thermoelectric performance.

A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine.

PubMed

Ciardiello, J J; Stewart, H L; Sore, H F; Galloway, W R J D; Spring, D R

2017-06-01

Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Elucidation of the structure and reaction mechanism of Sorghum bicolor hydroxycinnamoyltransferase and its structural relationship to other CoA-dependent transferases and synthases

USDA-ARS?s Scientific Manuscript database

Hydroxycinnamoyltransferase (SbHCT) from Sorghum bicolor participates in an early step of the phenylpropanoid pathway, exchanging CoA esterified to p-coumaric acid with shikimic or quinic acid, as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to...

Short-range magentic correlations and dynamic orbital ordering in the thermally activated spin state of LaCoO3

NASA Astrophysics Data System (ADS)

Rosenkranz, S.; Phelan, D.; Louca, D.; Lee, S. H.; Chupas, P. J.; Osborn, R.; Zheng, H.; Mitchell, J. F.

2006-03-01

The cobalt perovskites La1-xSrxCoO3 show intriguing spin, lattice, and orbital properties similar to the ones observed in colossal magnetoresistive manganites. The x=0 parent compound is a non-magnetic insulator at low temperatures, but shows evidence of a spin-state transition of the cobalt ions above 50K from a low-spin to an intermediate or high-spin configuration. Using high resolution, inelastic neutron scattering, we observe a distinct low energy excitation at 0.6meV coincident with the thermally induced spin state transition observed in susceptibility measurements. The thermal activation of this excited spin state also leads to short-range, dynamic ferro- and antiferromagnetic correlations. These observations are consistent with the activation of a zero-field split intermediate spin state as well as the presence of dynamic orbital ordering of these excited states. Work supported by US DOE BES-DMS W-31-109-ENG-38 and NSF DMR-0454672

Snapshots of a solid-state transformation: coexistence of three phases trapped in one crystal

DOE PAGES

Aromí, G.; Beavers, C. M.; Sánchez Costa, J.; ...

2016-01-05

Crystal-to-crystal transformations have been crucial in the understanding of solid-state processes, since these may be studied in detail by means of single crystal X-ray diffraction (SCXRD) techniques. The description of the mechanisms and potential intermediates of those processes remains very challenging. In fact, solid-state transient states have rarely been observed, at least to a sufficient level of detail. We have investigated the process of guest extrusion from the non-porous molecular material [Fe(bpp)(H 2L)](ClO 4) 2·1.5C 3H 6O (bpp = 2,6-bis(pyrazol-3-yl)pyridine; H 2L = 2,6-bis(5-(2-methoxyphenyl)-pyrazol-3-yl)pyridine; C 3H 6O = acetone), which occurs through ordered diffusion of acetone in a crystal-to-crystal manner,more » leading to dramatic structural changes. The slow kinetics of the transition allows thermal trapping of the system at various intermediate stages. The transiting single crystal can be then examined at these points through synchrotron SCXRD, offering a window upon the mechanism of the transformation at the molecular scale. These experiments have unveiled the development of an ordered intermediate phase, distinct from the initial and the final states, coexisting as the process advances with either of these two phases or, at a certain moment with both of them. The new intermediate phase has been structurally characterized in full detail by SCXRD, providing insights into the mechanism of this diffusion triggered solid-state phenomenon. Lastly, the process has been also followed by calorimetry, optical microscopy, local Raman spectroscopy and powder X-ray diffraction. The discovery and description of an intermediate ordered state in a molecular solid-state transformation is of great interest and will help to understand the mechanistic details and reaction pathways underlying these transformations.« less

Kinetic intermediates of unfolding of dimeric prostatic phosphatase.

PubMed

Kuciel, Radosława; Mazurkiewicz, Aleksandra; Dudzik, Paulina

2007-01-01

Kinetics of guanidine hydrochloride (GdnHCl)-induced unfolding of human prostatic acid phosphatase (hPAP), a homodimer of 50 kDa subunit molecular mass was investigated with enzyme activity measurements, capacity for binding an external hydrophobic probe, 1-anilinonaphtalene-8-sulfonate (ANS), accessibility of thiols to reaction with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and 2-(4'-maleimidylanilino)naphthalene-6-sulfonate (MIANS) and ability to bind Congo red dye. Kinetic analysis was performed to describe a possible mechanism of hPAP unfolding and dissociation that leads to generation of an inactive monomeric intermediate that resembles, in solution of 1.25 M GdnHCl pH 7.5, at 20 degrees C, in equilibrium, a molten globule state. The reaction of hPAP inactivation in 1.25 M GdnHCl followed first order kinetics with the reaction rate constant 0.0715 +/- 0.0024 min(-1) . The rate constants of similar range were found for the pseudo-first-order reactions of ANS and Congo red binding: 0.0366 +/- 0.0018 min(-1) and 0.0409 +/- 0.0052 min(-1), respectively. Free thiol groups, inaccessible in the native protein, were gradually becoming, with the progress of unfolding, exposed for the reactions with DTNB and MIANS, with the pseudo-first-order reaction rate constants 0.327 +/- 0.014 min(-1) and 0.216 +/- 0.010 min(-1), respectively. The data indicated that in the course of hPAP denaturation exposure of thiol groups to reagents took place faster than the enzyme inactivation and exposure of the protein hydrophobic surface. This suggested the existence of a catalytically active, partially unfolded, but probably dimeric kinetic intermediate in the process of hPAP unfolding. On the other hand, the protein inactivation was accompanied by exposure of a hydrophobic, ANS-binding surface, and with an increased capacity to bind Congo red. Together with previous studies these results suggest that the stability of the catalytically active conformation of the enzyme depends mainly on the dimeric structure of the native hPAP.

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

PubMed Central

Dyson, H. Jane; Wright, Peter E.

2017-01-01

Conspectus Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (~2 seconds) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ~ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this review was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question “What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?” PMID:28032989

Time-resolved distance determination by tryptophan fluorescence quenching: probing intermediates in membrane protein folding.

PubMed

Kleinschmidt, J H; Tamm, L K

1999-04-20

The mechanism of insertion and folding of an integral membrane protein has been investigated with the beta-barrel forming outer membrane protein A (OmpA) of Escherichia coli. This work describes a new approach to this problem by combining structural information obtained from tryptophan fluorescence quenching at different depths in the lipid bilayer with the kinetics of the refolding process. Experiments carried out over a temperature range between 2 and 40 degrees C allowed us to detect, trap, and characterize previously unidentified folding intermediates on the pathway of OmpA insertion and folding into lipid bilayers. Three membrane-bound intermediates were found in which the average distances of the Trps were 14-16, 10-11, and 0-5 A, respectively, from the bilayer center. The first folding intermediate is stable at 2 degrees C for at least 1 h. A second intermediate has been isolated at temperatures between 7 and 20 degrees C. The Trps move 4-5 A closer to the center of the bilayer at this stage. Subsequently, in an intermediate that is observable at 26-28 degrees C, the Trps move another 5-10 A closer to the center of the bilayer. The final (native) structure is observed at higher temperatures of refolding. In this structure, the Trps are located on average about 9-10 A from the bilayer center. Monitoring the evolution of Trp fluorescence quenching by a set of brominated lipids during refolding at various temperatures therefore allowed us to identify and characterize intermediate states in the folding process of an integral membrane protein.

Coupling between crystal structure and magnetism in transition-metal oxides

NASA Astrophysics Data System (ADS)

Barton, Phillip Thomas

Transition-metal oxides exhibit a fascinating array of phenomena ranging from superconductivity to negative thermal expansion to catalysis. This dissertation focuses on magnetism, which is integral to engineering applications such as data storage, electric motors/generators, and transformers. The investigative approach follows structure-property relationships from materials science and draws on intuition from solid-state chemistry. The interplay between crystal structure and magnetic properties is studied experimentally in order to enhance the understanding of magnetostructural coupling mechanisms and provide insight into avenues for tuning behavior. A combination of diffraction and physical property measurements were used to study structural and magnetic phase transitions as a function of chemical composition, temperature, and magnetic field. The systems examined are of importance in Li-ion battery electrochemistry, condensed-matter physics, solid-state chemistry, and p-type transparent conducting oxides. The materials were prepared by solid-state reaction of powder reagents at high temperatures for periods lasting tens of hours. The first project discussed is of a solid solution between NiO, a correlated insulator, and LiNiO2, a layered battery cathode. Despite the deceptive structural and compositional simplicity of this system, a complete understanding of its complex magnetic properties has remained elusive. This study shows that nanoscale domains of chemical order form at intermediate compositions, creating interfaces between antiferromagnetism and ferrimagnetism that give rise to magnetic exchange bias. A simple model of the magnetism is presented along with a comprehensive phase diagram. The second set of investigations focus on the Ge-Co-O system where the spin-orbit coupling of Co(II) plays a significant role. GeCo2O 4 is reported to exhibit unusual magnetic behavior that arises from Ising spin in its spinel crystal structure. Studies by variable-temperature synchrotron X-ray diffraction reveal a magnetostructural transition and capacitance measurements show evidence for magnetodielectric behavior. The above work uncovered a Co10Ge3O16 phase that had a known structure but whose physical properties were largely uncharacterized. This project examined its metamagnetic properties using detailed magnetometry experiments. Upon the application of a magnetic field, this material goes through a first-order phase transition from a noncollinear antiferromagnet to an unknown ferrimagnetic state. Lastly, this thesis explored the chemical dilution of magnetism in some perovskite and delafossite solid solutions. In the perovskite structure, compositions intermediate to the endmembers SrRuO3, a ferromagnetic metal, and LaRhO3, a diamagnetic semiconductor, were investigated. While the magnetism of this system is poised between localized and itinerant behavior, a compositionally-driven metal to insulator transition, revealed by electrical resistivity measurements, did not strongly impact the magnetic properties. Instead, both octahedral tilting and magnetic dilution had strong effects, and comparison of this characterization to Sr1-- x CaxRuO3 reinforces the important role of structural distortions in determining magnetic ground state. The final materials studied were of composition CuAl1-- xCrxO2 (0 < x < 1) in the delafossite structure. The primary interest was the geometric frustration of antiferromagnetism in CuCrO 2 and significant short-range correlations were observed above TN. The analysis found that reducing the number of degenerate states through Al substitution did not enhance magnetic ordering because of the weakening of magnetic exchange.

Crystal structure of the true Nasicon: Na/sub 3/Zr/sub 2/Si/sub 2/PO/sub 12/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boilot, J.P.; Collin, G.; Colomban, P.

For the first time, the results of single crystal determination of the true Nasicon are given. The structure refinement yielded the following composition: Na/sub 3.09(8)/Zr/sub 2.01(1)/P/sub 0.91/Si/sub 2.09/O/sub 12/. Evidence of the total occupancy of the Zr octahedron is found, displaying that only the Si/P non-stoichiometry mechanism is present in the Nasicon crystal. For the two temperatures which have been investigated (R.T. and 623K), the structures are very close to that of the Nasicon analog: Na/sub 3/Sc/sub 2/P/sub 3/O/sub 12/. However the Si/P substitution prevents the sodium long range ordering even in the monoclinic low temperature phase and therefore themore » cross over to the rhombohedral symmetry only involves very small atomic displacements. For both structures, a new sodium position (mid-Na) is displayed in the conduction channel, intermediate between the usual Na(1) and Na(2) sites.« less

Near-field thermal radiation of deep- subwavelength slits in the near infrared range.

PubMed

Guo, Yan; Li, Kuanbiao; Xu, Ying; Wei, Kaihua

2017-09-18

We numerically investigate the thermal radiation of one-dimensional deep subwavelength slits in the near infrared range. Using numerical calculations of single-slit and multi-slit structures, we find that high-level radiation efficiency can be achieved for a wide spectrum when ultra-thin intermediate layers are used, and it is less affected by structure parameters. The underlying mechanisms involve Surface Plasmon Polaritons resonance and Fabry-Perot interference at each slit and the interaction between adjacent slits. This structure helps understand and improve the design of thermal radiation control devices.

Influence of substrate and film thickness on polymer LIPSS formation

NASA Astrophysics Data System (ADS)

Cui, Jing; Nogales, Aurora; Ezquerra, Tiberio A.; Rebollar, Esther

2017-02-01

Here we focus on the influence of both, substrate and film thickness on polymer Laser Induced Periodic Surface Structures (LIPSS) formation in polymer films. For this aim a morphological description of ripples structures generated on spin-coated polystyrene (PS) films by a linearly polarized laser beam with a wavelength of 266 nm is presented. The influence of different parameters on the quality and characteristics of the formed laser-induced periodic surface structures (LIPSS) was investigated. We found that well-ordered LIPSS are formed either on PS films thinner than 200 nm or thicker than 400 nm supported on silicon substrates as well as on thicker free standing films. However less-ordered ripples are formed on silicon supported films with intermediate thicknesses in the range of 200-380 nm. The effect of the thermal and optical properties of the substrate on the quality of LIPSS was analyzed. Differences observed in the fluence and number of pulses needed for the onset of surface morphological modifications is explained considering two main effects which are: (1) The temperature increase on polymer surface induced by the action of cumulative laser irradiation and (2) The differences in thermal conductivity between the polymer and the substrate which strongly affect the heat dissipation generated by irradiation.

Cool Flames in Propane-Oxygen Premixtures at Low and Intermediate Temperatures at Reduced-Gravity

NASA Technical Reports Server (NTRS)

Pearlman, Howard; Foster, Michael; Karabacak, Devrez

2003-01-01

The Cool Flame Experiment aims to address the role of diffusive transport on the structure and the stability of gas-phase, non-isothermal, hydrocarbon oxidation reactions, cool flames and auto-ignition fronts in an unstirred, static reactor. These reactions cannot be studied on Earth where natural convection due to self-heating during the course of slow reaction dominates diffusive transport and produces spatio-temporal variations in the thermal and thus species concentration profiles. On Earth, reactions with associated Rayleigh numbers (Ra) less than the critical Ra for onset of convection (Ra(sub cr) approx. 600) cannot be achieved in laboratory-scale vessels for conditions representative of nearly all low-temperature reactions. In fact, the Ra at 1g ranges from 10(exp 4) - 10(exp 5) (or larger), while at reduced-gravity, these values can be reduced two to six orders of magnitude (below Ra(sub cr)), depending on the reduced-gravity test facility. Currently, laboratory (1g) and NASA s KC-135 reduced-gravity (g) aircraft studies are being conducted in parallel with the development of a detailed chemical kinetic model that includes thermal and species diffusion. Select experiments have also been conducted at partial gravity (Martian, 0.3gearth) aboard the KC-135 aircraft. This paper discusses these preliminary results for propane-oxygen premixtures in the low to intermediate temperature range (310- 350 C) at reduced-gravity.

Inhomogeneous structure in the chromospheres of dwarf M stars

NASA Technical Reports Server (NTRS)

Turner, N. J.; Cram, L. E.; Robinson, R. D.

1991-01-01

Linear combinations of observed spectra of the H-alpha and Ca-II resonance and IR lines from the chromospheres of a quiet (Gl 1) and an active (Gl 735) dwarf-M star are compared with the corresponding spectra from a star of intermediate activity (Gl 887). It is shown that the intermediate spectra cannot be explained as a simple juxtaposition of the extreme chromospheric states. It is concluded that the range of observed strengths of chromospheric activity indicators in dwarf-M stars is due, at least in part, to changes in the radial structure of the chromospheric heating function and not to changes in the area filling factor.

Protein Folding—How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry

PubMed Central

Englander, S. Walter; Mayne, Leland; Kan, Zhong-Yuan; Hu, Wenbing

2017-01-01

Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, development of the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with HX MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known. PMID:27145881

Structural transformations and disordering in zirconolite (CaZrTi2O7) at high pressure.

PubMed

Salamat, Ashkan; McMillan, Paul F; Firth, Steven; Woodhead, Katherine; Hector, Andrew L; Garbarino, Gaston; Stennett, Martin C; Hyatt, Neil C

2013-02-04

There is interest in identifying novel materials for use in radioactive waste applications and studying their behavior under high pressure conditions. The mineral zirconolite (CaZrTi(2)O(7)) exists naturally in trace amounts in diamond-bearing deep-seated metamorphic/igneous environments, and it is also identified as a potential ceramic phase for radionuclide sequestration. However, it has been shown to undergo radiation-induced metamictization resulting in amorphous forms. In this study we probed the high pressure structural properties of this pyrochlore-like structure to study its phase transformations and possible amorphization behavior. Combined synchrotron X-ray diffraction and Raman spectroscopy studies reveal a series of high pressure phase transformations. Starting from the ambient pressure monoclinic structure, an intermediate phase with P2(1)/m symmetry is produced above 15.6 GPa via a first order transformation resulting in a wide coexistence range. Upon compression to above 56 GPa a disordered metastable phase III with a cotunnite-related structure appears that is recoverable to ambient conditions. We examine the similarity between the zirconolite behavior and the structural evolution of analogous pyrochlore systems under pressure.

Unfolding Kinetics of β-Lactoglobulin Induced by Surfactant and Denaturant: A Stopped-Flow/Fluorescence Study

PubMed Central

Viseu, Maria Isabel; Melo, Eduardo P.; Carvalho, Teresa Isabel; Correia, Raquel F.; Costa, Sílvia M. B.

2007-01-01

The β→α transition of β-lactoglobulin, a globular protein abundant in the milk of several mammals, is investigated in this work. This transition, induced by the cationic surfactant dodecyltrimethylammonium chloride (DTAC), is accompanied by partial unfolding of the protein. In this work, unfolding of bovine β-lactoglobulin in DTAC is compared with its unfolding induced by the chemical denaturant guanidine hydrochloride (GnHCl). The final protein states attained in the two media have quite different secondary structure: in DTAC the α-helical content increases, leading to the so-called α-state; in GnHCl the amount of ordered secondary-structure decreases, resulting in a random coil-rich final state (denatured, or D, state). To obtain information on both mechanistic routes, in DTAC and GnHCl, and to characterize intermediates, the kinetics of unfolding were investigated in the two media. Equilibrium and kinetic data show the partial accumulation of an on-pathway intermediate in each unfolding route: in DTAC, an intermediate (I1) with mostly native secondary structure but loose tertiary structure appears between the native (β) and α-states; in GnHCl, another intermediate (I2) appears between states β and D. Kinetic rate constants follow a linear Chevron-plot representation in GnHCl, but show a more complex mechanism in DTAC, which acts like a stronger binding species. PMID:17693475

Diffraction of electrons at intermediate energies

NASA Astrophysics Data System (ADS)

Ascolani, H.; Barrachina, R. O.; Guraya, M. M.; Zampieri, G.

1992-08-01

We present a theory of the elastic scattering of electrons from crystalline surfaces that contains both low-energy-electron-diffraction (LEED) effects at low energies and x-ray-photoelectron- and Auger-electron-diffraction (XPD/AED) effects at intermediate energies. The theory is based on a cluster-type approach to the scattering problem and includes temperature effects. The transition from one regime to the other may be explained as follows: At low energies all the scattered waves add coherently, and the intensity is dominated by LEED effects. At intermediate energies the thermal vibration of the atoms destroys the long-range coherency responsible for the LEED peaks, but affects little the interference of those waves that share parts of their paths inside the solid. Thus, the interference of these waves comes to dominate the intensity, giving rise to structures similar to those observed in XPD/AED experiments. We perform a calculation of the elastic reflection of electrons from Cu(001) that is in good agreement with the experiment in the range 200-1500 eV. At low energies the intensity is dominated by LEED peaks; at 400 eV LEED peaks and XPD/AED structures coexist; and above this energy the intensity is dominated by the latter. We analyze the contributions to the intensity at intermediate energies of the interferences in the incoming and outgoing parts of the electron path.

Water clusters in amorphous pharmaceuticals.

PubMed

Authelin, Jean-Rene; MacKenzie, Alan P; Rasmussen, Don H; Shalaev, Evgenyi Y

2014-09-01

Amorphous materials, although lacking the long-range translational and rotational order of crystalline and liquid crystalline materials, possess certain local (short-range) structure. This paper reviews the distribution of one particular component present in all amorphous pharmaceuticals, that is, water. Based on the current understanding of the structure of water, water molecules can exist in either unclustered form or as aggregates (clusters) of different sizes and geometries. Water clusters are reported in a range of amorphous systems including carbohydrates and their aqueous solutions, synthetic polymers, and proteins. Evidence of water clustering is obtained by various methods that include neutron and X-ray scattering, molecular dynamics simulation, water sorption isotherm, concentration dependence of the calorimetric Tg , dielectric relaxation, and nuclear magnetic resonance. A review of the published data suggests that clustering depends on water concentration, with unclustered water molecules existing at low water contents, whereas clusters form at intermediate water contents. The transition from water clusters to unclustered water molecules can be expected to change water dependence of pharmaceutical properties, such as rates of degradation. We conclude that a mechanistic understanding of the impact of water on the stability of amorphous pharmaceuticals would require systematic studies of water distribution and clustering, while such investigations are lacking. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Multi-scale structures and functional properties of starches from Indica hybrid, Japonica and waxy rice.

PubMed

Wang, Shujun; Li, Peiyan; Yu, Jinglin; Guo, Peng; Wang, Shuo

2017-09-01

The structural and functional properties of starches from three rice grains differing in amylose content (19.9, 13.4 and 0.8% for Japonica, Indica hybrid and waxy rice, respectively) were investigated using a range of characterization methods Indica hybrid starch (IHS) had the highest proportion of intermediate (DP 13-24) and long branch chains (DP≥37) and the lowest proportion of short branch chains (DP 6-12), whereas the opposite results were observed for Japonica starch (JS). The results for waxy rice starch (WS) were between those of IHS and JS. Rice starches showed a typical A-type X-ray diffraction pattern with the relative crystallinity ranging from 33.4% for JS to 39.4% for WS. Significant differences were observed in lamellar distance and short-range molecular order characterized by IR ratio of absorbances at 1047/1022cm -1 and full width of half maximum (FWHM) of the band at 480cm -1 . WS showed a higher swelling power and a lower close packing concentration at temperatures from 60 to 90°C. The lower peak viscosity of WS was attributed to the formation of less rigid swollen granules at a concentrated regime. WS showed a higher in vitro digestibility compared with IHS and JS. Copyright © 2017 Elsevier B.V. All rights reserved.

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru; Sato, Yushi; Nomoto, Ken'ichi; Maeda, Keiichi; Nakasato, Naohito; Hachisu, Izumi

2017-04-01

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N, from a few 104 to a few 107 in order to check mass resolution convergence, where SPH simulations with N > 107 (or a space resolution of several 106 cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less active with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 104 to 107 cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲106 cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.

Structural relaxation in a binary metallic melt: Molecular dynamics computer simulation of undercooled Al80Ni20

NASA Astrophysics Data System (ADS)

Das, Subir K.; Horbach, Jürgen; Voigtmann, Thomas

2008-08-01

Molecular dynamics computer simulations are performed to study structure and structural relaxation in the glassforming metallic alloy Al80Ni20 . The interactions between the particles are modeled by an effective potential of the embedded atom type. Our model of Al80Ni20 exhibits chemical short-range order (CSRO) that is reflected in a broad prepeak around a wave number of 1.8Å-1 in the partial static structure factor for the Ni-Ni correlations. The CSRO is due to the preference of Ni atoms to have Al rather than Ni atoms as nearest neighbors. By analyzing incoherent and coherent intermediate scattering functions as well as self-diffusion constants and shear viscosity, we discuss how the chemical ordering is reflected in the dynamics of the deeply undercooled melt. The q dependence of the α relaxation time as well as the Debye-Waller factor for the Al-Al correlations show oscillations at the location of the prepeak in the partial static structure factor for the Ni-Ni correlations. The latter feature of the Debye-Waller factor is well reproduced by a calculation in the framework of the mode coupling theory (MCT) of the glass transition, using the partial static structure factors from the simulation as input. We also check the validity of the Stokes-Einstein-Sutherland formula that relates the self-diffusion coefficients with the shear viscosity. We show that it breaks down already far above the mode coupling critical temperature Tc . The failure of the Stokes-Einstein-Sutherland relation is not related to the specific chemical ordering in Al80Ni20 .

Coherent vector meson photoproduction from deuterium at intermediate energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rogers, T.C.; Strikman, M.I.; Sargsian, M.M.

2006-04-15

We analyze the cross section for vector meson photoproduction off a deuteron for the intermediate range of photon energies starting at a few giga-electron-volts above the threshold and higher. We reproduce the steps in the derivation of the conventional nonrelativistic Glauber expression based on an effective diagrammatic method while making corrections for Fermi motion and intermediate-energy kinematic effects. We show that, for intermediate-energy vector meson production, the usual Glauber factorization breaks down, and we derive corrections to the usual Glauber method to linear order in longitudinal nucleon momentum. The purpose of our analysis is to establish methods for probing interestingmore » physics in the production mechanism for {phi} mesons and heavier vector mesons. We demonstrate how neglecting the breakdown of Glauber factorization can lead to errors in measurements of basic cross sections extracted from nuclear data.« less

Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal.

PubMed

Morales, Piero; Lagerwall, Jan; Vacca, Paolo; Laschat, Sabine; Scalia, Giusy

2010-05-20

Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5), prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising during the solvent evaporation process. Moreover, in sufficiently thin films the crystallization seems to be suppressed, extending the uniform order of the liquid crystal phase down to room temperature. This should be compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C.

Computer simulation of CaSiO3 glass under compression: correlation between Si-Si pair radial distribution function and intermediate range order structure

NASA Astrophysics Data System (ADS)

Lan, Mai Thi; Thuy Duong, Tran; Iitaka, Toshiaki; Van Hong, Nguyen

2017-06-01

The structural organization of CaSiO3 glass at 600 K and under pressure of 0-100 GPa is investigated by molecular dynamics simulation (MDS). Results show that the atomic structure of CaSiO3 comprises SiO n and CaO m units considered as basic structural polyhedra. At low pressure, most of the basic structural polyhedra are SiO4, CaO5, CaO6 and CaO7. At high pressure most of the basic structural polyhedra are SiO5, SiO6 and CaO9, CaO10 and CaO11. The distribution of basic structural polyhedra is not uniform resulting in formation of Ca-rich and Si-rich regions. The distribution of SiO4, SiO5 and SiO6 polyhedra is also not uniform, but it tends to form SiO4-, SiO5-, and SiO6-clusters. For the Si-O network, under compression there is a gradual transition from the tetrahedral network (SiO4) to the octahedral network (SiO6) via SiO5 polyhedra. The SiO5-clusters are the same as immediate-phase in the transformation process. The size and shape of SiO4 tetrahedra change strongly under compression. While the size of SiO5 and SiO6 has also changed significantly, but the shape is almost unchanged under compression. The SiO n polyhedra can connect to each other via one common oxygen ion (corner-sharing bond), two common oxygen ions (edge-sharing bond) or three common oxygen ions (face-sharing bond). The Si-Si bond length in corner-sharing bonds is much longer than the ones in edge-sharing and face-sharing bonds. The change of intermediate range order (IRO) structure under compression relating to edge- and face-sharing bonds amongst SiO n at high pressure is the origin of the first peak splitting of the radial distribution functions of Si-Si pair. Under compression, the number of non-bridging oxygen (NBO) decreases. This makes the Si-O network more polymerized. At low pressure, most of the Ca2+ ions incorporate into the Si-O network via NBOs. At high pressure, the amount of NBO decreases, Ca2+ ions mainly incorporate into the Si-O network via bridging oxygen (BO) that belongs to SiO5 and SiO6 with a negative charge. And this is the principle for immobilization of heavy metal as well as fissile materials in hazardous waste (nuclear waste).

Mechanisms of deterioration of intermediate moisture food systems

NASA Technical Reports Server (NTRS)

Labuza, T. P.

1972-01-01

A study of shelf stability in intermediate moisture foods was made. Major efforts were made to control lipid oxidation and nonenzymatic browning. In order to determine means of preventing these reactions, model systems were developed having the same water activity content relationship of intermediate moisture foods. Models were based on a cellulose-lipid and protein-lipid system with glycerol added as the humectant. Experiments with both systems indicate that lipid oxidation is promoted significantly in the intermediate moisture range. The effect appeared to be related to increased mobility of either reactants or catalysts, since when the amount of water in the system reached a level where capillary condensation occurred and thus free water was present, the rates of oxidation increased. With added glycerol, which is water soluble and thus increases the amount of mobile phase, the increase in oxidation rate occurs at a lower relative humidity. The rates of oxidation were maximized at 61% RH and decreased again at 75% RH probably due to dilution. No significant non-enzymatic browning occurred in the protein-lipid systems. Prevention of oxidation by the use of metal chelating agents was enhanced in the cellulose system, whereas, with protein present, the lipid soluble chain terminating antioxidants (such as BHA) worked equally as well. Preliminary studies of foods adjusted to the intermediate moisture range bear out the results of oxidation in model systems. It can be concluded that for most fat containing intermediate moisture foods, rancidity will be the reaction most limiting stability.

Structural evolution in the crystallization of rapid cooling silver melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Z.A., E-mail: ze.tian@gmail.com; Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052; Dong, K.J.

2015-03-15

The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperaturemore » range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.« less

Influence Of Momentum Excess On The Pattern And Dynamics Of Intermediate-Range Stratified Wakes

DTIC Science & Technology

2016-06-01

excess in order to model the fundamental differences between signatures generated by towed and self- propelled bodies in various ocean states. In cases...which can be used on the operational level for developing and improving algorithms for non- acoustic signature prediction and detection. 14. SUBJECT...order to model the fundamental differences between signatures generated by towed and self- propelled bodies in various ocean states. In cases where

Optimization of Wireless Power Transfer Systems Enhanced by Passive Elements and Metasurfaces

NASA Astrophysics Data System (ADS)

Lang, Hans-Dieter; Sarris, Costas D.

2017-10-01

This paper presents a rigorous optimization technique for wireless power transfer (WPT) systems enhanced by passive elements, ranging from simple reflectors and intermedi- ate relays all the way to general electromagnetic guiding and focusing structures, such as metasurfaces and metamaterials. At its core is a convex semidefinite relaxation formulation of the otherwise nonconvex optimization problem, of which tightness and optimality can be confirmed by a simple test of its solutions. The resulting method is rigorous, versatile, and general -- it does not rely on any assumptions. As shown in various examples, it is able to efficiently and reliably optimize such WPT systems in order to find their physical limitations on performance, optimal operating parameters and inspect their working principles, even for a large number of active transmitters and passive elements.

Dramatic change of photoexcited quasiparticle relaxation dynamics across Yb valence state transition in YbInCu4

NASA Astrophysics Data System (ADS)

Zhang, M. Y.; Chen, R. Y.; Dong, T.; Wang, N. L.

2017-04-01

YbInCu4 undergoes a first-order structural phase transition near Tv=40 K associated with an abrupt change of Yb valence state. We perform an ultrafast pump-probe measurement on YbInCu4 and find that the expected heavy-fermion properties arising from the c -f hybridization exist only in a limited temperature range above Tv. Below Tv, the compound behaves as a normal metal though a prominent hybridization energy gap is still present in the infrared measurement. We elaborate that those seemingly controversial phenomena could be well explained by assuming that the Fermi level suddenly shifts up and moves away from the flat f -electron band as well as the indirect hybridization energy gap in the intermediate valence state below Tv.

Intermediate-filaments: from disordered building blocks to well-ordered cells

NASA Astrophysics Data System (ADS)

Kornreich, Micha; Malka-Gibor, Eti; Laser-Azogui, Adi; Doron, Ofer; Avinery, Ram; Herrmann, Harald; Beck, Roy

In the past decade it was found that ~50% of human proteins contain long disordered regions, which play significant functional roles. As these regions lack a defined 3D folded structure, their ensemble conformations can be studied using polymer physics statistical-mechanics arguments. We measure the structure and mechanical response of hydrogels composed of neuronal intermediate filaments proteins. In the nervous system, these proteins provide cells with their mechanical support and shape, via interactions of their long, highly charged and disordered protein chains. We employ synchrotron small-angle X-ray scattering and various microscopy techniques to investigate such hydrogels from the nano- to the macro-scale. In contrast to previous polymer physics theories and experiments, we find that shorter and less charged chains can promote network expansion. The results are explained by intricate interactions between specific domains on the interacting chains, and also suggest a novel structural justification for the changing protein compositions observed during neuronal development. We address the following questions: Can protein disorder have an important role in cellular architecture? Can structural disorder in the micro-scale induce orientational and translational order on the macro-scale? How do the physical properties of disordered protein regions, such as charge, length, and hydrophobicity, modulate the cellular super-structure?

Structural characterization of proteins in wheat flour doughs enriched with intermediate wheatgrass (Thinopyrum intermedium) flour.

PubMed

Marti, Alessandra; Bock, Jayne E; Pagani, Maria Ambrogina; Ismail, Baraem; Seetharaman, Koushik

2016-03-01

The high protein and fiber content of intermediate wheatgrass (IWG) - together with its interesting agronomic traits and environment-related benefits - make this perennial crop attractive also for human consumption. Structural characteristics of the proteins in IWG/hard wheat flour (HWF) doughs (at IWG:HWF ratios of 0:100, 50:50, 75:25 and 100:0) - including aggregate formation, thiols availability, and secondary structure changes during dough mixing - were investigated. Proteins in IWG-doughs had higher solubility and thiol content - as function of IWG content - suggesting that protein network was mostly based on non-covalent interactions. While 50% IWG-enrichment gave an increase in random structures, enrichment at ⩾75% resulted in a decrease in β-sheets with an increase in random structures, indicating a decrease in structural order. The observed differences in protein molecular configuration and interactions in HWF compared to IWG doughs necessitate further investigation to establish their impact on the quality of IWG-enriched bread. Copyright © 2015 Elsevier Ltd. All rights reserved.

From Solute, Fluidic and Particulate Precursors to Complex Organizations of Matter.

PubMed

Rao, Ashit; Cölfen, Helmut

2018-03-24

The organization of matter from its constitutive units recruits intermediate states with distinctive degrees of self-association and molecular order. Existing as clusters, droplets, gels as well as amorphous and crystalline nanoparticles, these precursor forms have fundamental contributions towards the composition and structure of inorganic and organic architectures. In this personal account, we show that the transitions from atoms, molecules or ionic species to superstructures of higher order are intertwined with the interfaces and interactions of precursor and intermediate states. Structural organizations distributed across different length scales are explained by the multistep nature of nucleation and crystallization, which can be guided towards functional hybrid materials by the strategic application of additives, templates and reaction environments. Thus, the non-classical pathways for material formation and growth offer conceptual frameworks for elucidating, inducing and directing fascinating material organizations of biogenic and synthetic origins. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermal collapse and hierarchy of polymorphs in a faujasite-type zeolite and its analogous melt-quenched glass

NASA Astrophysics Data System (ADS)

Palenta, Theresia; Fuhrmann, Sindy; Greaves, G. Neville; Schwieger, Wilhelm; Wondraczek, Lothar

2015-02-01

We examine the route of structural collapse and re-crystallization of faujasite-type (Na,K)-LSX zeolite. As the first step, a rather stable amorphous high density phase HDAcollapse is generated through an order-disorder transition from the original zeolite via a low density phase LDAcollapse, at around 790 °C. We find that the overall amorphization is driven by an increase in the bond angle distribution within T-O-T and a change in ring statistics to 6-membered TO4 (T = Si4+, Al3+) rings at the expense of 4-membered rings. The HDAamorph transforms into crystalline nepheline, though, through an intermediate metastable carnegieite phase. In comparison, the melt-derived glass of similar composition, HDAMQ, crystallizes directly into the nepheline phase without the occurrence of intermediate carnegieite. This is attributed to the higher structural order of the faujasite-derived HDAcollapse which prefers the re-crystallization into the highly symmetric carnegieite phase before transformation into nepheline with lower symmetry.

Variable character of O—O and M—O bonding in side-on (η2) 1:1 metal complexes of O2

PubMed Central

Cramer, Christopher J.; Tolman, William B.; Theopold, Klaus H.; Rheingold, Arnold L.

2003-01-01

The structures and the O—O and M—O bonding characters of a series of reported side-on (η2) 1:1 metal complexes of O2 are analyzed by using density functional theory calculations. Comparison of the calculated and experimental systems with respect to O—O bond distance, O—O stretching frequency, and O—O and M—O bond orders provides new insights into subtle influences relevant to O2 activation processes in biology and catalysis. The degree of charge transfer from the generally electron-rich metals to the dioxygen fragment is found to be variable, such that there are species well described as superoxides, others well described as peroxides, and several cases having intermediate character. Increased charge transfer to dioxygen takes place via overlap of the metal dxy orbital with the in-plane π* orbital of O2 and results in increased M—O bond orders and decreased O—O bond orders. Comparison of theory and experiment over the full range of compounds studied suggests that reevaluation of the O—O bond lengths determined from certain x-ray crystal structures is warranted; in one instance, an x-ray crystal structure redetermination was performed at low temperature, confirming the theoretical prediction. Librational motion of the coordinated O2 is identified as a basis for significant underestimation of the O—O distance at high temperature. PMID:12634422

Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump-Probe X-ray Solution Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyung Hwan; Muniyappan, Srinivasan; Oang, Key Young

2012-05-29

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps tomore » 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I 1, I 2, and I 3) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I 1 intermediate is generated within 100 ps and transforms to the R-like I 2 intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I 3 intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I 3 intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.« less

Presence of Peierls pairing and absence of insulator-to-metal transition in VO2 (A): a structure-property relationship study.

PubMed

Popuri, S R; Artemenko, A; Decourt, R; Villesuzanne, A; Pollet, M

2017-03-01

Layered vanadium oxides have been extensively explored due to their interesting metal-insulator transitions and energy conversion/storage applications. In the present study, we have successfully synthesized VO 2 (A) polymorph powder samples by a single-step hydrothermal synthesis process and consolidated them using spark plasma sintering. The structural and electronic properties of VO 2 (A) are measured over a large temperature range from liquid helium, across the structural transition (400-440 K) and up to 500 K. The structural analysis around this transition reveals an antiferrodistorsive to partially ferrodistorsive ordering upon cooling. It is followed by a progressive antiferromagnetic spin pairing which fully settles at about 150 K. The transport measurements show that, in contrast to the rutile archetype VO 2 (R/M1), the structural transition comes with a transition from semiconductor to band-type insulator. Under these circumstances, we propose a scenario with a high temperature antiferrodistorsive paramagnetic semiconducting phase, followed by an intermediate regime with a partially ferrodistorsive paramagnetic semiconducting phase, and finally a low temperature partially ferrodistorsive antiferromagnetic band insulator phase with a possible V-V Peierls-type pairing.

Thermal properties and phase transition in the fluoride, (NH{sub 4}){sub 3}SnF{sub 7}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kartashev, A.V.; Astafijev Krasnoyarsk State Pedagogical University, 660049 Krasnoyarsk; Gorev, M.V.

2016-05-15

Calorimetric, dilatometric and differential thermal analysis studies were performed on (NH{sub 4}){sub 3}SnF{sub 7} for a wide range of temperatures and pressures. Large entropy (δS{sub 0}=22 J/mol K) and elastic deformation (δ(ΔV/V){sub 0}=0.89%) jumps have proven that the Pa-3↔Pm-3m phase transition is a strong first order structural transformation. A total entropy change of ΔS{sub 0}=32.5 J/mol K is characteristic for the order–disorder phase transition, and is equal to the sum of entropy changes in the related material, (NH{sub 4}){sub 3}TiF{sub 7}, undergoing transformation between the two cubic phases through the intermediate phases. Hydrostatic pressure decreases the stability of the highmore » temperature Pm-3m phase in (NH{sub 4}){sub 3}SnF{sub 7}, contrary to (NH{sub 4}){sub 3}TiF{sub 7}, characterised by a negative baric coefficient. The effect of experimental conditions on the chemical stability of (NH{sub 4}){sub 3}SnF{sub 7} was observed. - Graphical abstract: Strong first order structural transformation Pa-3↔Pm-3m in (NH{sub 4}){sub 3}SnF{sub 7} is associated with very large total entropy change of ΔS{sub 0}=32.5 J/mol K characteristic for the ordering processes and equal to the sum of entropy changes in the related (NH{sub 4}){sub 3}TiF{sub 7} undergoing transformation between the same two cubic phases through the intermediate phases. - Highlights: • (NH{sub 4}){sub 3}SnF{sub 7} undergoes strong first order Pa-3↔Pm-3m phase transition. • Anomalous behaviour of ΔC{sub p} and ΔV/V exists far below phase transition temperature. • Structural distortions are accompanied by huge total entropy change ΔS≈Rln50. • High pressure strongly increases the stability of Pa-3 phase in (NH{sub 4}){sub 3}SnF{sub 7}. • Entropy of the Pa-3↔Pm-3m phase transition does not depend on pressure.« less

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

PubMed

Kameda, Hiroshi; Usugi, Sayaka; Kobayashi, Mana; Fukui, Naoya; Lee, Seki; Hongo, Kunihiro; Mizobata, Tomohiro; Sekiguchi, Yuki; Masaki, Yu; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi; Takayama, Yuki; Yamamoto, Masaki; Kawata, Yasushi

2017-01-01

The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells are still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis. Using coherent X-ray free electron laser pulses of SACLA, we analysed αSyn and GroES fibril intermediate species and characterized various aggregate structures. Unlike previous studies where an annular oligomeric form of αSyn was identified, particle reconstruction from scattering traces suggested that the specific forms of the toxic particles were varied, with the sizes of the particles falling within a specific range. We did however discover a common structural feature in both αSyn and GroES samples; the edges of the detected particles were nearly parallel and produced a characteristic diffraction pattern in the diffraction experiments. The presence of parallel-edged particles in toxic intermediates of αSyn and GroES fibrillogenesis pointed towards a plausible common molecular interface that leads to the formation of mature fibrils. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

On the Nature of Disorder in Solid 4He

NASA Astrophysics Data System (ADS)

Krainyukova, N. V.

2010-02-01

We apply a modified Debye approach to calculate the Gibbs free energy for different structural phases and crystallite sizes in 4He. Atoms are assumed to interact via the Aziz potential. We have found that some intermediate (between hcp and bcc) phase predicted previously is more favorable than hcp at low temperatures and for small sizes. We show that it can exist in a wide pressure range up to 60 bar in 4He for crystallite sizes about 3,000 atoms. For larger sizes (10,000 atoms or more) this phase becomes unfavorable. In multidomain structures the intermediate phase competes with hcp and metastable fcc that can be a reason for disorder in solid 4He.

Synthesis and Characterization of Metal Complexes with Schiff Base Ligands

ERIC Educational Resources Information Center

Wilkinson, Shane M.; Sheedy, Timothy M.; New, Elizabeth J.

2016-01-01

In order for undergraduate laboratory experiments to reflect modern research practice, it is essential that they include a range of elements, and that synthetic tasks are accompanied by characterization and analysis. This intermediate general chemistry laboratory exercise runs over 2 weeks, and involves the preparation of a Schiff base ligand and…

Establishing the solubility and local structure(s) of Amorphous Calcium Carbonate (ACC): Toward an understanding of invertebrate biomineralization

NASA Astrophysics Data System (ADS)

Mergelsberg, S. T.; Ulrich, R. N.; Michel, F. M.; Dove, P. M.

2017-12-01

Recent advances in high-resolution imaging show the widespreadd occurrence of multistep pathways to mineralization in biological and geological settings (De Yoreo et al., 2015, Science). For example, carbonate biomineralization often involves precipitation of amorphous calcium carbonate (ACC) as a reactive intermediate that subsequently transforms to crystalline products with diverse structures. Although current carbonate mineral proxies are based upon the composition of final crystalline products, the final signatures may be recording the properties of the initial amorphous phase. Thus, it is critical to establish the physical properties of ACC and understand the factors that influence its evolution to final products at conditions that approximate biological environments. This disconnect limits our ability to build a process-based understanding of when/how minor and trace elements are recorded in mineral composition proxies. In this experimental study, we quantified the chemical and physical properties of ACC and its evolution to final products. We first determined ACC solubility under controlled chemical conditions using a new type of flow-through reactor developed by our research group (Blue and Dove, 2015, GCA; Blue et al., 2017, GCA). The experimental design varied Mg concentration and total alkalinity while maintaining a mild pH that approximates biological environments. ACC solubility was measured at specific time points during the precipitation (from super- and undersaturated conditions) and during its subsequent evolution. Parallel experiments characterized the structure of the corresponding amorphous products using in situ pair distribution function (PDF) and small-angle x-ray scattering (SAXS) analyses. The measurements demonstrate at least two types of ACC can be produced by tuning Mg concentration and alkalinity. Each "phase" exhibits distinct short-range ordering that demonstrates structure-specific solubility. We also find temporal changes in the short-range order of each type of ACC that are dependent upon Mg content. Insights from this study hold promise for quantifying the chemical and structural properties of ACC and reconcile discrepancies in the literature.

Network structure of Mo-oxide glasses

NASA Astrophysics Data System (ADS)

Fabian, M.; Svab, E.; Milanova, M.; Krezhov, K.

2017-01-01

The structure of molybdate glasses have been investigated by neutron and high-energy X-ray diffraction coupled with Reverse Monte Carlo (RMC) simulation technique. From the modelling the partial atomic correlation functions g ij(r), the coordination number distributions CN ij and bond angle distributions have been revealed. For binary 90MoO3-10Nd2O3 glass composition the fraction of MoO4/MoO6 was 0.55/0.25. Three type of ternary system have been studied, where the most important structural units was authenticated. For MoO3-Nd2O3-B2O3 sample mixed MoO4-BO4 and MoO4-BO3 linkages form pronounced intermediate-range order. In case of MoO3-ZnO-B2O3 series the BO3 and BO4 units are linked to MoO4 and/or ZnO4, forming mixed MoO4-BO4(BO3), MoO4-ZnO4 and ZnO4-BO4(BO3) bond-linkages.

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation

NASA Astrophysics Data System (ADS)

Mereuta, Loredana; Roy, Mahua; Asandei, Alina; Lee, Jong Kook; Park, Yoonkyung; Andricioaei, Ioan; Luchian, Tudor

2014-01-01

The microscopic details of how peptides translocate one at a time through nanopores are crucial determinants for transport through membrane pores and important in developing nano-technologies. To date, the translocation process has been too fast relative to the resolution of the single molecule techniques that sought to detect its milestones. Using pH-tuned single-molecule electrophysiology and molecular dynamics simulations, we demonstrate how peptide passage through the α-hemolysin protein can be sufficiently slowed down to observe intermediate single-peptide sub-states associated to distinct structural milestones along the pore, and how to control residence time, direction and the sequence of spatio-temporal state-to-state dynamics of a single peptide. Molecular dynamics simulations of peptide translocation reveal the time- dependent ordering of intermediate structures of the translocating peptide inside the pore at atomic resolution. Calculations of the expected current ratios of the different pore-blocking microstates and their time sequencing are in accord with the recorded current traces.

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales.

PubMed

Márk, Géza I; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales

NASA Astrophysics Data System (ADS)

Márk, Géza I.; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P.

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Differentiating snail intermediate hosts of Schistosoma spp. using molecular approaches: fundamental to successful integrated control mechanism in Africa.

PubMed

Abe, Eniola Michael; Guan, Wei; Guo, Yun-Hai; Kassegne, Kokouvi; Qin, Zhi-Qiang; Xu, Jing; Chen, Jun-Hu; Ekpo, Uwem Friday; Li, Shi-Zhu; Zhou, Xiao-Nong

2018-03-26

Snail intermediate hosts play active roles in the transmission of snail-borne trematode infections in Africa. A good knowledge of snail-borne diseases epidemiology particularly snail intermediate host populations would provide the necessary impetus to complementing existing control strategy. This review highlights the importance of molecular approaches in differentiating snail hosts population structure and the need to provide adequate information on snail host populations by updating snail hosts genome database for Africa, in order to equip different stakeholders with adequate information on the ecology of snail intermediate hosts and their roles in the transmission of different diseases. Also, we identify the gaps and areas where there is need for urgent intervention to facilitate effective integrated control of schistosomiasis and other snail-borne trematode infections. Prioritizing snail studies, especially snail differentiation using molecular tools will boost disease surveillance and also enhance efficient schistosomaisis control programme in Africa.

Characterization of novel microstructures in Al-Fe-V-Si and Al-Fe-V-Si-Y alloys processed at intermediate cooling rates

NASA Astrophysics Data System (ADS)

Marshall, Ryan

Samples of an Al-Fe-V-Si alloy with and without small Y additions were prepared by copper wedge-mold casting. Analysis of the microstructures developed at intermediate cooling rates revealed the formation of an atypical morphology of the cubic alpha-Al12(Fe/V)3Si phase (Im 3 space group with a = 1.26 nm) in the form of a microeutectic with alpha-Al that forms in relatively thick sections. This structure was determined to exhibit promising hardness and thermal stability when compared to the commercial rapidly solidified and processed Al-Fe-V-Si (RS8009) alloy. In addition, convergent beam electron diffraction (CBED) and selected area electron diffraction (SAD) were used to characterize a competing intermetallic phase, namely, a hexagonal phase identified as h-AlFeSi (P6/mmm space group with a = 2.45 nm c = 1.25 nm) with evidence of a structural relationship to the icosahedral quasicrystalline (QC) phase (it is a QC approximant) and a further relationship to the more desirable alpha-Al12(Fe/V) 3Si phase, which is also a QC approximant. The analysis confirmed the findings of earlier studies in this system, which suggested the same structural relationships using different methods. As will be shown, both phases form across a range of cooling rates and appear to have good thermal stabilities. Additions of Y to the alloy were also studied and found to cause the formation of primary YV2Al20 particles on the order of 1 microm in diameter distributed throughout the microstructure, which otherwise appeared essentially identical to that of the Y-free 8009 alloy. The implications of these results on the possible development of these structures will be discussed in some detail.

Influence of the Ag concentration on the medium-range order in a CuZrAlAg bulk metallic glass

DOE PAGES

Gammer, C.; Escher, B.; Ebner, C.; ...

2017-03-21

Fluctuation electron microscopy of bulk metallic glasses of CuZrAl(Ag) demonstrates that medium-range order is sensitive to minor compositional changes. Furthermore, by analyzing nanodiffraction patterns medium-range order is detected with crystal-like motifs based on the B2 CuZr structure and its distorted structures resembling the martensitic ones. This result thus demonstrates some structural homology between the metallic glass and its high temperature crystalline phase. The amount of medium-range order seems slightly affected with increasing Ag concentration (0, 2, 5 at.%) but the structural motifs of the medium-range ordered clusters become more diverse at the highest Ag concentration. The decrease of dominant clustersmore » is consistent with the destabilization of the B2 structure measured by calorimetry and accounts for the increased glass-forming ability.« less

Influence of the Ag concentration on the medium-range order in a CuZrAlAg bulk metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gammer, C.; Escher, B.; Ebner, C.

Fluctuation electron microscopy of bulk metallic glasses of CuZrAl(Ag) demonstrates that medium-range order is sensitive to minor compositional changes. Furthermore, by analyzing nanodiffraction patterns medium-range order is detected with crystal-like motifs based on the B2 CuZr structure and its distorted structures resembling the martensitic ones. This result thus demonstrates some structural homology between the metallic glass and its high temperature crystalline phase. The amount of medium-range order seems slightly affected with increasing Ag concentration (0, 2, 5 at.%) but the structural motifs of the medium-range ordered clusters become more diverse at the highest Ag concentration. The decrease of dominant clustersmore » is consistent with the destabilization of the B2 structure measured by calorimetry and accounts for the increased glass-forming ability.« less

Kinetics of silicide formation over a wide range of heating rates spanning six orders of magnitude

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molina-Ruiz, Manel; Lopeandía, Aitor F.; Gonzalez-Silveira, Marta

Kinetic processes involving intermediate phase formation are often assumed to follow an Arrhenius temperature dependence. This behavior is usually inferred from limited data over narrow temperature intervals, where the exponential dependence is generally fully satisfied. However, direct evidence over wide temperature intervals is experimentally challenging and data are scarce. Here, we report a study of silicide formation between a 12 nm film of palladium and 15 nm of amorphous silicon in a wide range of heating rates, spanning six orders of magnitude, from 0.1 to 10{sup 5 }K/s, or equivalently more than 300 K of variation in reaction temperature. The calorimetric traces exhibit severalmore » distinct exothermic events related to interdiffusion, nucleation of Pd{sub 2}Si, crystallization of amorphous silicon, and vertical growth of Pd{sub 2}Si. Interestingly, the thickness of the initial nucleation layer depends on the heating rate revealing enhanced mass diffusion at the fastest heating rates during the initial stages of the reaction. In spite of this, the formation of the silicide strictly follows an Arrhenius temperature dependence over the whole temperature interval explored. A kinetic model is used to fit the calorimetric data over the complete heating rate range. Calorimetry is complemented by structural analysis through transmission electron microscopy and both standard and in-situ synchrotron X-ray diffraction.« less

Efficient near-field wireless energy transfer using adiabatic system variations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from themore » first resonator structure to the second resonator structure through the intermediate resonator structure.« less

Propylene oxidation mechanisms and intermediates using in situ soft X-ray fluorescence methods on the Pt(111) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gabelnick, A.M.; Capitano, A.T.; Kane, S.M.

2000-01-12

The oxidation of propylene preabsorbed on the Pt(111) surface has been characterized in oxygen pressures up to 0.02 Torr using fluorescence yield near-edge spectroscopy (FYNES) and temperature-programmed fluorescence yield near-edge spectroscopy (TP-FYNES) above the carbon K edge. During oxidation of adsorbed propylene, a stable intermediate was observed and characterized using these soft X-ray methods. A general in situ method for determining the stoichiometry of carbon-containing reaction intermediate species has been developed and demonstrated for the first time. Total carbon concentration measured during temperature-programmed reaction studies clearly indicates a reaction intermediate is formed in the 300 K temperature range with amore » surface concentration of 0.55 x 10{sup 15} carbon atoms/cm{sup 2}. By comparing the intensity of the C-H {sigma}* resonance at the magic angle with the intensity in the carbon continuum, the stoichiometry of this intermediate can be determined unambiguously. Based on calibration with molecular propylene (C{sub 3}H{sub 6}) and propylidyne (C{sub 3}H{sub 5}), the intermediate has a C{sub 3}H{sub 5} stoichiometry for oxygen pressures up to 0.02 Torr. A set of normal and glancing angle FYNES spectra above the carbon K edge was used to characterize the bonding and structure of this intermediate. Spectra of known coverages of adsorbed propylene and propylidyne served as standards. The spectra of di-{sigma} propylene, propylidyne, and the intermediate were curve fit as a group with consistent energies and widths of all primary features. Based on this procedure, the intermediate is 1,1,2-tri-{sigma} 1-methylvinyl. The stoichiometry and temperature stability range of the 1-methylvinyl intermediate formed in oxygen pressures up to 0.02 Torr is identical with the stoichiometry and stability of the same intermediate formed during oxidation of preadsorbed propylene by excess coadsorbed atomic oxygen.« less

The thermal properties of beeswaxes: unexpected findings.

PubMed

Buchwald, Robert; Breed, Michael D; Greenberg, Alan R

2008-01-01

Standard melting point analyses only partially describe the thermal properties of eusocial beeswaxes. Differential scanning calorimetry (DSC) revealed that thermal phase changes in wax are initiated at substantially lower temperatures than visually observed melting points. Instead of a sharp, single endothermic peak at the published melting point of 64 degrees C, DSC analysis of Apis mellifera Linnaeus wax yielded a broad melting curve that showed the initiation of melting at approximately 40 degrees C. Although Apis beeswax retained a solid appearance at these temperatures, heat absorption and initiation of melting could affect the structural characteristics of the wax. Additionally, a more complete characterization of the thermal properties indicated that the onset of melting, melting range and heat of fusion of beeswaxes varied significantly among tribes of social bees (Bombini, Meliponini, Apini). Compared with other waxes examined, the relatively malleable wax of bumblebees (Bombini) had the lowest onset of melting and lowest heat of fusion but an intermediate melting temperature range. Stingless bee (Meliponini) wax was intermediate between bumblebee and honeybee wax (Apini) in heat of fusion, but had the highest onset of melting and the narrowest melting temperature range. The broad melting temperature range and high heat of fusion in the Apini may be associated with the use of wax comb as a free-hanging structural material, while the Bombini and Meliponini support their wax structures with exogenous materials.

Synthesis and reversible hydration behavior of the thiosulfate intercalated layered double hydroxide of Zn and Al

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radha, S.; Milius, Wolfgang; Breu, Josef, E-mail: josef.breu@uni-bayreuth.de

2013-08-15

The thiosulfate-intercalated layered double hydroxide of Zn and Al undergoes reversible hydration with a variation in the relative humidity of the ambient. The hydrated and dehydrated phases, which represent the end members of the hydration cycle, both adopt the structure of the 3R{sub 1} polytype. In the intermediate range of relative humidity values (40–60%), the hydrated and dehydrated phases coexist. The end members of the hydration cycle adopt the structure of the same polytype, and vary only in their basal spacings. This points to the possibility that all the intermediate phases have a kinetic origin. - Graphical abstract: Basal spacingmore » evolution of the thiosulfate ion intercalated [Zn–Al] LDH during one complete hydration–dehydration cycle as a function of relative humidity. Display Omitted - Highlights: • Thiosulfate intercalated [Zn–Al] LDHs were synthesized by co-precipitation. • The LDH exhibits reversible hydration with variation in humidity. • Both the end members of the hydration cycle adopt the same polytype structure. • The interstratified intermediates observed are kinetic in origin.« less

Singular ferromagnetic susceptibility of the transverse-field Ising antiferromagnet on the triangular lattice

NASA Astrophysics Data System (ADS)

Biswas, Sounak; Damle, Kedar

2018-02-01

A transverse magnetic field Γ is known to induce antiferromagnetic three-sublattice order of the Ising spins σz in the triangular lattice Ising antiferromagnet at low enough temperature. This low-temperature order is known to melt on heating in a two-step manner, with a power-law ordered intermediate temperature phase characterized by power-law correlations at the three-sublattice wave vector Q : <σz(R ⃗) σz(0 ) > ˜cos(Q .R ⃗) /|R⃗| η (T ) with the temperature-dependent power-law exponent η (T )∈(1 /9 ,1 /4 ) . Here, we use a quantum cluster algorithm to study the ferromagnetic easy-axis susceptibility χu(L ) of an L ×L sample in this power-law ordered phase. Our numerical results are consistent with a recent prediction of a singular L dependence χu(L ) ˜L2 -9 η when η (T ) is in the range (1 /9 ,2 /9 ) . This finite-size result implies, via standard scaling arguments, that the ferromagnetic susceptibility χu(B ) to a uniform field B along the easy axis is singular at intermediate temperatures in the small B limit, χu(B ) ˜|B| -4/-18 η 4 -9 η for η (T )∈(1 /9 ,2 /9 ) , although there is no ferromagnetic long-range order in the low temperature state. Additionally we establish similar two-step melting behavior (via a study of the order parameter susceptibility χQ) in the case of the ferrimagnetic three-sublattice ordered phase which is stabilized by ferromagnetic next-neighbor couplings (J2) and confirm that the ferromagnetic susceptibility obeys the predicted singular form in the associated power-law ordered phase.

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters.

PubMed

Galavis, Paulina E; Hollensen, Christian; Jallow, Ngoneh; Paliwal, Bhudatt; Jeraj, Robert

2010-10-01

Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45-60 minutes post-injection of 10 mCi of [(18)F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor segmentation.

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters

PubMed Central

GALAVIS, PAULINA E.; HOLLENSEN, CHRISTIAN; JALLOW, NGONEH; PALIWAL, BHUDATT; JERAJ, ROBERT

2014-01-01

Background Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Material and methods Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45–60 minutes post-injection of 10 mCi of [18F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Results Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Conclusion Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor segmentation. PMID:20831489

Low-carbon martensitic steels. Alloying and properties

NASA Astrophysics Data System (ADS)

Kleiner, L. M.; Shatsov, A. A.; Larinin, D. M.

2011-03-01

Requirements on the structure of a steel with structural strength and a set of characteristics higher than those of medium-carbon steels with a structure of tempered sorbite are formulated. Principles for choosing compositions for process-adaptable low-carbon martensitic steels are presented. The combination of carbon and alloying elements providing high stability of austenite in the ranges of normal and intermediate transformations is determined, which makes it possible to obtain lath martensite in slow cooling.

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanikawa, Ataru; Sato, Yushi; Hachisu, Izumi

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N , from a few 10{sup 4} to a few 10{sup 7} in order to check mass resolution convergence, where SPH simulations with N > 10{sup 7} (or a space resolution of several 10{sup 6} cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less activemore » with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 10{sup 4} to 10{sup 7} cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲10{sup 6} cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.« less

Russian Compliance with the Intermediate Range Nuclear Forces (INF) Treaty: Background and Issues for Congress

DTIC Science & Technology

2017-01-27

Russian Compliance with the Intermediate Range Nuclear Forces (INF) Treaty: Background and Issues for Congress Amy F. Woolf Specialist in... Nuclear Weapons Policy January 27, 2017 Congressional Research Service 7-5700 www.crs.gov R43832 Russian Compliance with the Intermediate Range... Nuclear Forces (INF) Treaty Congressional Research Service Summary The United States and Soviet Union signed the Intermediate-Range Nuclear Forces

Transition-metal-substituted indium thiospinels as novel intermediate-band materials: prediction and understanding of their electronic properties.

PubMed

Palacios, P; Aguilera, I; Sánchez, K; Conesa, J C; Wahnón, P

2008-07-25

Results of density-functional calculations for indium thiospinel semiconductors substituted at octahedral sites with isolated transition metals (M=Ti,V) show an isolated partially filled narrow band containing three t2g-type states per M atom inside the usual semiconductor band gap. Thanks to this electronic structure feature, these materials will allow the absorption of photons with energy below the band gap, in addition to the normal light absorption of a semiconductor. To our knowledge, we demonstrate for the first time the formation of an isolated intermediate electronic band structure through M substitution at octahedral sites in a semiconductor, leading to an enhancement of the absorption coefficient in both infrared and visible ranges of the solar spectrum. This electronic structure feature could be applied for developing a new third-generation photovoltaic cell.

Mineralogy of Iron Microbial Mats from Loihi Seamount

PubMed Central

Toner, Brandy M.; Berquó, Thelma S.; Michel, F. Marc; Sorensen, Jeffry V.; Templeton, Alexis S.; Edwards, Katrina J.

2011-01-01

Extensive mats of Fe oxyhydroxides and associated Fe-oxidizing microbial organisms form in diverse geochemical settings – freshwater seeps to deep-sea vents – where ever opposing Fe(II)-oxygen gradients prevail. The mineralogy, reactivity, and structural transformations of Fe oxyhydroxides precipitated from submarine hydrothermal fluids within microbial mats remains elusive in active and fossil systems. In response, a study of Fe microbial mat formation at the Loihi Seamount was conducted to describe the physical and chemical characteristics of Fe-phases using extended X-ray absorption fine structure spectroscopy, powder X-ray diffraction, synchrotron radiation X-ray total scattering, low-temperature magnetic measurements, and Mössbauer spectroscopy. Particle sizes of 3.5–4.6 nm were estimated from magnetism data, and coherent scattering domain (CSD) sizes as small as 1.6 nm are indicated by pair distribution function (PDF) analysis. Disorder in the nanostructured Fe-bearing phases results in limited intermediate-range structural order: less than that of standard two-line ferrihydrite (Fh), except for the Pohaku site. The short-range ordered natural Fh (FhSRO) phases were stable at 4°C in the presence of oxygen for at least 1 year and during 400°C treatment. The observed stability of the FhSRO is consistent with magnetic observations that point to non-interacting nanoparticles. PDF analyses of total scattering data provide further evidence for FhSRO particles with a poorly ordered silica coating. The presence of coated particles explains the small CSD for the mat minerals, as well as the stability of the minerals over time and against heating. The mineral properties observed here provide a starting point from which progressively older and more extensively altered Fe deposits may be examined, with the ultimate goal of improved interpretation of past biogeochemical conditions and diagenetic processes. PMID:22485113

An infrared study of the nitro—nitrito linkage isomerization in solid nitro- and nitritopentamminecobalt(III) chloride

NASA Astrophysics Data System (ADS)

Heyns, A. M.; de Waal, D.

1989-01-01

The photochemical isomerization reaction of [Co(NH 3) 5NO 2]Cl 2 to [Co(NH 3) 5ONO]Cl 2 has been studied in the solid state by means of i.r. spectroscopy. The reaction is first order with k = 2.53±0.05 × 10 -4s -1 and is much faster ( t1/2=49min) than the well-known spontaneous nitrito → nitro isomerization ( t1/2 = 6 days). The i.r. bands of both the NH 3 and ONO - -groups in the range 4000-50 cm -1 indicate minor differences between the structures of freshly and photochemically prepared [Co(NH 3) 5ONO]Cl 2. The far i.r. spectra indicate the disorder existing in the intermediate products during the isomerization processes.

Microcanonical molecular simulations of methane hydrate nucleation and growth: evidence that direct nucleation to sI hydrate is among the multiple nucleation pathways.

PubMed

Zhang, Zhengcai; Walsh, Matthew R; Guo, Guang-Jun

2015-04-14

The results of six high-precision constant energy molecular dynamics (MD) simulations initiated from methane-water systems equilibrated at 80 MPa and 250 K indicate that methane hydrates can nucleate via multiple pathways. Five trajectories nucleate to an amorphous solid. One trajectory nucleates to a structure-I hydrate template with long-range order which spans the simulation box across periodic boundaries despite the presence of several defects. While experimental and simulation data for hydrate nucleation with different time- and length-scales suggest that there may exist multiple pathways for nucleation, including metastable intermediates and the direct formation of the globally-stable phase, this work provides the most compelling evidence that direct formation to the globally stable crystalline phase is one of the multiple pathways available for hydrate nucleation.

Correlation and nuclear distortion effects of Cr-substituted ZnSe.

PubMed

Tablero, C

2007-04-28

There is a great deal of interest in the effect of the correlation and effect of the atomic distortion in materials with a metallic intermediate band. This band, situated within the semiconductor band gaps, would be split, thus creating two bands, a full one below the Fermi energy and an empty one above it, i.e., a metal-insulator transition. This basic electronic band structure corresponds to intermediate band materials and is characteristic of transparent-conducting oxides, up and down converters, and intermediate band solar cells. A sufficiently high density of Cr in ZnSe substituting the Zn atoms leads to a microscopic intermediate band, in which these effects will be analyzed. A Hubbard term has been included to improve the description of the many-body effect. This term modifies the bandwidth of the intermediate band, the Fermi energy, and breaks the orbital-occupation degeneracy. From the results, the intermediate band is not split within the range of Hubbard term values analyzed and for Cr substituting Zn from 0.463% to 3.125% of Cr atomic concentration.

Intermediate honeycomb ordering to trigger oxygen redox chemistry in layered battery electrode

NASA Astrophysics Data System (ADS)

Mortemard de Boisse, Benoit; Liu, Guandong; Ma, Jiangtao; Nishimura, Shin-Ichi; Chung, Sai-Cheong; Kiuchi, Hisao; Harada, Yoshihisa; Kikkawa, Jun; Kobayashi, Yoshio; Okubo, Masashi; Yamada, Atsuo

2016-04-01

Sodium-ion batteries are attractive energy storage media owing to the abundance of sodium, but the low capacities of available cathode materials make them impractical. Sodium-excess metal oxides Na2MO3 (M: transition metal) are appealing cathode materials that may realize large capacities through additional oxygen redox reaction. However, the general strategies for enhancing the capacity of Na2MO3 are poorly established. Here using two polymorphs of Na2RuO3, we demonstrate the critical role of honeycomb-type cation ordering in Na2MO3. Ordered Na2RuO3 with honeycomb-ordered [Na1/3Ru2/3]O2 slabs delivers a capacity of 180 mAh g-1 (1.3-electron reaction), whereas disordered Na2RuO3 only delivers 135 mAh g-1 (1.0-electron reaction). We clarify that the large extra capacity of ordered Na2RuO3 is enabled by a spontaneously ordered intermediate Na1RuO3 phase with ilmenite O1 structure, which induces frontier orbital reorganization to trigger the oxygen redox reaction, unveiling a general requisite for the stable oxygen redox reaction in high-capacity Na2MO3 cathodes.

Intermediate honeycomb ordering to trigger oxygen redox chemistry in layered battery electrode.

PubMed

Mortemard de Boisse, Benoit; Liu, Guandong; Ma, Jiangtao; Nishimura, Shin-ichi; Chung, Sai-Cheong; Kiuchi, Hisao; Harada, Yoshihisa; Kikkawa, Jun; Kobayashi, Yoshio; Okubo, Masashi; Yamada, Atsuo

2016-04-18

Sodium-ion batteries are attractive energy storage media owing to the abundance of sodium, but the low capacities of available cathode materials make them impractical. Sodium-excess metal oxides Na2MO3 (M: transition metal) are appealing cathode materials that may realize large capacities through additional oxygen redox reaction. However, the general strategies for enhancing the capacity of Na2MO3 are poorly established. Here using two polymorphs of Na2RuO3, we demonstrate the critical role of honeycomb-type cation ordering in Na2MO3. Ordered Na2RuO3 with honeycomb-ordered [Na(1/3)Ru(2/3)]O2 slabs delivers a capacity of 180 mAh g(-1) (1.3-electron reaction), whereas disordered Na2RuO3 only delivers 135 mAh g(-1) (1.0-electron reaction). We clarify that the large extra capacity of ordered Na2RuO3 is enabled by a spontaneously ordered intermediate Na1RuO3 phase with ilmenite O1 structure, which induces frontier orbital reorganization to trigger the oxygen redox reaction, unveiling a general requisite for the stable oxygen redox reaction in high-capacity Na2MO3 cathodes.

Engineered disorder and light propagation in a planar photonic glass

PubMed Central

Romanov, Sergei G.; Orlov, Sergej; Ploss, Daniel; Weiss, Clemens K.; Vogel, Nicolas; Peschel, Ulf

2016-01-01

The interaction of light with matter strongly depends on the structure of the latter at wavelength scale. Ordered systems interact with light via collective modes, giving rise to diffraction. In contrast, completely disordered systems are dominated by Mie resonances of individual particles and random scattering. However, less clear is the transition regime in between these two extremes, where diffraction, Mie resonances and near-field interaction between individual scatterers interplay. Here, we probe this transitional regime by creating colloidal crystals with controlled disorder from two-dimensional self-assembly of bidisperse spheres. Choosing the particle size in a way that the small particles are transparent in the spectral region of interest enables us to probe in detail the effect of increasing positional disorder on the optical properties of the large spheres. With increasing disorder a transition from a collective optical response characterized by diffractive resonances to single particles scattering represented by Mie resonances occurs. In between these extremes, we identify an intermediate, hopping-like light transport regime mediated by resonant interactions between individual spheres. These results suggest that different levels of disorder, characterized not only by absence of long range order but also by differences in short-range correlation and interparticle distance, exist in colloidal glasses. PMID:27277521

Tailoring the Edge Structure of Molybdenum Disulfide toward Electrocatalytic Reduction of Carbon Dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abbasi, Pedram; Asadi, Mohammad; Liu, Cong

2017-01-24

Electrocatalytic conversion of carbon dioxide (CO2) into energy-rich fuels is considered to be the most efficient approach to achieve a carbon neutral cycle. Transition-metal dichalcogenides (TMDCs) have recently shown a very promising catalytic performance for CO2 reduction reaction in an ionic liquid electrolyte. Here, we report that the catalytic performance of molybdenum disulfide (MoS2), a member of TMDCs, can be significantly improved by using an appropriate dopant. Our electrochemical results indicate that 5% niobium (Nb)-doped vertically aligned MoS2 in ionic liquid exhibits 1 order of magnitude higher CO formation turnover frequency (TOF) than pristine MoS2 at an overpotential range ofmore » 50-150 mV. The TOF of this catalyst is also 2 orders of magnitude higher than that of Ag nanoparticles over the entire range of studied overpotentials (100-650 mV). Moreover, the in situ differential electrochemical mass spectrometry experiment shows the onset overpotential of 31 mV for this catalyst, which is the lowest onset potential for CO2 reduction reaction reported so far. Our density functional theory calculations reveal that low concentrations of Nb near the Mo edge atoms can enhance the TOF of CO formation by modifying the binding energies of intermediates to MoS2 edge atoms.« less

Altered structural development and accelerated succession from intermediate-scale wind disturbance in Quercus stands on the Cumberland Plateau, USA

Treesearch

Stephen D White; Justin L. Hart; Callie J. Schweitzer; Daniel C. Dey

2015-01-01

Natural disturbances play important roles in shaping the structure and composition of all forest ecosystems and can be used to inform silvicultural practices. Canopy disturbances are often classified along a gradient ranging from highly localized, gap-scale events to stand-replacing events. Wind storms such as downbursts, derechos, and low intensity tornadoes typically...

Effects of intermediate-scale wind disturbance on composition, structure, and succession in Quercus stands: Implications for natural disturbance-based silviculture

Treesearch

M.M. Cowden; J.L. Hart; C.J. Schweitzer; D.C. Dey

2014-01-01

Forest disturbances are discrete events in space and time that disrupt the biophysical environment and impart lasting legacies on forest composition and structure. Disturbances are often classified along a gradient of spatial extent and magnitude that ranges from catastrophic events where most of the overstory is removed to gap-scale events that modify local...

Orbital effects in cobaltites by neutron scattering

NASA Astrophysics Data System (ADS)

Louca, Despina

2005-03-01

The orbital degree of freedom can play a central role in the physics of transition metal perovskite oxides because of its intricate coupling with other degrees of freedom such as spin, charge and lattice. In this talk the case of La1-xSrxCoO3 will be presented. Using elastic and inelastic neutron scattering, we investigated the thermal evolution of the local atomic structure and lattice dynamics in the pure sample and with the addition of charge carriers as the system crosses over from a paramagnetic insulator to a ferromagnetic metal. In LaCoO3, the thermal activation of the Co ions from a nonmagnetic ground state to an intermediate spin state gives rise to orbital degeneracy. This leads to Jahn-Teller distortions that are dynamical in nature. Doping stabilizes the intermediate spin configuration of the Co ions in the paramagnetic insulating phase. Evidence for local static Jahn-Teller distortions is observed but without long-range ordering. The size of the JT lattice is proportional to the amount of charge. However, with cooling to the metallic phase, static JT distortions disappear for x <= 30 %, the percolation limit. This coincides with narrowing of two modes at φ=22,nd,4,eV in the phonon spectrum in which we argue is due to localized dynamical JT fluctuations^1. The implications of the orbital effects to the structural and magnetic properties will be discussed. ^1D. Louca and J. L. Sarrao, Phys. Rev. Lett. 91, 155501 (2003).

Driving Forces of the Self-Assembly of Supramolecular Systems: Partially Ordered Mesophases

NASA Astrophysics Data System (ADS)

Shcherbina, M. A.; Chvalun, S. N.

2018-06-01

The main aspects are considered of the self-organization of a new class of liquid crystalline compounds, rigid sector-shaped and cone-shaped dendrons. Theoretical approaches to the self-assembly of different amphiphilic compounds (lipids, bolaamphiphiles, block copolymers, and polyelectrolytes) are described. Particular attention is given to the mesophase structures that emerge during the self-organization of mesophases characterized by intermediate degrees of ordering, e.g., plastic crystals, the rotation-crystalline phase in polymers, ordered and disordered two-dimensional columnar phases, and bicontinuous cubic phases of different symmetry.

The development of quick, robust, quantitative phenotypic assays for describing the host–nonhost landscape to stripe rust

PubMed Central

Dawson, Andrew M.; Bettgenhaeuser, Jan; Gardiner, Matthew; Green, Phon; Hernández-Pinzón, Inmaculada; Hubbard, Amelia; Moscou, Matthew J.

2015-01-01

Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host–nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen’s ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon. PMID:26579142

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PubMed Central

Bian, Yunqiang; Zhang, Jian; Wang, Jun; Wang, Jihua; Wang, Wei

2015-01-01

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA. PMID:26030098

Surface nematic order in iron pnictides

NASA Astrophysics Data System (ADS)

Song, Kok Wee; Koshelev, Alexei E.

2016-09-01

Electronic nematicity plays an important role in iron-based superconductors. These materials have a layered structure and the theoretical description of their magnetic and nematic transitions has been well established in the two-dimensional approximation, i.e., when the layers can be treated independently. However, the interaction between iron layers mediated by electron tunneling may cause nontrivial three-dimensional behavior. Starting from the simplest model for orbital nematic in a single layer, we investigate the influence of interlayer tunneling on the bulk nematic order and a possible preemptive state where this order is only formed near the surface. We found that the interlayer tunneling suppresses the bulk nematicity, which makes favorable the formation of a surface nematic order above the bulk transition temperature. The purely electronic tunneling Hamiltonian, however, favors a nematic order parameter that alternates from layer to layer. The uniform bulk state typically observed experimentally may be stabilized by the coupling with the elastic lattice deformation. Depending on the strength of this coupling, we found three regimes: (i) surface nematic and alternating bulk order, (ii) surface nematic and uniform bulk order, and (iii) uniform bulk order without the intermediate surface phase. The intermediate surface-nematic state may resolve the current controversy about the existence of a weak nematic transition in the compound BaFe2As2 -xPx .

Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

Relating dynamics of model unentangled, crystallizable polymeric liquids to their local structure

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Hoy, Robert S.

We study the liquid-state dynamics of a recently developed, crystallizable bead-spring polymer model. The model possesses a single ground state (NCP, wherein monomers close-pack and chains are nematically aligned) for all finite bending stiffnesses kb, but the solid morphologies formed under cooling vary strongly with kb, varying from NCP to amorphous. We find that systems with kb producing amorphous order are good glass-formers exhibiting the classic Vogel-Fulcher slowdown with decreasing temperature T. In contrast, systems with kb producing crystalline solids exhibit a simpler dynamics when kb is small. Larger kb produce more complex dynamics, but these are associated with the existence of an intermediate nematic liquid rather than glassy slowdown. We relate these differences to local, cluster-level structure measured via TCC analyses. Formation propensities and lifetimes of various clusters (associated with amorphous or crystalline order) vary strongly with kb and T. We relate these differences to those measured by the self-intermediate scattering function and other macroscopic measures of dynamics. Our results should aid in understanding the competition between crystallization and glass-formation in synthetic polymers.

A modulation wave approach to the order hidden in disorder

PubMed Central

Withers, Ray

2015-01-01

The usefulness of a modulation wave approach to understanding and interpreting the highly structured continuous diffuse intensity distributions characteristic of the reciprocal spaces of the very large family of inherently flexible materials which exhibit ordered ‘disorder’ is pointed out. It is shown that both longer range order and truly short-range order are simultaneously encoded in highly structured diffuse intensity distributions. The long-range ordered crystal chemical rules giving rise to such diffuse distributions are highlighted, along with the existence and usefulness of systematic extinction conditions in these types of structured diffuse distributions. PMID:25610629

Productive Nanosystems: The Physics of Molecular Fabrication

ERIC Educational Resources Information Center

Drexler, K. Eric

2005-01-01

Fabrication techniques are the foundation of physical technology, and are thus of fundamental interest. Physical principles indicate that nanoscale systems will be able to fabricate a wide range of structures, operating with high productivity and precise molecular control. Advanced systems of this kind will require intermediate generations of…

Structures, phase transitions and microwave dielectric properties of the 6H perovskites Ba 3BSb 2O 9, B=Mg, Ca, Sr, Ba

NASA Astrophysics Data System (ADS)

Ling, Chris D.; Rowda, Budwy; Avdeev, Maxim; Pullar, Robert

2009-03-01

We present a complete temperature-composition phase diagram for Ba 3BSb 2O 9, B=Mg, Ca, Sr, Ba, along with their electrical behavior as a function of B. These compounds have long been recognized as 6H-type perovskites, but (with the exception of B=Mg) their exact structures and properties were unknown due to their low symmetries, temperature-dependent phase transitions, and difficulties in synthesizing pure samples. The full range of possible space group symmetries is observed, from ideal hexagonal P6 3/ mmc to monoclinic C2/ c to triclinic P1¯. Direct second-order transitions between these phases are plausible according to group theory, and no evidence was seen for any further intermediate phases. The phase diagram with respect to temperature and the effective ionic radius of B is remarkably symmetrical for B=Mg, Ca, and Sr. For B=Ba, a first-order phase transition to a locally distorted phase allows a metastable hexagonal phase to persist to lower temperatures than expected before decomposing around 600 K. Electrical measurements revealed that dielectric permittivity corrected for porosity does not change significantly as a function of B and is in a good agreement with the values predicted by the Clausius-Mossotti equation.

A conserved loop-wedge motif moderates reaction site search and recognition by FEN1.

PubMed

Thompson, Mark J; Gotham, Victoria J B; Ciani, Barbara; Grasby, Jane A

2018-06-07

DNA replication and repair frequently involve intermediate two-way junction structures with overhangs, or flaps, that must be promptly removed; a task performed by the essential enzyme flap endonuclease 1 (FEN1). We demonstrate a functional relationship between two intrinsically disordered regions of the FEN1 protein, which recognize opposing sides of the junction and order in response to the requisite substrate. Our results inform a model in which short-range translocation of FEN1 on DNA facilitates search for the annealed 3'-terminus of a primer strand, which is recognized by breaking the terminal base pair to generate a substrate with a single nucleotide 3'-flap. This recognition event allosterically signals hydrolytic removal of the 5'-flap through reaction in the opposing junction duplex, by controlling access of the scissile phosphate diester to the active site. The recognition process relies on a highly-conserved 'wedge' residue located on a mobile loop that orders to bind the newly-unpaired base. The unanticipated 'loop-wedge' mechanism exerts control over substrate selection, rate of reaction and reaction site precision, and shares features with other enzymes that recognize irregular DNA structures. These new findings reveal how FEN1 precisely couples 3'-flap verification to function.

Structure and Properties of Silica Glass Densified in Cold Compression and Hot Compression

NASA Astrophysics Data System (ADS)

Guerette, Michael; Ackerson, Michael R.; Thomas, Jay; Yuan, Fenglin; Bruce Watson, E.; Walker, David; Huang, Liping

2015-10-01

Silica glass has been shown in numerous studies to possess significant capacity for permanent densification under pressure at different temperatures to form high density amorphous (HDA) silica. However, it is unknown to what extent the processes leading to irreversible densification of silica glass in cold-compression at room temperature and in hot-compression (e.g., near glass transition temperature) are common in nature. In this work, a hot-compression technique was used to quench silica glass from high temperature (1100 °C) and high pressure (up to 8 GPa) conditions, which leads to density increase of ~25% and Young’s modulus increase of ~71% relative to that of pristine silica glass at ambient conditions. Our experiments and molecular dynamics (MD) simulations provide solid evidences that the intermediate-range order of the hot-compressed HDA silica is distinct from that of the counterpart cold-compressed at room temperature. This explains the much higher thermal and mechanical stability of the former than the latter upon heating and compression as revealed in our in-situ Brillouin light scattering (BLS) experiments. Our studies demonstrate the limitation of the resulting density as a structural indicator of polyamorphism, and point out the importance of temperature during compression in order to fundamentally understand HDA silica.

Discovery of Compact Quiescent Galaxies at Intermediate Redshifts in DEEP2

NASA Astrophysics Data System (ADS)

Blancato, Kirsten; Chilingarian, Igor; Damjanov, Ivana; Moran, Sean; Katkov, Ivan

2015-01-01

Compact quiescent galaxies in the redshift range 0.6 < z < 1.1 are the missing link needed to complete the evolutionary histories of these objects from the high redshift z ≥ 2 Universe to the local z ~ 0 Universe. We identify the first intermediate redshift compact quiescent galaxies by searching a sample of 1,089 objects in the DEEP2 Redshift Survey that have multi-band photometry, spectral fitting, and readily available structural parameters. We find 27 compact quiescent candidates between z = 0.6 and z = 1.1 where each candidate galaxy has archival Hubble Space Telescope (HST) imaging and is visually confirmed to be early-type. The candidates have half-light radii ranging from 0.83 < Re,c < 7.14 kpc (median Re,c = 1.77 kpc) and virial masses ranging from 2.2E10 < Mdyn < 5.6E11 Msun (median Mdyn = 7.7E10 Msun). Of our 27 compact quiescent candidates, 13 are truly compact with sizes at most half of the size of their z ~ 0 counterparts of the same mass. In addition to their structural properties bridging the gap between their high and low redshift counterparts, our sample of intermediate redshift quiescent galaxies span a large range of ages but is drawn from two distinct epochs of galaxy formation: formation at z > 2 which suggests these objects may be the relics of the observed high redshift compact galaxies and formation at z ≤ 2 which suggests there is an additional population of more recently formed massive compact galaxies. This work is supported in part by the NSF REU and DOD ASSURE programs under NSF grant no. 1262851 and by the Smithsonian Institution.

Boson mode, Medium Range Structure and Intermediate Phase (IP) in (Na2O)x(B2O3)1-x glasses

NASA Astrophysics Data System (ADS)

Vignarooban, K.; Boolchand, P.; Micoulaut, M.; Malki, M.

2012-02-01

Raman scattering of titled glasses are examined using a T64000 Dispersive system. Scattering strengths of the Boson mode (40 cm-1, 70 cm-1) and the Boroxyl ring (BR) mode (808 cm-1) are found to decrease with increasing x at the same rate in the 0 < x < 20% soda range. Apparently, the 2D character of BRs embedded in a 3D network gives rise to the Boson mode.ootnotetextM. Flores-Ruiz and G. Naumis, PRB, 2011. 83: p. 184204 The triad of modes (705, 740, 770 cm-1) near the 808 cm-1 mode are found to display a maximum in scattering strength near x = 37% (705 cm-1), 33% (740 cm-1) and 25% (770 cm-1), suggesting that these are also ring modes of Na-tripentaborate (STPB), Na-diborate (SDB) and Na-triborate (STB) super-structures. Variations in Raman scattering strengths also suggest that STB percolate near x = 20%, the stress transition, while the STPB and SDTB percolate near x = 40%, the rigidity transition. These transitions were inferred from m-DSC experiments that show an intermediate phase in the 20% < x < 40% range in dry and homogeneous glasses.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Kok Wee; Koshelev, Alexei E.

Electronic nematicity plays an important role in iron-based superconductors. These materials have a layered structure and the theoretical description of their magnetic and nematic transitions has been well established in the two-dimensional approximation, i.e., when the layers can be treated independently. However, the interaction between iron layers mediated by electron tunneling may cause nontrivial three-dimensional behavior. Starting from the simplest model for orbital nematic in a single layer, we investigate the influence of interlayer tunneling on the bulk nematic order and a possible preemptive state where this order is only formed near the surface. In addition, we found that themore » interlayer tunneling suppresses the bulk nematicity, which makes favorable the formation of a surface nematic order above the bulk transition temperature. The purely electronic tunneling Hamiltonian, however, favors a nematic order parameter that alternates from layer to layer. The uniform bulk state typically observed experimentally may be stabilized by the coupling with the elastic lattice deformation. Depending on the strength of this coupling, we found three regimes: (i) surface nematic and alternating bulk order, (ii) surface nematic and uniform bulk order, and (iii) uniform bulk order without the intermediate surface phase. Lastly, the intermediate surface-nematic state may resolve the current controversy about the existence of a weak nematic transition in the compound BaFe 2As 2-xP x .« less

EuNi 5 InH 1.5-x (x = 0–1.5): hydrogen induced structural and magnetic transitions

DOE PAGES

Bigun, Inna; Smetana, Volodymyr; Mudryk, Yaroslav; ...

2017-01-01

The new quaternary hydride EuNi 5InH 1.5 has been obtained by hydrogenation of the intermetallic parent EuNi5In under extremely mild conditions, hence, at room temperature and low hydrogen pressure. Hydrogenation at slightly elevated temperatures and pressures allows for the growth of large crystals, which is a rare observation for intermetallic hydrides. EuNi 5InH 1.5 crystallizes in its own structure type ( hP17, P6¯m2, a = 4.9437(6), c = 10.643(1) Å) with a unique arrangement of the intermetallic host. The hydrogen atoms prefer Ni-surrounded positions, occupying {EuNi 3} and {Eu 2Ni 2} tetrahedral voids in the structure. Upon hydrogenation of EuNimore » 5In an anisotropic volume expansion accompanied with a decrease of symmetry is observed. Magnetic measurements reveal antiferromagnetic ordering in the hydride below 4 K and indicate an intermediate +II/+III oxidation state for Eu both in the intermetallic phase and the hydride. X-ray photoemission spectroscopy confirms the existence of the two different oxidation states of Eu. The hydrogenation does not affect the oxidation state of Eu and the type of magnetic ordering, but exerts a strong influence on the transition temperature, crystal structure, mechanical and electrical properties. Crystallographic analysis suggests that Eu(II) and Eu(III) do not order but rather mix homogeneously on crystallographic sites. Electronic structure calculations reveal the metallic character of the hydride with several different types of chemical bonding interactions being present in the compound ranging from the formally ionic Eu–H to covalent Ni–H and delocalized metal–metal. As a result, geometry optimization confirm the thermodynamic instability of the intermetallic host lattice for the hydride and supports a transformation into the parental structure as observed experimentally.« less

Scale-by-scale energy budgets which account for the coherent motion

NASA Astrophysics Data System (ADS)

F, Thiesset; L, Danaila; A, Antonia R.; T, Zhou

2011-12-01

Scale-by-scale energy budget equations are written for flows where coherent structures may be prominent. Both general and locally isotropic formulations are provided. In particular, the contribution to the production, diffusion and energy transfer terms associated with the coherent motion is highlighted. Preliminary results are presented in the intermediate wake of a circular cylinder for phase-averaged second-and third-order structure functions. The experimental data provide adequate support for the scale-by-scale budgets.

Evolution of microstructure of Haynes 230 and Inconel 617 under mechanical testing at high temperatures

NASA Astrophysics Data System (ADS)

Hrutkay, Kyle

Haynes 230 and Inconel 617 are austenitic nickel based superalloys, which are candidate structural materials for next generation high temperature nuclear reactors. High temperature deformation behavior of Haynes 230 and Inconel 617 have been investigated at the microstructural level in order to gain a better understanding of mechanical properties. Tensile tests were performed at strain rates ranging from 10-3-10-5 s -1 at room temperature, 600 °C, 800 °C and 950 °C. Subsequent microstructural analysis, including Scanning Electron Microscopy, Transmission Electron Microscopy, Energy-Dispersive X-ray Spectroscopy, and X-Ray Diffraction were used to relate the microstructural evolution at high temperatures to that of room temperature samples. Grain sizes and precipitate morphologies were used to determine high temperature behavior and fracture mechanics. Serrated flow was observed at intermediate and high temperatures as a result of discontinuous slip and dynamic recrystallization. The amplitude of serration increased with a decrease in the strain rate and increase in the temperature. Dynamic strain ageing was responsible for serrations at intermediate temperatures by means of a locking and unlocking phenomenon between dislocations and solute atoms. Dynamic recrystallization nucleated by grain and twin bulging resulting in a refinement of grain size. Existing models found in the literature were discussed to explain both of these phenomena.

Symplectic no-core shell-model approach to intermediate-mass nuclei

NASA Astrophysics Data System (ADS)

Tobin, G. K.; Ferriss, M. C.; Launey, K. D.; Dytrych, T.; Draayer, J. P.; Dreyfuss, A. C.; Bahri, C.

2014-03-01

We present a microscopic description of nuclei in the intermediate-mass region, including the proximity to the proton drip line, based on a no-core shell model with a schematic many-nucleon long-range interaction with no parameter adjustments. The outcome confirms the essential role played by the symplectic symmetry to inform the interaction and the winnowing of shell-model spaces. We show that it is imperative that model spaces be expanded well beyond the current limits up through 15 major shells to accommodate particle excitations, which appear critical to highly deformed spatial structures and the convergence of associated observables.

Heterogeneity of Equilibrium Molten Globule State of Cytochrome c Induced by Weak Salt Denaturants under Physiological Condition

PubMed Central

Rahaman, Hamidur; Alam Khan, Md. Khurshid; Hassan, Md. Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε 400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N. PMID:25849212

Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition.

PubMed

Rahaman, Hamidur; Alam Khan, Md Khurshid; Hassan, Md Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.

Methods for using novel cathode and electrolyte materials for solid oxide fuel cells and ion transport membranes

DOEpatents

Jacobson, Allan J.; Wang, Shuangyan; Kim, Gun Tae

2016-01-12

Methods using novel cathode, electrolyte and oxygen separation materials operating at intermediate temperatures for use in solid oxide fuel cells and ion transport membranes include oxides with perovskite related structures and an ordered arrangement of A site cations. The materials have significantly faster oxygen kinetics than in corresponding disordered perovskites.

Cathode and electrolyte materials for solid oxide fuel cells and ion transport membranes

DOEpatents

Jacobson, Allan J; Wang, Shuangyan; Kim, Gun Tae

2014-01-28

Novel cathode, electrolyte and oxygen separation materials are disclosed that operate at intermediate temperatures for use in solid oxide fuel cells and ion transport membranes based on oxides with perovskite related structures and an ordered arrangement of A site cations. The materials have significantly faster oxygen kinetics than in corresponding disordered perovskites.

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels.

PubMed

Hansing, Johann; Netz, Roland R

2018-06-05

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Spin-orbit quenching of the C+(2P) ion by collisions with para- and ortho-H2.

PubMed

Lique, François; Werfelli, Ghofran; Halvick, Philippe; Stoecklin, Thierry; Faure, Alexandre; Wiesenfeld, Laurent; Dagdigian, Paul J

2013-05-28

Spin-orbit (de-)excitation of C(+)((2)P) by collisions with H2, a key process for astrochemistry, is investigated. Quantum-mechanical calculations of collisions between C(+) ions and para- and ortho-H2 have been performed in order to determine the cross section for the C(+) (2)P3∕2 → (2)P1∕2 fine-structure transition at low and intermediate energies. The calculation are based on new ab initio potential energy surfaces obtained using the multireference configuration interaction method. Corresponding rate coefficients were obtained for temperatures ranging from 5 to 500 K. These rate coefficients are compared to previous estimations, and their impact is assessed through radiative transfer computation. They are found to increase the flux of the (2)P3∕2 → (2)P1∕2 line at 158 μm by up to 30% for typical diffuse interstellar cloud conditions.

Normal mode-guided transition pathway generation in proteins

PubMed Central

Lee, Byung Ho; Seo, Sangjae; Kim, Min Hyeok; Kim, Youngjin; Jo, Soojin; Choi, Moon-ki; Lee, Hoomin; Choi, Jae Boong

2017-01-01

The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this. PMID:29020017

Non-integer viscoelastic constitutive law to model soft biological tissues to in-vivo indentation.

PubMed

Demirci, Nagehan; Tönük, Ergin

2014-01-01

During the last decades, derivatives and integrals of non-integer orders are being more commonly used for the description of constitutive behavior of various viscoelastic materials including soft biological tissues. Compared to integer order constitutive relations, non-integer order viscoelastic material models of soft biological tissues are capable of capturing a wider range of viscoelastic behavior obtained from experiments. Although integer order models may yield comparably accurate results, non-integer order material models have less number of parameters to be identified in addition to description of an intermediate material that can monotonically and continuously be adjusted in between an ideal elastic solid and an ideal viscous fluid. In this work, starting with some preliminaries on non-integer (fractional) calculus, the "spring-pot", (intermediate mechanical element between a solid and a fluid), non-integer order three element (Zener) solid model, finally a user-defined large strain non-integer order viscoelastic constitutive model was constructed to be used in finite element simulations. Using the constitutive equation developed, by utilizing inverse finite element method and in vivo indentation experiments, soft tissue material identification was performed. The results indicate that material coefficients obtained from relaxation experiments, when optimized with creep experimental data could simulate relaxation, creep and cyclic loading and unloading experiments accurately. Non-integer calculus viscoelastic constitutive models, having physical interpretation and modeling experimental data accurately is a good alternative to classical phenomenological viscoelastic constitutive equations.

Identification of an Unfolding Intermediate for a DNA Lesion Bypass Polymerase

PubMed Central

Sherrer, Shanen M.; Maxwell, Brian A.; Pack, Lindsey R.; Fiala, Kevin A.; Fowler, Jason D.; Zhang, Jun; Suo, Zucai

2012-01-01

Sulfolobus solfataricusDNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C. PMID:22667759

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction.

PubMed

Elsässer, Brigitta; Valiev, Marat; Weare, John H

2009-03-25

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

Influence of electron doping on the ground state of (Sr 1-xLa x) 2IrO 4

DOE PAGES

Chen, Xiang; Hogan, Tom; Walkup, D.; ...

2015-08-17

The evolution of the electronic properties of electron-doped (Sr 1-xLa x) 2IrO 4 is experimentally explored as the doping limit of La is approached. As electrons are introduced, the electronic ground state transitions from a spin-orbit Mott phase into an electronically phase separated state, where long-range magnetic order vanishes beyond x = 0:02 and charge transport remains percolative up to the limit of La substitution (x =0:06). In particular, the electronic ground state remains inhomogeneous even beyond the collapse of the parent state's long-range antiferromagnetic order, while persistent short-range magnetism survives up to the highest La-substitution levels. Furthermore, as electronsmore » are doped into Sr 2IrO 4, we observe the appearance of a low temperature magnetic glass-like state intermediate to the complete suppression of antiferromagnetic order. Universalities and di erences in the electron-doped phase diagrams of single layer and bilayer Ruddlesden-Popper strontium iridates are discussed.« less

Theoretical Determination of Optimal Material Parameters for ZnCdTe/ZnCdSe Quantum Dot Intermediate Band Solar Cells

NASA Astrophysics Data System (ADS)

Imperato, C. M.; Ranepura, G. A.; Deych, L. I.; Kuskovsky, I. L.

2018-03-01

Intermediate band solar cells (IBSCs) are designed to enhance the photovoltaic efficiency significantly over that of a single-junction solar cell as determined by the Shockley-Queisser limit. In this work we present calculations to determine parameters of type-II Zn1-xCdxTe/Zn1-yCdySe quantum dots (QDs) grown on the InP substrate suitable for IBSCs. The calculations are done via the self-consistent variational method, accounting for the disk form of the QDs, presence of the strained ZnSe interfacial layer, and under conditions of a strain-free device structure. We show that to achieve the required parameters relatively thick QDs are required. Barriers must contain Cd concentration in the range of 35-44%, while Cd concentration in QD can vary widely from 0% to 70%, depending on their thickness to achieve the intermediate band energies in the range of 0.50-0.73 eV. It is also shown that the results are weakly dependent on the barrier thickness.

Intermediate honeycomb ordering to trigger oxygen redox chemistry in layered battery electrode

PubMed Central

Mortemard de Boisse, Benoit; Liu, Guandong; Ma, Jiangtao; Nishimura, Shin-ichi; Chung, Sai-Cheong; Kiuchi, Hisao; Harada, Yoshihisa; Kikkawa, Jun; Kobayashi, Yoshio; Okubo, Masashi; Yamada, Atsuo

2016-01-01

Sodium-ion batteries are attractive energy storage media owing to the abundance of sodium, but the low capacities of available cathode materials make them impractical. Sodium-excess metal oxides Na2MO3 (M: transition metal) are appealing cathode materials that may realize large capacities through additional oxygen redox reaction. However, the general strategies for enhancing the capacity of Na2MO3 are poorly established. Here using two polymorphs of Na2RuO3, we demonstrate the critical role of honeycomb-type cation ordering in Na2MO3. Ordered Na2RuO3 with honeycomb-ordered [Na1/3Ru2/3]O2 slabs delivers a capacity of 180 mAh g−1 (1.3-electron reaction), whereas disordered Na2RuO3 only delivers 135 mAh g−1 (1.0-electron reaction). We clarify that the large extra capacity of ordered Na2RuO3 is enabled by a spontaneously ordered intermediate Na1RuO3 phase with ilmenite O1 structure, which induces frontier orbital reorganization to trigger the oxygen redox reaction, unveiling a general requisite for the stable oxygen redox reaction in high-capacity Na2MO3 cathodes. PMID:27088834

Double scattering of light from Biophotonic Nanostructures with short-range order

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noh, Heeso; Liew, Seng Fatt; Saranathan, Vinodkumar

2010-07-28

We investigate the physical mechanism for color production by isotropic nanostructures with short-range order in bird feather barbs. While the primary peak in optical scattering spectra results from constructive interference of singly-scattered light, many species exhibit secondary peaks with distinct characteristic. Our experimental and numerical studies show that these secondary peaks result from double scattering of light by the correlated structures. Without an analog in periodic or random structures, such a phenomenon is unique for short-range ordered structures, and has been widely used by nature for non-iridescent structural coloration.

An experimental and kinetic modeling study on dimethyl carbonate (DMC) pyrolysis and combustion

DOE PAGES

Sun, Wenyu; Yang, Bin; Hansen, Nils; ...

2015-12-08

Because of the absence of C–C bonds and the large oxygen content in its molecular structure, dimethyl carbonate (DMC) is a promising oxygenated additive or substitute for hydrocarbon fuels. In order to understand its chemical oxidation and combustion kinetics, flow reactor pyrolysis at different pressures (40, 200 and 1040 mbar) and low-pressure laminar premixed flames with different equivalence ratios (1.0 and 1.5) were investigated. Mole fraction profiles of many reaction intermediates and products were obtained within estimated experimental uncertainties. From theoretical calculations and estimations, a detailed kinetic model for DMC pyrolysis and high-temperature combustion consisting of 257 species and 1563more » reactions was developed. The performance of the kinetic model was then analyzed using detailed chemical composition information, primarily from the present measurements. In addition, it was examined against the chemical structure of an opposed-flow diffusion flame, relying on global combustion properties such as the ignition delay times and laminar burning velocities. Furthermore, these extended comparisons yielded overall satisfactory agreement, demonstrating the applicability of the present model over a wide range of high-temperature conditions.« less

A Multiwavelength Study of POX 52, a Dwarf Seyfert Galaxy with an Intermediate-Mass Black Hole

NASA Astrophysics Data System (ADS)

Barth, Aaron

2004-07-01

We propose a comprehensive optical, UV, and X-ray investigation of the unique galaxy POX 52. POX 52 is a Seyfert 1 galaxy with unprecedented properties: its host galaxy appears to be a dwarf elliptical, and its stellar velocity dispersion is only 36 km/s. The stellar velocity dispersion and the broad emission-line widths both suggest a black hole mass of order 10^5 solar masses, placing POX 52 in a region of AGN parameter space that is almost completely unexplored at present. We request ACS/HRC imaging to perform a definitive measurement of the host galaxy structure; STIS UV and optical spectroscopy to study the nonstellar continuum and the structure of the broad-line region; and Chandra ACS imaging to detect the X-ray emission from the nucleus and investigate its spectral and variability properties. The results of this program will give a detailed understanding of the host galaxy and accretion properties of one of the very few known black holes in the mass range around 10^5 solar masses.

Spectroscopic and Thermal Behavior of Chromium Soaps

NASA Astrophysics Data System (ADS)

Mehrotra, K. N.; Jain, Mamta

1996-02-01

The physicochemical characteristics of chromium soaps (myristate and stearate) were investigated in the solid state (thermal, X-ray, and IR measurements) and in solutions (spectrophotometric measurements). The thermal measurements showed that the decomposition of chromium soaps is a two-step process. The soap decomposed into chromium oxycarboxylate, ketone, and carbon dioxide in the first step and the intermediate oxycarboxylate underwent further decomposition to chromium trioxide in the second step. The results showed that the second step is kinetically of zero order and the values of energy of activation for the first and second steps lie in the ranges 6-7 and 17-18 kcal mol-1, respectively. The X-ray diffraction results showed that these soaps possess double-layer structure with molecular axes slightly inclined to the basal plane. The infrared results revealed that the fatty acids exist with dimeric structure through hydrogen bonding between two molecules of fatty acids whereas the metal-to-oxygen bonds in chromium soaps are not purely ionic but possess considerable covalent character. The results of spectrophotometric measurements also confirmed the somewhat covalent nature of chromium soaps in solutions in dichloromethane.

A Multi-spectroscopic Investigation of Sulphur Speciation in Silicate Glasses and Slags

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingham, P.; Connelly, A; Hand, R

2010-01-01

Sulphur K-edge x-ray absorption near-edge structure (XANES), sulphur K{sub {alpha}} and K{sub {beta}} high resolution x-ray emission spectroscopies (XES), electron paramagnetic resonance (EPR) and optical absorption spectroscopies have been used to study the speciation of sulphur in a range of soda-lime-silica glasses and silicate slags. Several inorganic standards with known sulphur oxidation states and structural environments have also been analysed. Results confirm that the average oxidation state of sulphur in glasses decreases, as expected, in the order (colourless>light olive>dark olive>light amber>dark amber). This behaviour is consistent with decreasing S{sup 6+}/{Sigma}S ratio, which has been quantified by linear combination fitting ofmore » XES S K{alpha} spectra, and with analysed sulphur contents which exhibit a characteristic relationship with oxygen partial pressure, pO{sub 2}. A combination of S{sup 6+}, S{sup 5+}, S{sup 4+} and more reduced sulphur species has been detected in olive and amber glasses. The S{sup 4+} and S{sup 5+} species are most evident in olive-coloured glasses produced under moderately reducing conditions that coincide with minimum sulphur solubilities. The reduced form of sulphur, present in all reduced glasses, is interpreted as being present as S{sup 2-} on the basis of XANES, XES, EPR and optical measurements. An alternative interpretation of the data is that there is a continuum of less strongly reduced species, primarily S{sup +} and S{sup 2+}; this interpretation has less merit. In this paper we show that the established relationship that describes sulphur redox only in terms of S{sup 6+} and S{sup 2-}, and which states that only these two species co-exist over a narrow, moderately reducing range of pO{sub 2}, does not fully describe the behaviour of S in the industrial, non-equilibrated glasses studied. Hence this relationship requires slight modification for non-equilibrated systems to explain the existence of intermediate sulphur oxidation states such as S{sup 4+} and S{sup 5+}, particularly within the intermediate pO{sub 2} range that corresponds with sulphur solubility minima.« less

Surface nematic order in iron pnictides

DOE PAGES

Song, Kok Wee; Koshelev, Alexei E.

2016-09-09

Electronic nematicity plays an important role in iron-based superconductors. These materials have a layered structure and the theoretical description of their magnetic and nematic transitions has been well established in the two-dimensional approximation, i.e., when the layers can be treated independently. However, the interaction between iron layers mediated by electron tunneling may cause nontrivial three-dimensional behavior. Starting from the simplest model for orbital nematic in a single layer, we investigate the influence of interlayer tunneling on the bulk nematic order and a possible preemptive state where this order is only formed near the surface. In addition, we found that themore » interlayer tunneling suppresses the bulk nematicity, which makes favorable the formation of a surface nematic order above the bulk transition temperature. The purely electronic tunneling Hamiltonian, however, favors a nematic order parameter that alternates from layer to layer. The uniform bulk state typically observed experimentally may be stabilized by the coupling with the elastic lattice deformation. Depending on the strength of this coupling, we found three regimes: (i) surface nematic and alternating bulk order, (ii) surface nematic and uniform bulk order, and (iii) uniform bulk order without the intermediate surface phase. Lastly, the intermediate surface-nematic state may resolve the current controversy about the existence of a weak nematic transition in the compound BaFe 2As 2-xP x .« less

The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase Kinetic and Structural Evidence Supporting a Key Role for Histidine 265 of the Catalytic triad

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horsman, Geoff P.; Bhowmik, Shiva; Seah, Stephen Y.K.

2010-01-07

BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA ({lambda}{sub max} is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum ({lambda}{sub max} is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T.,more » and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate ({lambda}{sub max} is 506 nm) with a similar rate, 1/{tau} {approx} 500 s{sup -1}. The crystal structure of the S112A:HOPDA complex at 1.8-{angstrom} resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7{angstrom} away.« less

Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State

PubMed Central

Strauss, Mike; Schotte, Lise; Karunatilaka, Krishanthi S.; Filman, David J.

2016-01-01

ABSTRACT By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. IMPORTANCE When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events. PMID:27852863

Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.

PubMed

Strauss, Mike; Schotte, Lise; Karunatilaka, Krishanthi S; Filman, David J; Hogle, James M

2017-02-01

By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events. Copyright © 2017 American Society for Microbiology.

Fast ancestral gene order reconstruction of genomes with unequal gene content.

PubMed

Feijão, Pedro; Araujo, Eloi

2016-11-11

During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree. Since this problem is NP-hard for most rearrangement models, exact solutions are practical only for small instances, and heuristics have to be used for larger datasets. This type of approach can be called event-based. Another common approach is based on finding conserved structures between the input genomes, such as adjacencies between genes, possibly also assigning weights that indicate a measure of confidence or probability that this particular structure is present on each ancestral genome, and then finding a set of non conflicting adjacencies that optimize some given function, usually trying to maximize total weight and minimizing character changes in the tree. We call this type of methods homology-based. In previous work, we proposed an ancestral reconstruction method that combines homology- and event-based ideas, using the concept of intermediate genomes, that arise in DCJ rearrangement scenarios. This method showed better rate of correctly reconstructed adjacencies than other methods, while also being faster, since the use of intermediate genomes greatly reduces the search space. Here, we generalize the intermediate genome concept to genomes with unequal gene content, extending our method to account for gene insertions and deletions of any length. In many of the simulated datasets, our proposed method had better results than MLGO and MGRA, two state-of-the-art algorithms for ancestral reconstruction with unequal gene content, while running much faster, making it more scalable to larger datasets. Studing ancestral reconstruction problems under a new light, using the concept of intermediate genomes, allows the design of very fast algorithms by greatly reducing the solution search space, while also giving very good results. The algorithms introduced in this paper were implemented in an open-source software called RINGO (ancestral Reconstruction with INtermediate GenOmes), available at https://github.com/pedrofeijao/RINGO .

Posthodiplostomum cuticola (Digenea: Diplostomatidae) in intermediate fish hosts: factors contributing to the parasite infection and prey selection by the definitive bird host.

PubMed

Ondracková, M; Simková, A; Gelnar, M; Jurajda, P

2004-12-01

Infection parameters of Posthodiplostomum cuticola, a digenean parasite with a complex life-cycle, were investigated in fish (the second intermediate host) from 6 floodplain water bodies over 2 years. A broad range of factors related to abiotic characteristics of localities, density of the first intermediate (planorbid snails) and definitive (wading birds) hosts and fish community structure were tested for their effects on P. cuticola infection in juvenile and adult fish. Characters of the littoral zone and flood duration were found to be important factors for the presence of the first intermediate and definitive hosts. Visitation time of definitive bird hosts was also related to adult fish host density. Localities with P. cuticola infected fish were visited by a higher number of bird species. Infection of P. cuticola in fish and similarities in infection among fish host assemblages were correlated with fish host density and fish species composition. Parasite infection in both adult and juvenile fishes was associated with the slope of the bank and the bottom type, in particular in juvenile fish assemblages with snail host density. We conclude that habitat characteristics, snail host density and fish community structure contribute significantly to P. cuticola infection in fish hosts.

High resolution absolute absorption cross sections of the B ̃(1)A'-X ̃(1)A' transition of the CH2OO biradical.

PubMed

Foreman, Elizabeth S; Kapnas, Kara M; Jou, YiTien; Kalinowski, Jarosław; Feng, David; Gerber, R Benny; Murray, Craig

2015-12-28

Carbonyl oxides, or Criegee intermediates, are formed from the gas phase ozonolysis of alkenes and play a pivotal role in night-time and urban area atmospheric chemistry. Significant discrepancies exist among measurements of the strong B ̃(1)A'-X ̃(1)A' electronic transition of the simplest Criegee intermediate, CH2OO in the visible/near-UV. We report room temperature spectra of the B ̃(1)A'-X ̃(1)A' electronic absorption band of CH2OO acquired at higher resolution using both single-pass broadband absorption and cavity ring-down spectroscopy. The new absorption spectra confirm the vibrational structure on the red edge of the band that is absent from ionization depletion measurements. The absolute absorption cross sections over the 362-470 nm range are in good agreement with those reported by Ting et al. Broadband absorption spectra recorded over the temperature range of 276-357 K were identical within their mutual uncertainties, confirming that the vibrational structure is not due to hot bands.

Structural transitions in vortex systems with anisotropic interactions

DOE PAGES

Olszewski, Maciej W.; Eskildsen, M. R.; Reichhardt, Charles; ...

2017-12-29

We introduce a model of vortices in type-II superconductors with a four-fold anisotropy in the vortex–vortex interaction potential. Using numerical simulations we show that the vortex lattice undergoes structural transitions as the anisotropy is increased, with a triangular lattice at low anisotropy, a rhombic intermediate state, and a square lattice for high anisotropy. In some cases we observe a multi-q state consisting of an Archimedean tiling that combines square and triangular local ordering. At very high anisotropy, domains of vortex chain states appear. We discuss how this model can be generalized to higher order anisotropy as well as its applicabilitymore » to other particle-based systems with anisotropic particle–particle interactions.« less

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

PubMed

Baird, Nathan J; Ludtke, Steven J; Khant, Htet; Chiu, Wah; Pan, Tao; Sosnick, Tobin R

2010-11-24

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Intermediate Filaments Play a Pivotal Role in Regulating Cell Architecture and Function*

PubMed Central

Lowery, Jason; Kuczmarski, Edward R.; Herrmann, Harald; Goldman, Robert D.

2015-01-01

Intermediate filaments (IFs) are composed of one or more members of a large family of cytoskeletal proteins, whose expression is cell- and tissue type-specific. Their importance in regulating the physiological properties of cells is becoming widely recognized in functions ranging from cell motility to signal transduction. IF proteins assemble into nanoscale biopolymers with unique strain-hardening properties that are related to their roles in regulating the mechanical integrity of cells. Furthermore, mutations in the genes encoding IF proteins cause a wide range of human diseases. Due to the number of different types of IF proteins, we have limited this short review to cover structure and function topics mainly related to the simpler homopolymeric IF networks composed of vimentin, and specifically for diseases, the related muscle-specific desmin IF networks. PMID:25957409

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

PubMed Central

Granata, Daniele; Camilloni, Carlo; Vendruscolo, Michele; Laio, Alessandro

2013-01-01

The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The determination of the free-energy landscapes of proteins by computational methods is, however, very challenging as it requires an extensive sampling of their conformational spaces. We describe here a technique to achieve this goal with relatively limited computational resources by incorporating nuclear magnetic resonance (NMR) chemical shifts as collective variables in metadynamics simulations. As in this approach the chemical shifts are not used as structural restraints, the resulting free-energy landscapes correspond to the force fields used in the simulations. We illustrate this approach in the case of the third Ig-binding domain of protein G from streptococcal bacteria (GB3). Our calculations reveal the existence of a folding intermediate of GB3 with nonnative structural elements. Furthermore, the availability of the free-energy landscape enables the folding mechanism of GB3 to be elucidated by analyzing the conformational ensembles corresponding to the native, intermediate, and unfolded states, as well as the transition states between them. Taken together, these results show that, by incorporating experimental data as collective variables in metadynamics simulations, it is possible to enhance the sampling efficiency by two or more orders of magnitude with respect to standard molecular dynamics simulations, and thus to estimate free-energy differences among the different states of a protein with a kBT accuracy by generating trajectories of just a few microseconds. PMID:23572592

Effect of film multi-scale structure on the water vapor permeability in hydroxypropyl starch (HPS)/Na-MMT nanocomposites.

PubMed

Liu, Siyuan; Cai, Panfu; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing

2016-12-10

To improve the water vapor resistance of starch-based films, Na-MMT (Na-montmorillonite) as nanofillers were fabricated into hydroxypropyl starch and the multi-scale structural changes (including intermolecular interaction, short-range conformation, long-range ordered structure and the aggregated structure of the film) were revealed. The elongation of the water vapor molecule pathway by tortuous path is generally recognized as the main reason for the improvement of water resistance. However this study observed the lowest water vapor permeability (WVP) was at the 3% Na-MMT/hydroxypropyl starch (HPS) ratio instead of 5% even nanofillers were partially exfoliated at both ratio. Except for the "tortuous path" caused by nanofillers, this observation proposed that the short-range conformation of HPS chains, long-range ordered structure and the aggregated structure likely influenced the water barrier property. The relationship between WVP and multi-scale structure of the film was investigated. The results suggested that a good balance of short-range conformationin the amorphous region, long-range ordered structure and the aggregated structure of the film was required for the improvement of water vapor barrier property. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet

PubMed Central

Buchanan, Lauren E.; Dunkelberger, Emily B.; Tran, Huong Q.; Cheng, Pin-Nan; Chiu, Chi-Cheng; Cao, Ping; Raleigh, Daniel P.; de Pablo, Juan J.; Nowick, James S.; Zanni, Martin T.

2013-01-01

Amyloid formation is implicated in more than 20 human diseases, yet the mechanism by which fibrils form is not well understood. We use 2D infrared spectroscopy and isotope labeling to monitor the kinetics of fibril formation by human islet amyloid polypeptide (hIAPP or amylin) that is associated with type 2 diabetes. We find that an oligomeric intermediate forms during the lag phase with parallel β-sheet structure in a region that is ultimately a partially disordered loop in the fibril. We confirm the presence of this intermediate, using a set of homologous macrocyclic peptides designed to recognize β-sheets. Mutations and molecular dynamics simulations indicate that the intermediate is on pathway. Disrupting the oligomeric β-sheet to form the partially disordered loop of the fibrils creates a free energy barrier that is the origin of the lag phase during aggregation. These results help rationalize a wide range of previous fragment and mutation studies including mutations in other species that prevent the formation of amyloid plaques. PMID:24218609

Generic approach to access barriers in dehydrogenation reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Corrosion behaviour of steel rebars embedded in a concrete designed for the construction of an intermediate-level radioactive waste disposal facility

NASA Astrophysics Data System (ADS)

Duffó, G. S.; Arva, E. A.; Schulz, F. M.; Vazquez, D. R.

2013-07-01

The National Atomic Energy Commission of the Argentine Republic is developing a nuclear waste disposal management programme that contemplates the design and construction of a facility for the final disposal of intermediate-level radioactive wastes. The repository is based on the use of multiple, independent and redundant barriers. The major components are made in reinforced concrete so, the durability of these structures is an important aspect for the facility integrity. This work presents an investigation performed on an instrumented reinforced concrete prototype specifically designed for this purpose, to study the behaviour of an intermediate level radioactive waste disposal facility from the rebar corrosion point of view. The information obtained will be used for the final design of the facility in order to guarantee a service life more or equal than the foreseen durability for this type of facilities.

Generic approach to access barriers in dehydrogenation reactions

DOE PAGES

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

2018-03-08

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Durability of a reinforced concrete designed for the construction of an intermediate-level radioactive waste disposal facility

NASA Astrophysics Data System (ADS)

Duffó, G. S.; Arva, E. A.; Schulz, F. M.; Vazquez, D. R.

2012-01-01

The National Atomic Energy Commission of the Argentine Republic is developing a nuclear waste disposal management programme that contemplates the design and construction of a facility for the final disposal of intermediate-level radioactive wastes. The repository is based on the use of multiple, independent and redundant barriers. The major components are made in reinforced concrete so, the durability of these structures is an important aspect for the facility integrity. This work presents an investigation performed on a reinforced concrete specifically designed for this purpose, to predict the service life of the intermediate level radioactive waste disposal facility from data obtained with several techniques. Results obtained with corrosion sensors embedded in a concrete prototype are also included. The information obtained will be used for the final design of the facility in order to guarantee a service life more or equal than the foreseen durability for this type of facilities.

The ferromagnetic-spin glass transition in PdMn alloys: symmetry breaking of ferromagnetism and spin glass studied by a multicanonical method.

PubMed

Kato, Tomohiko; Saita, Takahiro

2011-03-16

The magnetism of Pd(1-x)Mn(x) is investigated theoretically. A localized spin model for Mn spins that interact with short-range antiferromagnetic interactions and long-range ferromagnetic interactions via itinerant d electrons is set up, with no adjustable parameters. A multicanonical Monte Carlo simulation, combined with a procedure of symmetry breaking, is employed to discriminate between the ferromagnetic and spin glass orders. The transition temperature and the low-temperature phase are determined from the temperature variation of the specific heat and the probability distributions of the ferromagnetic order parameter and the spin glass order parameter at different concentrations. The calculation results reveal that only the ferromagnetic phase exists at x < 0.02, that only the spin glass phase exists at x > 0.04, and that the two phases coexist at intermediate concentrations. This result agrees semi-quantitatively with experimental results.

Spectral multiplexing using stacked volume-phase holographic gratings - I

NASA Astrophysics Data System (ADS)

Zanutta, A.; Landoni, M.; Riva, M.; Bianco, A.

2017-08-01

Many focal-reducer spectrographs, currently available at state-of-the-art telescopes facilities, would benefit from a simple refurbishing that could increase both the resolution and spectral range in order to cope with the progressively challenging scientific requirements, but, in order to make this update appealing, it should minimize the changes in the existing structure of the instrument. In the past, many authors proposed solutions based on stacking subsequently layers of dispersive elements and recording multiple spectra in one shot (multiplexing). Although this idea is promising, it brings several drawbacks and complexities that prevent the straightforward integration of such a device in a spectrograph. Fortunately, nowadays, the situation has changed dramatically, thanks to the successful experience achieved through photopolymeric holographic films, used to fabricate common volume-phase holographic gratings (VPHGs). Thanks to the various advantages made available by these materials in this context, we propose an innovative solution to design a stacked multiplexed VPHG that is able to secure efficiently different spectra in a single shot. This allows us to increase resolution and spectral range enabling astronomers to greatly economize their awarded time at the telescope. In this paper, we demonstrate the applicability of our solution, both in terms of expected performance and feasibility, supposing the upgrade of the Gran Telescopio CANARIAS (GTC) Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy (OSIRIS).

Cryo-EM structures of two bovine adenovirus type 3 intermediates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin

2014-02-15

Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure representsmore » a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.« less

Probing with and into fingerprints.

PubMed

Dahiya, Ravinder S; Gori, Monica

2010-07-01

A recent report by Scheibert et al. highlights the role of fingerprints in enhancing tactile sensitivity. By scanning a surface with a biometric force sensor they demonstrate the dominance of the frequencies that fall within the optimal sensitivity range of Pacinian afferents. The sensor, in this study, has a soft cover patterned with parallel ridges-mimicking the fingerprints. However, the skin structure is quite complex. Elasticity of the skin varies with depth and the ridge like pattern is comprised of not just papillary ridges or fingerprints. Besides fingerprints there exist intermediate ridges, positioned exactly under the papillary ridges, and limiting ridges at dermis-epidermis junction. These structures are usually considered as single unit. If so, it is important to revisit and see if the role of fingerprints remains the same, should the sensor cover have both fingerprints and intermediate ridges.

Structural characteristics and properties of the regenerated silk fibroin prepared from formic acid.

PubMed

Um, I C; Kweon, H Y; Park, Y H; Hudson, S

2001-08-20

Structural characteristics and thermal and solution properties of the regenerated silk fibroin (SF) prepared from formic acid (FU) were compared with those of SF from water (AU). According to the turbidity and shear viscosity measurement, SF formic acid solution was stable and transparent, no molecular aggregations occurred. The sample FU exhibited the beta-sheet structure, while AU random coil conformation using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and differential scanning calorimetry. The effects of methanol treatment on samples were also examined. According to the measurement of crystallinity (XRD) and crystallinity index (FTIR), the concept of long/short-range ordered structure formation was proposed. Long-range ordered crystallites are predominantly formed for methanol treated SF film while SF film cast from formic acid favors the formation of short-range ordered structure. The relaxation temperatures of SF films measured by dynamic thermomechanical analysis supported the above mechanism due to the sensitivity of relaxation temperature on the short-range order.

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

PubMed

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

Discussing religion and spirituality is an advanced communication skill: an exploratory structural equation model of physician trainee self-ratings.

PubMed

Ford, Dee W; Downey, Lois; Engelberg, Ruth; Back, Anthony L; Curtis, J Randall

2012-01-01

Communication about religious and spiritual issues is fundamental to palliative care, yet little empirical data exist to guide curricula in this area. The goal of this study was to develop an improved understanding of physicians' perspectives on their communication competence about religious and spiritual issues. We examined surveys of physician trainees (n=297) enrolled in an ongoing communication skills study at two medical centers in the northwestern and southeastern United States. Our primary outcome was self-assessed competence in discussing religion and spirituality. We used exploratory structural equation modeling (SEM) to develop measurement and full models for acquisition of self-assessed communication competencies. Our measurement SEM identified two latent constructs that we label Basic and Intermediate Competence, composed of five self-assessed communication skills. The Basic Competence construct included overall satisfaction with palliative care skills and with discussing do not resuscitate (DNR) status. The Intermediate Competence construct included responding to inappropriate treatment requests, maintaining hope, and addressing fears about the end-of-life. Our full SEM model found that Basic Competence predicted Intermediate Competence and that Intermediate Competence predicted competence in religious and spiritual discussions. Years of clinical training directly influenced Basic Competence. Increased end-of-life discussions positively influenced Basic Competence and had a complex association with Intermediate Competence. Southeastern trainees perceived more competence in religious and spiritual discussions than northwestern trainees. This study suggests that discussion of religious and spiritual issues is a communication skill that trainees consider more advanced than other commonly taught communication skills, such as discussing DNR orders.

Array design considerations for exploitation of stable weakly dispersive modal pulses in the deep ocean

NASA Astrophysics Data System (ADS)

Udovydchenkov, Ilya A.

2017-07-01

Modal pulses are broadband contributions to an acoustic wave field with fixed mode number. Stable weakly dispersive modal pulses (SWDMPs) are special modal pulses that are characterized by weak dispersion and weak scattering-induced broadening and are thus suitable for communications applications. This paper investigates, using numerical simulations, receiver array requirements for recovering information carried by SWDMPs under various signal-to-noise ratio conditions without performing channel equalization. Two groups of weakly dispersive modal pulses are common in typical mid-latitude deep ocean environments: the lowest order modes (typically modes 1-3 at 75 Hz), and intermediate order modes whose waveguide invariant is near-zero (often around mode 20 at 75 Hz). Information loss is quantified by the bit error rate (BER) of a recovered binary phase-coded signal. With fixed receiver depths, low BERs (less than 1%) are achieved at ranges up to 400 km with three hydrophones for mode 1 with 90% probability and with 34 hydrophones for mode 20 with 80% probability. With optimal receiver depths, depending on propagation range, only a few, sometimes only two, hydrophones are often sufficient for low BERs, even with intermediate mode numbers. Full modal resolution is unnecessary to achieve low BERs. Thus, a flexible receiver array of autonomous vehicles can outperform a cabled array.

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

DOE PAGES

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.; ...

2017-10-25

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qingteng; Bahadur, Divya; Dufresne, Eric M.

Here, we have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scatter- ing (SAXS), x-ray photon correlation spectroscopy (XPCS), and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically-determined gel temperature, T gel, was characterized via the slow-down of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT = T quench - T gel), wave vector, and formation time (t f). We findmore » similar patterns in the slow-down of dynamics that maps the wave-vector-dependent dynamics at a particular ΔT and t f to that at other ΔTs and t fs via an effective scaling temperature, Ts. A single Ts applies to a broad range of ΔT and tf but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than that of the attraction strength between colloids. Finally, we interpret this strong temperature de- pendence in terms of changes in cooperative bonding required to form stable, energetically favored, local structures.« less

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

DOE PAGES

Zarzycki, Piotr; Gilbert, Benjamin

2016-04-27

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short-and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without externalmore » water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.« less

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

PubMed Central

Zarzycki, Piotr; Gilbert, Benjamin

2016-01-01

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species. PMID:27118164

Structure of carbonate melts at high pressure

NASA Astrophysics Data System (ADS)

Hudspeth, J.; Sanloup, C.; Cochain, B.; Konopkova, Z.; Afonina, V.; Morgenroth, W.

2015-12-01

Carbonate melts are rare magmas with only a single active volcano (Oldoinyo Lengai,Tanzania [1]). They are of fundamental interest for their role in the Earth's deep carbon cycle and are of immense economic importance due to their affinity for REE strategic metals (niobium, uranium, tantalum, etc). They have remarkable physical properties such as very low viscosity [2] and magmatic temperatures for alkaline carbonate lavas [3] and it has been predicted that their compressibility could be significantly higher than that of silicate melts [4,5]. Despite the atomic structure of carbonate melts being fundamental for controlling their physical and chemical behavior in natural systems, very few structural studies have been reported and these have been largely computational. Here we present initial structural investigations of carbonate melts at mantle pressures using in situ x-ray diffraction in diamond anvil cells. The structure factor S(Q) is transformed to obtain the real space pair distribution function G(R) which describes the local and intermediate range atomic ordering allowing bond length and coordination number changes with pressure to be determined. [1] Krafft and Keller, Science 245:168-170, 1989 [2] Yono et al., Nat. Commun. 5:5091, 2014 [3] Dobson et al., Earth Planet. Sci. Lett. 143:207-215, 1996 [4] Genge et al., Earth Planet. Sci. Lett. 131:225-238, 1995 [5] Jones et al., Rev. Mineral. Geochem. 75:289-322, 2013

Highly efficient tandem polymer solar cells with a photovoltaic response in the visible light range.

PubMed

Zheng, Zhong; Zhang, Shaoqing; Zhang, Maojie; Zhao, Kang; Ye, Long; Chen, Yu; Yang, Bei; Hou, Jianhui

2015-02-18

Highly efficient polymer solar cells with a tandem structure are fabricated by using two excellent photovoltaic polymers and a highly transparent intermediate recombination layer. Power conversion -efficiencies over 10% can be realized with a photovoltaic response within 800 nm. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amorphous calcium carbonate controls avian eggshell mineralization: A new paradigm for understanding rapid eggshell calcification.

PubMed

Rodríguez-Navarro, Alejandro B; Marie, Pauline; Nys, Yves; Hincke, Maxwell T; Gautron, Joel

2015-06-01

Avian eggshell mineralization is the fastest biogenic calcification process known in nature. How this is achieved while producing a highly crystalline material composed of large calcite columnar single crystals remains largely unknown. Here we report that eggshell mineral originates from the accumulation of flat disk-shaped amorphous calcium carbonate (ACC) particles on specific organic sites on the eggshell membrane, which are rich in proteins and sulfated proteoglycans. These structures known as mammillary cores promote the nucleation and stabilization of a amorphous calcium carbonate with calcitic short range order which predetermine the calcite composition of the mature eggshell. The amorphous nature of the precursor phase was confirmed by the diffuse scattering of X-rays and electrons. The nascent calcitic short-range order of this transient mineral phase was revealed by infrared spectroscopy and HRTEM. The ACC mineral deposited around the mammillary core sites progressively transforms directly into calcite crystals without the occurrence of any intermediate phase. Ionic speciation data suggest that the uterine fluid is equilibrated with amorphous calcium carbonate, throughout the duration of eggshell mineralization process, supporting that this mineral phase is constantly forming at the shell mineralization front. On the other hand, the transient amorphous calcium carbonate mineral deposits, as well as the calcite crystals into which they are converted, form by the ordered aggregation of nanoparticles that support the rapid mineralization of the eggshell. The results of this study alter our current understanding of avian eggshell calcification and provide new insights into the genesis and formation of calcium carbonate biominerals in vertebrates. Copyright © 2015 Elsevier Inc. All rights reserved.

Spectral analysis of near-wall turbulence in channel flow at Reτ=4200 with emphasis on the attached-eddy hypothesis

NASA Astrophysics Data System (ADS)

Agostini, Lionel; Leschziner, Michael

2017-01-01

Direct numerical simulation data for channel flow at a friction Reynolds number of 4200, generated by Lozano-Durán and Jiménez [J. Fluid Mech. 759, 432 (2014), 10.1017/jfm.2014.575], are used to examine the properties of near-wall turbulence within subranges of eddy-length scale. Attention is primarily focused on the intermediate layer (mesolayer) covering the logarithmic velocity region within the range of wall-scaled wall-normal distance of 80-1500. The examination is based on a number of statistical properties, including premultiplied and compensated spectra, the premultiplied derivative of the second-order structure function, and three scalar parameters that characterize the anisotropic or isotropic state of the various length-scale subranges. This analysis leads to the delineation of three regions within the map of wall-normal-wise premultiplied spectra, each characterized by distinct turbulence properties. A question of particular interest is whether the Townsend-Perry attached-eddy hypothesis (AEH) can be shown to be valid across the entire mesolayer, in contrast to the usual focus on the outer portion of the logarithmic-velocity layer at high Reynolds numbers, which is populated with very-large-scale motions. This question is addressed by reference to properties in the premultiplied scalewise derivative of the second-order structure function (PMDS2) and joint probability density functions of streamwise-velocity fluctuations and their streamwise and spanwise derivatives. This examination provides evidence, based primarily on the existence of a plateau region in the PMDS2, for the qualified validity of the AEH right down the lower limit of the logarithmic velocity range.

Anisotropy of the monomer random walk in a polymer melt: local-order and connectivity effects

NASA Astrophysics Data System (ADS)

Bernini, S.; Leporini, D.

2016-05-01

The random walk of a bonded monomer in a polymer melt is anisotropic due to local order and bond connectivity. We investigate both effects by molecular-dynamics simulations on melts of fully-flexible linear chains ranging from dimers (M  =  2) up to entangled polymers (M  =  200). The corresponding atomic liquid is also considered a reference system. To disentangle the influence of the local geometry and the bond arrangements, and to reveal their interplay, we define suitable measures of the anisotropy emphasising either the former or the latter aspect. Connectivity anisotropy, as measured by the correlation between the initial bond orientation and the direction of the subsequent monomer displacement, shows a slight enhancement due to the local order at times shorter than the structural relaxation time. At intermediate times—when the monomer displacement is comparable to the bond length—a pronounced peak and then decays slowly as t -1/2, becoming negligible when the displacement is as large as about five bond lengths, i.e. about four monomer diameters or three Kuhn lengths. Local-geometry anisotropy, as measured by the correlation between the initial orientation of a characteristic axis of the Voronoi cell and the subsequent monomer dynamics, is affected at shorter times than the structural relaxation time by the cage shape with antagonistic disturbance by the connectivity. Differently, at longer times, the connectivity favours the persistence of the local-geometry anisotropy, which vanishes when the monomer displacement exceeds the bond length. Our results strongly suggest that the sole consideration of the local order is not enough to understand the microscopic origin of the rattling amplitude of the trapped monomer in the cage of the neighbours.

Critical Intermediate Structure That Directs the Crystalline Texture and Surface Morphology of Organo-Lead Trihalide Perovskite.

PubMed

Chia, Hao-Chung; Sheu, Hwo-Shuenn; Hsiao, Yu-Yun; Li, Shao-Sian; Lan, Yi-Kang; Lin, Chung-Yao; Chang, Je-Wei; Kuo, Yen-Chien; Chen, Chia-Hao; Weng, Shih-Chang; Su, Chun-Jen; Su, An-Chung; Chen, Chun-Wei; Jeng, U-Ser

2017-10-25

We have identified an often observed yet unresolved intermediate structure in a popular processing with dimethylformamide solutions of lead chloride and methylammonium iodide for perovskite solar cells. With subsecond time-resolved grazing-incidence X-ray scattering and X-ray photoemission spectroscopy, supplemental with ab initio calculation, the resolved intermediate structure (CH 3 NH 3 ) 2 PbI 2 Cl 2 ·CH 3 NH 3 I features two-dimensional (2D) perovskite bilayers of zigzagged lead-halide octahedra and sandwiched CH 3 NH 3 I layers. Such intermediate structure reveals a hidden correlation between the intermediate phase and the composition of the processing solution. Most importantly, the 2D perovskite lattice of the intermediate phase is largely crystallographically aligned with the [110] planes of the three-dimensional perovskite cubic phase; consequently, with sublimation of Cl ions from the organo-lead octahedral terminal corners in prolonged annealing, the zigzagged octahedral layers of the intermediate phase can merge with the intercalated methylammonium iodide layers for templated growth of perovskite crystals. Regulated by annealing temperature and the activation energies of the intermediate and perovskite, deduced from analysis of temperature-dependent structural kinetics, the intermediate phase is found to selectively mature first and then melt along the layering direction for epitaxial conversion into perovskite crystals. The unveiled epitaxial conversion under growth kinetics controls might be general for solution-processed and intermediate-templated perovskite formation.

Chiral symmetry and the nucleon-nucleon interaction

DOE PAGES

Machleidt, Ruprecht

2016-04-20

We review how nuclear forces emerge from low-energy quantum chromodynamics (QCD) via chiral effective field theory (EFT). During the past two decades, this approach has evolved into a powerful tool to derive nuclear two- and many-body forces in a systematic and model-independent way. We then focus on the nucleon-nucleon (NN) interaction and show in detail how, governed by chiral symmetry, the long- and intermediate-range of the NN potential builds up order by order. We proceed up to sixth order in small momenta, where convergence is achieved. Lastly, the final result allows for a full assessment of the validity of themore » chiral EFT approach to the NN interaction.« less

Ground-state phases of the spin-1 J1-J2 Heisenberg antiferromagnet on the honeycomb lattice

NASA Astrophysics Data System (ADS)

Li, P. H. Y.; Bishop, R. F.

2016-06-01

We study the zero-temperature quantum phase diagram of a spin-1 Heisenberg antiferromagnet on the honeycomb lattice with both nearest-neighbor exchange coupling J1>0 and frustrating next-nearest-neighbor coupling J2≡κ J1>0 , using the coupled cluster method implemented to high orders of approximation, and based on model states with different forms of classical magnetic order. For each we calculate directly in the bulk thermodynamic limit both ground-state low-energy parameters (including the energy per spin, magnetic order parameter, spin stiffness coefficient, and zero-field uniform transverse magnetic susceptibility) and their generalized susceptibilities to various forms of valence-bond crystalline (VBC) order, as well as the energy gap to the lowest-lying spin-triplet excitation. In the range 0 <κ <1 we find evidence for four distinct phases. Two of these are quasiclassical phases with antiferromagnetic long-range order, one with two-sublattice Néel order for κ <κc1=0.250(5 ) , and another with four-sublattice Néel-II order for κ >κc 2=0.340 (5 ) . Two different paramagnetic phases are found to exist in the intermediate region. Over the range κc1<κ<κci=0.305 (5 ) we find a gapless phase with no discernible magnetic order, which is a strong candidate for being a quantum spin liquid, while over the range κci<κ <κc 2 we find a gapped phase, which is most likely a lattice nematic with staggered dimer VBC order that breaks the lattice rotational symmetry.

Dynamic study of sub-micro sized LiFePO4 cathodes by in-situ tender X-ray absorption near edge structure

NASA Astrophysics Data System (ADS)

Wang, Dongniu; Wang, Huixin; Yang, Jinli; Zhou, Jigang; Hu, Yongfeng; Xiao, Qunfeng; Fang, Haitao; Sham, Tsun-Kong

2016-01-01

Olivine-type phosphates (LiMPO4, M = Fe, Mn, Co) are promising cathode materials for lithium-ion batteries that are generally accepted to follow first order equilibrium phase transformations. Herein, the phase transformation dynamics of sub-micro sized LiFePO4 particles with limited rate capability at a low current density of 0.14 C was investigated. An in-situ X-ray Absorption Near Edge Structure (XANES) measurement was conducted at the Fe and P K-edge for the dynamic studies upon lithiation and delithiation. Fe K-edge XANES spectra demonstrate that not only lithium-rich intermediate phase LixFePO4 (x = 0.6-0.75), but also lithium-poor intermediate phase LiyFePO4 (y = 0.1-0.25) exist during the charge and discharge, respectively. Furthermore, during charge and discharge, a fluctuation of the FePO4 and LiFePO4 fractions obtained by liner combination fitting around the imaginary phase fractions followed Faraday's law and the equilibrium first-order two-phase transformation versus reaction time is present, respectively. The charging and discharging process has a reversible phase transformation dynamics with symmetric structural evolution routes. P K-edge XANES spectra reveal an enrichment of PF6-1 anions at the surface of the electrode during charging.

Transition and post-transition metal ions in borate glasses: Borate ligand speciation, cluster formation, and their effect on glass transition and mechanical properties.

PubMed

Möncke, D; Kamitsos, E I; Palles, D; Limbach, R; Winterstein-Beckmann, A; Honma, T; Yao, Z; Rouxel, T; Wondraczek, L

2016-09-28

A series of transition and post-transition metal ion (Mn, Cu, Zn, Pb, Bi) binary borate glasses was studied with special consideration of the cations impact on the borate structure, the cations cross-linking capacity, and more generally, structure-property correlations. Infrared (IR) and Raman spectroscopies were used for the structural characterization. These complementary techniques are sensitive to the short-range order as in the differentiation of tetrahedral and trigonal borate units or regarding the number of non-bridging oxygen ions per unit. Moreover, vibrational spectroscopy is also sensitive to the intermediate-range order and to the presence of superstructural units, such as rings and chains, or the combination of rings. In order to clarify band assignments for the various borate entities, examples are given from pure vitreous B 2 O 3 to meta-, pyro-, ortho-, and even overmodified borate glass compositions. For binary metaborate glasses, the impact of the modifier cation on the borate speciation is shown. High field strength cations such as Zn 2+ enhance the disproportionation of metaborate to polyborate and pyroborate units. Pb 2+ and Bi 3+ induce cluster formation, resulting in PbO n - and BiO n -pseudophases. Both lead and bismuth borate glasses show also a tendency to stabilize very large superstructural units in the form of diborate polyanions. Far-IR spectra reflect on the bonding states of modifier cations in glasses. The frequency of the measured cation-site vibration band was used to obtain the average force constant for the metal-oxygen bonding, F M-O . A linear correlation between glass transition temperature (T g ) and F M-O was shown for the metaborate glass series. The mechanical properties of the glasses also correlate with the force constant F M-O , though for cations of similar force constant the fraction of tetrahedral borate units (N 4 ) strongly affects the thermal and mechanical properties. For paramagnetic Cu- and Mn-borate glasses, N 4 was determined from the IR spectra after deducing the relative absorption coefficient of boron tetrahedral versus boron trigonal units, α = α 4 /α 3 , using NMR literature data of the diamagnetic glasses.

An operando FTIR spectroscopic and kinetic study of carbon monoxide pressure influence on rhodium-catalyzed olefin hydroformylation.

PubMed

Kubis, Christoph; Sawall, Mathias; Block, Axel; Neymeyr, Klaus; Ludwig, Ralf; Börner, Armin; Selent, Detlef

2014-09-08

The influence of carbon monoxide concentration on the kinetics of the hydroformylation of 3,3-dimethyl-1-butene with a phosphite-modified rhodium catalyst has been studied for the pressure range p(CO)=0.20-3.83 MPa. Highly resolved time-dependent concentration profiles of the organometallic intermediates were derived from IR spectroscopic data collected in situ for the entire olefin-conversion range. The dynamics of the catalyst and organic components are described by enzyme-type kinetics with competitive and uncompetitive inhibition reactions involving carbon monoxide taken into account. Saturation of the alkyl-rhodium intermediates with carbon monoxide as a cosubstrate occurs between 1.5 and 2 MPa of carbon monoxide pressure, which brings about a convergence of aldehyde regioselectivity. Hydrogenolysis of the acyl intermediate is fast at 30 °C and low pressure of p(CO)=0.2 MPa, but is of minus first order with respect to the solution concentration of carbon monoxide. Resting 18-electron hydrido and acyl complexes that correspond to early and late rate-determining states, respectively, coexist as long as the conversion of the substrate is not complete. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermediate Filaments Play a Pivotal Role in Regulating Cell Architecture and Function.

PubMed

Lowery, Jason; Kuczmarski, Edward R; Herrmann, Harald; Goldman, Robert D

2015-07-10

Intermediate filaments (IFs) are composed of one or more members of a large family of cytoskeletal proteins, whose expression is cell- and tissue type-specific. Their importance in regulating the physiological properties of cells is becoming widely recognized in functions ranging from cell motility to signal transduction. IF proteins assemble into nanoscale biopolymers with unique strain-hardening properties that are related to their roles in regulating the mechanical integrity of cells. Furthermore, mutations in the genes encoding IF proteins cause a wide range of human diseases. Due to the number of different types of IF proteins, we have limited this short review to cover structure and function topics mainly related to the simpler homopolymeric IF networks composed of vimentin, and specifically for diseases, the related muscle-specific desmin IF networks. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Dynamic-load-enabled ultra-low power multiple-state RRAM devices.

PubMed

Yang, Xiang; Chen, I-Wei

2012-01-01

Bipolar resistance-switching materials allowing intermediate states of wide-varying resistance values hold the potential of drastically reduced power for non-volatile memory. To exploit this potential, we have introduced into a nanometallic resistance-random-access-memory (RRAM) device an asymmetric dynamic load, which can reliably lower switching power by orders of magnitude. The dynamic load is highly resistive during on-switching allowing access to the highly resistive intermediate states; during off-switching the load vanishes to enable switching at low voltage. This approach is entirely scalable and applicable to other bipolar RRAM with intermediate states. The projected power is 12 nW for a 100 × 100 nm(2) device and 500 pW for a 10 × 10 nm(2) device. The dynamic range of the load can be increased to allow power to be further decreased by taking advantage of the exponential decay of wave-function in a newly discovered nanometallic random material, reaching possibly 1 pW for a 10×10 nm(2) nanometallic RRAM device.

Synthesis of Novel 1,4- Dihydropyridine Derivatives Bearing Biphenyl-2'-Tetrazole Substitution as Potential Dual Angiotensin II Receptors and Calcium Channel Blockers

PubMed Central

Shahbazi Mojarrad, Javid; Zamani, Zahra; Nazemiyeh, Hossein; Ghasemi, Saeed; Asgari, Davoud

2011-01-01

Introduction: We report the synthesis of novel 1,4-dihydropyridine derivatives containing biphenyl-2'-tetrazole moieties. We hypothesized that merging the key structural elements present in an AT1 receptor antagonist with key structural elements in 1,4-dihydropyridine calcium channel blockers would yield novel analogs with potential dual activity for both receptors. This strategy led to the design and synthesis of dialkyl 1,4-dihydro-2,6-dimethyl-4-[2-n-alkyl-1-[2΄-(1H-tetrazole-5-yl) biphenyl -4-yl] methyl] imidazole-4(or 5)-yl]- 3, 5-pyridinedicarboxylate analogs. Methods: These compounds were obtained by two methods starting from biphenyltetrazolyl-4-(or 5)-imidazolecarboxaldehyde intermediates employing in classical Hantzsch condensation reaction. In the first method, triphenylmethyl protecting group of 4- or 5-carboxaldehyde intermediate was first removed in acidic media and then classical Hantzsch reaction was employed in order to obtain the final products. In the second method, without further deprotection process, protected 4- or 5-carboxaldehyde intermediate directly was used in Hantzsch reaction. Results: The second method was more efficient than the first method since the deprotection and ring closure reaction occurs simultaneously in one pot. Conclusion: Eight novel dihydropridines analogs were synthesized using classic Hantzsch condensation reaction. Chemical structures of the compounds were characterized by 1H NMR, infrared and mass spectroscopy. PMID:24312750

Effects of competition among fertility centers on pregnancy and high-order multiple gestation rates.

PubMed

Steiner, Anne Z; Paulson, Richard J; Hartmann, Katherine E

2005-05-01

To measure the effect of competition among fertility centers on pregnancy and high-order multiple (HOM) gestation rates after IVF. Retrospective cohort study. Four hundred eight fertility clinics registered with the Society for Assisted Reproductive Technology as providing IVF services in 2000. Competition was defined as number of clinics in a geographically defined area. Demand for services was based on the population of reproductive-aged women. Three hundred eighty-one fertility clinics reporting clinical outcomes. Pregnancy rates, HOM gestation rates, population of reproductive-aged women, and number of competing clinics were calculated for each clinic from Society for Assisted Reproductive Technology and census data. The clinic HOM gestation rate (percentage of pregnancies that were HOM) and age-adjusted pregnancy rate. The number of clinics in an area of competition ranged from 1 to 22. The HOM gestation rate per clinic ranged from 0% to 50%. As demand increased, competition increased. As competition increased, the number of HOM pregnancies per clinic decreased. In areas of low competition (1 to 2 clinics) the clinic HOM gestation rate was 8.43%, in areas of intermediate competition (3-7 clinics) 8.39%, and in areas of high competition (8-22 clinics) 8.24%. In areas with intermediate demand, high levels of competition resulted in fewer HOM pregnancies than intermediate competition (relative risk 0.56, 95% confidence interval 0.36-0.89) or low levels of competition (RR 0.57, 95% confidence interval 0.35-0.94). Age-adjusted pregnancy rates did not differ by level of competition. According to these data, the risk of HOM gestation decreases with increasing competition among clinics; however, pregnancy rates are unaffected.

Long-Range Self-Assembly via the Mutual Lorentz Force of Plasmon Radiation.

PubMed

Ji, Haojie; Trevino, Jacob; Tu, Raymond; Knapp, Ellen; McQuade, James; Yurkiv, Vitaliy; Mashayek, Farzad; Vuong, Luat T

2018-04-11

Long-range interactions often proceed as a sequence of hopping through intermediate, statistically favored events. Here, we demonstrate predictable mechanical dynamics of particles that arise from the Lorentz force between plasmons. Even if the radiation is weak, the nonconservative Lorentz force produces stable locations perpendicular to the plasmon oscillation; over time, distinct patterns emerge. Experimentally, linearly polarized light illumination leads to the formation of 80 nm diameter Au nanoparticle chains, perpendicularly aligned, with lengths that are orders of magnitude greater than their plasmon near-field interaction. There is a critical intensity threshold and optimal concentration for observing self-assembly.

Human molecular cytogenetics: From cells to nucleotides

PubMed Central

Riegel, Mariluce

2014-01-01

The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed. PMID:24764754

Effect of chain stiffness on the competition between crystallization and glass-formation in model unentangled polymers

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Smith, Tyler B.; Hoy, Robert S.; Karayiannis, Nikos Ch.

2015-10-01

We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of chain stiffness, spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter (lK/r0) increases monotonically with increasing bending stiffness kb and yields a one-parameter model that relates chain shape to bulk morphology. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order. In the rodlike limit, nematic chain ordering typical of lamellar precursors coexists with close-packing. At intermediate values of bending stiffness, the competition between random-walk-like and nematic chain ordering produces glass-formation; the range of kb over which this occurs increases with the thermal cooling rate | T ˙ | implemented in our molecular dynamics simulations. Finally, values of kb between the glass-forming and rodlike ranges produce complex ordered phases such as close-packed spirals. Our results should provide a useful initial step in a coarse-grained modeling approach to systematically determining the effect of chain stiffness on the crystallization-vs-glass-formation competition in both synthetic and colloidal polymers.

Does sex matter? Temporal and spatial patterns of cougar-human conflict in British Columbia.

PubMed

Teichman, Kristine J; Cristescu, Bogdan; Nielsen, Scott E

2013-01-01

Wildlife-human conflicts occur wherever large carnivores overlap human inhabited areas. Conflict mitigation can be facilitated by understanding long-term dynamics and examining sex-structured conflict patterns. Predicting areas with high probability of conflict helps focus management strategies in order to proactively decrease carnivore mortality. We investigated the importance of cougar (Puma concolor) habitat, human landscape characteristics and the combination of habitat and human features on the temporal and spatial patterns of cougar-human conflicts in British Columbia. Conflicts (n = 1,727; 1978-2007) involved similar numbers of male and female cougars with conflict rate decreasing over the past decade. Conflicts were concentrated within the southern part of the province with the most conflicts per unit area occurring on Vancouver Island. For both sexes, the most supported spatial models for the most recent (1998-2007) conflicts contained both human and habitat variables. Conflicts were more likely to occur close to roads, at intermediate elevations and far from the northern edge of the cougar distribution range in British Columbia. Male cougar conflicts were more likely to occur in areas of intermediate human density. Unlike cougar conflicts in other regions, cattle density was not a significant predictor of conflict location. With human populations expanding, conflicts are expected to increase. Conservation tools, such as the maps predicting conflict hotspots from this study, can help focus management efforts to decrease carnivore-human conflict.

Investigating the structure and fragmentation of a highly filamentary IRDC

NASA Astrophysics Data System (ADS)

Henshaw, J. D.; Caselli, P.; Fontani, F.; Jiménez-Serra, I.; Tan, J. C.; Longmore, S. N.; Pineda, J. E.; Parker, R. J.; Barnes, A. T.

2016-11-01

We present 3.7 arcsec (˜0.05 pc) resolution 3.2 mm dust continuum observations from the Institut de Radioastronomie Millimétrique Plateau de Bure Interferometer, with the aim of studying the structure and fragmentation of the filamentary infrared dark cloud (IRDC) G035.39-00.33. The continuum emission is segmented into a series of 13 quasi-regularly spaced (λobs ˜ 0.18 pc) cores, following the major axis of the IRDC. We compare the spatial distribution of the cores with that predicted by theoretical work describing the fragmentation of hydrodynamic fluid cylinders, finding a significant (a factor of ≳ 8) discrepancy between the two. Our observations are consistent with the picture emerging from kinematic studies of molecular clouds suggesting that the cores are harboured within a complex network of independent sub-filaments. This result emphasizes the importance of considering the underlying physical structure, and potentially, dynamically important magnetic fields, in any fragmentation analysis. The identified cores exhibit a range in (peak) beam-averaged column density (3.6 × 1023 cm-2 < NH, c < 8.0 × 1023 cm-2), mass (8.1 M⊙ < Mc < 26.1 M⊙), and number density (6.1 × 105 cm-3 < nH, c, eq < 14.7 × 105 cm-3). Two of these cores, dark in the mid-infrared, centrally concentrated, monolithic (with no traceable substructure at our PdBI resolution), and with estimated masses of the order ˜20-25 M⊙, are good candidates for the progenitors of intermediate-to-high-mass stars. Virial parameters span a range 0.2 < αvir < 1.3. Without additional support, possibly from dynamically important magnetic fields with strengths of the order of 230 μG < B < 670 μG, the cores are susceptible to gravitational collapse. These results may imply a multilayered fragmentation process, which incorporates the formation of sub-filaments, embedded cores, and the possibility of further fragmentation.

The impact of chemical doping on the magnetic state of the Sr{sub 2}YRuO{sub 6} double perovskite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kayser, Paula; Ranjbar, Ben; Kennedy, Brendan J.

The impact of chemical doping of the type Sr{sub 2−x}A{sub x}YRuO{sub 6} (A=Ca, Ba) on the low temperature magnetic properties of Sr{sub 2}YRuO{sub 6}, probed using variable temperature magnetic susceptibility, neutron diffraction and heat capacity measurements, are described. Specific-heat measurements of un-doped Sr{sub 2}YRuO{sub 6} reveal two features at ∼26 and ∼30 K. Neutron scattering measurements at these temperatures are consistent with a change from a 2D ordered state to the 3D type 1 AFM state. Magnetic and structural studies of a number of doped oxides are described that highlight the unique low temperature behavior of Sr{sub 2}YRuO{sub 6} andmore » demonstrate that doping destabilizes the intermediate 2D ordered state. - Graphical abstract: Neutron diffraction measurements of the ordered double perovskite Sr{sub 2}YRuO{sub 6}reveal a with a change from a 2D ordered state to the 3D type 1 AFM state upon cooling. The impact of chemical doping Sr{sub 2−x}A{sub x}YRuO{sub 6} (A=Ca, Ba) on the low temperature magnetic properties have also been investigated and these highlight the unique low temperature behavior of Sr{sub 2}YRuO{sub 6} with doping destabilizing the intermediate 2D ordered state. - Highlights: • Crystal and Magnetic Structure of Sr{sub 2}YRuO{sub 3} was studied using Neutron Diffraction. • Effect of doping on the magnetic ground state established. • Origin of two low temperature transitions discussed.« less

Physical properties and evolutionary time scales of disks around solar-type and intermediate mass stars

NASA Technical Reports Server (NTRS)

Strom, Stephen E.; Edwards, Suzan

1993-01-01

Recent observations of circumstellar disks and their evolutionary timescales are reviewed. It is concluded that disks appear to be a natural outcome of the star-formation process. The disks surrounding young stars initially are massive, with optically thick structures comprised of gas and micron-sized grains. Disk masses are found to range from 0.01 to 0.2 solar masses for solar-type PMS stars, and from 0.01 to 6 solar masses for young, intermediate mass stars. Massive, optically thick accretion disks have accretion rates between 10 exp -8 and 10 exp -6 solar masses/yr for solar type PMS stars and between 10 exp -6 and 10 exp -4 solar masses/yr for intermediate stars. The results suggest that a significant fraction of the mass comprising the star may have passed through a circumstellar accretion disk.

Geometric and electronic structure contributions to function in non-heme iron enzymes.

PubMed

Solomon, Edward I; Light, Kenneth M; Liu, Lei V; Srnec, Martin; Wong, Shaun D

2013-11-19

Mononuclear non-heme Fe (NHFe) enzymes play key roles in DNA repair, the biosynthesis of antibiotics, the response to hypoxia, cancer therapy, and many other biological processes. These enzymes catalyze a diverse range of oxidation reactions, including hydroxylation, halogenation, ring closure, desaturation, and electrophilic aromatic substitution (EAS). Most of these enzymes use an Fe(II) site to activate dioxygen, but traditional spectroscopic methods have not allowed researchers to insightfully probe these ferrous active sites. We have developed a methodology that provides detailed geometric and electronic structure insights into these NHFe(II) active sites. Using these data, we have defined a general mechanistic strategy that many of these enzymes use: they control O2 activation (and limit autoxidation and self-hydroxylation) by allowing Fe(II) coordination unsaturation only in the presence of cosubstrates. Depending on the type of enzyme, O2 activation either involves a 2e(-) reduced Fe(III)-OOH intermediate or a 4e(-) reduced Fe(IV)═O intermediate. Nuclear resonance vibrational spectroscopy (NRVS) has provided the geometric structure of these intermediates, and magnetic circular dichroism (MCD) has defined the frontier molecular orbitals (FMOs), the electronic structure that controls reactivity. This Account emphasizes that experimental spectroscopy is critical in evaluating the results of electronic structure calculations. Therefore these data are a key mechanistic bridge between structure and reactivity. For the Fe(III)-OOH intermediates, the anticancer drug activated bleomycin (BLM) acts as the non-heme Fe analog of compound 0 in heme (e.g., P450) chemistry. However BLM shows different reactivity: the low-spin (LS) Fe(III)-OOH can directly abstract a H atom from DNA. The LS and high-spin (HS) Fe(III)-OOHs have fundamentally different transition states. The LS transition state goes through a hydroxyl radical, but the HS transition state is activated for EAS without O-O cleavage. This activation is important in one class of NHFe enzymes that utilizes a HS Fe(III)-OOH intermediate in dioxygenation. For Fe(IV)═O intermediates, the LS form has a π-type FMO activated for attack perpendicular to the Fe-O bond. However, the HS form (present in the NHFe enzymes) has a π FMO activated perpendicular to the Fe-O bond and a σ FMO positioned along the Fe-O bond. For the NHFe enzymes, the presence of π and σ FMOs enables enzymatic control in determining the type of reactivity: EAS or H-atom extraction for one substrate with different enzymes and halogenation or hydroxylation for one enzyme with different substrates.

Multiple intermediates on the energy landscape of a 15-HEAT-repeat protein

PubMed Central

Tsytlonok, Maksym; Craig, Patricio O.; Sivertsson, Elin; Serquera, David; Perrett, Sarah; Best, Robert B.; Wolynes, Peter G.; Itzhaki, Laura S.

2014-01-01

Repeat proteins are a special class of modular, non-globular proteins composed of small structural motifs arrayed to form elongated architectures and stabilised solely by short-range contacts. We find a remarkable complexity in the unfolding of the large HEAT repeat protein PR65/A. In contrast to what has been seen for small repeat proteins in which unfolding propagates from one end, the HEAT array of PR65/A ruptures at multiple distant sites, leading to intermediate states with non-contiguous folded subdomains. Kinetic analysis allows us to define a network of intermediates and to delineate the pathways that connect them. There is a dominant sequence of unfolding, reflecting a non-uniform distribution of stability across the repeat array; however the unfolding of certain intermediates is competitive, leading to parallel pathways. Theoretical models accounting for the heterogeneous contact density in the folded structure are able to rationalize the variation in stability across the array. This variation in stability also suggests how folding may direct function in a large repeat protein: The stability distribution enables certain regions to present rigid motifs for molecular recognition while affording others flexibility to broaden the search area as in a fly-casting mechanism. Thus PR65/A uses the two ends of the repeat array to bind diverse partners and thereby coordinate the dephosphorylation of many different substrates and of multiple sites within hyperphosphorylated substrates. PMID:24120762

Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

2017-10-01

Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes.

PubMed

Li, Guangyue; Wang, Jian-Bo; Reetz, Manfred T

2018-04-01

Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magnetic structure in Mn1 -xCoxGe compounds

NASA Astrophysics Data System (ADS)

Altynbaev, E.; Siegfried, S.-A.; Strauß, P.; Menzel, D.; Heinemann, A.; Fomicheva, L.; Tsvyashchenko, A.; Grigoriev, S.

2018-04-01

The magnetic system of the pseudobinary compound Mn1 -xCoxGe has been studied using small-angle neutron scattering and susceptibility measurements. It is found that Mn1 -xCoxGe orders magnetically at low temperatures in the whole concentration range of x ∈[0 /0.9 ] . Four different states of the magnetic structure have been found at low temperatures: the long-range-ordered (LRO) short-period helical magnetic structure at x

Properties of tetrahedral clusters and medium range order in GaN during rapid solidification

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Yao, Zhenzhen; Hu, Xuechen; Xie, Quan

2017-12-01

The solidification process of liquid gallium nitride has been studied by molecular dynamics simulation using the Stillinger-Weber potential at cooling rate of 10 K/ps. The structural properties of gallium nitride during the rapid cooling process were investigated in detail by the radial distribution functions, Voronoi polyhedron index and the visualization technology. The amorphous structures were formed with many medium range order structures at 200 K. The <4 0 0 0> polyhedron as the main polyhedron was more stable than other polyhedron in GaN during the quenching process. The cubic and hexahedral medium range order structures were formed by the close link between <4 0 0 0> polyhedron. The cubic crystal structures grew up through the crystalline surface by a layer-by-layer method to become more stable structures during the quenching process.

Amyloidogenesis of Natively Unfolded Proteins

PubMed Central

Uversky, Vladimir N.

2009-01-01

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis. PMID:18537543

Probing the thermal stability and the decomposition mechanism of a magnesium-fullerene polymer via X-ray Raman spectroscopy, X-ray diffraction and molecular dynamics simulations.

PubMed

Aramini, Matteo; Niskanen, Johannes; Cavallari, Chiara; Pontiroli, Daniele; Musazay, Abdurrahman; Krisch, Michael; Hakala, Mikko; Huotari, Simo

2016-02-21

We report the microscopic view of the thermal structural stability of the magnesium intercalated fullerene polymer Mg2C60. With the application of X-ray Raman spectroscopy and X-ray diffraction, we study in detail the decomposition pathways of the polymer system upon annealing at temperatures between 300 and 700 °C. We show that there are at least two energy scales involved in the decomposition reaction. Intermolecular carbon bonds, which are responsible for the formation of a 2D fullerene polymer, are broken with a relatively modest thermal energy, while the long-range order of the original polymer remains intact. With an increased thermal energy, the crystal structure in turn is found to undergo a transition to a novel intercalated cubic phase that is stable up to the highest temperature studied here. The local structure surrounding magnesium ions gets severely modified close to, possibly at, the phase transition. We used density functional theory based calculations to study the thermodynamic and kinetic aspects of the collapse of the fullerene network, and to explain the intermediate steps as well as the reaction pathways in the break-up of this peculiar C60 intermolecular bonding architecture.

Local atomic order of a metallic glass made visible by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Luo, Yuansu; Samwer, Konrad

2018-06-01

Exploring the atomic level structure in amorphous materials by STM becomes extremely difficult due to the localized electronic states. Here we carried out STM studies on a quasi-low-dimensional film of metallic glass Zr65Cu27.5Al7.5 which is ‘ultrathin’ compared with the localization length and/or the length scale of short range order. The local electronic structure must appear more inherent, having states at E f available for tip-sample tunneling current. To enhance imaging contrasts between long-range and short-range orders, the highly oriented pyrolytic graphite was chosen as substrate, so that the structural heterogeneity arising from competition between the glass former ability and the epitaxy can be ascertained. A chemical order predicted for this system was observed in atomic ordered regimes (1–2 monolayers), accompanied with a superstructure with the period Zr–Cu(Al)–Zr along three hexagonal axes. The result implies a chemical short range order in disordered regimes, where polyhedral clusters are dominant with the solute atom Cu(Al) in the center. An attempt for the structural modelling was made based on high resolution STM images, giving icosahedral order on the surface and different Voronoi clusters in 3D space.

On debris flows, river networks, and the spatial structure of channel morphology.

Treesearch

P.E. Bigelow; L.E. Benda; D.J. Miller; K.M. Burnett

2007-01-01

In this paper, we examine the influence of debris-flow deposits and fans on channels and habitat characteristics in small to intermediate-size watersheds in the Oregon Coast Range. We evaluate: (1) the proportion of stream length bordered by debris fans and the spacing between fans, (2) the recurrence interval of debris flows in unmanaged watersheds, (3) the proportion...

Theoretical Heterogeneous Catalysis: Scaling Relationships and Computational Catalyst Design.

PubMed

Greeley, Jeffrey

2016-06-07

Scaling relationships are theoretical constructs that relate the binding energies of a wide variety of catalytic intermediates across a range of catalyst surfaces. Such relationships are ultimately derived from bond order conservation principles that were first introduced several decades ago. Through the growing power of computational surface science and catalysis, these concepts and their applications have recently begun to have a major impact in studies of catalytic reactivity and heterogeneous catalyst design. In this review, the detailed theory behind scaling relationships is discussed, and the existence of these relationships for catalytic materials ranging from pure metal to oxide surfaces, for numerous classes of molecules, and for a variety of catalytic surface structures is described. The use of the relationships to understand and elucidate reactivity trends across wide classes of catalytic surfaces and, in some cases, to predict optimal catalysts for certain chemical reactions, is explored. Finally, the observation that, in spite of the tremendous power of scaling relationships, their very existence places limits on the maximum rates that may be obtained for the catalyst classes in question is discussed, and promising strategies are explored to overcome these limitations to usher in a new era of theory-driven catalyst design.

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

COBALAMIN- AND COBAMIDE-DEPENDENT METHYLTRANSFERASES

PubMed Central

Matthews, Rowena G.; Koutmos, Markos; Datta, Supratim

2008-01-01

Methyltransferases that employ cobalamin cofactors, or their analogues the cobamides, as intermediates in catalysis of methyl transfer play vital roles in energy generation in anaerobic unicellular organisms. In a broader range of organisms they are involved in the conversion of homocysteine to methionine. Although the individual methyl transfer reactions catalyzed are simple SN2 displacements, the required change in coordination at the cobalt of the cobalamin or cobamide cofactors and the lability of the reduced Co+1 intermediates introduces the necessity for complex conformational changes during the catalytic cycle. Recent spectroscopic and structural studies on several of these methyltransferases have helped to reveal the strategies by which these conformational changes are facilitated and controlled. PMID:19059104

Chemical Probes for the Functionalization of Polyketide Intermediates**

PubMed Central

Riva, Elena; Wilkening, Ina; Gazzola, Silvia; Li, W M Ariel; Smith, Luke; Leadlay, Peter F; Tosin, Manuela

2014-01-01

A library of functionalized chemical probes capable of reacting with ketosynthase-bound biosynthetic intermediates was prepared and utilized to explore in vivo polyketide diversification. Fermentation of ACP mutants of S. lasaliensis in the presence of the probes generated a range of unnatural polyketide derivatives, including novel putative lasalocid A derivatives characterized by variable aryl ketone moieties and linear polyketide chains (bearing alkyne/azide handles and fluorine) flanking the polyether scaffold. By providing direct information on microorganism tolerance and enzyme processing of unnatural malonyl-ACP analogues, as well as on the amenability of unnatural polyketides to further structural modifications, the chemical probes constitute invaluable tools for the development of novel mutasynthesis and synthetic biology. PMID:25212788

Visual performance after bilateral implantation of 2 new presbyopia-correcting intraocular lenses: Trifocal versus extended range of vision.

PubMed

Monaco, Gaspare; Gari, Mariangela; Di Censo, Fabio; Poscia, Andrea; Ruggi, Giada; Scialdone, Antonio

2017-06-01

To compare the visual outcomes and quality of vision of 2 new diffractive multifocal intraocular lenses (IOLs) with those of a monofocal IOL. Fatebenefratelli e Oftalmico Hospital, Milan, Italy. Prospective case series. Patients had bilateral cataract surgery with implantation of a trifocal IOL (Panoptix), an extended-range-of-vision IOL (Symfony), or a monofocal IOL (SN60WF). Postoperative examinations included assessing distance, intermediate, and near visual acuity; binocular defocus; intraocular and total aberrations; point-spread function (PSF); modulation transfer function (MTF); retinal straylight; and quality-of-vision (QoV) and spectacle-dependence questionnaires. Seventy-six patients (152 eyes) were assessed for study eligibility. Twenty patients (40 eyes) in each arm of the study (60 patients, 120 eyes) completed the outcome assessment. At the 4-month follow-up, the trifocal group had significantly better near visual acuity than the extended-range-of-vision group (P = .005). The defocus curve showed the trifocal IOL had better intermediate/near performance than the extended-range-of-vision IOL and both multifocal IOLs performed better than the monofocal IOL. Intragroup comparison of the total higher-order aberrations, PSF, MTF, and retinal straylight were not statistically different. The QoV questionnaire results showed no differences in dysphotopsia between the multifocal IOL groups; however, the results were significantly higher than in the monofocal IOL group. Both multifocal IOLs seemed to be good options for patients with intermediate-vision requirements, whereas the trifocal IOL might be better for patients with near-vision requirements. The significant perception of visual side effects indicates that patients still must be counseled about these effects before a multifocal IOL is implanted. Copyright © 2017 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Identifying the Structure of the Intermediate, Li 2/3CoPO 4, Formed during Electrochemical Cycling of LiCoPO 4

DOE PAGES

Strobridge, Fiona C.; Clément, Raphaële J.; Leskes, Michal; ...

2014-11-03

In situ synchrotron diffraction measurements and subsequent Rietveld refinements are used to show that the high energy density cathode material LiCoPO 4 (space group Pnma) undergoes two distinct two-phase reactions upon charge and discharge, both occurring via an intermediate Li 2/3(Co 2+) 2/3(Co 3+) 1/3PO 4 phase. Two resonances are observed for Li 2/3CoPO 4 with intensity ratios of 2:1 and 1:1 in the 31P and 7Li NMR spectra, respectively. An ordering of Co 2+/Co 3+ oxidation states is proposed within a (a × 3b × c) supercell, and Li +/vacancy ordering is investigated using experimental NMR data in combinationmore » with first-principles solid-state DFT calculations. In the lowest energy configuration, both the Co 3+ ions and Li vacancies are found to order along the b-axis. Two other low energy Li +/vacancy ordering schemes are found only 5 meV per formula unit higher in energy. All three configurations lie below the LiCoPO 4–CoPO 4 convex hull and they may be readily interconverted by Li + hops along the b-direction.« less

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

PubMed Central

Surana, Parag

2016-01-01

Abstract The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly‐Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

Optical properties and progressive sterical hindering in pyridinium phenoxides

NASA Astrophysics Data System (ADS)

Boeglin, A.; Barsella, A.; Fort, A.; Mançois, F.; Rodriguez, V.; Diemer, V.; Chaumeil, H.; Defoin, A.; Jacques, P.; Carré, C.

2007-07-01

Pyridinium phenoxides are model compounds associating large dipole moments with high optical nonlinearities. A progression of sterically hindered forms of such zwitterions has been synthesized in order to investigate their structure/property relationships. Their UV-vis absorption in acetonitrile has been analyzed as a function of concentration in order to assess the presence of aggregates and the level of protonation. The quadratic optical properties have been measured by the EFISH and hyper-Rayleigh techniques and are interpreted via semi-empirical calculations. The solvation model used leads to results that agree with our experimental findings indicating an increased response for intermediate twist angles.

a Structure of Experienced Time

NASA Astrophysics Data System (ADS)

Havel, Ivan M.

2005-10-01

The subjective experience of time will be taken as a primary motivation for an alternative, essentially discontinuous conception of time. Two types of such experience will be discussed, one based on personal episodic memory, the other on the theoretical fine texture of experienced time below the threshold of phenomenal awareness. The former case implies a discrete structure of temporal episodes on a large scale, while the latter case suggests endowing psychological time with a granular structure on a small scale, i.e. interpreting it as a semi-ordered flow of smeared (not point-like) subliminal time grains. Only on an intermediate temporal scale would the subjectively felt continuity and fluency of time emerge. Consequently, there is no locally smooth mapping of phenomenal time onto the real number continuum. Such a model has certain advantages; for instance, it avoids counterintuitive interpretations of some neuropsychological experiments (e.g. Libet's measurement) in which the temporal order of events is crucial.

Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis

DOE Office of Scientific and Technical Information (OSTI.GOV)

K Harris; G Cockrell; D Puleo

2011-12-31

Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered releasemore » of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.« less

A Feasibility Study of the Flare-Cylinder Configuration as a Reentry Body Shape for an Intermediate Range Ballistic Missile

NASA Technical Reports Server (NTRS)

Garland, B. J.; Hall, J. R.

1958-01-01

A study has been made of a flare-cylinder configuration to investigate its feasibility as a reentry body of an intermediate range ballistic missile. Factors considered were heating, weight, stability, and impact velocity. A series of trajectories covering the possible range of weight-drag ratios were computed for simple truncated nose shapes of varying pointedness, and hence varying weight-drag ratios. Four trajectories were chosen for detailed temperature computation from among those trajectories estimated to be possible. Temperature calculations were made for both "conventional" (for example, copper, Inconel, and stainless steel) and "unconventional" (for example, beryllium and graphite) materials. Results of the computations showed that an impact Mach number of 0.5 was readily obtainable for a body constructed from conventional materials. A substantial increase in subsonic impact velocity above a Mach number of 0.5 was possible without exceeding material temperature limits. A weight saving of up to 134 pounds out of 822 was possible with unconventional materials. This saving represents 78 percent of the structural weight. Supersonic impact would require construction of the body from unconventional materials but appeared to be well within the range of attainability.

Non-Native α-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the β-Barrel in β-Lactoglobulin.

PubMed

Sakurai, Kazumasa; Yagi, Masanori; Konuma, Tsuyoshi; Takahashi, Satoshi; Nishimura, Chiaki; Goto, Yuji

2017-09-12

The roles of non-native α-helices frequently observed in the initial folding stage of β-sheet proteins have been examined for many years. We herein investigated the residue-level structures of several mutants of bovine β-lactoglobulin (βLG) in quenched-flow pH-pulse labeling experiments. βLG assumes a collapsed intermediate with a non-native α-helical structure (I 0 ) in the early stage of folding, although its native form is predominantly composed of β-structures. The protection profile in I 0 of pseudo-wild type (WT*) βLG was found to deviate from the pattern of the "average area buried upon folding" (AABUF). In particular, the level of protection at the region of strand A, at which non-native α-helices form in the I 0 state, was significantly low compared to AABUF. G17E, the mutant with an increased helical propensity, showed a similar protection pattern. In contrast, the protection pattern for I 0 of E44L, the mutant with an increased β-sheet propensity, was distinct from that of WT* and resembled the AABUF pattern. Transverse relaxation measurements demonstrated that the positions of the residual structures in the unfolded states of these mutants were consistent with those of the protected residues in the respective I 0 states. On the basis of the slower conversion of I 0 to the native state for E44L to that for WT*, non-native α-helices facilitate the ordered assembly of the β-barrel by preventing interactions that trap folding.

Role of core excitation in (d ,p ) transfer reactions

NASA Astrophysics Data System (ADS)

Deltuva, A.; Ross, A.; Norvaišas, E.; Nunes, F. M.

2016-10-01

Background: Recent work found that core excitations can be important in extracting structure information from (d ,p ) reactions. Purpose: Our objective is to systematically explore the role of core excitation in (d ,p ) reactions and to understand the origin of the dynamical effects. Method: Based on the particle-rotor model of n +10Be , we generate a number of models with a range of separation energies (Sn=0.1 -5.0 MeV), while maintaining a significant core excited component. We then apply the latest extension of the momentum-space-based Faddeev method, including dynamical core excitation in the reaction mechanism to all orders, to the 10Be(d ,p )11Be -like reactions, and study the excitation effects for beam energies Ed=15 -90 MeV. Results: We study the resulting angular distributions and the differences between the spectroscopic factor that would be extracted from the cross sections, when including dynamical core excitation in the reaction, and that of the original structure model. We also explore how different partial waves affect the final cross section. Conclusions: Our results show a strong beam-energy dependence of the extracted spectroscopic factors that become smaller for intermediate beam energies. This dependence increases for loosely bound systems.

Evidence of an Intermediate Phase in bulk alloy oxide glass sysem

NASA Astrophysics Data System (ADS)

Chakraborty, S.; Boolchand, P.

2011-03-01

Reversibility windows have been observed in modified oxides (alkali-silicates and -germanates) and identified with Intermediate Phases(IPs). Here we find preliminary evidence of an IP in a ternary oxide glass, (B2 O3)5 (Te O2)95-x (V2O5)x , which is composed of network formers. Bulk glasses are synthesized across the 18% x 35 % composition range, and examined in Raman scattering, modulated DSC and molar volume experiments. Glass transition temperatures Tg (x) steadily decrease with V2O5 content x, and reveal the enthalpy of relaxation at Tg to show a global minimum in the 24% x < 27 range, the reversibility window (IP). Molar volumes reveal a minimum in this window. Raman scattering reveals a Boson mode, and at least six other vibrational bands in the 100cm-1 < ν < 1700cm-1 range. Compositional trends in vibrational mode strengths and frequency are established. These results will be presented in relation to glass structure evolution with vanadia content and the underlying elastic phases. Supported by NSF grant DMR 08-53957.

A Multi-Wavelength Survey of Intermediate-Mass Star-Forming Regions

NASA Astrophysics Data System (ADS)

Lundquist, Michael J.; Kobulnicky, Henry A.; Kerton, Charles R.

2015-01-01

Current research into Galactic star formation has focused on either massive star-forming regions or nearby low-mass regions. We present results from a survey of Galactic intermediate-mass star-forming regions (IM SFRs). These regions were selected from IRAS colors that specify cool dust and large PAH contribution, suggesting that they produce stars up to but not exceeding about 8 solar masses. Using WISE data we have classified 984 candidate IM SFRs as star-like objects, galaxies, filamentary structures, or blobs/shells based on their mid-infrared morphologies. Focusing on the blobs/shells, we combined follow-up observations of deep near-infrared (NIR) imaging with optical and NIR spectroscopy to study the stellar content, confirming the intermediate-mass nature of these regions. We also gathered CO data from OSO and APEX to study the molecular content and dynamics of these regions. We compare these results to those of high-mass star formation in order to better understand their role in the star-formation paradigm.

Measuring the Impact of Financial Intermediation: Linking Contract Theory to Econometric Policy Evaluation *

PubMed Central

Townsend, Robert M.; Urzua, Sergio S.

2010-01-01

We study the impact that financial intermediation can have on productivity through the alleviation of credit constraints in occupation choice and/or an improved allocation of risk, using both static and dynamic structural models as well as reduced form OLS and IV regressions. Our goal in this paper is to bring these two strands of the literature together. Even though, under certain assumptions, IV regressions can recover accurately the true model-generated local average treatment effect, these are quantitatively different, in order of magnitude and even sign, from other policy impact parameters (e.g., ATE and TT). We also show that laying out clearly alternative models can guide the search for instruments. On the other hand adding more margins of decision, i.e., occupation choice and intermediation jointly, or adding more periods with promised utilities as key state variables, as in optimal multi-period contracts, can cause the misinterpretation of IV as the causal effect of interest. PMID:20436953

Formation of single-walled aluminosilicate nanotubes from molecular precursors and curved nanoscale intermediates.

PubMed

Yucelen, G Ipek; Choudhury, Rudra Prosad; Vyalikh, Anastasia; Scheler, Ulrich; Beckham, Haskell W; Nair, Sankar

2011-04-13

We report the identification and elucidation of the mechanistic role of molecular precursors and nanoscale (1-3 nm) intermediates with intrinsic curvature in the formation of single-walled aluminosilicate nanotubes. We characterize the structural and compositional evolution of molecular and nanoscale species over a length scale of 0.1-100 nm by electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy ((27)Al liquid-state, (27)Al and (29)Si solid-state MAS), and dynamic light scattering. Together with structural optimization of key experimentally identified species by solvated density functional theory calculations, this study reveals the existence of intermediates with bonding environments, as well as intrinsic curvature, similar to the structure of the final nanotube product. We show that "proto-nanotube-like" intermediates with inherent curvature form in aqueous synthesis solutions immediately after initial hydrolysis of reactants, disappear from the solution upon heating to 95 °C due to condensation accompanied by an abrupt pH decrease, and finally form ordered single-walled aluminosilicate nanotubes. Detailed quantitative analysis of NMR and ESI-MS spectra from the relevant aluminosilicate, aluminate, and silicate solutions reveals the presence of a variety of monomeric and polymeric aluminate and aluminosilicate species (Al(1)Si(x)-Al(13)Si(x)), such as Keggin ions [AlO(4)Al(12)(OH)(24)(H(2)O)(12)](7+) and polynuclear species with a six-membered Al oxide ring unit. Our study also directly reveals the complexation of aluminate and aluminosilicate species with perchlorate species that most likely inhibit the formation of larger condensates or nontubular structures. Integration of all of our results leads to the construction of the first molecular-level mechanism of single-walled metal oxide nanotube formation, incorporating the role of monomeric and polymeric aluminosilicate species as well as larger nanoparticles. © 2011 American Chemical Society

Magnetic Structure and Quadrupolar Order Parameter Driven by Geometrical Frustration Effect in NdB 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamauchi, Hiroki; Metoki, Naoto; Watanuki, Ryuta

2017-04-15

Neutron diffraction experiments have been carried out to characterize the magnetic structures and order parameters in an intermediate phase of NdB 4 showing the successive phase transitions at T 0 = 17.2 K, T N1 = 7.0 K, and T N2 = 4.8 K. We have revealed the antiferromagnetic ordering with the propagation vectors q0=(0,0,0), q0 and qs1=(δ,δ,0.4) (δ ~ 0.14), and q 0 and q s2=(0.2,0,0.4) in phase II (T N1 < T < T 0), phase III (T N2 < T < T N1), and phase IV (T < T N2), respectively. The observed patterns in phase IImore » are successfully explained by postulating a coplanar structure with static magnetic moments in the tetragonal ab-plane. We have found that the magnetic structure in phase II can be uniquely determined to be a linear combination of antiferromagnetic “all-in/all-out”-type (Γ 4) and “vortex”-type (Γ 2) structures, consisting of a Γ 4 main component (77%) with a small amplitude of Γ 2 (23%). Finally, we propose that the quadrupolar interaction holds the key to stabilizing the noncollinear magnetic structure and quadrupolar order. Here, the frustration in the Shastry–Sutherland lattice would play an essential role in suppressing the dominance of the magnetic interaction.« less

Magnetic Structure and Quadrupolar Order Parameter Driven by Geometrical Frustration Effect in NdB4

NASA Astrophysics Data System (ADS)

Yamauchi, Hiroki; Metoki, Naoto; Watanuki, Ryuta; Suzuki, Kazuya; Fukazawa, Hiroshi; Chi, Songxue; Fernandez-Baca, Jaime A.

2017-04-01

Neutron diffraction experiments have been carried out to characterize the magnetic structures and order parameters in an intermediate phase of NdB4 showing the successive phase transitions at T0 = 17.2 K, TN1 = 7.0 K, and TN2 = 4.8 K. We have revealed the antiferromagnetic ordering with the propagation vectors q0 = (0,0,0), q0 and qs1 = (δ ,δ ,0.4) (δ ˜ 0.14), and q0 and qs2 = (0.2,0,0.4) in phase II (TN1 < T < T0), phase III (TN2 < T < TN1), and phase IV (T < TN2), respectively. The observed patterns in phase II are successfully explained by postulating a coplanar structure with static magnetic moments in the tetragonal ab-plane. We have found that the magnetic structure in phase II can be uniquely determined to be a linear combination of antiferromagnetic "all-in/all-out"-type (Γ4) and "vortex"-type (Γ2) structures, consisting of a Γ4 main component (77%) with a small amplitude of Γ2 (23%). We propose that the quadrupolar interaction holds the key to stabilizing the noncollinear magnetic structure and quadrupolar order. Here, the frustration in the Shastry-Sutherland lattice would play an essential role in suppressing the dominance of the magnetic interaction.

Two-photon direct frequency comb spectroscopy of alkali atoms

NASA Astrophysics Data System (ADS)

Palm, Christopher; Pradhananga, Trinity; Nguyen, Khoa; Montcrieffe, Caitlin; Kimball, Derek

2012-11-01

We have studied transition frequencies and excited state hyperfine structure in rubidium using 2-photon transitions excited directly with the frequency-doubled output of a erbium fiber optical frequency comb. The frequency comb output is directed in two counterpropagating directions through a vapor cell containing the rubidium vapor. A pair of optical filters is used to select teeth of the comb in order to identify the transition wavelengths. A photomultiplier tube (PMT) measures fluorescence from a decay channel wavelength selected with another optical filter. Using different combinations of filters enables a wide range of transitions to be investigated. By scanning the repetition rate, a Doppler-free spectrum can be obtained enabling kHz-resolution spectral measurements. An interesting dependence of the 2-photon spectrum on the energy of the intermediate state of the 2-photon transition is discussed. Our investigations are laying the groundwork for a long-term research program to use direct frequency comb spectroscopy to understand the complex spectra of rare-earth atoms.

Mechanical and Transport Properties of Poly(propylene-co-1-heptene) Copolymers and Their Dependence on Monoclinic and/or Mesomorphic Polymorphs.

PubMed

García-Peñas, Alberto; Gómez-Elvira, José M; Lorenzo, Vicente; Pérez, Ernesto; Cerrada, María L

2016-02-25

Poly(propylene-co-1-heptene) copolymers have been evaluated in a wide 1-heptene content range. Two different polymorphs can be observed in this interval under the processing conditions imposed: monoclinic crystallites and mesomorphic entities. The unique presence of one or the other lattice at specific content or the coexistence of both of them at the intermediate composition interval is a key factor affecting some of the exhibited properties. The influence is observed in characteristics mainly dependent on either crystalline structure, like rigidity, or the amorphous regions, as location and intensity of glass transition. To get a deeper understanding, the transition from mesophase to monoclinic crystallites has also been studied by DSC and by WAXS and SAXS experiments using synchrotron radiation. It is observed that this transformation is only partial and just involves one-third of the initial ordered mesomorphic entities. Permeability to different gases is mainly dependent on amorphous content and hindrance that monoclinic or mesomorphic entities impose on those disordered regions.

Stellar models for a wide range of initial chemical compositions until helium burning IV. From X = 0.65 to X = 0.80, for Z = 0.004

NASA Astrophysics Data System (ADS)

Claret, A.; Gimenez, A.

1998-11-01

As a continuation of previous papers in a series devoted to the computation of stellar structure and evolution models we present a grid specifically obtained for detailed studies of the stellar content of the Small Magellanic Cloud. The initial metal content has thus been adopted to be Z = 0.004 while the hydrogen content varies from 0.65 to 0.80 leaving as an intermediate value that given by standard laws of enrichment, X = 0.744. Interpolation for different environment is therefore possible with these new models. Other input physics parameters, e.g. convective overshooting, mixing-length, opacities or nuclear reaction rates, have been adopted to be homogeneous with the previously published models in order to facilitate comparative studies. Tables 1-72 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/Abstract.html}

Ethylene Epoxidation with Nitrous Oxide over Fe-BTC Metal-Organic Frameworks: A DFT Study.

PubMed

Maihom, Thana; Choomwattana, Saowapak; Wannakao, Sippakorn; Probst, Michael; Limtrakul, Jumras

2016-11-04

The epoxidation of ethylene with N 2 O over the metal-organic framework Fe-BTC (BTC=1,3,5-benzentricarboxylate) is investigated by means of density functional calculations. Two reaction paths for the production of ethylene oxide or acetaldehyde are systematically considered in order to assess the efficiency of Fe-BTC for the selective formation of ethylene oxide. The reaction starts with the decomposition of N 2 O to form an active surface oxygen atom on the Fe site of Fe-BTC, which subsequently reacts with an ethylene molecule to form an ethyleneoxy intermediate. This intermediate can then be selectively transformed either by 1,2-hydride shift into the undesired product acetaldehyde or into the desired product ethylene oxide by way of ring closure of the intermediate. The production of ethylene oxide requires an activation energy of 5.1 kcal mol -1 , which is only about one-third of the activation energy of acetaldehyde formation (14.3 kcal mol -1 ). The predicted reaction rate constants for the formation of ethylene oxide in the relevant temperature range are approximately 2-4 orders of magnitude higher than those for acetaldehyde. Altogether, the results suggest that Fe-BTC is a good candidate catalyst for the epoxidation of ethylene by molecular N 2 O. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schotte, Friedrich; Cho, Hyun Sun; Kaila, Ville R.I.

2012-11-06

To understand how signaling proteins function, it is necessary to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotatedmore » nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (~600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.« less

Manganese containing layer for magnetic recording media

DOEpatents

Lambeth, David N.; Lee, Li-Lien; Laughlin, David E.

1999-01-01

The present invention provides for a magnetic recording media incorporating Mn-containing layers between a substrate and a magnetic layer to provide media having increased coercivity and lower noise. The Mn-containing layer can be incorporated in a rotating, translating or stationary recording media to operate in conjunction with magnetic transducing heads for recording and reading of magnetic data, as well as other applications. The magnetic recording medium of the invention preferably includes a Co or Co alloy film magnetic layer, and Mn-containing layer, preferably comprised of VMn, TiMn, MnZn, CrMnMo, CrMnW, CrMnV, and CrMnTi, and most preferably a CrMn alloy, disposed between the substrate and the magnetic layer to promote an epitaxial crystalline structure in the magnetic layer. The medium can further include seed layers, preferably polycrystalline MgO for longitudinal media, underlayers, and intermediate layers. Underlayers and intermediate layers are comprised of materials having either an A2 structure or a B2-ordered crystalline structure disposed between the seed layer and the magnetic layer. Materials having an A2 structure are preferably Cr or Cr alloys, such as CrV, CrMo, CrW and CrTi. Materials having a B2-ordered structure having a lattice constant that is substantially comparable to that of Cr, such as those preferably selected from the group consisting of NiAl, AILCo, FeAl, FeTi, CoFe, CoTi, CoHf, CoZr, NiTi, CuBe, CuZn, A-LMn, AlRe, AgMg, and Al.sub.2 FeMn.sub.2, and is most preferably FeAl or NiAl.

Protein folding and misfolding: mechanism and principles

PubMed Central

Englander, S. Walter; Mayne, Leland; Krishna, Mallela M. G.

2012-01-01

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding. PMID:18405419

Rogue waves in the multicomponent Mel'nikov system and multicomponent Schrödinger-Boussinesq system

NASA Astrophysics Data System (ADS)

Sun, Baonan; Lian, Zhan

2018-02-01

By virtue of the bilinear method and the KP hierarchy reduction technique, exact explicit rational solutions of the multicomponent Mel'nikov equation and the multicomponent Schrödinger-Boussinesq equation are constructed, which contain multicomponent short waves and single-component long wave. For the multicomponent Mel'nikov equation, the fundamental rational solutions possess two different behaviours: lump and rogue wave. It is shown that the fundamental (simplest) rogue waves are line localised waves which arise from the constant background with a line profile and then disappear into the constant background again. The fundamental line rogue waves can be classified into three: bright, intermediate and dark line rogue waves. Two subclasses of non-fundamental rogue waves, i.e., multirogue waves and higher-order rogue waves are discussed. The multirogue waves describe interaction of several fundamental line rogue waves, in which interesting wave patterns appear in the intermediate time. Higher-order rogue waves exhibit dynamic behaviours that the wave structures start from lump and then retreat back to it. Moreover, by taking the parameter constraints further, general higher-order rogue wave solutions for the multicomponent Schrödinger-Boussinesq system are generated.

Redox-Mediated Stabilization in Zinc Molybdenum Nitrides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arca, Elisabetta; Lany, Stephan; Perkins, John D.

We report on the theoretical prediction and experimental realization of new ternary zinc molybdenum nitride compounds. We used theory to identify previously unknown ternary compounds in the Zn-Mo-N systems, Zn 3MoN 4 and ZnMoN 2, and to analyze their bonding environment. Experiments show that Zn-Mo-N alloys can form in broad composition range from Zn 3MoN 4 to ZnMoN 2 in the wurtzite-derived structure, accommodating very large off-stoichiometry. Interestingly, the measured wurtzite-derived structure of the alloys is metastable for the ZnMoN 2 stoichiometry, in contrast to the Zn 3MoN 4 stoichiometry, where ordered wurtzite is predicted to be the ground state.more » The formation of Zn 3MoN 4-ZnMoN 2 alloy with wurtzite-derived crystal structure is enabled by the concomitant ability of Mo to change oxidation state from +VI in Zn 3MoN 4 to +IV in ZnMoN 2, and the capability of Zn to contribute to the bonding states of both compounds, an effect that we define as 'redox-mediated stabilization.' The stabilization of Mo in both the +VI and +IV oxidation states is due to the intermediate electronegativity of Zn, which enables significant polar covalent bonding in both Zn 3MoN 4 and ZnMoN 2 compounds. The smooth change in the Mo oxidation state between Zn 3MoN 4 and ZnMoN 2 stoichiometries leads to a continuous change in optoelectronic properties - from resistive and semitransparent Zn 3MoN 4 to conductive and absorptive ZnMoN 2. The reported redox-mediated stabilization in zinc molybdenum nitrides suggests there might be many undiscovered ternary compounds with one metal having an intermediate electronegativity, enabling significant covalent bonding, and another metal capable of accommodating multiple oxidation states, enabling stoichiometric flexibility.« less

Redox-Mediated Stabilization in Zinc Molybdenum Nitrides

DOE PAGES

Arca, Elisabetta; Lany, Stephan; Perkins, John D.; ...

2018-03-01

We report on the theoretical prediction and experimental realization of new ternary zinc molybdenum nitride compounds. We used theory to identify previously unknown ternary compounds in the Zn-Mo-N systems, Zn 3MoN 4 and ZnMoN 2, and to analyze their bonding environment. Experiments show that Zn-Mo-N alloys can form in broad composition range from Zn 3MoN 4 to ZnMoN 2 in the wurtzite-derived structure, accommodating very large off-stoichiometry. Interestingly, the measured wurtzite-derived structure of the alloys is metastable for the ZnMoN 2 stoichiometry, in contrast to the Zn 3MoN 4 stoichiometry, where ordered wurtzite is predicted to be the ground state.more » The formation of Zn 3MoN 4-ZnMoN 2 alloy with wurtzite-derived crystal structure is enabled by the concomitant ability of Mo to change oxidation state from +VI in Zn 3MoN 4 to +IV in ZnMoN 2, and the capability of Zn to contribute to the bonding states of both compounds, an effect that we define as 'redox-mediated stabilization.' The stabilization of Mo in both the +VI and +IV oxidation states is due to the intermediate electronegativity of Zn, which enables significant polar covalent bonding in both Zn 3MoN 4 and ZnMoN 2 compounds. The smooth change in the Mo oxidation state between Zn 3MoN 4 and ZnMoN 2 stoichiometries leads to a continuous change in optoelectronic properties - from resistive and semitransparent Zn 3MoN 4 to conductive and absorptive ZnMoN 2. The reported redox-mediated stabilization in zinc molybdenum nitrides suggests there might be many undiscovered ternary compounds with one metal having an intermediate electronegativity, enabling significant covalent bonding, and another metal capable of accommodating multiple oxidation states, enabling stoichiometric flexibility.« less

Molecular Dynamics of Peptide Folding at Aqueous Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Chipot, Christophe; Chang, Sherwood (Technical Monitor)

1997-01-01

Even though most monomeric peptides are disordered in water they can adopt sequence-dependent, ordered structures, such as a-helices, at aqueous interfaces. This property is relevant to cellular signaling, membrane fusion, and the action of toxins and antibiotics. The mechanism of folding nonpolar peptides at the water-hexane interface was studied in the example of an 11-mer, of poly-L-leucine. Initially placed as a random coil on the water side of the interface, the peptide folded into an a-helix in 36 ns. Simultaneously, the peptide translocated into the hexane side of the interface. Folding was not sequential and involved a 3/10-helix as an intermediate. The folded peptide was either parallel to the interface or had its C-terminus exposed to water. An 11-mer, LQQLLQQLLQL, composed of leucine (L) and glutamine (G), was taken as a model amphiphilic peptide. It rapidly adopted an amphiphilic, disordered structure at the interface. Further folding proceeded through a series of amphiphilic intermediates.

Secuencias evolutivas e isocronas para estrellas de baja masa e intermedia

NASA Astrophysics Data System (ADS)

Panei, J.; Baume, G.

2016-08-01

We present theoretical evolutionary sequences for low- and intermediate-mass stars. The masses calculated range from 1.7 to 10 M. The initial chemical composition is . In addition, we have taken into account a nuclear network with 17 isotopes and 34 nuclear reactions. With respect to the mix, we considered overshooting with a parameter . The evolutionary calculations were initialized from the region of instability of Hayashi, in order to calculate isochrones of pre-sequence, too.

Simulation of Peptides at Aqueous Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, M.; Chipot, C.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Integrating photonic crystals in thin film silicon photovoltaics

NASA Astrophysics Data System (ADS)

O'Brien, P. G.; Chutinan, A.; Ozin, G. A.; Kherani, N. P.; Zukotynski, S.

2010-06-01

Wave-optics analysis is performed to investigate the benefits of integrating photonic crystals into micromorph cells. Specifically, we theoretically investigate two novel micromorph cells which integrate photonic crystals and compare their optical performance with that of conventional micromorph cells. In the first innovative micromorph cell configuration the intermediate reflector is a selectively transparent and conducting photonic crystal (STCPC). In the second micromorph cell its bottom μc-Si:H cell is structured in the form of an inverted opal. Our results show that with the AM1.5 solar spectrum at normal incidence the current generated in a conventional micromorph cell is increased from 12.1 mA/cm2 to 13.0 mA/cm2 when the bottom μc-Si:H cell is structured in the form of an inverted opal. However, the current generated in the micromorph cell can be increased to as much as 13.7 mA/cm2 when an STCPC is utilized as the intermediate reflector. Furthermore, the thickness of the μc-Si:H opal must be relatively large in order to absorb a sufficient amount of the solar irradiance, which is expected to degrade the electrical performance of the device. In contrast, our results suggest that STCPC intermediate reflectors are a viable technology that could potentially enhance the performance of micromorph cells.

Mechanism of insulin fibrillation: the structure of insulin under amyloidogenic conditions resembles a protein-folding intermediate.

PubMed

Hua, Qing-xin; Weiss, Michael A

2004-05-14

Insulin undergoes aggregation-coupled misfolding to form a cross-beta assembly. Such fibrillation has long complicated its manufacture and use in the therapy of diabetes mellitus. Of interest as a model for disease-associated amyloids, insulin fibrillation is proposed to occur via partial unfolding of a monomeric intermediate. Here, we describe the solution structure of human insulin under amyloidogenic conditions (pH 2.4 and 60 degrees C). Use of an enhanced sensitivity cryogenic probe at high magnetic field avoids onset of fibrillation during spectral acquisition. A novel partial fold is observed in which the N-terminal segments of the A- and B-chains detach from the core. Unfolding of the N-terminal alpha-helix of the A-chain exposes a hydrophobic surface formed by native-like packing of the remaining alpha-helices. The C-terminal segment of the B-chain, although not well ordered, remains tethered to this partial helical core. We propose that detachment of N-terminal segments makes possible aberrant protein-protein interactions in an amyloidogenic nucleus. Non-cooperative unfolding of the N-terminal A-chain alpha-helix resembles that observed in models of proinsulin folding intermediates and foreshadows the extensive alpha --> beta transition characteristic of mature fibrils.

Thermal and Denaturation Studies of the Time-Resolved Fluorescence Decay of Human Superoxide Dismutase

NASA Astrophysics Data System (ADS)

Silva, Norberto De Jesus

Previous studies have shown that time-resolved fluorescence decay of various single tryptophan proteins is best described by a distribution of fluorescence lifetimes rather than one or two lifetimes. The thermal dependence of the lifetime distributions is consistent with the hypothesis that proteins fluctuate between a hierarchy of many conformational substates. With this scenario as a theoretical framework, the correlations between protein dynamic and structure are investigated by studying the time-resolved fluorescence and anisotropy decay of the single tryptophan (Trp) residue of human superoxide dismutase (HSOD) over a wide range of temperatures and at different denaturant concentrations. First, it is demonstrated that the center of the lifetime distribution can characterize the average deactivation environment of the excited Trp-protein system. A qualitative model is introduced to explain the time-resolved fluorescence decay of HSOD in 80% glycerol over a wide range of temperatures. The dynamical model features isoenergetic conformational substates separated by a hierarchy of energy barriers. The HSOD system is also investigated as a function of denaturant concentration in aqueous solution. As a function of guanidine hydrochloride (GdHCl), the width of the fluorescence lifetime distribution of HSOD displays a maximum which is not coincident with the fully denatured form of HSOD at 6.5M GdHCl. Furthermore, the width for the fully denatured form of HSOD is greater than that of the native form. This is consistent with the scenario that more conformational substates are being created upon denaturation of HSOD. HSOD is a dimeric protein and it was observed that the width of the lifetime distribution of HSOD at intermediate GdHCl concentrations increased with decreasing protein concentration. In addition, the secondary structure of HSOD at intermediate GdHCl concentration does not change with protein concentration. These results suggest that HSOD display structural microheterogeneity which is consistent with the hypothesis of conformational substates. Further analysis show that, during denaturation, the monomeric form of HSOD is an intermediate which displays native-like secondary structure and fluctuating tertiary structure; i.e., the monomeric form of HSOD is a molten globule.

Minimally nonlocal nucleon-nucleon potentials with chiral two-pion exchange including Δ resonances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piarulli, M.; Girlanda, L.; Schiavilla, R.

In this study, we construct a coordinate-space chiral potential, including Δ-isobar intermediate states in its two-pion-exchange component up to order Q 3 (Q denotes generically the low momentum scale). The contact interactions entering at next-to-leading and next-to-next-to-next-to-leading orders (Q 2 and Q 4, respectively) are rearranged by Fierz transformations to yield terms at most quadratic in the relative momentum operator of the two nucleons. The low-energy constant multiplying these contact interactions are fitted to the 2013 Granada database, consisting of 2309 pp and 2982 np data (including, respectively, 148 and 218 normalizations) in the laboratory-energy range 0–300 MeV. For themore » total 5291 $pp$ and $np$ data in this range, we obtain a Χ 2 /datum of roughly 1.3 for a set of three models characterized by long- and short-range cutoffs, R L and R S respectively, ranging from (R L,R S)=(1.2,0.8) fm down to (0.8,0.6) fm. The long-range (short-range) cutoff regularizes the one- and two-pion exchange (contact) part of the potential.« less

Minimally nonlocal nucleon-nucleon potentials with chiral two-pion exchange including Δ resonances

DOE PAGES

Piarulli, M.; Girlanda, L.; Schiavilla, R.; ...

2015-02-26

In this study, we construct a coordinate-space chiral potential, including Δ-isobar intermediate states in its two-pion-exchange component up to order Q 3 (Q denotes generically the low momentum scale). The contact interactions entering at next-to-leading and next-to-next-to-next-to-leading orders (Q 2 and Q 4, respectively) are rearranged by Fierz transformations to yield terms at most quadratic in the relative momentum operator of the two nucleons. The low-energy constant multiplying these contact interactions are fitted to the 2013 Granada database, consisting of 2309 pp and 2982 np data (including, respectively, 148 and 218 normalizations) in the laboratory-energy range 0–300 MeV. For themore » total 5291 $pp$ and $np$ data in this range, we obtain a Χ 2 /datum of roughly 1.3 for a set of three models characterized by long- and short-range cutoffs, R L and R S respectively, ranging from (R L,R S)=(1.2,0.8) fm down to (0.8,0.6) fm. The long-range (short-range) cutoff regularizes the one- and two-pion exchange (contact) part of the potential.« less

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

PubMed

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

Lattice Boltzmann simulation of shear-induced particle migration in plane Couette-Poiseuille flow: Local ordering of suspension

NASA Astrophysics Data System (ADS)

Chun, Byoungjin; Kwon, Ilyoung; Jung, Hyun Wook; Hyun, Jae Chun

2017-12-01

The shear-induced migration of concentrated non-Brownian monodisperse suspensions in combined plane Couette-Poiseuille (C-P) flows is studied using a lattice Boltzmann simulation. The simulations are mainly performed for a particle volume fraction of ϕbulk = 0.4 and H/a = 44.3, 23.3, where H and a denote the channel height and radius of suspended particles, respectively. The simulation method is validated in two simple flows, plane Poiseuille and plane Couette flows. In the Poiseuille flow, particles migrate to the mid-plane of the channel where the local concentration is close to the limit of random-close-packing, and a random structure is also observed at the plane. In the Couette flow, the particle distribution remains in the initial uniform distribution. In the combined C-P flows, the behaviors of migration are categorized into three groups, namely, Poiseuille-dominant, Couette-dominant, and intermediate regimes, based on the value of a characteristic force, G, where G denotes the relative magnitude of the body force (P) against the wall-driving force (C). With respect to the Poiseuille-dominant regime, the location of the maximum concentration is shifted from the mid-plane to the lower wall moving in the same direction as the external body force, when G decreases. With respect to the Couette-dominant regime, the behavior is similar to that of a simple shear flow with the exception that a slightly higher concentration of particles is observed near the lower wall. However, with respect to the intermediate value of G, several layers of highly ordered particles are unexpectedly observed near the lower wall where the plane of maximum concentration is located. The locally ordered structure is mainly due to the lateral migration of particles and wall confinement. The suspended particles migrate toward a vanishingly small shear rate at the wall, and they are consequently layered into highly ordered two-dimensional structures at the high local volume fraction.

Preparing for War: The Structure and Conduct of Peacetime Maneuvers

DTIC Science & Technology

2013-06-01

today.8 Documents such as Army TRADOC 525 series pamphlets and the current National Security Strategy will be examined to determine scenarios the...conduct training exercises.10 TRADOC Pamphlet 525-3-0, The Army Capstone Concept, Operational Adaptability: Operations under Conditions of Uncertainty...intermediate objectives to achieve long range goals, this base force provides the planning foundation for program requirements.it 11 TRADOC Pamphlet

Extended x-ray absorption fine structure spectroscopy and x-ray absorption near edge spectroscopy study of aliovalent doped ceria to correlate local structural changes with oxygen vacancies clustering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirbhate, S. C.; Acharya, S. A., E-mail: saha275@yahoo.com; Yadav, A. K.

2016-04-04

This study provides atomic scale insight to understand the role of aliovalent dopants on oxygen vacancies clustering and dissociation mechanism in ceria system in order to enhance the performance of oxy-ion conductor. Dopants induced microscale changes in ceria are probed by extended X-ray absorption fine structure spectroscopy, X-ray absorption near edge spectra, and Raman spectroscopy. The results are explored to establish a correlation between atomic level structural changes (coordination number, interatomic spacing) → formation of dimer and trimer type cation-oxygen vacancies defect complex (intrinsic and extrinsic) → dissociation of oxygen vacancies from defect cluster → ionic conductivity temperature. It ismore » a strategic approach to understand key physics of ionic conductivity mechanism in order to reduce operating temperature of electrolytes for intermediate temperature (300–450 °C) electrochemical devices for the first time.« less

Thiol reactivity and its impact on the ciliate toxicity of α,β-unsaturated aldehydes, ketones, and esters.

PubMed

Böhme, Alexander; Thaens, Diana; Schramm, Franziska; Paschke, Albrecht; Schüürmann, Gerrit

2010-12-20

A recently introduced chemoassay has been used to determine second-order rate constants of the electrophile-nucleophile reaction of 15 α,β-unsaturated aldehydes with glutathione. The respective kGSH values vary for more than 3 orders of magnitude, and are within the range determined previously for 31 α,β-unsaturated ketones and esters. Structure-reactivity analyses yield distinct relationships between kGSH and structural features of the compounds. Moreover, increasing kGSH increases the aldehyde toxicity toward ciliates in terms of 48 h-EC50 values (effective concentration yielding 50% growth inhibition of Tetrahymena pyriformis within 48 h). A respective log-log regression equation including both kGSH and the octanol/water partition coefficient, Kow, yields a squared correlation coefficient of 0.96. Comparative analysis with corresponding data for 15 ketones and 16 esters reveals systematic differences between the three compound classes with regard to the individual contributions of hydrophobicity and electrophilic reactivity to aquatic toxicity. The former is particularly pronounced for aldehydes, while the ester toxicity is largely governed by reactivity, with ketones showing an intermediate pattern that is more similar to the one of esters than of aldehydes. It follows that within the Michael acceptor domain of α,β-unsaturated carbonyls, a distinction between aldehydes and nonaldehydic derivatives appears necessary when employing electrophilic reactivity as a component for the quantitative prediction of their reactive toxicity toward aquatic organisms.

Study of the electrochemical oxidation and reduction of C.I. Reactive Orange 4 in sodium sulphate alkaline solutions.

PubMed

del Río, A I; Molina, J; Bonastre, J; Cases, F

2009-12-15

Synthetic solutions of hydrolysed C.I. Reactive Orange 4, a monoazo textile dye commercially named Procion Orange MX-2R (PMX2R) and colour index number C.I. 18260, was exposed to electrochemical treatment under galvanostatic conditions and Na2SO4 as electrolyte. The influence of the electrochemical process as well as the applied current density was evaluated. Ti/SnO2-Sb-Pt and stainless steel electrodes were used as anode and cathode, respectively, and the intermediates generated on the cathode during electrochemical reduction were investigated. Aliquots of the solutions treated were analysed by UV-visible and FTIR-ATR spectroscopy confirming the presence of aromatic structures in solution when an electro-reduction was carried out. Electro-oxidation degraded both the azo group and aromatic structures. HPLC measures revealed that all processes followed pseudo-first order kinetics and decolourisation rates showed a considerable dependency on the applied current density. CV experiments and XPS analyses were carried out to study the behaviour of both PMX2R and intermediates and to analyse the state of the cathode after the electrochemical reduction, respectively. It was observed the presence of a main intermediate in solution after an electrochemical reduction whose chemical structure is similar to 2-amino-1,5-naphthalenedisulphonic acid. Moreover, the analysis of the cathode surface after electrochemical reduction reveals the presence of a coating layer with organic nature.

Correlated bursts and the role of memory range

NASA Astrophysics Data System (ADS)

Jo, Hang-Hyun; Perotti, Juan I.; Kaski, Kimmo; Kertész, János

2015-08-01

Inhomogeneous temporal processes in natural and social phenomena have been described by bursts that are rapidly occurring events within short time periods alternating with long periods of low activity. In addition to the analysis of heavy-tailed interevent time distributions, higher-order correlations between interevent times, called correlated bursts, have been studied only recently. As the underlying mechanism behind such correlated bursts is far from being fully understood, we devise a simple model for correlated bursts using a self-exciting point process with a variable range of memory. Whether a new event occurs is stochastically determined by a memory function that is the sum of decaying memories of past events. In order to incorporate the noise and/or limited memory capacity of systems, we apply two memory loss mechanisms: a fixed number or a variable number of memories. By analysis and numerical simulations, we find that too much memory effect may lead to a Poissonian process, implying that there exists an intermediate range of memory effect to generate correlated bursts comparable to empirical findings. Our conclusions provide a deeper understanding of how long-range memory affects correlated bursts.

Structure and Microhardness of Cu-Ta Joints Produced by Explosive Welding

PubMed Central

Maliutina, Iu. N.; Mali, V. I.; Bataev, I. A.; Bataev, A. A.; Esikov, M. A.; Smirnov, A. I.; Skorokhod, K. A.

2013-01-01

The structure and microhardness of Cu-Ta joints produced by explosive welding were studied. It was found that, during explosive welding, an intermediate layer 20⋯40 μm thick with a finely dispersed heterophase structure, formed between the welded copper and tantalum plates. The structure of the layer was studied by scanning and transmission electron microscopy. Microvolumes with tantalum particles distributed in a copper matrix and microvolumes of copper particles in a tantalum matrix were detected. The tantalum particles in copper have a size of 5⋯500 nm, with a predominance of 5⋯50 nm particles. A mechanism for the formation of the finely dispersed heterophase structure in explosive welding is proposed. The microhardness of interlayers with the heterophase structure reaches 280 HV, which far exceeds the microhardness of copper (~130 HV) and tantalum (~160 HV). Many twins of deformation origin were found in the structure of the copper plate. The effect of heating temperature in the range from 100 to 900°C on the microhardness of copper, tantalum, and the Cu-Ta welded joint was studied. Upon heating to 900°C, the microhardness of the intermediate layer decreases from 280 to 150 HV. The reduction in the strength properties of the weld material is mainly due to structural transformations in copper. PMID:24453818

A-thermal elastic behavior of silicate glasses.

PubMed

Rabia, Mohammed Kamel; Degioanni, Simon; Martinet, Christine; Le Brusq, Jacques; Champagnon, Bernard; Vouagner, Dominique

2016-02-24

Depending on the composition of silicate glasses, their elastic moduli can increase or decrease as function of the temperature. Studying the Brillouin frequency shift of these glasses versus temperature allows the a-thermal composition corresponding to an intermediate glass to be determined. In an intermediate glass, the elastic moduli are independent of the temperature over a large temperature range. For sodium alumino-silicate glasses, the a-thermal composition is close to the albite glass (NaAlSi3O8). The structural origin of this property is studied by in situ high temperature Raman scattering. The structure of the intermediate albite glass and of silica are compared at different temperatures between room temperature and 600 °C. When the temperature increases, it is shown that the high frequency shift of the main band at 440 cm(-1) in silica is a consequence of the cristobalite-like alpha-beta transformation of 6-membered rings. This effect is stronger in silica than bond elongation (anharmonic effects). As a consequence, the elastic moduli of silica increase as the temperature increases. In the albite glass, the substitution of 25% of Si(4+) ions by Al(3+) and Na(+) ions decreases the proportion of SiO2 6-membered rings responsible for the silica anomaly. The effects of the silica anomaly balance the anharmonicity in albite glass and give rise to an intermediate a-thermal glass. Different networks, formers or modifiers, can be added to produce different a-thermal glasses with useful mechanical or chemical properties.

Genetic admixture and lineage separation in a southern Andean plant

PubMed Central

Morello, Santiago; Sede, Silvana M.

2016-01-01

Mountain uplifts have generated new ecologic opportunities for plants, and triggered evolutionary processes, favouring an increase on the speciation rate in all continents. Moreover, mountain ranges may act as corridors or barriers for plant lineages and populations. In South America a high rate of diversification has been linked to Andean orogeny during Pliocene/Miocene. More recently, Pleistocene glacial cycles have also shaped species distribution and demography. The endemic genus Escallonia is known to have diversified in the Andes. Species with similar morphology obscure species delimitation and plants with intermediate characters occur naturally. The aim of this study is to characterize genetic variation and structure of two widespread species of Escallonia: E. alpina and E. rubra. We analyzed the genetic variation of populations of the entire distribution range of the species and we also included those with intermediate morphological characters; a total of 94 accessions from 14 populations were used for the Amplified Fragment Length Polymorphism (AFLP) analysis. Plastid DNA sequences (trnS-trnG, 3′trnV-ndhC intergenic spacers and the ndhF gene) from sixteen accessions of Escallonia species were used to construct a Statistical Parsimony network. Additionally, we performed a geometric morphometrics analysis on 88 leaves from 35 individuals of the two E. alpina varieties to further study their differences. Wright’s Fst and analysis of molecular variance tests performed on AFLP data showed a significant level of genetic structure at the species and population levels. Intermediate morphology populations showed a mixed genetic contribution from E. alpina var. alpina and E. rubra both in the Principal Coordinates Analysis (PCoA) and STRUCTURE. On the other hand, E. rubra and the two varieties of E. alpina are well differentiated and assigned to different genetic clusters. Moreover, the Statistical Parsimony network showed a high degree of divergence between the varieties of E. alpina: var. alpina is more closely related to E. rubra and other species than to its own counterpart E. alpina var. carmelitana. Geometric morphometrics analysis (Elliptic Fourier descriptors) revealed significant differences in leaf shape between varieties. We found that diversity in Escallonia species analyzed here is geographically structured and deep divergence between varieties of E. alpina could be associated to ancient evolutionary events like orogeny. Admixture in southern populations could be the result of hybridization at the margins of the parental species’ distribution range. PMID:27179539

Phase diagram of the underdoped cuprates at high magnetic field

NASA Astrophysics Data System (ADS)

Chakraborty, Debmalya; Morice, Corentin; Pépin, Catherine

2018-06-01

The experimentally measured phase diagram of cuprate superconductors in the temperature-applied magnetic field plane illuminates key issues in understanding the physics of these materials. At low temperature, the superconducting state gives way to a long-range charge order with increasing magnetic field; both the orders coexist in a small intermediate region. The charge order transition is strikingly insensitive to temperature and quickly reaches a transition temperature close to the zero-field superconducting Tc. We argue that such a transition along with the presence of the coexisting phase is difficult to obtain in a weak coupling competing orders formalism. We demonstrate that for some range of parameters there is an enlarged symmetry of the strongly coupled charge and superconducting orders in the system depending on their relative masses and the coupling strength of the two orders. We establish that this sharp switch from the superconducting phase to the charge order phase can be understood in the framework of a composite SU(2) order parameter comprising the charge and superconducting orders. Finally, we illustrate that there is a possibility of the coexisting phase of the competing charge and superconducting orders only when the SU(2) symmetry between them is weakly broken due to biquadratic terms in the free energy. The relation of this sharp transition to the proximity to the pseudogap quantum critical doping is also discussed.

Infrared spectroscopy as a tool to characterise starch ordered structure--a joint FTIR-ATR, NMR, XRD and DSC study.

PubMed

Warren, Frederick J; Gidley, Michael J; Flanagan, Bernadine M

2016-03-30

Starch has a heterogeneous, semi-crystalline granular structure and the degree of ordered structure can affect its behaviour in foods and bioplastics. A range of methodologies are employed to study starch structure; differential scanning calorimetry, (13)C nuclear magnetic resonance, X-ray diffraction and Fourier transform infrared spectroscopy (FTIR). Despite the appeal of FTIR as a rapid, non-destructive methodology, there is currently no systematically defined quantitative relationship between FTIR spectral features and other starch structural measures. Here, we subject 61 starch samples to structural analysis, and systematically correlate FTIR spectra with other measures of starch structure. A hydration dependent peak position shift in the FTIR spectra of starch is observed, resulting from increased molecular order, but with complex, non-linear behaviour. We demonstrate that FTIR is a tool that can quantitatively probe short range interactions in starch structure. However, the assumptions of linear relationships between starch ordered structure and peak ratios are overly simplistic. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interface structure and composition of MoO3/GaAs(0 0 1)

NASA Astrophysics Data System (ADS)

Sarkar, Anirban; Ashraf, Tanveer; Grafeneder, Wolfgang; Koch, Reinhold

2018-04-01

We studied growth, structure, stress, oxidation state as well as surface and interface structure and composition of thermally-evaporated thin MoO3 films on the technologically important III/V-semiconductor substrate GaAs(0 0 1). The MoO3 films grow with Mo in the 6+  oxidation state. The electrical resistance is tunable by the oxygen partial pressure during deposition from transparent insulating to semi-transparant halfmetallic. In the investigated growth temperature range (room temperature to 200 °C) no diffraction spots are detected by x-ray diffraction. However, high resolution transmission electron microscopy reveals the formation of MoO3 nanocrystal grains with diameters of 5–8 nm. At the interface a  ≈3 nm-thick intermediate layer has formed, where the single-crystal lattice of GaAs gradually transforms to the nanocrystalline MoO3 structure. This interpretation is corroborated by our in situ and real-time stress measurements evidencing a two-stage growth process as well as by elemental interface analysis revealing coexistance of Ga, As, Mo, and oxygen in a intermediate layer of 3–4 nm.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Biogenic mixing induced by intermediate Reynolds number swimming in stratified fluids

PubMed Central

Wang, Shiyan; Ardekani, Arezoo M.

2015-01-01

We study fully resolved motion of interacting swimmers in density stratified fluids using an archetypal swimming model called “squirmer”. The intermediate Reynolds number regime is particularly important, because the vast majority of organisms in the aphotic ocean (i.e. regions that are 200 m beneath the sea surface) are small (mm-cm) and their motion is governed by the balance of inertial and viscous forces. Our study shows that the mixing efficiency and the diapycnal eddy diffusivity, a measure of vertical mass flux, within a suspension of squirmers increases with Reynolds number. The mixing efficiency is in the range of O(0.0001–0.04) when the swimming Reynolds number is in the range of O(0.1–100). The values of diapycnal eddy diffusivity and Cox number are two orders of magnitude larger for vertically swimming cells compared to horizontally swimming cells. For a suspension of squirmers in a decaying isotropic turbulence, we find that the diapycnal eddy diffusivity enhances due to the strong viscous dissipation generated by squirmers as well as the interaction of squirmers with the background turbulence. PMID:26628288

Biogenic mixing induced by intermediate Reynolds number swimming in stratified fluids.

PubMed

Wang, Shiyan; Ardekani, Arezoo M

2015-12-02

We study fully resolved motion of interacting swimmers in density stratified fluids using an archetypal swimming model called "squirmer". The intermediate Reynolds number regime is particularly important, because the vast majority of organisms in the aphotic ocean (i.e. regions that are 200 m beneath the sea surface) are small (mm-cm) and their motion is governed by the balance of inertial and viscous forces. Our study shows that the mixing efficiency and the diapycnal eddy diffusivity, a measure of vertical mass flux, within a suspension of squirmers increases with Reynolds number. The mixing efficiency is in the range of O(0.0001-0.04) when the swimming Reynolds number is in the range of O(0.1-100). The values of diapycnal eddy diffusivity and Cox number are two orders of magnitude larger for vertically swimming cells compared to horizontally swimming cells. For a suspension of squirmers in a decaying isotropic turbulence, we find that the diapycnal eddy diffusivity enhances due to the strong viscous dissipation generated by squirmers as well as the interaction of squirmers with the background turbulence.

Long-range interactions of hydrogen atoms in excited states. III. n S -1 S interactions for n ≥3

NASA Astrophysics Data System (ADS)

Adhikari, C. M.; Debierre, V.; Jentschura, U. D.

2017-09-01

The long-range interaction of excited neutral atoms has a number of interesting and surprising properties such as the prevalence of long-range oscillatory tails and the emergence of numerically large van der Waals C6 coefficients. Furthermore, the energetically quasidegenerate n P states require special attention and lead to mathematical subtleties. Here we analyze the interaction of excited hydrogen atoms in n S states (3 ≤n ≤12 ) with ground-state hydrogen atoms and find that the C6 coefficients roughly grow with the fourth power of the principal quantum number and can reach values in excess of 240 000 (in atomic units) for states with n =12 . The nonretarded van der Waals result is relevant to the distance range R ≪a0/α , where a0 is the Bohr radius and α is the fine-structure constant. The Casimir-Polder range encompasses the interatomic distance range a0/α ≪R ≪ℏ c /L , where L is the Lamb shift energy. In this range, the contribution of quasidegenerate excited n P states remains nonretarded and competes with the 1 /R2 and 1 /R4 tails of the pole terms, which are generated by lower-lying m P states with 2 ≤m ≤n -1 , due to virtual resonant emission. The dominant pole terms are also analyzed in the Lamb shift range R ≫ℏ c /L . The familiar 1 /R7 asymptotics from the usual Casimir-Polder theory is found to be completely irrelevant for the analysis of excited-state interactions. The calculations are carried out to high precision using computer algebra in order to handle a large number of terms in intermediate steps of the calculation for highly excited states.

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

PubMed

Armen, Roger S; Daggett, Valerie

2005-12-13

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.

Optimized equation of the state of the square-well fluid of variable range based on a fourth-order free-energy expansion.

PubMed

Espíndola-Heredia, Rodolfo; del Río, Fernando; Malijevsky, Anatol

2009-01-14

The free energy of square-well (SW) systems of hard-core diameter sigma with ranges 1 < or = lambda < or = 3 is expanded in a perturbation series. This interval covers most ranges of interest, from short-ranged SW fluids (lambda approximately 1.2) used in modeling colloids to long ranges (lambda approximately 3) where the van der Waals classic approximation holds. The first four terms are evaluated by means of extensive Monte Carlo simulations. The calculations are corrected for the thermodynamic limit and care is taken to evaluate and to control the various sources of error. The results for the first two terms in the series confirm well-known independent results but have an increased estimated accuracy and cover a wider set of well ranges. The results for the third- and fourth-order terms are novel. The free-energy expansion for systems with short and intermediate ranges, 1 < or = lambda < or = 2, is seen to have properties similar to those of systems with longer ranges, 2 < or = lambda < or = 3. An equation of state (EOS) is built to represent the free-energy data. The thermodynamics given by this EOS, confronted against independent computer simulations, is shown to predict accurately the internal energy, pressure, specific heat, and chemical potential of the SW fluids considered and for densities 0 < or = rho sigma(3) < or = 0.9 including subcritical temperatures. This fourth-order theory is estimated to be accurate except for a small region at high density, rho sigma(3) approximately 0.9, and low temperature where terms of still higher order might be needed.

NMR Evidences of the Coupling between Conduction Electrons and Molecular Degrees of Freedom in the Exotic Member of the Bechgaard Salt (TMTSF)2FSO3

NASA Astrophysics Data System (ADS)

Satsukawa, Hidetaka; Yajima, Akio; Hiraki, Ko-ichi; Takahashi, Toshihiro; Kang, Haeyong; Jo, Younjung; Kang, Woun; Chung, Ok-Hee

2016-12-01

We performed 77Se- and 19F-NMR measurements on single crystals of (TMTSF)2FSO3 to characterize the electronic structures of different phases in the temperature-pressure phase diagram, determined by precise transport measurements [Jo et al., Phys. Rev. B 67, 014516 (2003)]. We claim that such varieties of electronic states in the refined phase diagram are caused by strong couplings of the conduction electrons with FSO3 anions, especially with the permanent electric dipoles on the anions. We suggest that as temperature decreases, the FSO3 anions form orientational ordering through two steps; first, only the tetrahedrons form an orientational order leaving the orientations of the electronic dipoles in random (transition I); then the dipoles form a perfect orientational order at a lower temperature (transition II). In the intermediate temperature range between transitions I and II, we found an appreciable enhancement of homogeneous and inhomogeneous widths of the 77Se-NMR spectrum. From the analysis of the angular dependence of the linewidth, we attributed these anomalies to the intramolecular charge disproportionation or imbalance and its slow dynamics caused by the coupling with the permanent electric dipole of the anion. Results of 19F-NMR relaxation and lineshape measurements support this picture very well. Electronic structures at higher pressures up to 1.25 GPa are discussed on the basis of the results of the 77Se- and 19F-NMR measurements.

Phase equilibria, crystal structure and oxygen content of intermediate phases in the Y-Ba-Co-O system

NASA Astrophysics Data System (ADS)

Urusova, A. S.; Cherepanov, V. A.; Aksenova, T. V.; Gavrilova, L. Ya.; Kiselev, E. A.

2013-06-01

The phase equilibria in the Y-Ba-Co-O system were systematically studied at 1373 K in air. The intermediate phases formed in the Y-Ba-Co-O system at 1373 K in air were: YBaCo2O5+δ, YBaCo4O7 and BaCo1-yYyO3-δ (0.09≤y≤0.42). It was shown that YBaCo2O5+δ possesses tetragonal structure with the 3ap×3ap×2ap superstructure (sp. gr. P4/mmm). High-temperature X-ray diffraction analysis of the YBaCo2O5+δ in the temperature range from 298 K up to 1073 K under Po2=0.21 аtm has not shown any phase transformations. The value of oxygen content for the YBaCo2O5+δ at room temperature was estimated as 5.40 and at 1323 K it was equal to 5.04. Thermal expansion of sample shows a linear characteristics and the average thermal expansion coefficient (TEC) is about 13.8×10-6, K-1 in the temperature range 298-1273 K. The homogeneity range and crystal structure of the BaCo1-yYyO3-δ (0.09≤y≤0.42) solid solutions were determined by X-ray diffraction of quenched samples. All BaCo1-yYyO3-δ solid solutions were found to have cubic structure (sp. gr. Pm3m). The unit cell parameters were refined using Rietveld full-profile analysis. Oxygen nonstoichiometry of BaCo1-yYyO3-δ solid solutions with 0.1≤y≤0.4 was measured by means of thermogravimetric technique within the temperature range 298-1373 K in air. Thermal expansion of BaCo1-yYyO3-δ (у=0.0; 0.1; 0.2; 0.3) samples was studied within the temperature range 298-1200 K in air. The projection of isothermal-isobaric phase diagram for the Y-Ba-Co-O system to the compositional triangle of metallic components was presented.

Radioactive fallout projections and arms control agreements: INF (Intermediate-range Nuclear Forces) and START (Strategic Arms Reduction Treaty)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, C.S.

1988-02-01

Projections of levels of radioactive fallout from a nuclear war are sensitive to assumptions about the structure of the nuclear stockpiles as well as the assumed scenarios for a nuclear war. Recent arms control proposals would change these parameters. This paper examines the implications of the proposed (Intermediate-range Nuclear Forces) INF treaty and (Strategic Arms Reduction Treaty) START on fallout projections from a major nuclear war. We conclude that the INF reductions are likely to have negligible effects on estimates of global and local fallout, whereas the START reductions could result in reductions in estimates of local fallout that rangemore » from significant to dramatic, depending upon the nature of the reduced strategic forces. Should a major war occur, projections of total fatalities from direct effects of blast, thermal radiation, a nd fallout, and the phenomenon known as nuclear winter, would not be significantly affected by INF and START initiatives as now drafted. 14 refs.« less

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

DOE PAGES

Huo, Lu; Davis, Ian; Liu, Fange; ...

2015-01-07

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD +-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp 3-to-sp 2 transition during enzyme-mediated oxidation.« less

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

PubMed Central

2017-01-01

As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal–oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal–oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron–oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs. PMID:29286645

Bond-orientational order in liquid Si

NASA Technical Reports Server (NTRS)

Wang, Z. Q.; Stroud, D.

1991-01-01

Bond-orientational order in liquid Si via Monte Carlo simulation in conjuncation with empirical two- and three-body potentials of the form proposed by Stillinger and Weber are studied. Bond-orientational order (BOO) is described in terms of combinations of spherical harmonic functions. Liquid Si is found to have pronounced short-range BOO corresponding to l = 3, as expected for a structure with local tetrahedral order. No long-range BOO is found either in the equilibrium or the supercooled liquid. When the three-body potential is artificially removed, the tetrahedral bond-orientation order disappears and the liquid assumes a close-packed structure.

Photo-crystallization in a-Se layer structures: Effects of film-substrate interface-rigidity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindberg, G. P.; Gross, N.; Weinstein, B. A.

Amorphous selenium (a-Se) films deposited on rigid substrates can undergo photo-induced crystallization (PC) even at temperatures (T) well below the glass transition, T{sub g} ∼ 313 K. Substrate-generated shear strain is known to promote the PC process. In the present work, we explore the influence of different substrates (Si and glass), and different film-layer-substrate combinations, on the PC in a variety of a-Se films and film-structures. The intermediate layers (indium tin oxide and polyimide) are chosen to promote conductivity and/or to be a buffer against interface strain in structures of interest for digital imaging applications. The PC characteristics in these samples are evaluatedmore » and compared using optical microscopy, atomic-force microscopy, Raman mapping, and T-dependent Raman spectroscopy. Both the presence of a soft intermediate layer, and the thermal softening that occurs for T increasing through T{sub g}, inhibit the tendency for the onset of PC. The extensive PC mapping results in the wide range of samples studied here, as well as the suppression of PC near T{sub g} in this array of samples, strongly support the generality of this behavior. As a consequence, one may expect that the stability of a-Se films against PC can be enhanced by decreasing the rigidity of the film-substrate interface. In this regard, advanced film structures that employ flexible substrates, soft intermediate layers, and/or are designed to be operated near T{sub g} should be explored.« less

Amorphous photonic crystals with only short-range order.

PubMed

Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

2013-10-04

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Concentration of small ring structures in vitreous silica from a first-principles analysis of the Raman spectrum.

PubMed

Umari, P; Gonze, Xavier; Pasquarello, Alfredo

2003-01-17

Using a first-principles approach, we calculate Raman spectra for a model structure of vitreous silica. We develop a perturbational method for calculating the dielectric tensor in an ultrasoft pseudopotential scheme and obtain Raman coupling tensors by finite differences with respect to atomic displacements. For frequencies below 1000 cm(-1), the parallel-polarized Raman spectrum of vitreous silica is dominated by oxygen bending motions, showing a strong sensitivity to the intermediate range structure. By modeling the Raman coupling, we derive estimates for the concentrations of three- and four-membered rings from the experimental intensities of the Raman defect lines.

Structure of exoplanets

PubMed Central

Spiegel, David S.; Fortney, Jonathan J.; Sotin, Christophe

2014-01-01

The hundreds of exoplanets that have been discovered in the past two decades offer a new perspective on planetary structure. Instead of being the archetypal examples of planets, those of our solar system are merely possible outcomes of planetary system formation and evolution, and conceivably not even especially common outcomes (although this remains an open question). Here, we review the diverse range of interior structures that are both known and speculated to exist in exoplanetary systems—from mostly degenerate objects that are more than 10× as massive as Jupiter, to intermediate-mass Neptune-like objects with large cores and moderate hydrogen/helium envelopes, to rocky objects with roughly the mass of Earth. PMID:24379369

Structure of exoplanets.

PubMed

Spiegel, David S; Fortney, Jonathan J; Sotin, Christophe

2014-09-02

The hundreds of exoplanets that have been discovered in the past two decades offer a new perspective on planetary structure. Instead of being the archetypal examples of planets, those of our solar system are merely possible outcomes of planetary system formation and evolution, and conceivably not even especially common outcomes (although this remains an open question). Here, we review the diverse range of interior structures that are both known and speculated to exist in exoplanetary systems--from mostly degenerate objects that are more than 10× as massive as Jupiter, to intermediate-mass Neptune-like objects with large cores and moderate hydrogen/helium envelopes, to rocky objects with roughly the mass of Earth.

A two-step spin crossover mononuclear iron(II) complex with a [HS-LS-LS] intermediate phase.

PubMed

Bonnet, Sylvestre; Siegler, Maxime A; Costa, José Sánchez; Molnár, Gábor; Bousseksou, Azzedine; Spek, Anthony L; Gamez, Patrick; Reedijk, Jan

2008-11-21

The two-step spin crossover of a new mononuclear iron(ii) complex is studied by magnetic, crystallographic and calorimetric methods revealing two successive first-order phase transitions and an ordered intermediate phase built by the repetition of the unprecedented [HS-LS-LS] motif.

Field dependence of the magnetic correlations of the frustrated magnet SrDy 2 O 4

DOE PAGES

Gauthier, N.; Fennell, A.; Prévost, B.; ...

2017-05-30

Tmore » he frustrated magnet SrDy 2 O 4 exhibits a field-induced phase with a magnetization plateau at 1 / 3 of the saturation value for magnetic fields applied along the b axis. We report here a neutron scattering study of the nature and symmetry of the magnetic order in this field-induced phase. Below ≈ 0.5 K, there are strong hysteretic effects, and the order is short- or long-ranged for zero-field and field cooling, respectively. We find that the long-range ordered magnetic structure within the zigzag chains is identical to that expected for the one-dimensional axial next-nearest neighbor Ising (ANNNI) model in longitudinal fields. he long-range ordered structure in field contrasts with the short-range order found at zero field, and is most likely reached through enhanced quantum fluctuations with increasing fields.« less

Field dependence of the magnetic correlations of the frustrated magnet SrDy2O4

NASA Astrophysics Data System (ADS)

Gauthier, N.; Fennell, A.; Prévost, B.; Désilets-Benoit, A.; Dabkowska, H. A.; Zaharko, O.; Frontzek, M.; Sibille, R.; Bianchi, A. D.; Kenzelmann, M.

2017-05-01

The frustrated magnet SrDy2O4 exhibits a field-induced phase with a magnetization plateau at 1 /3 of the saturation value for magnetic fields applied along the b axis. We report here a neutron scattering study of the nature and symmetry of the magnetic order in this field-induced phase. Below T ≈0.5 K, there are strong hysteretic effects, and the order is short- or long-ranged for zero-field and field cooling, respectively. We find that the long-range ordered magnetic structure within the zigzag chains is identical to that expected for the one-dimensional axial next-nearest neighbor Ising (ANNNI) model in longitudinal fields. The long-range ordered structure in field contrasts with the short-range order found at zero field, and is probably reached through enhanced quantum fluctuations with increasing fields.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

PubMed

Gsponer, Joerg; Hopearuoho, Harri; Whittaker, Sara B-M; Spence, Graham R; Moore, Geoffrey R; Paci, Emanuele; Radford, Sheena E; Vendruscolo, Michele

2006-01-03

We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.

Final Technical Report: Vibrational Spectroscopy of Transient Combustion Intermediates Trapped in Helium Nanodroplets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douberly, Gary Elliott

The objective of our experimental research program is to isolate and stabilize transient intermediates and products of prototype combustion reactions. This will be accomplished by Helium Nanodroplet Isolation, a novel technique where liquid helium droplets freeze out high energy metastable configurations of a reacting system, permitting infrared spectroscopic characterizations of products and intermediates that result from hydrocarbon radical reactions with molecular oxygen and other small molecules relevant to combustion environments. The low temperature (0.4 K) and rapid cooling associated with He droplets provides a perfectly suited medium to isolate and probe a broad range of molecular radical and carbene systemsmore » important to combustion chemistry. The sequential addition of molecular species to He droplets often leads to the stabilization of high-energy, metastable cluster configurations that represent regions of the potential energy surface far from the global minimum. Single and double resonance IR laser spectroscopy techniques, along with Stark and Zeeman capabilities, are being used to probe the structural and dynamical properties of these systems.« less

Does Sex Matter? Temporal and Spatial Patterns of Cougar-Human Conflict in British Columbia

PubMed Central

Teichman, Kristine J.; Cristescu, Bogdan; Nielsen, Scott E.

2013-01-01

Wildlife-human conflicts occur wherever large carnivores overlap human inhabited areas. Conflict mitigation can be facilitated by understanding long-term dynamics and examining sex-structured conflict patterns. Predicting areas with high probability of conflict helps focus management strategies in order to proactively decrease carnivore mortality. We investigated the importance of cougar (Puma concolor) habitat, human landscape characteristics and the combination of habitat and human features on the temporal and spatial patterns of cougar-human conflicts in British Columbia. Conflicts (n = 1,727; 1978–2007) involved similar numbers of male and female cougars with conflict rate decreasing over the past decade. Conflicts were concentrated within the southern part of the province with the most conflicts per unit area occurring on Vancouver Island. For both sexes, the most supported spatial models for the most recent (1998–2007) conflicts contained both human and habitat variables. Conflicts were more likely to occur close to roads, at intermediate elevations and far from the northern edge of the cougar distribution range in British Columbia. Male cougar conflicts were more likely to occur in areas of intermediate human density. Unlike cougar conflicts in other regions, cattle density was not a significant predictor of conflict location. With human populations expanding, conflicts are expected to increase. Conservation tools, such as the maps predicting conflict hotspots from this study, can help focus management efforts to decrease carnivore-human conflict. PMID:24040312

Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins.

PubMed

Ayuso-Tejedor, Sara; Angarica, Vladimir Espinosa; Bueno, Marta; Campos, Luis A; Abián, Olga; Bernadó, Pau; Sancho, Javier; Jiménez, M Angeles

2010-07-23

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Short-range order of undercooled melts of PdZr2 intermetallic compound studied by X-ray and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Klein, S.; Holland-Moritz, D.; Herlach, D. M.; Mauro, N. A.; Kelton, K. F.

2013-05-01

The short-range order in undercooled melts of the intermetallic Zr2Pd glass-forming alloy is investigated by combining electrostatic levitation (ESL) with high-energy X-ray diffraction and neutron diffraction. Experimentally determined structure factors are measured and analyzed with respect to various structures of short-range order. The comparative X-ray and neutron scattering experiments allow for investigations of topological and chemical short-range order. Based on these studies, no preference of a specific short-range order is found for the liquid Zr2Pd glass-forming alloy, even in the metastable state of the deeply undercooled melt. This is in agreement with an earlier report from X-ray diffraction and molecular-dynamics studies of a Zr75.5Pd24.5 liquid, which showed a broad distribution of cluster types. The results for the Zr2Pd liquid are discussed with respect to the glass-forming ability of this melt.

Complex Fluids at Interfaces and Interfaces of Complex Fluids

NASA Astrophysics Data System (ADS)

Nouri, Mariam

The present thesis deals with two independent projects and is consequently divided into two parts. The first part details a computational study of the fluid structure of ring-shaped molecules and their positional and orientational molecular organizations in different degrees of confinement, while the second part concerns an experimental study of phase behavior and interfacial phenomena in confined colloid-polymer systems. In the first part, ring-shaped molecules are studied using Monte Carlo simulation techniques in one, two and three dimensions. The model used to describe ring-shaped molecules is composed of hard-spheres linked together to form planar rigid rings. For rings of various sizes and for a wide range of densities, positional and orientational orderings are reported in forms of pair distribution functions of the ring centers and correlation functions of the ring normal orientations. Special emphasis is given to understand structural formation at interfaces, i.e., the structure and orderings of these molecules when they are confined to two dimensions. In a plane but the rings themselves are free to rotate around all axes, nematic ordering is observed at sufficiently high densities. In the second part, phase equilibria of confined aqueous colloid-polymer systems are studied experimentally using fluorescence microscopy. Aqueous mixtures of fluorescent polystyrene spheres and polyacrylamide are confined between a glass slide and a coverslip. The phase diagram is determined as a function of the colloidal and polymer concentrations. Liquid-liquid phase coexistence between a colloid-rich phase and a polymer-rich phase occurs at intermediate polymer concentrations, while liquid-solid phase coexistence between a polymer-rich liquid and a colloid-rich solid is observed at high polymer concentrations. Interfacial thickness and tension of the interface between these coexisting phases are measured using image analysis techniques. It is also observed that the colloid-rich solid and liquid domains coarsen mainly by Ostwald ripening.

Kinetic theory of turbulence for parallel propagation revisited: Low-to-intermediate frequency regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Peter H., E-mail: yoonp@umd.edu; School of Space Research, Kyung Hee University, Yongin, Gyeonggi 446-701

2015-09-15

A previous paper [P. H. Yoon, “Kinetic theory of turbulence for parallel propagation revisited: Formal results,” Phys. Plasmas 22, 082309 (2015)] revisited the second-order nonlinear kinetic theory for turbulence propagating in directions parallel/anti-parallel to the ambient magnetic field, in which the original work according to Yoon and Fang [Phys. Plasmas 15, 122312 (2008)] was refined, following the paper by Gaelzer et al. [Phys. Plasmas 22, 032310 (2015)]. The main finding involved the dimensional correction pertaining to discrete-particle effects in Yoon and Fang's theory. However, the final result was presented in terms of formal linear and nonlinear susceptibility response functions. Inmore » the present paper, the formal equations are explicitly written down for the case of low-to-intermediate frequency regime by making use of approximate forms for the response functions. The resulting equations are sufficiently concrete so that they can readily be solved by numerical means or analyzed by theoretical means. The derived set of equations describe nonlinear interactions of quasi-parallel modes whose frequency range covers the Alfvén wave range to ion-cyclotron mode, but is sufficiently lower than the electron cyclotron mode. The application of the present formalism may range from the nonlinear evolution of whistler anisotropy instability in the high-beta regime, and the nonlinear interaction of electrons with whistler-range turbulence.« less

The Compressed Baryonic Matter experiment at FAIR

NASA Astrophysics Data System (ADS)

Höhne, Claudia

2018-02-01

The CBM experiment will investigate highly compressed baryonic matter created in A+A collisions at the new FAIR research center. With a beam energy range up to 11 AGeV for the heaviest nuclei at the SIS 100 accelerator, CBM will investigate the QCD phase diagram in the intermediate range, i.e. at moderate temperatures but high net-baryon densities. This intermediate range of the QCD phase diagram is of particular interest, because a first order phase transition ending in a critical point and possibly new highdensity phases of strongly interacting matter are expected. In this range of the QCD phase diagram only exploratory measurements have been performed so far. CBM, as a next generation, high-luminosity experiment, will substantially improve our knowledge of matter created in this region of the QCD phase diagram and characterize its properties by measuring rare probes such as multi-strange hyperons, dileptons or charm, but also with event-by-event fluctuations of conserved quantities, and collective flow of identified particles. The experimental preparations with special focus on hadronic observables and strangeness is presented in terms of detector development, feasibility studies and fast track reconstruction. Preparations are progressing well such that CBM will be ready with FAIR start. As quite some detectors are ready before, they will be used as upgrades or extensions of already running experiments allowing for a rich physics program prior to FAIR start.

Hydrothermally processed 1D hydroxyapatite: mechanism of formation and biocompatibility studies

PubMed Central

Stojanović, Zoran S.; Ignjatović, Nenad; Wu, Victoria; Žunič, Vojka; Veselinović, Ljiljana; Škapin, Srečo; Miljković, Miroslav; Uskoković, Vuk; Uskoković, Dragan

2016-01-01

Recent developments in bone tissue engineering have led to an increased interest in one-dimensional (1D) hydroxyapatite (HA) nano- and micro-structures such as wires, ribbons and tubes. They have been proposed for use as cell substrates, reinforcing phases in composites and carriers for biologically active substances. Here we demonstrate the synthesis of 1D HA structures using an optimized, urea-assisted, high-yield hydrothermal batch process. The one-pot process, yielding HA structures composed of bundles of ribbons and wires, was typified by the simultaneous occurrence of a multitude of intermediate reactions, failing to meet the uniformity criteria over particle morphology and size. To overcome these issues, the preparation procedure was divided to two stages: dicalcium phosphate platelets synthesized in the first step were used as a precursor for the synthesis of 1D HA in the second stage. Despite the elongated particle morphologies, both the precursor and the final product exhibited excellent biocompatibility and caused no reduction of viability when tested against osteoblastic MC3T3-E1 cells in 2D culture up to the concentration of 2.6 mg/cm2. X-ray powder diffraction combined with a range of electron microscopies and laser diffraction analyses was used to elucidate the formation mechanism and the microstructure of the final particles. The two-step synthesis involved a more direct transformation of DCP to 1D HA with the average diameter of 37 nm and the aspect ratio exceeding 100:1. The comparison of crystalline domain sizes along different crystallographic directions showed no signs of significant anisotropy, while indicating that individual nanowires are ordered in bundles in the b crystallographic direction of the P63/m space group of HA. Intermediate processes, e.g., dehydration of dicalcium phosphate, are critical for the formation of 1D HA alongside other key aspects of this phase transformation, it must be investigated in more detail in the continuous design of smart HA micro- and nano-structures with advanced therapeutic potentials. PMID:27524076

A Reaction Center-dependent Photoprotection Mechanism in a Highly Robust Photosystem II from an Extremophilic Red Alga, Cyanidioschyzon merolae*

PubMed Central

Krupnik, Tomasz; Kotabová, Eva; van Bezouwen, Laura S.; Mazur, Radosław; Garstka, Maciej; Nixon, Peter J.; Barber, James; Kaňa, Radek; Boekema, Egbert J.; Kargul, Joanna

2013-01-01

Members of the rhodophytan order Cyanidiales are unique among phototrophs in their ability to live in extremely low pH levels and moderately high temperatures. The photosynthetic apparatus of the red alga Cyanidioschyzon merolae represents an intermediate type between cyanobacteria and higher plants, suggesting that this alga may provide the evolutionary link between prokaryotic and eukaryotic phototrophs. Although we now have a detailed structural model of photosystem II (PSII) from cyanobacteria at an atomic resolution, no corresponding structure of the eukaryotic PSII complex has been published to date. Here we report the isolation and characterization of a highly active and robust dimeric PSII complex from C. merolae. We show that this complex is highly stable across a range of extreme light, temperature, and pH conditions. By measuring fluorescence quenching properties of the isolated C. merolae PSII complex, we provide the first direct evidence of pH-dependent non-photochemical quenching in the red algal PSII reaction center. This type of quenching, together with high zeaxanthin content, appears to underlie photoprotection mechanisms that are efficiently employed by this robust natural water-splitting complex under excess irradiance. In order to provide structural details of this eukaryotic form of PSII, we have employed electron microscopy and single particle analyses to obtain a 17 Å map of the C. merolae PSII dimer in which we locate the position of the protein mass corresponding to the additional extrinsic protein stabilizing the oxygen-evolving complex, PsbQ′. We conclude that this lumenal subunit is present in the vicinity of the CP43 protein, close to the membrane plane. PMID:23775073

The nature of photoinduced phase transition and metastable states in vanadium dioxide

DOE PAGES

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; ...

2016-12-16

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO 2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M 2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picosecondsmore » at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.« less

The nature of photoinduced phase transition and metastable states in vanadium dioxide

PubMed Central

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

2016-01-01

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium. PMID:27982066

The nature of photoinduced phase transition and metastable states in vanadium dioxide

NASA Astrophysics Data System (ADS)

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

2016-12-01

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO 2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M 2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picosecondsmore » at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.« less

Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connor, Sean E.; Capodagli, Glenn C.; Deaton, Michelle K.

Tuberculosis (TB) is a major infectious disease that accounts for over 1.7 million deaths every year. Mycobacterium tuberculosis, the causative agent of tuberculosis, enters the human host by the inhalation of infectious aerosols. Additionally, one third of the world's population is likely to be infected with latent TB. The incidence of TB is on the rise owing in part to the emergence of multidrug-resistant strains. As a result, there is a growing need to focus on novel M. tuberculosis enzyme targets. M. tuberculosis triosephosphate isomerase (MtTPI) is an essential enzyme for gluconeogenetic pathways, making it a potential target for futuremore » therapeutics. In order to determine its structure, the X-ray crystal structure of MtTPI has been determined, as well as that of MtTPI bound with a reaction-intermediate analog. As a result, two forms of the active site were revealed. In conjunction with the kinetic parameters obtained for the MtTPI-facilitated conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (D-GAP), this provides a greater structural and biochemical understanding of this enzyme. Additionally, isothermal titration calorimetry was used to determine the binding constant for a reaction-intermediate analog bound to the active site of MtTPI.« less

Globular, Sponge-like to Layer-like Morphological Transition in 1-n-Alkyl-3-methylimidazolium Octylsulfate Ionic Liquid Homologous Series.

PubMed

Kapoor, Utkarsh; Shah, Jindal K

2018-01-11

Segregation of polar and nonpolar domains in ionic liquids for which either the cation or anion is responsible for inducing nonpolar domains is well understood. On the other hand, information regarding the nanoscale heterogeneities originating due to the presence of nonpolar content on both the ions is rudimentary at this point. The present contribution is aimed at addressing this question and focuses on a molecular dynamics simulation study to probe nanoscale structural and aggregation features of the 1-n-alkyl-3-methylimidazolium [C n mim] octylsulfate [C 8 SO 4 ] ionic liquid homologous series (n = 2, 4, 6, 8, 10, and 12). The objective of this work is to determine the effect of increasing alkyl chain length in the cation on nonpolar domain formation, especially when the alkyl chain lengths from both the ions participate in defining such domains. The results indicate that all the ionic liquids form nonpolar domains, morphology of which gradually changes from globular, sponge-like to layer-like structure with increase in the cationic alkyl chain length. The length of the nonpolar domains calculated from the total structure factor for [C 10 mim][C 8 SO 4 ] is considerably higher than that reported for other imidazolium-based ionic liquid containing smaller anions. The structure factor for [C 12 mim][C 8 SO 4 ] ionic liquid contains multiple intermediate peaks separating the charge alternation peak and pre-peak, which points to nonpolar domains of varying lengths, an observation that remains to be validated. Analysis of the heterogeneous order parameters and orientational correlation functions of the alkyl chains further suggests an increase in the spatial heterogeneity and long-range order along the homologous series. The origin of rich diversity of structures obtained by introducing nonpolar content on both the ions is discussed.

Memory and long-range correlations in chess games

NASA Astrophysics Data System (ADS)

Schaigorodsky, Ana L.; Perotti, Juan I.; Billoni, Orlando V.

2014-01-01

In this paper we report the existence of long-range memory in the opening moves of a chronologically ordered set of chess games using an extensive chess database. We used two mapping rules to build discrete time series and analyzed them using two methods for detecting long-range correlations; rescaled range analysis and detrended fluctuation analysis. We found that long-range memory is related to the level of the players. When the database is filtered according to player levels we found differences in the persistence of the different subsets. For high level players, correlations are stronger at long time scales; whereas in intermediate and low level players they reach the maximum value at shorter time scales. This can be interpreted as a signature of the different strategies used by players with different levels of expertise. These results are robust against the assignation rules and the method employed in the analysis of the time series.

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.

PubMed

Vonrhein, C; Schlauderer, G J; Schulz, G E

1995-05-15

There are 17 crystal structures of nucleoside monophosphate kinases known. As expected for kinases, they show large conformational changes upon binding of substrates. These are concentrated in two chain segments, or domains, of 30 and 38 residues that are involved in binding of the substrates N1TP and N2MP (nucleoside tri- and monophosphates with bases N1 and N2), respectively. After aligning the 17 structures on the main parts of their polypeptide chains, two domains in various conformational states were revealed. These states were caused by bound substrate (or analogues) and by crystal-packing forces, and ranged between a 'closed' conformation and a less well defined 'open' conformation. The structures were visually sorted yielding an approximately evenly spaced series of domain states that outlines the closing motions when the substrates bind. The packing forces in the crystals are weak, leaving the natural domain trajectories essentially intact. Packing is necessary, however, to produce stable intermediates. The ordered experimental structures were then recorded as still pictures of a movie and animated to represent the motions of the molecule during a catalytic cycle. The motions were smoothed out by adding interpolated structures to the observed ones. The resulting movies are available through the World Wide Web (http:@bio5.chemie.uni-freiburg.de/ak movie.html). Given the proliferating number of homologous proteins known to exist in different conformational states, it is becoming possible to outline the motions of chain segments and combine them into a movie, which can then represent protein action much more effectively than static pictures alone are able to do.

Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

PubMed Central

Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

2015-01-01

Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state. PMID:26630011

Anelastic attenuation structure of the southern Aegean subduction area

NASA Astrophysics Data System (ADS)

Ventouzi, Chrisanthi; Papazachos, Constantinos; Papaioannou, Christos; Hatzidimitriou, Panagiotis

2014-05-01

The study of the anelastic attenuation structure plays a very important role for seismic wave propagation and provides not only valuable constraints for the Earth's interior (temperature, relative viscosity, slab dehydration and melt transport) but also significant information for the simulation of strong ground motions. In order to investigate the attenuation structure of the broader Southern Aegean subduction area, acceleration spectra of intermediate depth earthquakes produced from data provided by two local networks which operated in the area were used. More specifically, we employed data from approximately 400 intermediate-depth earthquakes, as these were recorded from the EGELADOS seismic monitoring project which consisted of 65 land stations and 24 OBS recorders and operated during 2005-2007, as well as data from the earlier installed CYCNET local network, which operated during 2002-2005. A frequency-independent path attenuation operator t* was computed for both P and S arrivals for each waveform, using amplitude spectra generated by the recorded data of the aforementioned networks. Initially, estimated P and S traveltimes were examined and modeled as a function of epicentral distance for different groups of focal depths, using data from the CYCNET network in order to obtain the expected arrival information when original arrival times were not available. Two approaches to assess the spectral-decay were adopted for t* determination. Initially, an automated approach was used, where t* was automatically calculated from the slope of the acceleration spectrum, assuming an ω2 source model for frequencies above the corner frequency, fc. Estimation of t* was performed in the frequency band of 0.2 to 25 Hz, using only spectra with a signal-to-noise ratio larger than 3 for a frequency range of at least 4Hz for P-waves and 1Hz for S-waves, respectively. In the second approach, the selection of the linearly-decaying part of the spectra where t* was calculated, was carried out manually, after a visual inspection by the user for optimal spectral fitting. The observed t* data from both approaches were examined against hypocentral distance. In general, no significant linear trend, revealing dependence of t* with distance, could be observed on the original data, clearly a result of the significant spatial and depth variations of the anelastic attenuation structure that superimposes the distance effect. In order to further investigate this issue, a spatial variation of t* values for different hypocentral-depth groups was performed. The obtained results show that along-arc stations exhibit very low values of t*, while back-arc stations present much larger values. The observed t* along-arc/back-arc differences becomes more significant as the depth of the earthquakes increases, indicating the effect of the high-attenuation (low-Q) mantle wedge beneath the volcanic arc. For a more detailed view of the spatial variations of the whole path attenuation operator, we performed preliminary spatial interpolation of t* values for different hypocentral depth ranges. For "shallower" hypocentral depths, low values of t*, appear to be sparsely observed mainly in the back-arc area, but as hypocentral depths increase, a much larger area with higher attenuation is identified along the volcanic arc. This work has been partly supported by the 3D-SEGMENTS project #1337 funded by EC European Social Fund and the Operational Programme "Education and Lifelong Learning" of the ARISTEIA-I call of the Greek Secretariat of Research and Technology.

Local self-uniformity in photonic networks.

PubMed

Sellers, Steven R; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-17

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

Local self-uniformity in photonic networks

NASA Astrophysics Data System (ADS)

Sellers, Steven R.; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-01

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

(13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

PubMed

Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

2015-12-03

Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate.

Analysis and numerical study of inertia-gravity waves generated by convection in the tropics

NASA Astrophysics Data System (ADS)

Evan, Stephanie

2011-12-01

Gravity waves transport momentum and energy upward from the troposphere and by dissipation affect the large-scale structure of the middle atmosphere. An accurate representation of these waves in climate models is important for climate studies, but is still a challenge for most global and climate models. In the tropics, several studies have shown that mesoscale gravity waves and intermediate scale inertia-gravity waves play an important role in the dynamics of the upper atmosphere. Despite observational evidence for the importance of forcing of the tropical circulation by inertia-gravity waves, their exact properties and forcing of the tropical stratospheric circulation are not fully understood. In this thesis, properties of tropical inertia-gravity waves are investigated using radiosonde data from the 2006 Tropical Warm Pool International Cloud Experiment (TWP-ICE), the European Centre for Medium-Range Weather Forecasts (ECMWF) dataset and high-resolution numerical experiments. Few studies have characterized inertia-gravity wave properties using radiosonde profiles collected on a campaign basis. We first examine the properties of intermediate-scale inertia-gravity waves observed during the 2006 TWP-ICE campaign in Australia. We show that the total vertical flux of horizontal momentum associated with the waves is of the same order of magnitude as previous observations of Kelvin waves. This constitutes evidence for the importance of the forcing of the tropical circulation by intermediate-scale inertia-gravity waves. Then, we focus on the representation of inertia-gravity waves in analysis data. The wave event observed during TWP-ICE is also present in the ECMWF data. A comparison between the characteristics of the inertia-gravity wave derived with the ECMWF data to the properties of the wave derived with the radiosonde data shows that the ECMWF data capture similar structure for this wave event but with a larger vertical wavelength. The Weather Research and Forecasting (WRF) modeling system is used to understand the representation of the wave event in the ECMWF data. The model is configured as a tropical channel with a high top at 1 hPa. WRF is used with the same horizontal resolution (˜ 40 km) as the operational ECMWF in 2006 while using a finer vertical grid-spacing than ECMWF. Different experiments are performed to determine the sensitivity of the wave structure to cumulus schemes, initial conditions and vertical resolution. We demonstrate that high vertical resolution would be required for ECMWF to accurately resolve the vertical structure of inertia-gravity waves and their effect on the middle atmosphere circulation. Lastly we perform WRF simulations in January 2006 and 2007 to assess gravity wave forcing of the tropical stratospheric circulation. In these simulations a large part of the gravity wave spectrum is explicitly simulated. The WRF model is able to reproduce the evolution of the mean tropical stratospheric zonal wind when compared to observational data and the ECMWF reanalysis. It is shown that gravity waves account for 60% up to 80% of the total wave forcing of the tropical stratospheric circulation. We also compute wave forcing associated with intermediate-scale inertiagravity waves. In the WRF simulations this wave type represents ˜ 30% of the total gravity wave forcing. This suggests that intermediate-scale inertia-gravity waves can play an important role in the tropical middle-atmospheric circulation. In addition, the WRF high-resolution simulations are used to provide some guidance for constraining gravity wave parameterizations in coarse-grid climate models.

A review of neosporosis and pathologic findings of Neospora caninum infection in wildlife

PubMed Central

Donahoe, Shannon L.; Lindsay, Scott A.; Krockenberger, Mark; Phalen, David; Šlapeta, Jan

2015-01-01

Neospora caninum is an apicomplexan parasite that is the etiologic agent of neosporosis, a devastating infectious disease regarded as a major cause of reproductive loss in cattle and neuromuscular disease in dogs worldwide. This protozoan pathogen is maintained in the environment by a heteroxenous life cycle that involves a definitive canid host and a wide range of intermediate hosts. In recent years, a number of wildlife species have been investigated for their possible involvement in the N. caninum life cycle and many have been implicated as intermediate hosts. However, in many instances these studies have utilized serological and molecular techniques to detect infection in clinically normal animals, and investigation of possible associated morbidity, mortality, and pathology has been neglected. As such, the occurrence and importance of Neospora-associated disease in wildlife species are unknown. In order to improve our understanding of the significance of N. caninum infection in nondomestic species, the present review provides an up-to-date summary of clinical neosporosis and N. caninum-associated pathologic lesions in naturally and experimentally infected wildlife species. We provide a list of all free-ranging and captive wildlife species identified with N. caninum infection to date using currently available diagnostic tools. The advantages and disadvantages of diagnostic methods in wildlife are addressed in order to recommend optimal diagnosis of confirming N. caninum infection and neosporosis in nondomestic species. Although current data would suggest that N. caninum infection does not adversely impact wildlife populations, there is a need for greater international uniformity in the diagnosis of N. caninum infection and neosporosis in nondomestic species in order to assess the true consequences of parasite infection. PMID:25973393

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

DOE PAGES

Wen, Tongqi; Sun, Yang; Ye, Beilin; ...

2018-01-31

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wen, Tongqi; Sun, Yang; Ye, Beilin

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

Cooling rate dependence of structural order in Ni62Nb38 metallic glass

NASA Astrophysics Data System (ADS)

Wen, Tongqi; Sun, Yang; Ye, Beilin; Tang, Ling; Yang, Zejin; Ho, Kai-Ming; Wang, Cai-Zhuang; Wang, Nan

2018-01-01

Molecular dynamics (MD) simulations are performed to study the structure of Ni62Nb38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni62Nb38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfect icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.

Well-ordered structure of methylene blue monolayers on Au(111) surface: electrochemical scanning tunneling microscopy studies.

PubMed

Song, Yonghai; Wang, Li

2009-02-01

Well-ordered structure of methylene blue (MB) monolayers on Au(111) surface has been successfully obtained by controlling the substrate potential. Electrochemical scanning tunneling microscopy (ECSTM) examined the monolayers of MB on Au(111) in 0.1 M HClO(4) and showed long-range ordered, interweaved arrays of MB with quadratic symmetry on the substrate in the potential range of double-layer charging. High-resolution ECSTM image further revealed the details of the MB monolayers structure of c(5 x 5 radical 3)rect and the flat-lying orientation of ad-molecules. The dependence of molecular organization on the substrate potential and the formation mechanism of well-ordered structure on Au(111) surface were investigated in detail. The obtained well-ordered structure at the interface between a metal and an aqueous electrolyte might possibly be used as high-density device for signal memory and templates for the advanced nanopatterning of surfaces. (c) 2008 Wiley-Liss, Inc.

Reaction kinetics and transformation of carbadox and structurally related compounds with aqueous chlorine.

PubMed

Shah, Amisha D; Kim, Jae-Hong; Huang, Ching-Hua

2006-12-01

The potential release of carbadox (CDX), a commonly used antibacterial agent in swine husbandry, into water systems is of a concern due to its carcinogenic and genotoxic effects. Until this study, the reactivity of carbadox (possessing quinoxaline N,N'-dioxide and hydrazone moieties) toward aqueous chlorine has yetto be investigated in depth. Chemical reactivity, reaction kinetics, and transformation pathways of carbadox and structurally related compounds with free chlorine under typical water treatment conditions were determined. This study found that only CDX and desoxycarbadox (DCDX), a main metabolite of CDX with no ring N-oxide groups, react rapidly with free chlorine while other structurally related compounds including olaquindox, quindoxin, quinoxaline N-oxide, quinoxaline, and quinoline N-oxide do not. The reaction kinetics of CDX and DCDX with chlorine are highly pH dependent (e.g., the apparent second-order rate constant, kapp, for CDX ranges from 51.8 to 3.15 x 10(4) M(-1)s(-1) at pH 4-11). The high reactivity of CDX and DCDX to chlorine involves deprotonation of their hydrazone N-H moieties where initial chlorine attack results in a reactive intermediate that is further attacked by nucleophiles in the matrix to yield non-chlorinated, hydroxylated, and larger molecular weight byproducts. All of the CDX's byproducts retain their biologically active N-oxide groups, suggesting that they may remain as active antibacterial agents.

An integral-factorized implementation of the driven similarity renormalization group second-order multireference perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hannon, Kevin P.; Li, Chenyang; Evangelista, Francesco A., E-mail: francesco.evangelista@emory.edu

2016-05-28

We report an efficient implementation of a second-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT2) [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)]. Our implementation employs factorized two-electron integrals to avoid storage of large four-index intermediates. It also exploits the block structure of the reference density matrices to reduce the computational cost to that of second-order Møller–Plesset perturbation theory. Our new DSRG-MRPT2 implementation is benchmarked on ten naphthyne isomers using basis sets up to quintuple-ζ quality. We find that the singlet-triplet splittings (Δ{sub ST}) of the naphthyne isomers strongly depend onmore » the equilibrium structures. For a consistent set of geometries, the Δ{sub ST} values predicted by the DSRG-MRPT2 are in good agreements with those computed by the reduced multireference coupled cluster theory with singles, doubles, and perturbative triples.« less

Spin-reorientation transitions in the Cairo pentagonal magnet Bi 4 Fe 5 O 13 F

DOE PAGES

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; ...

2017-09-19

Here, we show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi 4Fe 5O 13F, on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi 4Fe 5O 13F is very far from the relevant parametermore » regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe 3+ spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.« less

Spin-reorientation transitions in the Cairo pentagonal magnet Bi4Fe5O13F

NASA Astrophysics Data System (ADS)

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; Batuk, Dmitry; Frontzek, Matthias; Abakumov, Artem M.

2017-09-01

We show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi4Fe5O13F , on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi4Fe5O13F is very far from the relevant parameter regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe3 + spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.

Elucidating the breathing of the metal-organic framework MIL-53(Sc) with ab initio molecular dynamics simulations and in situ X-ray powder diffraction experiments.

PubMed

Chen, Linjiang; Mowat, John P S; Fairen-Jimenez, David; Morrison, Carole A; Thompson, Stephen P; Wright, Paul A; Düren, Tina

2013-10-23

Ab initio molecular dynamics (AIMD) simulations have been used to predict structural transitions of the breathing metal-organic framework (MOF) MIL-53(Sc) in response to changes in temperature over the range 100-623 K and adsorption of CO2 at 0-0.9 bar at 196 K. The method has for the first time been shown to predict successfully both temperature-dependent structural changes and the structural response to variable sorbate uptake of a flexible MOF. AIMD employing dispersion-corrected density functional theory accurately simulated the experimentally observed closure of MIL-53(Sc) upon solvent removal and the transition of the empty MOF from the closed-pore phase to the very-narrow-pore phase (symmetry change from P2(1)/c to C2/c) with increasing temperature, indicating that it can directly take into account entropic as well as enthalpic effects. We also used AIMD simulations to mimic the CO2 adsorption of MIL-53(Sc) in silico by allowing the MIL-53(Sc) framework to evolve freely in response to CO2 loadings corresponding to the two steps in the experimental adsorption isotherm. The resulting structures enabled the structure determination of the two CO2-containing intermediate and large-pore phases observed by experimental synchrotron X-ray diffraction studies with increasing CO2 pressure; this would not have been possible for the intermediate structure via conventional methods because of diffraction peak broadening. Furthermore, the strong and anisotropic peak broadening observed for the intermediate structure could be explained in terms of fluctuations of the framework predicted by the AIMD simulations. Fundamental insights from the molecular-level interactions further revealed the origin of the breathing of MIL-53(Sc) upon temperature variation and CO2 adsorption. These simulations illustrate the power of the AIMD method for the prediction and understanding of the behavior of flexible microporous solids.

Probing New Long-Range Interactions by Isotope Shift Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berengut, Julian C.; Budker, Dmitry; Delaunay, Cédric

We explore a method to probe new long- and intermediate-range interactions using precision atomic isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the standard model nuclear effects. We apply our method to existing Ca + data and project its sensitivity to conjectured new bosons with spin-independent couplings to the electron and the neutron using narrow transitions in other atoms and ions, specifically, Sr and Yb. Future measurements are expected to improve themore » relative precision by 5 orders of magnitude, and they can potentially lead to an unprecedented sensitivity for bosons within the 0.3 to 10 MeV mass range.« less

Probing New Long-Range Interactions by Isotope Shift Spectroscopy.

PubMed

Berengut, Julian C; Budker, Dmitry; Delaunay, Cédric; Flambaum, Victor V; Frugiuele, Claudia; Fuchs, Elina; Grojean, Christophe; Harnik, Roni; Ozeri, Roee; Perez, Gilad; Soreq, Yotam

2018-03-02

We explore a method to probe new long- and intermediate-range interactions using precision atomic isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the standard model nuclear effects. We apply our method to existing Ca^{+} data and project its sensitivity to conjectured new bosons with spin-independent couplings to the electron and the neutron using narrow transitions in other atoms and ions, specifically, Sr and Yb. Future measurements are expected to improve the relative precision by 5 orders of magnitude, and they can potentially lead to an unprecedented sensitivity for bosons within the 0.3 to 10 MeV mass range.

Probing New Long-Range Interactions by Isotope Shift Spectroscopy

DOE PAGES

Berengut, Julian C.; Budker, Dmitry; Delaunay, Cédric; ...

2018-02-26

We explore a method to probe new long- and intermediate-range interactions using precision atomic isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the standard model nuclear effects. We apply our method to existing Ca + data and project its sensitivity to conjectured new bosons with spin-independent couplings to the electron and the neutron using narrow transitions in other atoms and ions, specifically, Sr and Yb. Future measurements are expected to improve themore » relative precision by 5 orders of magnitude, and they can potentially lead to an unprecedented sensitivity for bosons within the 0.3 to 10 MeV mass range.« less

A reconnaissance space sensing investigation of crustal structure for a strip from the eastern Sierra Nevada to the Colorado Plateau

NASA Technical Reports Server (NTRS)

Bechtold, I. C. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Analysis of ERTS-1 MSS imagery over the sourthern Basin-Range Province of California, Nevada, and Arizona has led to recognition of regional tectonic control of volcanism, plutonism, mineralization, and fault patterns. This conclusion is the result of geologic reconnaissance of anomalies observed in ERTS-1 and Apollo-9 data, guided by intermediate scale U-2 photography, SLAR, and relevant geologic literature. In addition to regional tectonic studies, the ERTS-1 imagery provides a basis for detailed research of relatively small geologic features. Interpretation of ERTS-1 and Apollo-9 space imagery and intermediate scale X-15 and U-2 photography indicates the presence of a major fault zone along the California-Nevada state line, here named the Pahrump fault zone. Field mapping confirms previously unreported evidence of fault breaks in bedrock, along range fronts and in Quaternary alluvium and lake sediments. Regional gravity lows and fault traces within the Pahrump fault zone from a general left stepping en echelon pattern. The trend and postulated diplacement for this fault are similar to other major strike slip fault zones in the southern Basin-Range Province.

Glyoxal Oxidation Mechanism: Implications for the Reactions HCO + O2 and OCHCHO + HO2.

PubMed

Faßheber, Nancy; Friedrichs, Gernot; Marshall, Paul; Glarborg, Peter

2015-07-16

A detailed mechanism for the thermal decomposition and oxidation of the flame intermediate glyoxal (OCHCHO) has been assembled from available theoretical and experimental literature data. The modeling capabilities of this extensive mechanism have been tested by simulating experimental HCO profiles measured at intermediate and high temperatures in previous glyoxal photolysis and pyrolysis studies. Additionally, new experiments on glyoxal pyrolysis and oxidation have been performed with glyoxal and glyoxal/oxygen mixtures in Ar behind shock waves at temperatures of 1285-1760 K at two different total density ranges. HCO concentration-time profiles have been detected by frequency modulation spectroscopy at a wavelength of λ = 614.752 nm. The temperature range of available direct rate constant data of the high-temperature key reaction HCO + O2 → CO + HO2 has been extended up to 1705 K and confirms a temperature dependence consistent with a dominating direct abstraction channel. Taking into account available literature data obtained at lower temperatures, the following rate constant expression is recommended over the temperature range 295 K < T < 1705 K: k1/(cm(3) mol(-1) s(-1)) = 6.92 × 10(6) × T(1.90) × exp(+5.73 kJ/mol/RT). At intermediate temperatures, the reaction OCHCHO + HO2 becomes more important. A detailed reanalysis of previous experimental data as well as more recent theoretical predictions favor the formation of a recombination product in contrast to the formerly assumed dominating and fast OH-forming channel. Modeling results of the present study support the formation of HOCH(OO)CHO and provide a 2 orders of magnitude lower rate constant estimate for the OH channel. Hence, low-temperature generation of chain carriers has to be attributed to secondary reactions of HOCH(OO)CHO.

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

PubMed Central

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. PMID:26394388

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

JPL self pulsed laser surface measurement system development. [large space deployed antenna structures

NASA Technical Reports Server (NTRS)

Berdahl, M.

1980-01-01

The use of a self pulsed laser system for accurately describing the surface shape of large space deployed antenna structures was evaluated. Tests with a breadboard system verified functional operation with short time resolution on the order of .2 mm, nonambiguous ranging, and a maximum range capability on the order of 150 m. The projected capability of the system is resolution of less than .1 mm over a reasonable time period and a range extension to over 300 m.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

Intermediate visual acuity of presbyopic individuals with and without distance and bifocal lens corrections.

DOT National Transportation Integrated Search

1977-03-01

Visual acuity was determined at the intermediate range for older individuals with various combinations of ocular refractive error (nine subcategories) and accommodative power (three subcategories). Subjects (N=249) read numerals ranging in size to me...

Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids

PubMed Central

Jarchow-Choy, Sarah K; Koppisch, Andrew T; Fox, David T

2014-01-01

Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined. PMID:25009443

Efficient synthesis and physicochemical characterization of natural danshensu, its S isomer and intermediates thereof

NASA Astrophysics Data System (ADS)

Sidoryk, Katarzyna; Filip, Katarzyna; Cmoch, Piotr; Łaszcz, Marta; Cybulski, Marcin

2018-02-01

The synthesis and molecular structure details of R- 3,4-dihydroxyphenyl lactic acid (danshensu) and related compounds, i.e. S isomer and the key intermediates have been described. Danshensu is an important water soluble phenolic acid of Salvia miltiorrhiza herb (danshen or red sag) with numerous applications in traditional Chinese medicine (TCM). Our synthetic approach was based on the Knoevenagel condensation of the protected 3,4-dihydroxybenzaldehyd and Meldrum acid derivative, followed by asymmetric Sharples dihydroxylation, reductive mono dehydroxylation and final deprotection. All compounds were characterized by various spectroscopic techniques: 1H-, 13C- magnetic resonance (NMR); Fourier-transformed infrared (FTIR); Raman, HR mass spectroscopy. For the determination of compound optical purities original HPLC methods were developed which allowed for the efficient resolution of danshensu R and S enantiomers as well as its intermediate enantiomers, using commercially available chiral stationary phases. Furthermore, in order to better understand danshensu specificity as a potential API in drug formulation, the physicochemical properties of the compounds were studied by thermal analysis, including differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA).

Self-ordered, controlled structure nanoporous membranes using constant current anodization.

PubMed

Lee, Kwan; Tang, Yun; Ouyang, Min

2008-12-01

We report a constant current (CC) based anodization technique to fabricate and control structure of mechanically stable anodic aluminum oxide (AAO) membranes with a long-range ordered hexagonal nanopore pattern. For the first time we show that interpore distance (Dint) of a self-ordered nanopore feature can be continuously tuned over a broad range with CC anodization and is uniquely defined by the conductivity of sulfuric acid as electrolyte. We further demonstrate that this technique can offer new degrees of freedom for engineering planar nanopore structures by fine tailoring the CC based anodization process. Our results not only facilitate further understanding of self-ordering mechanism of alumina membranes but also provide a fast, simple (without requirement of prepatterning or preoxide layer), and flexible methodology for controlling complex nanoporous structures, thus offering promising practical applications in nanotechnology.

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

PubMed Central

NISHIMURA, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate. PMID:28077807

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

PubMed

Nishimura, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Choosing order of operations to accelerate strip structure analysis in parameter range

NASA Astrophysics Data System (ADS)

Kuksenko, S. P.; Akhunov, R. R.; Gazizov, T. R.

2018-05-01

The paper considers the issue of using iteration methods in solving the sequence of linear algebraic systems obtained in quasistatic analysis of strip structures with the method of moments. Using the analysis of 4 strip structures, the authors have proved that additional acceleration (up to 2.21 times) of the iterative process can be obtained during the process of solving linear systems repeatedly by means of choosing a proper order of operations and a preconditioner. The obtained results can be used to accelerate the process of computer-aided design of various strip structures. The choice of the order of operations to accelerate the process is quite simple, universal and could be used not only for strip structure analysis but also for a wide range of computational problems.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

DOE PAGES

Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

2014-12-29

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe 3+ to activate O 2 and catecholic substrates for reaction. The inability of Fe 3+ to directly bind O 2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surroundingmore » solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe 3+ species, and the anhydride-Fe 3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe 2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe 2+ intermediate that could bind O 2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

Pathways for virus assembly around nucleic acids

PubMed Central

Perlmutter, Jason D; Perkett, Matthew R

2014-01-01

Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single molecule fluorescence correlation spectroscopy or bulk time resolved small angle x-ray scattering experiments. PMID:25036288

Energetics of a uranothorite (Th 1–xU xSiO 4) solid solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaofeng; Szenknect, Stephanie; Mesbah, Adel

High-temperature oxide melt solution calorimetric measurements were completed to determine the enthalpies of formation of the uranothorite, (USiO 4) x–(ThSiO 4) 1–x, solid solution. Phase-pure samples with x values of 0, 0.11, 0.21, 0.35, 0.71, and 0.84 were prepared, purified, and characterized by powder X-ray diffraction, electron probe microanalysis, thermogravimetric analysis and differential scanning calorimetry coupled with in situ mass spectrometry, and high-temperature oxide melt solution calorimetry. This work confirms the energetic metastability of coffinite, USiO 4, and U-rich intermediate silicate phases with respect to a mixture of binary oxides. Furthermore, variations in unit cell parameters and negative excess volumesmore » of mixing, coupled with strongly exothermic enthalpies of mixing in the solid solution, suggest short-range cation ordering that can stabilize intermediate compositions, especially near x = 0.5.« less

Energetics of a uranothorite (Th 1–xU xSiO 4) solid solution

DOE PAGES

Guo, Xiaofeng; Szenknect, Stephanie; Mesbah, Adel; ...

2016-10-11

High-temperature oxide melt solution calorimetric measurements were completed to determine the enthalpies of formation of the uranothorite, (USiO 4) x–(ThSiO 4) 1–x, solid solution. Phase-pure samples with x values of 0, 0.11, 0.21, 0.35, 0.71, and 0.84 were prepared, purified, and characterized by powder X-ray diffraction, electron probe microanalysis, thermogravimetric analysis and differential scanning calorimetry coupled with in situ mass spectrometry, and high-temperature oxide melt solution calorimetry. This work confirms the energetic metastability of coffinite, USiO 4, and U-rich intermediate silicate phases with respect to a mixture of binary oxides. Furthermore, variations in unit cell parameters and negative excess volumesmore » of mixing, coupled with strongly exothermic enthalpies of mixing in the solid solution, suggest short-range cation ordering that can stabilize intermediate compositions, especially near x = 0.5.« less

Topology of zigzag chromatin.

PubMed

Strogatz, S

1983-08-21

An enormous length of DNA is packaged in the nuclei of eukaryotic cells. This is achieved through several intermediate levels of compaction, ranging from the double helix to the chromosome. The nucleosome is now firmly established as the first level of chromatin structure. Next it appears that the nucleosomes are themselves stacked in a two-track array, with a dinucleosome repeat. Several winding patterns of DNA are compatible with such a structure. It is shown here that, compared to other feasible DNA paths, the observed winding pattern has remarkable topological properties. The possible biological significance of this peculiarity is discussed.

Hydrolysis of ZrCl4 and HfCl4: The Initial Steps in the High-Temperature Oxidation of Metal Chlorides to Produce ZrO2 and HfO2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, Zongtang; Dixon, David A.

2013-03-08

The gas-phase hydrolysis of MCl4 (M = Zr, Hf) to produce the initial particles on the way to zirconia and hafnia nanoparticles has been studied with electronic structure theory. The potential energy surfaces, the themochemistry of the reaction species, and the reaction paths for the initial steps of MCl4 reacting with H2O have been calculated. The hydrolysis of MCl4 at higher temperatures begins with the formation of oxychlorohydroxides followed by the elimination of HCl instead of the direct production of MOCl2 and HCl or MO2 and HCl due to the substantial endothermicities associated with the formation of gas-phase MO2. Themore » structural properties and heats of formation of the reactants and products are consistent with the available experimental results. A number of metal oxychlorides (oxychlorohydroxides) intermediate clusters have been studied to assess their role in the production of MO2 nanoparticles. The calculated clustering reaction energies of those intermediates are highly exothermic, so they could be readily formed in the hydrolysis process. These intermediate clusters can be formed exothermically from metal oxychlorohydroxides by the elimination of one HCl or H2O molecule. Our calculations show that the mechanisms leading to the formation of MO2 nanoparticles are complicated and are accompanied by the potential production of a wide range of intermediates, as found for the production of TiO2 particles from the high-temperature oxidation of TiCl4.« less

Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors.

PubMed

Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi

2017-01-01

In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (k cat ) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of k cat were also lower. The hydrolytic water molecule with favorable Gibbs free energy may hydrolyze acylated serine slowly. Gibbs free energy of hydrolytic water molecule might be a useful descriptor for computer-aided discovery of mechanism-based reversible covalent inhibitors of hydrolytic enzymes.

Local structure of human hair spatially resolved by sub-micron X-ray beam.

PubMed

Stanić, Vesna; Bettini, Jefferson; Montoro, Fabiano Emmanuel; Stein, Aaron; Evans-Lutterodt, Kenneth

2015-11-30

Human hair has three main regions, the medulla, the cortex, and the cuticle. An existing model for the cortex suggests that the α-keratin- based intermediate filaments (IFs) align with the hair's axis, but are orientationally disordered in-plane. We found that there is a new region in the cortex near the cuticle's boundary in which the IFs are aligned with the hair's axis, but additionally, they are orientationally ordered in-plane due to the presence of the cuticle/hair boundary. Further into the cortex, the IF arrangement becomes disordered, eventually losing all in-plane orientation. We also find that in the cuticle, a key diffraction feature is absent, indicating the presence of the β-keratin rather than that of the α-keratin phase. This is direct structural evidence that the cuticle contains β-keratin sheets. This work highlights the importance of using a sub-micron x-ray beam to unravel the structures of poorly ordered, multi-phase systems.

First X-ray crystal structure and internal reference diffusion-ordered NMR spectroscopy study of the prototypical Posner reagent, MeCu(SPh)Li(THF)3.

PubMed

Bertz, Steven H; Hardin, Richard A; Heavey, Thomas J; Jones, Daniel S; Monroe, T Blake; Murphy, Michael D; Ogle, Craig A; Whaley, Tara N

2013-07-29

Grow slow: The usual direct treatment of MeLi and CuSPh did not yield X-ray quality crystals of MeCu(SPh)Li. An indirect method starting from Me2CuLi⋅LiSPh and chalcone afforded the desired crystals by the slow reaction of the intermediate π-complex (see scheme). This strategy produced the first X-ray crystal structure of a Posner cuprate. A complementary NMR study showed that the contact ion pair was also the main species in solution. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and property of metal melt I: The number of residual bonds after solid-liquid phase changes

NASA Astrophysics Data System (ADS)

Mi, Guangbao; Li, Peijie; He, Liangju

2010-09-01

Based on the mechanism of metal solid-liquid phase change and the theory of liquid metal’s micro-inhomogeneity, a physical model is established between latent heats of fusion and vaporization and the numbers of residual bonds and short-range ordered atoms at the melting point inside a metal melt. Meanwhile, the mathematical derivation and proof are also offered. This model produces the numbers of residual bonds and short-range ordered atoms after the solid-liquid phase change only by using basic parameters and thermophysical properties of the crystal structure. Therefore, it presents a more effective way to analyze the melt’s structural information. By using this model, this study calculates the numbers of residual bonds and short-range ordered atoms in Al and Ni melts. The calculated results are consistent with the experimental results. Simultaneously, this study discusses the atomic number’s influence on the numbers of residual bonds and short-range ordered atoms in the melts within the first (IA) and second main group (IIA) elements.

Comparison of liquid-state anomalies in Stillinger-Weber models of water, silicon, and germanium

NASA Astrophysics Data System (ADS)

Dhabal, Debdas; Chakravarty, Charusita; Molinero, Valeria; Kashyap, Hemant K.

2016-12-01

We use molecular dynamics simulations to compare and contrast the liquid-state anomalies in the Stillinger-Weber models of monatomic water (mW), silicon (Si), and germanium (Ge) over a fairly wide range of temperatures and densities. The relationships between structure, entropy, and mobility, as well as the extent of the regions of anomalous behavior, are discussed as a function of the degree of tetrahedrality. We map out the cascade of density, structural, pair entropy, excess entropy, viscosity, and diffusivity anomalies for these three liquids. Among the three liquids studied here, only mW displays anomalies in the thermal conductivity, and this anomaly is evident only at very low temperatures. Diffusivity and viscosity, on the other hand, show pronounced anomalous regions for the three liquids. The temperature of maximum density of the three liquids shows re-entrant behavior consistent with either singularity-free or liquid-liquid critical point scenarios proposed to explain thermodynamic anomalies. The order-map, which shows the evolution of translational versus tetrahedral order in liquids, is different for Ge than for Si and mW. We find that although the monatomic water reproduces several thermodynamic and dynamic properties of rigid-body water models (e.g., SPC/E, TIP4P/2005), its sequence of anomalies follows, the same as Si and Ge, the silica-like hierarchy: the region of dynamic (diffusivity and viscosity) anomalies encloses the region of structural anomalies, which in turn encloses the region of density anomaly. The hierarchy of the anomalies based on excess entropy and Rosenfeld scaling, on the other hand, reverses the order of the structural and dynamic anomalies, i.e., predicts that the three Stillinger-Weber liquids follow a water-like hierarchy of anomalies. We investigate the scaling of diffusivity, viscosity, and thermal conductivity with the excess entropy of the liquid and find that for dynamical properties that present anomalies there is no universal scaling of the reduced property with excess entropy for the whole range of temperatures and densities. Instead, Rosenfeld's scaling holds for all the three liquids at high densities and high temperatures, although deviations from simple exponential dependence are observed for diffusivity and viscosity at lower temperatures and intermediate densities. The slope of the scaling of transport properties obtained for Ge is comparable to that obtained for simple liquids, suggesting that this low tetrahedrality liquid, although it stabilizes a diamond crystal, is already close to simple liquid behavior for certain properties.

Comparison of liquid-state anomalies in Stillinger-Weber models of water, silicon, and germanium.

PubMed

Dhabal, Debdas; Chakravarty, Charusita; Molinero, Valeria; Kashyap, Hemant K

2016-12-07

We use molecular dynamics simulations to compare and contrast the liquid-state anomalies in the Stillinger-Weber models of monatomic water (mW), silicon (Si), and germanium (Ge) over a fairly wide range of temperatures and densities. The relationships between structure, entropy, and mobility, as well as the extent of the regions of anomalous behavior, are discussed as a function of the degree of tetrahedrality. We map out the cascade of density, structural, pair entropy, excess entropy, viscosity, and diffusivity anomalies for these three liquids. Among the three liquids studied here, only mW displays anomalies in the thermal conductivity, and this anomaly is evident only at very low temperatures. Diffusivity and viscosity, on the other hand, show pronounced anomalous regions for the three liquids. The temperature of maximum density of the three liquids shows re-entrant behavior consistent with either singularity-free or liquid-liquid critical point scenarios proposed to explain thermodynamic anomalies. The order-map, which shows the evolution of translational versus tetrahedral order in liquids, is different for Ge than for Si and mW. We find that although the monatomic water reproduces several thermodynamic and dynamic properties of rigid-body water models (e.g., SPC/E, TIP4P/2005), its sequence of anomalies follows, the same as Si and Ge, the silica-like hierarchy: the region of dynamic (diffusivity and viscosity) anomalies encloses the region of structural anomalies, which in turn encloses the region of density anomaly. The hierarchy of the anomalies based on excess entropy and Rosenfeld scaling, on the other hand, reverses the order of the structural and dynamic anomalies, i.e., predicts that the three Stillinger-Weber liquids follow a water-like hierarchy of anomalies. We investigate the scaling of diffusivity, viscosity, and thermal conductivity with the excess entropy of the liquid and find that for dynamical properties that present anomalies there is no universal scaling of the reduced property with excess entropy for the whole range of temperatures and densities. Instead, Rosenfeld's scaling holds for all the three liquids at high densities and high temperatures, although deviations from simple exponential dependence are observed for diffusivity and viscosity at lower temperatures and intermediate densities. The slope of the scaling of transport properties obtained for Ge is comparable to that obtained for simple liquids, suggesting that this low tetrahedrality liquid, although it stabilizes a diamond crystal, is already close to simple liquid behavior for certain properties.

CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

EPA Science Inventory

Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

The pressure-induced structural response of rare earth hafnate and stannate pyrochlore from 0.1-50 GPa

NASA Astrophysics Data System (ADS)

Turner, K. M.; Rittman, D.; Heymach, R.; Turner, M.; Tracy, C.; Mao, W. L.; Ewing, R. C.

2017-12-01

Complex oxides with the pyrochlore (A2B2O7) and defect-fluorite ((A,B)4O7) structure-types undergo structural transformations under high-pressure. These compounds are under consideration for applications including as a proposed waste-form for actinides generated in the nuclear fuel cycle. High-pressure transformations in rare earth hafnates (A2Hf2O7, A=Sm, Eu, Gd, Dy, Y, Yb) and stannates (A2Sn2O7, A=Nd, Gd, Er) were investigated to 50 GPa by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Rare-earth hafnates form the pyrochlore structure for A=La-Tb and the defect-fluorite structure for A=Dy-Lu. Lanthanide stannates form the pyrochlore structure. Raman spectra revealed that at ambient pressure all compositions have pyrochlore-type short-range order. Stannate compositions show a larger degree of pyrochlore-type short-range ordering relative to hafnates. In situ high-pressure synchrotron XRD showed that rare earth hafnates and stannates underwent a pressure-induced phase transition to a cotunnite-like (Pnma) structure that begins between 18-25 GPa in hafnates and between 30-33 GPa in stannates. The phase transition is not complete at 50 GPa, and upon decompression, XRD indicates that all compositions transform to defect-fluorite with an amorphous component. In situ Raman spectroscopy showed that disordering in stannates and hafnates occurs gradually upon compression. Pyrochlore-structured hafnates retain short-range order to a higher pressure (30 GPa vs. <10 GPa) than defect-fluorite-structured hafnates. Hafnates and stannates decompressed from 50 GPa show Raman spectra consistent with weberite-type structures, also reported in irradiated stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of 250 GPa for hafnate compositions with the pyrochlore structure, and 400 GPa for hafnate compositions with the defect-fluorite structure. Stannates have a lower bulk modulus relative to hafnates (between 80-150 GPa). Stannate and hafnate pyrochlore compositions taken to high pressure show structural transformations consistent with irradiated pyrochlore, and compositionally disordered pyrochlore: a long-range structure best described by defect-fluorite, and a short-range structure best described by weberite.

Self-organized colloidal quantum dots and metal nanoparticles for plasmon-enhanced intermediate-band solar cells.

PubMed

Mendes, Manuel J; Hernández, Estela; López, Esther; García-Linares, Pablo; Ramiro, Iñigo; Artacho, Irene; Antolín, Elisa; Tobías, Ignacio; Martí, Antonio; Luque, Antonio

2013-08-30

A colloidal deposition technique is presented to construct long-range ordered hybrid arrays of self-assembled quantum dots and metal nanoparticles. Quantum dots are promising for novel opto-electronic devices but, in most cases, their optical transitions of interest lack sufficient light absorption to provide a significant impact in their implementation. A potential solution is to couple the dots with localized plasmons in metal nanoparticles. The extreme confinement of light in the near-field produced by the nanoparticles can potentially boost the absorption in the quantum dots by up to two orders of magnitude.In this work, light extinction measurements are employed to probe the plasmon resonance of spherical gold nanoparticles in lead sulfide colloidal quantum dots and amorphous silicon thin-films. Mie theory computations are used to analyze the experimental results and determine the absorption enhancement that can be generated by the highly intense near-field produced in the vicinity of the gold nanoparticles at their surface plasmon resonance.The results presented here are of interest for the development of plasmon-enhanced colloidal nanostructured photovoltaic materials, such as colloidal quantum dot intermediate-band solar cells.

Hydrogeology of the surficial and intermediate aquifer systems in Sarasota and adjacent counties, Florida

USGS Publications Warehouse

Barr, G.L.

1996-01-01

From 1991 to 1995, the hydrogeology of the surficial aquifer system and the major permeable zones and confining units of the intermediate aquifer system in southwest Florida was studied. The study area is a 1,400-square-mile area that includes Sarasota County and parts of Manatee, De Soto, Charlotte, and Lee Counties. Lithologic, geophysical, hydraulic property, and water-level data were used to correlate the hydrogeology and map the extent of the aquifer systems. Water chemistry was evaluated in southwest Sarasota County to determine salinity of the surficial and intermediate aquifer systems. The surficial aquifer is an unconfined aquifer system that overlies the intermediate aquifer system and ranges from a few feet to over 60 feet in thickness in the study area. Hydraulic properties of the surficial aquifer system determined from aquifer and laboratory tests, and model simulations vary considerably across the study area. The intermediate aquifer system, a confined aquifer system that lies between the surficial and the Upper Floridan aquifers, is composed of alternating confining units and permeable zones. The intermediate aquifer system has three major permeable zones that exhibit a wide range of hydraulic properties. Horizontal flow in the intermediate aquifer system is northeast to southwest. Most of the study area is in a discharge area of the intermediate aquifer system. Water ranges naturally from fresh in the surficial aquifer system and upper permeable zones of the intermediate aquifer system to moderately saline in the lower permeable zone. Water-quality data collected in coastal southwest Sarasota County indicate that ground-water withdrawals from major pumping centers have resulted in lateral seawater intrusion and upconing into the surficial and intermediate aquifer systems.

Role of core excitation in ( d , p ) transfer reactions

DOE PAGES

Deltuva, A.; Ross, A.; Norvaišas, E.; ...

2016-10-24

In our recent work we found that core excitations can be important in extracting structure information from (d,p) reactions. Our objective is to systematically explore the role of core excitation in (d,p) reactions and to understand the origin of the dynamical effects. Based on the particle-rotor model of n+Be 10, we generate a number of models with a range of separation energies (S n=0.1–5.0 MeV), while maintaining a significant core excited component. We then apply the latest extension of the momentum-space-based Faddeev method, including dynamical core excitation in the reaction mechanism to all orders, to the Be 10(d,p)Be 11-like reactions,more » and study the excitation effects for beam energies E d=15–90 MeV. We study the resulting angular distributions and the differences between the spectroscopic factor that would be extracted from the cross sections, when including dynamical core excitation in the reaction, and that of the original structure model. We also explore how different partial waves affect the final cross section. Our results show a strong beam-energy dependence of the extracted spectroscopic factors that become smaller for intermediate beam energies. Finally, this dependence increases for loosely bound systems.« less

The Oligomeric Nature of Triosephosphate Isomerase. Studies of Monomerization

NASA Astrophysics Data System (ADS)

Zárate-Pérez, Francisco; Vázquez-Contreras, Edgar

2008-02-01

In this work, we report the implications of the monomerization of triosephosphate isomerase (TIM) from T. cruzi (TcTIM). A monomeric mutant (monoTcTIM) of this species was constructed by genetic engineering, shortening the main loop of interdigitation, which is fundamental for its dimerization. The properties of monoTcTIM were compared with those of the other TIM monomeric versions: genetically engineered mutants, or equilibrium intermediates obtained by chemical denaturation. The stability for almost all the monomeric variants so far reported appears in the same range, and also presents similar structural characteristics. Regarding the catalytic activity of monomeric mutants, when it is present is in several orders of magnitude lower than those observed in their respective wild-type enzyme. The change in the hydrophobic surface of TcTIM after and before monomerization was also studied and corresponds to an extensive area of the interface region, which becomes exposed when monomers are dissociated. This fact could be related with conformational changes in the local environment of the catalytic amino acids responsible for the isomerization of the substrate and consequently the inactivation of its catalytic properties. Comparison of the structural, folding and unfolding properties, as well as stability studies could give answers on why this enzyme is an obligate oligomer.

Structure and thermoelectric property of Te doped paracostibite CoSb1-xTexS compounds

NASA Astrophysics Data System (ADS)

You, Yonghui; Su, Xianli; Liu, Wei; Yan, Yonggao; Fu, Jiefei; Cheng, Xin; Zhang, Cheng; Tang, Xinfeng

2018-06-01

Paracostibite (CoSbS), a newly developed thermoelectric material, has aroused lots of interest due to its highly earth abundant and inexpensive constituent elements and potential application for thermoelectric power generation in the intermediate temperature range. Herein, a series of CoSb1-xTexS (x = 0-0.09) compounds were prepared by vacuum melting and annealing followed by SPS processing, and the effects of Te doping on the structure and thermoelectric properties were systematically investigated. Doping Te on the Sb site increases the carrier concentration up to 7.24 × 1020 cm-3 for CoSb0.93Te0.07S compound which is several orders of magnitude higher than that of un-doped CoSbS, and enhances the power factor. The maximum power factor of 14.07 μW cm-1 K-2 is attained at 900 K. Concomitantly, doping with Te on the Sb site leads to effective scattering of heat carrying phonon, accompanying with a strong suppression of the thermal conductivity with the increase of Te content, resulting in an increase of the ZT. A maximum ZT of 0.43 at 900 K is attained for CoSb0.93Te0.07S compound, which is 139% higher than that of un-doped CoSbS compound.

Retrospection of Chernobyl nuclear accident for decision analysis concerning remedial actions in Ukraine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Georgievskiy, Vladimir

2007-07-01

It is considered the efficacy of decisions concerning remedial actions when of-site radiological monitoring in the early and (or) in the intermediate phases was absent or was not informative. There are examples of such situations in the former Soviet Union where many people have been exposed: releases of radioactive materials from 'Krasnoyarsk-26' into Enisey River, releases of radioactive materials from 'Chelabinsk-65' (the Kishtim accident), nuclear tests at the Semipalatinsk Test Site, the Chernobyl nuclear accident etc. If monitoring in the early and (or) in the intermediate phases is absent the decisions concerning remedial actions are usually developed on the basemore » of permanent monitoring. However decisions of this kind may be essentially erroneous. For these cases it is proposed to make retrospection of radiological data of the early and intermediate phases of nuclear accident and to project decisions concerning remedial actions on the base of both retrospective data and permanent monitoring data. In this Report the indicated problem is considered by the example of the Chernobyl accident for Ukraine. Their of-site radiological monitoring in the early and intermediate phases was unsatisfactory. In particular, the pasture-cow-milk monitoring had not been made. All official decisions concerning dose estimations had been made on the base of measurements of {sup 137}Cs in body (40 measurements in 135 days and 55 measurements in 229 days after the Chernobyl accident). For the retrospection of radiological data of the Chernobyl accident dynamic model has been developed. This model has structure similar to the structure of Pathway model and Farmland model. Parameters of the developed model have been identified for agricultural conditions of Russia and Ukraine. By means of this model dynamics of 20 radionuclides in pathways and dynamics of doses have been estimated for the early, intermediate and late phases of the Chernobyl accident. The main results are following: - During the first year after the Chernobyl accident 75-93% of Commitment Effective Dose had been formed; - During the first year after the Chernobyl accident 85-90% of damage from radiation exposure had been formed. During the next 50 years (the late phase of accident) only 10-15% of damage from radiation exposure will have been formed; - Remedial actions (agricultural remedial actions as most effective) in Ukraine are intended for reduction of the damage from consumption of production which is contaminated in the late phase of accident. I.e. agricultural remedial actions have been intended for minimization only 10 % of the total damage from radiation exposure; - Medical countermeasures can minimize radiation exposure damage by an order of magnitude greater than agricultural countermeasures. - Thus, retrospection of nuclear accident has essentially changed type of remedial actions and has given a chance to increase effectiveness of spending by an order of magnitude. This example illustrates that in order to optimize remedial actions it is required to use data of retrospection of nuclear accidents in all cases when monitoring in the early and (or) intermediate phases is unsatisfactory. (author)« less

High pressure spectroscopic studies of phase transition in VO2

NASA Astrophysics Data System (ADS)

Basu, Raktima; Mishra, K. K.; Ravindran, T. R.; Dhara, Sandip

2018-04-01

Vanadium dioxide (VO2) exhibits a reversible first-order metal to insulator transition (MIT) at a technologically important temperature of 340K. A structural phase transition (SPT) from monoclinic M1 to rutile tetragonal R is also reported via another two intermediate phases of monoclinic M2 and triclinic T. Metastable monoclinic M2 phase of VO2 was synthesized by Mg doping in the vapour transport process. Raman spectroscopic measurements were carried out at high pressure on V1-xMgxO2 microrods. Two reversible structural phase transitions from monoclinic M2 to triclinic T at 1.6 GPa and T to monoclinic M1 at 3.2 GPa are observed and are explained by structural relaxation of the strained phases.

Mechanisms of the Wurtzite to Rocksalt Transformation in CdSe Nanocrystals

NASA Astrophysics Data System (ADS)

Grünwald, Michael; Rabani, Eran; Dellago, Christoph

2006-06-01

We study the pressure-driven phase transition from the four-coordinate wurtzite to the six-coordinate rocksalt structure in CdSe nanocrystals with molecular dynamics computer simulations. With an ideal gas as the pressure medium, we apply hydrostatic pressure to spherical and faceted nanocrystals ranging in diameter from 25 to 62 Å. In spherical crystals, the main mechanism of the transformation involves the sliding of (100) planes, but depending on the specific surface structure we also observe a second mechanism proceeding through the flattening of (100) planes. In faceted crystals, the transition proceeds via a five-coordinated hexagonal structure, which is stabilized at intermediate pressures due to dominant surface energetics.

A Theoretical Probe for Excitation Mechanisms of Sun-like and Mira-like Oscillations of Stars

NASA Astrophysics Data System (ADS)

Xiong, Da-run; Deng, Li-cai

2013-01-01

The linear nonadiabatic oscillations for evolutionary models of 0.6- 3M8 stars are calculated by using a nonlocal and time-dependent convection theory. The results show that in the HR diagram the pulsation-unstable low- temperature stars on the right side of instability strip can be divided into two groups. One group indicates the Sun-like oscillation stars composed of the main- sequence dwarfs, sub-giants and red giants (RGs) of low and intermediate lu- minosities, which are unstable in the intermediate- and high-order (n ≥ 12) p- modes, and stable in the low-order (n ≤ 5) p-modes. Another group indicates the Mira-like stars composed of the bright RGs and asymptotic giant branch (AGB) stars, which are just contrary to Sun-like stars, unstable in low-order (n ≤ 5) p-modes and stable in the intermediate- and high-order (n ≥ 12) p-modes. The oscillations for the red edge of Cepheid (δ Scuti) instability strip, Sun-like and Mira-like stars can be explained uniformly by the coupling between convection and oscillation (CCO). For the low-temperature stars on the right side of in- stability strip, CCO is the dominant excitation and damping mechanism of the oscillations of low- and intermediate-order p-modes, and the turbulent stochas- tic excitation becomes important only for the high-order p-modes of Sun-like oscillations.

Projecting non-diffracting waves with intermediate-plane holography.

PubMed

Mondal, Argha; Yevick, Aaron; Blackburn, Lauren C; Kanellakopoulos, Nikitas; Grier, David G

2018-02-19

We introduce intermediate-plane holography, which substantially improves the ability of holographic trapping systems to project propagation-invariant modes of light using phase-only diffractive optical elements. Translating the mode-forming hologram to an intermediate plane in the optical train can reduce the need to encode amplitude variations in the field, and therefore complements well-established techniques for encoding complex-valued transfer functions into phase-only holograms. Compared to standard holographic trapping implementations, intermediate-plane holograms greatly improve diffraction efficiency and mode purity of propagation-invariant modes, and so increase their useful non-diffracting range. We demonstrate this technique through experimental realizations of accelerating modes and long-range tractor beams.

Weak arrest-like and field-driven first order magnetic phase transitions of itinerant Fe3Ga4 revealed by magnetization and magnetoresistance isotherms

NASA Astrophysics Data System (ADS)

Samatham, S. Shanmukharao; Suresh, K. G.

2017-01-01

The detailed magnetic study of complex 3d-electron based Fe3Ga4 is reported. It undergoes paramagnetic to antiferromagnetic (TN) and antiferromagnetic to ferromagnetic (TC) transitions respectively around 380 and 70 K. The thermal hysteresis of field-cooled cooling (FCC) and field-cooled warming (FCW) hints at first order phase transition below Curie temperature. A weak phase coexistence of ferro and antiferromagnetic phases is suggested by exploring the arrest-like first-order phenomenon. In the intermediate temperature range, field-driven metamagnetic transition from antiferro to ferromagnetic phase is confirmed. Further bringing the system very near to TN, field-induced transitions disappear and above TN predominant paramagnetic contribution is evident. The magnetic H-T phase diagram distinguishing different magnetic phases of Fe3Ga4 is obtained.

Intermediate couplings: NMR at the solids-liquids interface

NASA Astrophysics Data System (ADS)

Spence, Megan

2006-03-01

Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics.

Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis.

PubMed

Pratt, Andrew C; Dewage, Sajeewa W; Pang, Allan H; Biswas, Tapan; Barnard-Britson, Sandra; Cisneros, G Andrés; Tsodikov, Oleg V

2015-10-01

Family I inorganic pyrophosphatases (PPiases) are ubiquitous enzymes that are critical for phosphate metabolism in all domains of life. The detailed catalytic mechanism of these enzymes, including the identity of the general base, is not fully understood. We determined a series of crystal structures of the PPiase from Mycobacterium tuberculosis (Mtb PPiase) bound to catalytic metals, inorganic pyrophosphate (PPi; the reaction substrate) and to one or two inorganic phosphate ions (Pi; the reaction product), ranging in resolution from 1.85 to 3.30Å. These structures represent a set of major kinetic intermediates in the catalytic turnover pathway for this enzyme and suggest an order of association and dissociation of the divalent metals, the substrate and the two products during the catalytic turnover. The active site of Mtb PPiase exhibits significant structural differences from the well characterized Escherichia coli PPiase in the vicinity of the bound PPi substrate. Prompted by these differences, quantum mechanics/molecular mechanics (QM/MM) analysis yielded an atomic description of the hydrolysis step for Mtb PPiase and, unexpectedly, indicated that Asp89, rather than Asp54 that was proposed for E. coli PPiase, can abstract a proton from a water molecule to activate it for a nucleophilic attack on the PPi substrate. Mutagenesis studies of the key Asp residues of Mtb PPiase supported this mechanism. This combination of structural and computational analyses clarifies our understanding of the mechanism of family I PPiases and has potential utility for rational development of drugs targeting this enzyme. Copyright © 2015 Elsevier Inc. All rights reserved.

In Situ Probing and Synthetic Control of Cationic Ordering in Ni-Rich Layered Oxide Cathodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Jianqing; Zhang, Wei; Huq, Ashfia

Ni-rich layered oxides (LiNi1-xMxO2; M = Co, Mn, ...) are appealing alternatives to conventional LiCoO2 as cathodes in Li-ion batteries for automobile and other large-scale applications due to their high theoretical capacity and low cost. However, preparing stoichiometric LiNi1-xMxO2 with ordered layer structure and high reversible capacity, has proven difficult due to cation mixing in octahedral sites. Herein, in situ studies of synthesis reactions and the associated structural ordering in preparing LiNiO2 and the Co-substituted variant, LiNi0.8Co0.2O2, are made, to gain insights into synthetic control of the structure and electrochemical properties of Ni-rich layered oxides. Results from this study indicatemore » a direct transformation of the intermediate from the rock salt structure into hexagonal phase, and during the process, Co substitution facilities the nucleation of a Co-rich layered phase at low temperatures and subsequent growth and stabilization of solid solution Li(Ni, Co)O-2 upon further heat treatment. Optimal conditions are identified from the in situ studies and utilized to obtain stoichiometric LiNi0.8Co0.2O2 that exhibits high capacity (up to 200 mA h g(-1) ) with excellent retention. The findings shed light on designing high performance Ni-rich layered oxide cathodes through synthetic control of the structural ordering in the materials.« less

A DNA-based nanomechanical device with three robust states.

PubMed

Chakraborty, Banani; Sha, Ruojie; Seeman, Nadrian C

2008-11-11

DNA has been used to build a variety of devices, ranging from those that are controlled by DNA structural transitions to those that are controlled by the addition of specific DNA strands. These sequence-dependent devices fulfill the promise of DNA in nanotechnology because a variety of devices in the same physical environment can be controlled individually. Many such devices have been reported, but most of them contain one or two structurally robust end states, in addition to a floppy intermediate or even a floppy end state. We describe a system in which three different structurally robust end states can be obtained, all resulting from the addition of different set strands to a single floppy intermediate. This system is an extension of the PX-JX(2) DNA device. The three states are related to each other by three different motions, a twofold rotation, a translation of approximately 2.1-2.5 nm, and a twofold screw rotation, which combines these two motions. We demonstrate the transitions by gel electrophoresis, by fluorescence resonance energy transfer, and by atomic force microscopy. The control of this system by DNA strands opens the door to trinary logic and to systems containing N devices that are able to attain 3(N) structural states.

A DNA-based nanomechanical device with three robust states

PubMed Central

Chakraborty, Banani; Sha, Ruojie; Seeman, Nadrian C.

2008-01-01

DNA has been used to build a variety of devices, ranging from those that are controlled by DNA structural transitions to those that are controlled by the addition of specific DNA strands. These sequence-dependent devices fulfill the promise of DNA in nanotechnology because a variety of devices in the same physical environment can be controlled individually. Many such devices have been reported, but most of them contain one or two structurally robust end states, in addition to a floppy intermediate or even a floppy end state. We describe a system in which three different structurally robust end states can be obtained, all resulting from the addition of different set strands to a single floppy intermediate. This system is an extension of the PX-JX2 DNA device. The three states are related to each other by three different motions, a twofold rotation, a translation of ≈2.1–2.5 nm, and a twofold screw rotation, which combines these two motions. We demonstrate the transitions by gel electrophoresis, by fluorescence resonance energy transfer, and by atomic force microscopy. The control of this system by DNA strands opens the door to trinary logic and to systems containing N devices that are able to attain 3N structural states. PMID:18474862

Interface properties of MIS structures based on hetero-epitaxial graded-gap Hg1-xCdxTe with CdTe interlayer created in situ during MBE growth

NASA Astrophysics Data System (ADS)

Voitsekhovskii, Alexander V.; Nesmelov, Sergey N.; Dzyadukh, Stanislav M.; Varavin, Vasily S.; Dvoretsky, Sergey A.; Mikhailov, Nikolay N.; Yakushev, Maksim V.; Sidorov, Georgy Yu.

2017-11-01

Heterostructures based on n-Hg1-xCdxTe (x = 0.23-0.40) with near-surface graded-gap layers were grown by molecular beam epitaxy on Si (013) substrates. At 77 K, the admittance of the In/Al2O3/Hg1-xCdxTe metal-insulator-semiconductor (MIS) structures with grown in situ CdTe intermediate layer and without such a layer was investigated. It has been established that MIS structures of In/Al2O3/Hg1-xCdxTe with an interlayer of in situ grown CdTe are characterized by the electrical strength of the dielectric and the qualitative interface. The hysteresis of the capacitive characteristics is practically absent within a small range of variation in the bias voltage. The density of fast surface states at the minimum does not exceed 2.2 × 1010 eV-1 cm-2. MIS structures of In/Al2O3/Hg1-xCdxTe without an intermediate layer of CdTe have significantly higher densities of fast and slow surface states, as well as lower values of the differential resistance of the space-charge region in the regime of strong inversion.

Communication: Microphase equilibrium and assembly dynamics.

PubMed

Zhuang, Yuan; Charbonneau, Patrick

2017-09-07

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

Novel Inhibitor Cystine Knot Peptides from Momordica charantia

PubMed Central

Clark, Richard J.; Tang, Jun; Zeng, Guang-Zhi; Franco, Octavio L.; Cantacessi, Cinzia; Craik, David J.; Daly, Norelle L.; Tan, Ning-Hua

2013-01-01

Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III), were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK) motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature. PMID:24116036

Theoretical study of bismuth-doped cadmium telluride

NASA Astrophysics Data System (ADS)

Menendez-Proupin, E.; Rios-Gonzalez, J. A.; Pena, J. L.

Cadmium telluride heavily doped with bismuth has been proposed as an absorber with an intermediate band for solar cells. Increase in the photocurrent has been shown recently, although the overall cell efficiency has not improved. In this work, we study the electronic structure and the formation energies of the defects associated to bismuth impurities. We have performed electronic structure calculations within generalized density functional theory, using the exchange-correlation functional HSE(w) , where the range-separation parameter w has been tuned to reproduce the CdTe bandgap. Improving upon previous reports, we have included the spin-orbit interaction, which modifies the structure of the valence band and the energy levels of bismuth. We have found that interstitial Bi (Bii) tends to occupy Cd vacancies, cadmium substitution (BiCd) creates single donor level, while tellurium substitution (BiTe) is a shallow single acceptor. We investigate the interaction between these point defects and how can they be combined to create a partially filled intermediate band. Supported by FONDECYT Grant 1130437, CONACYT-SENER SUSTENTABILIDAD ENERGETICA/project CeMIE-Sol PY-207450/25 and PY-207450/26. JARG acknowledges CONACYT fellowship for research visit. Powered@NLHPC (ECM-02).

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.

PubMed

Ma, Buyong; Nussinov, Ruth

2006-05-15

The structure and stabilities of the intermediates affect protein folding as well as misfolding and amyloid formation. By applying Kramer's theory of barrier crossing and a Morse-function-like energy landscape, we show that intermediates with medium stability dramatically increase the rate of amyloid formation; on the other hand, very stable and very unstable intermediates sharply decrease amyloid formation. Remarkably, extensive molecular dynamics simulations and conformational energy landscape analysis of Abeta25-35 and its N27Q mutant corroborate the mathematical description. Both experimental and current simulation results indicate that the core of the amyloid structure of Abeta25-35 formed from residues 28-35. A single mutation of N27Q of Abeta25-35 makes the Abeta25-35 N27Q amyloid-free. Energy landscape calculations show that Abeta25-35 has extended intermediates with medium stability that are prone to form amyloids, whereas the extended intermediates for Abeta25-35 N27Q split into stable and very unstable species that are not disposed to form amyloids. The results explain the contribution of both alpha-helical and beta-strand intermediates to amyloid formation. The results also indicate that the structure and stability of the intermediates, as well as of the native folded and the amyloid states can be targeted in drug design. One conceivable approach is to stabilize the intermediates to deter amyloid formation.

Hierarchical personality traits and the distinction between unipolar and bipolar disorders.

PubMed

Quilty, Lena C; Pelletier, Marianne; Deyoung, Colin G; Michael Bagby, R

2013-05-01

The association between personality and psychopathology can provide an insight into the structure of mental disorders and the shared etiology and pathophysiology underlying diagnoses with overlapping symptomatology. The majority of personality-psychopathology research pertinent to the mood disorders has focused upon traits at the higher-order levels of the personality hierarchy, rather than those at intermediate or lower levels. The purpose of the current investigation was to investigate whether unipolar and bipolar mood disorders, and the severity of depressive and manic symptoms, show differential associations with traits at multiple levels of the personality hierarchy. Participants (N=275; 63% women; mean age 42.95 years) with depressive disorders (n=139) and bipolar disorders (n=136), as assessed by the Structured Clinical Interview for DSM-IV, Axis I Disorders, Patient Version (SCID-I/P; First et al., 1995), completed the Hamilton Depression Rating Scale, Young Mania Scale, Revised NEO Personality Inventory and Big Five Aspect Scales. Results support the hypothesis that lower levels of the personality hierarchy provide additional differentiation of affective pathology. As compared to the widespread association of depressive symptoms with traits across the personality hierarchy, manic symptoms demonstrated more specific associations with traits at lower levels of the personality hierarchy. Patients with severe mania were excluded, thus the full range of mania is not represented in the current sample. These results support the use of lower-order personality traits to discriminate between unipolar versus bipolar mood disorder, and are consistent with changes proposed to the psychiatric nosology to increase diagnostic precision. Copyright © 2012 Elsevier B.V. All rights reserved.

The dichotomy between strong and ultra-weak magnetic fields among intermediate-mass stars

NASA Astrophysics Data System (ADS)

Lignières, François; Petit, Pascal; Aurière, Michel; Wade, Gregg A.; Böhm, Torsten

2014-08-01

Until recently, the detection of magnetic fields at the surface of intermediate-mass main-sequence stars has been limited to Ap/Bp stars, a class of chemically peculiar stars. This class represents no more than 5-10% of the stars in this mass range. This small fraction is not explained by the fossil field paradigm that describes the Ap/Bp type magnetism as a remnant of an early phase of the star-life. Also, the limitation of the field measurements to a small and special group of stars is obviously a problem to study the effect of the magnetic fields on the stellar evolution of a typical intermediate-mass star. Thanks to the improved sensitivity of a new generation of spectropolarimeters, a lower bound to the magnetic fields of Ap/Bp stars, a two orders of magnitude desert in the longitudinal magnetic field and a new type of sub-gauss magnetism first discovered on Vega have been identified. These advances provide new clues to understand the origin of intermediate-mass magnetism as well as its influence on stellar evolution. In particular, a scenario has been proposed whereby the magnetic dichotomy between Ap/Bp and Vega-like magnetism originate from the bifurcation between stable and unstable large scale magnetic configurations in differentially rotating stars. In this paper, we review these recent observational findings and discuss this scenario.

High-energy X-ray powder diffraction and atomic-pair distribution-function studies of charged/discharged structures in carbon-hybridized Li2MnSiO4 nanoparticles as a cathode material for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Moriya, Maki; Miyahara, Masahiko; Hokazono, Mana; Sasaki, Hirokazu; Nemoto, Atsushi; Katayama, Shingo; Akimoto, Yuji; Hirano, Shin-ichi; Ren, Yang

2014-10-01

The stable cycling performance with a high discharge capacity of ∼190 mAh g-1 in a carbon-hybridized Li2MnSiO4 nanostructured powder has prompted an experimental investigation of the charged/discharged structures using synchrotron-based and laboratory-based X-rays and atomic-pair distribution-function (PDF) analyses. A novel method of in-situ spray pyrolysis of a precursor solution with glucose as a carbon source enabled the successful synthesis of the carbon-hybridized Li2MnSiO4 nanoparticles. The XRD patters of the discharged (lithiated) samples exhibit a long-range ordered structure characteristic of the (β) Li2MnSiO4 crystalline phase (space group Pmn21) which dissipates in the charged (delithiated) samples. However, upon discharging the long-range ordered structure recovers in each cycle. The disordered structure, according to the PDF analysis, is mainly due to local distortions of the MnO4 tetrahedra which show a mean Mn-O nearest neighbor distance shorter than that of the long-range ordered phase. These results corroborate the notion of the smaller Mn3+/Mn4+ ionic radii in the Li extracted phase versus the larger Mn2+ ionic radius in Li inserted phase. Thus Li extraction/insertion drives the fluctuation between the disordered and the long-range ordered structures.

Characterization of ultrafast laser-ablation plasma plumes at various Ar ambient pressures

DOE PAGES

Diwakar, P. K.; Harilal, S. S.; Phillips, M. C.; ...

2015-07-30

Expansion dynamics and internal plume structures of fs laser ablated brass plasma in Ar at various pressure levels ranging from vacuum to atmospheric were studied using multitude of diagnostic tools including time resolved and time integrated 2-dimensional imaging, optical time of flight measurements and visible emission spectroscopy. Temporal evolution of excited Cu and Zn species in the plume were imaged using band pass interference filters and compared its hydrodynamic expansion features with spectrally integrated images of the plume. 2D imaging coupled with monochromatic line selection showed several interesting features at various pressure levels which include velocity differences among the plumemore » species, emission intensity distribution, plasma temperature, electron density etc. Plume confinement, enhanced signal intensity, and dual peak structures in time-of-flight profiles were observed at intermediate pressure range of ~10 Torr. Optimum signal to background ratio was also observed in this pressure range. As a result, possible mechanisms for observed changes in plume shape, optical emission intensity and dual peak structures in time-of-flight profiles were discussed.« less

Synthesis and magnetic properties of the high-pressure scheelite-type GdCrO{sub 4} polymorph

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dos santos-Garcia, A.J., E-mail: adossant@quim.ucm.es; Climent-Pascual, E.; Gallardo-Amores, J.M.

The scheelite-type polymorph of GdCrO{sub 4} has been obtained from the corresponding zircon-type compound under high pressure and temperature conditions, namely 4 GPa and 803 K. The crystal structure has been determined by X-ray powder diffraction. This GdCrO{sub 4} scheelite crystallizes in a tetragonal symmetry with space group I4{sub 1}/a (No. 88, Z=4), a=5.0501(1) A, c=11.4533(2) A and V=292.099(7) A{sup 3}. The thermal decomposition leads to the formation of the zircon-polymorph as intermediate phase at 773 K to end in the corresponding GdCrO{sub 3} distorted perovskite-structure at higher temperatures. Magnetic susceptibility and magnetization measurements suggest the existence of long-range antiferromagneticmore » interactions which have been also confirmed from specific heat measurements. Neutron powder diffraction data reveal the simultaneous antiferromagnetic Gd{sup 3+} and Cr{sup 5+} ordering in the scheelite-type GdCrO{sub 4} with a T{sub N}{approx}20 K. The magnetic propagation vector was found to be k=(0 0 0). Combined with group theory analysis, the best neutron powder diffraction fit was obtained with a collinear antiferromagnetic coupling in which the m{sub Cr{sup 5}{sup +}} and m{sub Gd{sup 3}{sup +}} magnetic moments are confined in the tetragonal basal plane according to the mixed representation {Gamma}{sub 6} Circled-Plus {Gamma}{sub 8}. Thermal decomposition of the GdCrO{sub 4} high pressure polymorph, from the scheelite-type through the zircon-type structure as intermediate to end in the GdCrO{sub 3} perovskite. Highlights: Black-Right-Pointing-Pointer New high pressure GdCrO{sub 4} polymorph crystallizing in the scheelite type structure. Black-Right-Pointing-Pointer It is an antiferromagnet with a metamagnetic transition at low magnetic fields. Black-Right-Pointing-Pointer We have determined its magnetic structure from powder neutron diffraction data. Black-Right-Pointing-Pointer Otherwise, the room pressure zircon-polymorph is a ferromagnet. Black-Right-Pointing-Pointer The paper will be a great contribution in the study of 3d-4f magnetic interactions.« less

Out-of-equilibrium dynamics of photoexcited spin-state concentration waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marino, Andrea; Buron-Le Cointe, M.; Lorenc, M.

2015-01-28

The spin crossover compound [Fe IIH 2L 2-Me][PF 6]2 presents a two-step phase transition. In the intermediate phase, a spin state concentration wave (SSCW) appears resulting from a symmetry breaking (cell doubling) associated with a long-range order of alternating high and low spin molecular states. Lastly, by combining time-resolved optical and X-ray diffraction measurements on a single crystal, we study how such a system responds to femtosecond laser excitation and we follow in real time the erasing and rewriting of the SSCW

Relocation of Intermediate-depth Seismicity in the Relic Alboran Slab: Clustering and Relationship to Tearing and Dehydration Embrittlement.

NASA Astrophysics Data System (ADS)

Sun, M.; Bezada, M.

2017-12-01

Intermediate-depth seismicity outside active subduction zones is rare. However, there is a well-known occurrence of such events in a N-S elongated volume between Spain and Morocco, within what most researchers consider to be the relic Alboran slab. Partial subduction of, and tearing from the adjoining continental lithosphere have been suggested in this area. We investigate whether dehydration embrittlement or shear instability is more consistent with the Alboran intermediate depth seismicity by considering their location relative to the expected thermal structure and expected areas of high strain rate associated with thinning or tearing of the slab. We use a dense temporary seismograph deployment in Spain and Morocco to relocate 65 intermediate-depth events occurring between 2010 and 2013 in this region. The relocation procedure is realized by a grid-search approach that minimizes the normalized misfit between the picked times and travel times calculated using a regional 3D velocity model. Results indicate that, compared with catalog results, hypocenters after relocation are more concentrated in space; they tend to shift southward and eastward while no systematic shift in depth is observed. Relocated hypocenters concentrate at a depth range between 50-100 km and along a narrow longitude range around 4.5W. Investigation of the earthquake density distribution indicates these earthquakes concentrate into several clusters. One such cluster sits above the spain-arm of the Alboran slab and beneath the Spain continental lithosphere, indicating that it is likely associated to the thinning process of the Alboran slab. The other four clusters all lie within the interior of the slab. Interestingly, two of them are near the middle of the subducted lithosphere and the other two lie near its base. This observation seems at odds with expectations based on the two leading hypotheses for enabling brittle failure at intermediate depths.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

A Temporospatial Map That Defines Specific Steps at Which Critical Surfaces in the Gag MA and CA Domains Act during Immature HIV-1 Capsid Assembly in Cells

PubMed Central

Robinson, Bridget A.; Reed, Jonathan C.; Geary, Clair D.; Swain, J. Victor

2014-01-01

ABSTRACT During HIV-1 assembly, Gag polypeptides target to the plasma membrane, where they multimerize to form immature capsids that undergo budding and maturation. Previous mutational analyses identified residues within the Gag matrix (MA) and capsid (CA) domains that are required for immature capsid assembly, and structural studies showed that these residues are clustered on four exposed surfaces in Gag. Exactly when and where the three critical surfaces in CA function during assembly are not known. Here, we analyzed how mutations in these four critical surfaces affect the formation and stability of assembly intermediates in cells expressing the HIV-1 provirus. The resulting temporospatial map reveals that critical MA residues act during membrane targeting, residues in the C-terminal CA subdomain (CA-CTD) dimer interface are needed for the stability of the first membrane-bound assembly intermediate, CA-CTD base residues are necessary for progression past the first membrane-bound intermediate, and residues in the N-terminal CA subdomain (CA-NTD) stabilize the last membrane-bound intermediate. Importantly, we found that all four critical surfaces act while Gag is associated with the cellular facilitators of assembly ABCE1 and DDX6. When correlated with existing structural data, our findings suggest the following model: Gag dimerizes via the CA-CTD dimer interface just before or during membrane targeting, individual CA-CTD hexamers form soon after membrane targeting, and the CA-NTD hexameric lattice forms just prior to capsid release. This model adds an important new dimension to current structural models by proposing the potential order in which key contacts within the immature capsid lattice are made during assembly in cells. IMPORTANCE While much is known about the structure of the completed HIV-1 immature capsid and domains of its component Gag proteins, less is known about the sequence of events leading to formation of the HIV-1 immature capsid. Here we used biochemical and ultrastructural analyses to generate a temporospatial map showing the precise order in which four critical surfaces in Gag act during immature capsid formation in provirus-expressing cells. Because three of these surfaces make important contacts in the hexameric lattices that are found in the completed immature capsid, these data allow us to propose a model for the sequence of events leading to formation of the hexameric lattices. By providing a dynamic view of when and where critical Gag-Gag contacts form during the assembly process and how those contacts function in the nascent capsid, our study provides novel insights into how an immature capsid is built in infected cells. PMID:24623418

Rates of manganese oxidation in aqueous systems

USGS Publications Warehouse

Hem, J.D.

1981-01-01

The rate of crystal growth of Mn3O4 (hausmannite) and ??MnOOH (feitknechtite) in aerated aqueous manganous perchlorate systems, near 0.01 M in total manganese, was determined at pH levels ranging from 7.00 to 9.00 and at temperatures from 0.5 to 37.4??C. The process is autocatalytic, but becomes psuedo first-order in dissolved Mn2+ activity when the amount of precipitate surface is large compared to the amount of unreacted manganese. Reaction rates determined by titrations using an automated pH-stat were fitted to an equation for precipitate growth. The rates are proportional to surface area of oxide and degree of supersaturation with respect to Mn2+. The oxide obtained at the higher temperature was Mn3O4, but at 0.5?? C only ??MnOOH was formed. At intermediate temperatures, mixtures of these solids were formed. The rate of precipitation of hausmannite is strongly influenced by temperature, and that of feitknechtite much less so. The difference in activation energy may be related to differences in crystal structure of the oxides and the geometry of polymeric hydroxy ion precursors. ?? 1981.

Amorphization and Directional Crystallization of Metals Confined in Carbon Nanotubes Investigated by in Situ Transmission Electron Microscopy.

PubMed

Tang, Dai-Ming; Ren, Cui-Lan; Lv, Ruitao; Yu, Wan-Jing; Hou, Peng-Xiang; Wang, Ming-Sheng; Wei, Xianlong; Xu, Zhi; Kawamoto, Naoyuki; Bando, Yoshio; Mitome, Masanori; Liu, Chang; Cheng, Hui-Ming; Golberg, Dmitri

2015-08-12

The hollow core of a carbon nanotube (CNT) provides a unique opportunity to explore the physics, chemistry, biology, and metallurgy of different materials confined in such nanospace. Here, we investigate the nonequilibrium metallurgical processes taking place inside CNTs by in situ transmission electron microscopy using CNTs as nanoscale resistively heated crucibles having encapsulated metal nanowires/crystals in their channels. Because of nanometer size of the system and intimate contact between the CNTs and confined metals, an efficient heat transfer and high cooling rates (∼10(13) K/s) were achieved as a result of a flash bias pulse followed by system natural quenching, leading to the formation of disordered amorphous-like structures in iron, cobalt, and gold. An intermediate state between crystalline and amorphous phases was discovered, revealing a memory effect of local short-to-medium range order during these phase transitions. Furthermore, subsequent directional crystallization of an amorphous iron nanowire formed by this method was realized under controlled Joule heating. High-density crystalline defects were generated during crystallization due to a confinement effect from the CNT and severe plastic deformation involved.

TiO2-SiO2 Coatings with a Low Content of AuNPs for Producing Self-Cleaning Building Materials

PubMed Central

Gil, M. L. Almoraima; Mosquera, María J.

2018-01-01

The high pollution levels in our cities are producing a significant increase of dust on buildings. An application of photoactive coatings on building materials can produce buildings with self-cleaning surfaces. In this study, we have developed a simple sol-gel route for producing Au-TiO2/SiO2 photocatalysts with application on buildings. The gold nanoparticles (AuNPs) improved the TiO2 photoactivity under solar radiation because they promoted absorption in the visible range. We varied the content of AuNPs in the sols under study, in order to investigate their effect on self-cleaning properties. The sols obtained were sprayed on a common building stone, producing coatings which adhere firmly to the stone and preserve their aesthetic qualities. We studied the decolourization efficiency of the photocatalysts under study against methylene blue and against soot (a real staining agent for buildings). Finally, we established that the coating with an intermediate Au content presented the best self-cleaning performance, due to the role played by its structure and texture on its photoactivity. PMID:29558437

NMR Characterization of Self-Association Domains Promoted by Interactions with LC8 Hub Protein

PubMed Central

Barbar, Elisar; Nyarko, Afua

2014-01-01

Most proteins in interaction networks have a small number of partners, while a few, called hubs, participate in a large number of interactions and play a central role in cell homeostasis. One highly conserved hub is a protein called LC8 that was originally identified as an essential component of the multi-subunit complex dynein but later shown to be also critical in multiple protein complexes in diverse systems. What is intriguing about this hub protein is that it does not passively bind its various partners but emerging evidence suggests that LC8 acts as a dimerization engine that promotes self-association and/or higher order organization of its primarily disordered monomeric partners. This structural organization process does not require ATP but is triggered by long-range allosteric regulation initiated by LC8 binding a pair of disordered chains forming a bivalent or polybivalent scaffold. This review focuses on the role of LC8 in promoting self-association of two of its binding partners, a dynein intermediate chain and a non dynein protein called Swallow. PMID:24757501

Computer simulation results for bounds on the effective conductivity of composite media

NASA Astrophysics Data System (ADS)

Smith, P. A.; Torquato, S.

1989-02-01

This paper studies the determination of third- and fourth-order bounds on the effective conductivity σe of a composite material composed of aligned, infinitely long, identical, partially penetrable, circular cylinders of conductivity σ2 randomly distributed throughout a matrix of conductivity σ1. Both bounds involve the microstructural parameter ζ2 which is a multifold integral that depends upon S3, the three-point probability function of the composite. This key integral ζ2 is computed (for the possible range of cylinder volume fraction φ2) using a Monte Carlo simulation technique for the penetrable-concentric-shell model in which cylinders are distributed with an arbitrary degree of impenetrability λ, 0≤λ≤1. Results for the limiting cases λ=0 (``fully penetrable'' or randomly centered cylinders) and λ=1 (``totally impenetrable'' cylinders) compare very favorably with theoretical predictions made by Torquato and Beasley [Int. J. Eng. Sci. 24, 415 (1986)] and by Torquato and Lado [Proc. R. Soc. London Ser. A 417, 59 (1988)], respectively. Results are also reported for intermediate values of λ: cases which heretofore have not been examined. For a wide range of α=σ2/σ1 (conductivity ratio) and φ2, the third-order bounds on σe significantly improve upon second-order bounds which just depend upon φ2. The fourth-order bounds are, in turn, narrower than the third-order bounds. Moreover, when the cylinders are highly conducting (α≫1), the fourth-order lower bound provides an excellent estimate of the effective conductivity for a wide range of volume fractions.

Similar local order in disordered fluorite and aperiodic pyrochlore structures

DOE PAGES

Shamblin, Jacob; Tracy, Cameron; Palomares, Raul; ...

2017-10-01

A major challenge to understanding the response of materials to extreme environments (e.g., nuclear fuels/waste forms and fusion materials) is to unravel the processes by which a material can incorporate atomic-scale disorder, and at the same time, remain crystalline. While it has long been known that all condensed matter, even liquids and glasses, possess short-range order, the relation between fully-ordered, disordered, and aperiodic structures over multiple length scales is not well understood. For example, when defects are introduced (via pressure or irradiation) into materials adopting the pyrochlore structure, these complex oxides either disorder over specific crystallographic sites, remaining crystalline, ormore » become aperiodic. Here we present neutron total scattering results characterizing the irradiation response of two pyrochlores, one that is known to disorder (Er2Sn2O7) and the other to amorphize (Dy2Sn2O7) under ion irradiation. The results demonstrate that in both cases, the local pyrochlore structure is transformed into similar short range configurations that are best fit by the orthorhombic weberite structure, even though the two compositions have distinctly different structures, aperiodic vs. disordered-crystalline, at longer length scales. Thus, a material's resistance to amorphization may not depend primarily on local defect formation energies, but rather on the structure's compatibility with meso-scale modulations of the local order in a way that maintains long-range periodicity.« less

Short range orders of an adsorbed layer: gold on the Si(111)7 × 7 surface

NASA Astrophysics Data System (ADS)

Takahashi, S.; Tanishiro, Y.; Takayanagi, K.

1991-02-01

Ordered phases of 5 × 2, 3× 3 and 6 × 6 structures formed by gold deposition on a Si(11)7 × 7 surface were observed by transmission electron diffraction (TED). Short-range orders of the 3× 3 phase of low and high coverages are analyzed from diffuse TED intensities. Phasons which displace the adsorption site by a at every translation of 6 a are found to be introduced in the 3× 3 structure of the saturation coverage. The phasons, which create 2 a correlation between gold clusters, prohibit formation of a completely ordered 3× 3 phase.

Local Structure and Short-Range Order in a NiCoCr Solid Solution Alloy

DOE PAGES

Zhang, F. X.; Zhao, Shijun; Jin, Ke; ...

2017-05-19

Multi-element solid solution alloys are intrinsically disordered on the atomic scale, and many of their advanced properties originate from the unique local structural characteristics. We measured the local structure of a NiCoCr solid solution alloy with X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) techniques. The atomic pair distribution function analysis (PDF) did not exhibit distinct structural distortion. But, EXAFS analysis suggested that the Cr atoms are favorably bonded with Ni and Co in the solid solution alloys. This short-range order (SRO) plays a role in the distinct low values of electrical and thermal conductivities in Ni-based solidmore » solution alloys when Cr is incorporated. Both the long-range and local structures of the NiCoCr alloy upon Ni ion irradiation were studied and an irradiation-induced enhancement of SRO was found.« less

Rain Characteristics and Large-Scale Environments of Precipitation Objects with Extreme Rain Volumes from TRMM Observations

NASA Technical Reports Server (NTRS)

Zhou, Yaping; Lau, William K M.; Liu, Chuntao

2013-01-01

This study adopts a "precipitation object" approach by using 14 years of Tropical Rainfall Measuring Mission (TRMM) Precipitation Feature (PF) and National Centers for Environmental Prediction (NCEP) reanalysis data to study rainfall structure and environmental factors associated with extreme heavy rain events. Characteristics of instantaneous extreme volumetric PFs are examined and compared to those of intermediate and small systems. It is found that instantaneous PFs exhibit a much wider scale range compared to the daily gridded precipitation accumulation range. The top 1% of the rainiest PFs contribute over 55% of total rainfall and have 2 orders of rain volume magnitude greater than those of the median PFs. We find a threshold near the top 10% beyond which the PFs grow exponentially into larger, deeper, and colder rain systems. NCEP reanalyses show that midlevel relative humidity and total precipitable water increase steadily with increasingly larger PFs, along with a rapid increase of 500 hPa upward vertical velocity beyond the top 10%. This provides the necessary moisture convergence to amplify and sustain the extreme events. The rapid increase in vertical motion is associated with the release of convective available potential energy (CAPE) in mature systems, as is evident in the increase in CAPE of PFs up to 10% and the subsequent dropoff. The study illustrates distinct stages in the development of an extreme rainfall event including: (1) a systematic buildup in large-scale temperature and moisture, (2) a rapid change in rain structure, (3) explosive growth of the PF size, and (4) a release of CAPE before the demise of the event.

Interplay between magnetic order at Mn and Tm sites alongside the structural distortion in multiferroic films of o -TmMn O3

NASA Astrophysics Data System (ADS)

Windsor, Y. W.; Ramakrishnan, M.; Rettig, L.; Alberca, A.; Bothschafter, E. M.; Staub, U.; Shimamoto, K.; Hu, Y.; Lippert, T.; Schneider, C. W.

2015-06-01

We employ resonant soft x-ray diffraction to individually study the magnetic ordering of the Mn and the Tm sublattices in single-crystalline films of orthorhombic (o -) TmMn O3 . The same magnetic ordering wave vector of (0 q 0 ) with q ≈0.46 is found for both ionic species, suggesting that the familiar antiferromagnetic order of the Mn ions induces a magnetic order on the Tm unpaired 4 f electrons. Indeed, intensity variations of magnetic reflections with temperature corroborate this scenario. Calculated magnetic fields at the Tm sites are used as a model magnetic structure for the Tm, which correctly predicts intensity variations at the Tm resonance upon azimuthal rotation of the sample. The model allows ruling out a b c -cycloid modulation of the Mn ions as the cause for the incommensurate ordering, as found in TbMn O3 . The structural distortion, which occurs in the ferroelectric phase below TC, was followed through nonresonant diffraction of structural reflections forbidden by the high-temperature crystal symmetry. The (0 q 0 ) magnetic reflection appears at the Mn resonance well above TC, indicating that this reflection is sensitive also to the intermediate sinusoidal magnetic phase. The model presented suggests that the Tm 4 f electrons are polarized well above the ferroelectric transition and are possibly not affected by the transition at TC. The successful description of the induced order observed at the Tm resonance is a promising example for future element-selective studies in which "spectator" ions may allow access to previously unobtainable information about other constituent ions.

Low-loss waveguides for THz guidance and devices

NASA Astrophysics Data System (ADS)

Rahman, B. M. A.; Themistos, C.; Tanvir, H.; Uthman, M.; Quadir, A.; Markides, C.

2013-03-01

The terahertz (THz) region occupies a large portion of the electromagnetic spectrum, located between the microwave and optical frequencies and normally is defined as the band ranging from 0.1 to 10 THz. In recent years, this intermediate THz radiation band has attracted considerable interest, because it offers significant scientific and technological potential for applications in many fields, such as sensing [1], imaging [2] and spectroscopy [3]. However, waveguiding in this intermediate spectral region is a major challenge and strong dielectric and conductive losses in the terahertz frequency range have been a major problem for waveguiding. The conventional guiding structures exemplified by microstrips, coplanar striplines and coplanar waveguides [4] are highly lossy and dispersive. However, so far the most promising dielectric waveguides have been the use of photonic crystal fibers at terahertz frequencies [5, 6] and metal coated guides [7] at terahertz frequencies. In this paper, various types of practical dielectric and metal coated waveguides are evaluated and design optimization of Quantum Cascade Lasers, MMI-based power splitters and narrow-band filters are presented, by using full-vectorial finite element method [8].

Improved conductivity of indium-tin-oxide film through the introduction of intermediate layer

NASA Astrophysics Data System (ADS)

Ng, S. W.; Yam, F. K.; Beh, K. P.; Tneh, S. S.; Hassan, Z.

2016-09-01

A thin intermediate layer (Ag, AuSn, In, Ni, Sn, SiO2) was individually deposited on glass substrates prior to the deposition of indium-tin-oxide (ITO) thin film by radio-frequency (RF) magnetron sputtering employing ITO target (composition ratio of In2O3:SnO2 = 9:1). The structural, optical and electrical properties were investigated to compare the ITO thin film with and without an intermediate layer. The preferential orientation of all ITO films was along (222) plane. Although all thin films were polycrystalline, the presence of intermediate layer promoted the overall crystallinity. The sheet resistance and resistivity of the ITO film were reduced from ∼68 Ω/□ to ∼29-45 Ω/□, and 16.2 × 10-4 Ω cm up to 7.58 × 10-4 Ω cm, respectively, by inserting a thin metal layer underneath the ITO film, and it is dependent on the degree of crystallization. The optical transmittance in the visible region varies from 40 to 88% for different samples. Based on the evaluation from Tauc plot, the optical band gap falls in the range of 4.02-4.12 eV. Physical film thickness was compared with that evaluated by optical measurement in the visible range and the physical thickness was found to be smaller. Similarly, the carrier concentration/scattering time from Hall effect measurement were also compared with that from optical measurement in the infrared region. Haacke's figure of merit (FOM) was employed to assess the quality of the ITO films, and the highest FOM is credited to ITO/In up to ∼8 × 10-3 Ω-1 in the visible light region.

Contact area of rough spheres: Large scale simulations and simple scaling laws

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pastewka, Lars, E-mail: lars.pastewka@kit.edu; Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218; Robbins, Mark O., E-mail: mr@pha.jhu.edu

2016-05-30

We use molecular simulations to study the nonadhesive and adhesive atomic-scale contact of rough spheres with radii ranging from nanometers to micrometers over more than ten orders of magnitude in applied normal load. At the lowest loads, the interfacial mechanics is governed by the contact mechanics of the first asperity that touches. The dependence of contact area on normal force becomes linear at intermediate loads and crosses over to Hertzian at the largest loads. By combining theories for the limiting cases of nominally flat rough surfaces and smooth spheres, we provide parameter-free analytical expressions for contact area over the wholemore » range of loads. Our results establish a range of validity for common approximations that neglect curvature or roughness in modeling objects on scales from atomic force microscope tips to ball bearings.« less

Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis

NASA Astrophysics Data System (ADS)

Booth, David R.; Sunde, Margaret; Bellotti, Vittorio; Robinson, Carol V.; Hutchinson, Winston L.; Fraser, Paul E.; Hawkins, Philip N.; Dobson, Christopher M.; Radford, Sheena E.; Blake, Colin C. F.; Pepys, Mark B.

1997-02-01

Tissue deposition of soluble proteins as amyloid fibrils underlies a range of fatal diseases. The two naturally occurring human lysozyme variants are both amyloidogenic, and are shown here to be unstable. They aggregate to form amyloid fibrils with transformation of the mainly helical native fold, observed in crystal structures, to the amyloid fibril cross-β fold. Biophysical studies suggest that partly folded intermediates are involved in fibrillogenesis, and this may be relevant to amyloidosis generally.

Waveform inversion for D″ structure beneath northern Asia using Hi-net tiltmeter data

NASA Astrophysics Data System (ADS)

Kawai, Kenji; Sekine, Shutaro; Fuji, Nobuaki; Geller, Robert J.

2009-10-01

We invert shear-wave waveform data for the radial variation of (isotropic) shear-velocity in D″ beneath Northern Asia. We reduce source and receiver effects by using data for intermediate and deep events beneath Italy and Japan recorded respectively at stations in East Asia and Europe. Relative to PREM, we find a significantly higher S-wave velocity in the depth range from 150 to 300 km above the core-mantle boundary (CMB) and a slightly lower S-wave velocity in the depth range 0-150 km above the CMB. As our previous studies of D″ structure beneath Central America and the Arctic obtained similar S-wave velocity models, we suggest that this pattern of vertical dependence of shear wave velocity in D″ may be a general phenomenon, at least in relatively cold regions.

Structure of short-range-ordered iron(III)-precipitates formed by iron(II) oxidation in water containing phosphate, silicate, and calcium

NASA Astrophysics Data System (ADS)

Voegelin, A.; Frommer, J.; Vantelon, D.; Kaegi, R.; Hug, S. J.

2009-04-01

The oxidation of Fe(II) in water leads to the formation of Fe(III)-precipitates that strongly affect the fate of nutrients and contaminants in natural and engineered systems. Examples include the cycling of As in rice fields irrigated with As-rich groundwater or the treatment of drinking water for As removal. Knowledge of the types of Fe(III)-precipitates forming in such systems is essential for the quantitative modeling of nutrient and contaminant dynamics and for the optimization of water purification techniques on the basis of a mechanistic understanding of the relevant biogeochemical processes. In this study, we investigated the local coordination of Fe, P, and Ca in Fe(III)-precipitates formed by aeration of synthetic Fe(II)-containing groundwater with variable composition (pH 7, 2-30 mg/L Fe(II), 2-20 mg/L phosphate-P, 2-20 mg/L silicate-Si, 8 mM Na-bicarbonate or 2.5 mM Ca-&1.5 mM Mg-bicarbonate). After 4 hours of oxidation, Fe(III)-precipitates were collected on 0.2 µm nylon filters and dried. The precipitates were analyzed by Fe K-edge EXAFS (XAS beamline, ANKA, Germany) and by P and Ca K-edge XANES spectroscopy (LUCIA beamline, SLS, Switzerland). The Fe K-edge EXAFS spectra indicated that local Fe coordination in the precipitates systematically shifted with water composition. As long as water contained P, mainly short-range-ordered Fe(III)-phosphate formed (with molar P/Fe ~0.5). In the absence of P, Fe(III) precipitated as hydrous ferric oxide at high Si/Fe>0.5, as ferrihydrite at intermediate Si/Fe, and mainly as lepidocrocite at Si/Fe<0.2. Analysis of the EXAFS by shell-fitting indicated that Fe(III)-phosphates mainly contained mono- or oligomeric (edge- or corner-sharing) Fe and that the linkage between neighboring Fe(III)-octahedra changed from predominantly edge-sharing in Si-rich hydrous ferric oxide to edge- and corner-sharing in ferrihydrite. Electron microscopic data showed that changes in local precipitate structure were systematically reflected in particle morphology and SAED patterns. The P K-edge XANES spectra revealed that phosphate was bound to both Fe as well as Ca (if present). The Ca K-edge XANES spectra showed that the mode of Ca uptake by the Fe(III)-precipitates shifted from mainly adsorption at high Fe/P to coprecipitation at low Fe/P ratio. Despite oversaturation, neither calcite nor hydroxyapatite formed to a significant extent. The results from this study indicated that, depending on water composition, Fe(II) oxidation in natural waters leads to different types of short-range-ordered Fe(III)-phases. Since these phases are expected to differ in their effect on contaminant and nutrient dynamics, their specific physical and chemical properties warrant further research. Methodologically, this work demonstrated the usefulness of investigating the local structure of short-range-ordered precipitates along compositional gradients and by combining the element-selective information from different X-ray absorption edges.

O 2 Activation by Non-Heme Iron Enzymes

DOE PAGES

Solomon, Edward I.; Goudarzi, Serra; Sutherlin, Kyle D.

2016-10-28

The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O 2 activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods have now been developed that provide significant insight into the correlation of structure with function. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O 2 activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O 2 activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin Fe III-OOHmore » non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin Fe IV=O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Lastly, for several subclasses of non-heme Fe enzymes, substrate binding to the Fe II site leads to the one electron reductive activation of O 2 to an Fe III-superoxide capable of H-atom abstraction and electrophilic attack.« less

O 2 Activation by Non-Heme Iron Enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solomon, Edward I.; Goudarzi, Serra; Sutherlin, Kyle D.

The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O 2 activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods have now been developed that provide significant insight into the correlation of structure with function. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O 2 activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O 2 activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin Fe III-OOHmore » non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin Fe IV=O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Lastly, for several subclasses of non-heme Fe enzymes, substrate binding to the Fe II site leads to the one electron reductive activation of O 2 to an Fe III-superoxide capable of H-atom abstraction and electrophilic attack.« less

Tailoring vibration mode shapes using topology optimization and functionally graded material concepts

NASA Astrophysics Data System (ADS)

Montealegre Rubio, Wilfredo; Paulino, Glaucio H.; Nelli Silva, Emilio Carlos

2011-02-01

Tailoring specified vibration modes is a requirement for designing piezoelectric devices aimed at dynamic-type applications. A technique for designing the shape of specified vibration modes is the topology optimization method (TOM) which finds an optimum material distribution inside a design domain to obtain a structure that vibrates according to specified eigenfrequencies and eigenmodes. Nevertheless, when the TOM is applied to dynamic problems, the well-known grayscale or intermediate material problem arises which can invalidate the post-processing of the optimal result. Thus, a more natural way for solving dynamic problems using TOM is to allow intermediate material values. This idea leads to the functionally graded material (FGM) concept. In fact, FGMs are materials whose properties and microstructure continuously change along a specific direction. Therefore, in this paper, an approach is presented for tailoring user-defined vibration modes, by applying the TOM and FGM concepts to design functionally graded piezoelectric transducers (FGPT) and non-piezoelectric structures (functionally graded structures—FGS) in order to achieve maximum and/or minimum vibration amplitudes at certain points of the structure, by simultaneously finding the topology and material gradation function. The optimization problem is solved by using sequential linear programming. Two-dimensional results are presented to illustrate the method.

Highly Stable Hierarchical Flower-like β-In2S3 Assembled from 2D Nanosheets with high Adsorption-Photodecolorization Activities for the Treatment of Wastewater

NASA Astrophysics Data System (ADS)

Cheng, Yang; Niu, Helin; Chen, Jingshuai; Song, Jiming; Mao, Changjie; Zhang, Shengyi; Chen, Changle; Gao, Yuanhao

2017-05-01

The hierarchical flower-like β-In2S3 catalyst assembled from 2D nanosheets was prepared using an organic-component depletion method utilizing inorganic-organic hybrids indium diethyldithiocarbamate (In-DDTC) as a single-source precursor. The crystallization, morphology and composition of the as-synthesized β-In2S3 were characterized by XRD, SEM, TEM, EDS and XPS, respectively. The β-In2S3 possessed high specific surface area of 134.1 m2 g-1, adsorption capacity of 195.5 mg g-1 for methylene blue, and extreme photodecolorization speed under visible light irradiation for the complete removal of methyl orange (MO) dye within 15 min and tetracycline within 60 min. Although methyl orange concentration decreased quickly, the total organic carbon (TOC) decreased slowly. UV-vis and mass spectrometry (MS) were applied to analyze the intermediates coming from the photodecolorization of MO. In order to estimate the roles of active species during the decolorization of MO, trapping experiments were conducted to determine the main active species during the decolorization process. The results indicated that . O2 - radicals and e-1 were the key intermediates. This enhanced activity was attributed to its unique structures assembled from 2D nanosheets with thickness of ca. 5-7 nm, leading to high specific surface area, wide range of pore size distribution and great efficiency in absorbing light and electron/hole separation. The hierarchical flower-like β-In2S3 demonstrated great advantages in the treatment of various wastewater pollutants including textile dyes and antibiotics.

Thermal algebraic-decay charge liquid driven by competing short-range Coulomb repulsion

NASA Astrophysics Data System (ADS)

Kaneko, Ryui; Nonomura, Yoshihiko; Kohno, Masanori

2018-05-01

We explore the possibility of a Berezinskii-Kosterlitz-Thouless-like critical phase for the charge degrees of freedom in the intermediate-temperature regime between the charge-ordered and disordered phases in two-dimensional systems with competing short-range Coulomb repulsion. As the simplest example, we investigate the extended Hubbard model with on-site and nearest-neighbor Coulomb interactions on a triangular lattice at half filling in the atomic limit by using a classical Monte Carlo method, and find a critical phase, characterized by algebraic decay of the charge correlation function, belonging to the universality class of the two-dimensional XY model with a Z6 anisotropy. Based on the results, we discuss possible conditions for the critical phase in materials.

Initial Assessment of U.S. Refineries for Purposes of Potential Bio-Based Oil Insertions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Charles J.; Jones, Susanne B.; Padmaperuma, Asanga B.

2013-04-01

In order to meet U.S. biofuel objectives over the coming decade the conversion of a broad range of biomass feedstocks, using diverse processing options, will be required. Further, the production of both gasoline and diesel biofuels will employ biomass conversion methods that produce wide boiling range intermediate oils requiring treatment similar to conventional refining processes (i.e. fluid catalytic cracking, hydrocracking, and hydrotreating). As such, it is widely recognized that leveraging existing U.S. petroleum refining infrastructure is key to reducing overall capital demands. This study examines how existing U.S. refining location, capacities and conversion capabilities match in geography and processing capabilitiesmore » with the needs projected from anticipated biofuels production.« less

Reaction of iminopropadienones with amines--formation of zwitterionic intermediates, ketenes, and ketenimines.

PubMed

Veedu, Rakesh Naduvile; Kokas, Okanya J; Couturier-Tamburelli, Isabelle; Koch, Rainer; Aycard, Jean-Pierre; Borget, Fabien; Wentrup, Curt

2008-10-09

Five aryliminopropadienones 4a- d have been synthesized by flash vacuum thermolysis (FVT) by using two different precursors in each case. These compounds were deposited at 50 K at a pressure of ca. 10(-6) mbar together with three different nucleophiles, namely, trimethylamine (TMA), dimethylamine (DMA), and diethylamine (DEA), in order to study their reactions as neat solids during warm-up by FTIR spectroscopy. The reaction with TMA showed that a zwitterionic species (5 and/or 6) was formed in all the cases. With DMA and DEA, an alpha-oxoketenimine and/or an imidoylketene (7 and 8 or 9 and 10) was formed as the final product. In addition, several bands were observed, which can be assigned to zwitterionic intermediates (11 or 12). Optimized structures and vibrational spectra for all products were calculated at the B3LYP/6-31G(d) level of theory by using the polarizable continuum model (epsilon = 5).

Fatigue Lifetime of Ceramic Matrix Composites at Intermediate Temperature by Acoustic Emission

PubMed Central

Racle, Elie; Godin, Nathalie; Reynaud, Pascal; Fantozzi, Gilbert

2017-01-01

The fatigue behavior of a Ceramic Matrix Composite (CMC) at intermediate temperature under air is investigated. Because of the low density and the high tensile strength of CMC, they offer a good technical solution to design aeronautical structural components. The aim of the present study is to compare the behavior of this composite under static and cyclic loading. Comparison between incremental static and cyclic tests shows that cyclic loading with an amplitude higher than 30% of the ultimate tensile strength has significant effects on damage and material lifetimes. In order to evaluate the remaining lifetime, several damage indicators, mainly based on the investigation of the liberated energy, are introduced. These indicators highlight critical times or characteristic times, allowing an evaluation of the remaining lifetime. A link is established with the characteristic time around 25% of the total test duration and the beginning of the matrix cracking during cyclic fatigue. PMID:28773019

Herschel Far Infrared Spectra of Dusty Star-Forming Galaxies

NASA Astrophysics Data System (ADS)

Wilson, Derek; Cooray, Asantha R.; Nayyeri, Hooshang

2017-01-01

We stack archival spectra from the Herschel Space Observatory's SPIRE Spectrometer in three redshift bins from low redshifts (z < 0.2), through intermediate redshifts (0.2 < z < 1), and up to high redshifts (z > 1) in order to determine the average properties of the gas and dust in dusty, star-forming galaxies and (U)LIRGs. In the lower-redshift stack, we detect a host of water and carbon monoxide rotational transition lines, as well as some fine structure lines such as [NII]. At intermediate redshifts, only a [CII] line appears. The high-redshift stack displays strong [CII] emission, as well as faint emission from [OI] and [OIII]. The observed emission lines are used to model the average number density and radiation field strength in the photodissociation regions of our high-redshift sample, and the spectral line energy distributions of CO rotational transitions from the low-redshift stack are presented.

Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.

PubMed

Bruijnincx, Pieter C A; van Koten, Gerard; Klein Gebbink, Robertus J M

2008-12-01

Iron-containing enzymes are one of Nature's main means of effecting key biological transformations. The mononuclear non-heme iron oxygenases and oxidases have received the most attention recently, primarily because of the recent availability of crystal structures of many different enzymes and the stunningly diverse oxidative transformations that these enzymes catalyze. The wealth of available structural data has furthermore established the so-called 2-His-1-carboxylate facial triad as a new common structural motif for the activation of dioxygen. This superfamily of mononuclear iron(ii) enzymes catalyzes a wide range of oxidative transformations, ranging from the cis-dihydroxylation of arenes to the biosynthesis of antibiotics such as isopenicillin and fosfomycin. The remarkable scope of oxidative transformations seems to be even broader than that associated with oxidative heme enzymes. Not only are many of these oxidative transformations of key biological importance, many of these selective oxidations are also unprecedented in synthetic organic chemistry. In this critical review, we wish to provide a concise background on the chemistry of the mononuclear non-heme iron enzymes characterized by the 2-His-1-carboxylate facial triad and to discuss the many recent developments in the field. New examples of enzymes with unique reactivities belonging to the superfamily have been reported. Furthermore, key insights into the intricate mechanistic details and reactive intermediates have been obtained from both enzyme and modeling studies. Sections of this review are devoted to each of these subjects, i.e. the enzymes, biomimetic models, and reactive intermediates (225 references).

Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

DOE PAGES

Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

2013-09-04

The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. Themore » range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.« less

Cooling rate dependence of structural order in Al90Sm10 metallic glass

NASA Astrophysics Data System (ADS)

Sun, Yang; Zhang, Yue; Zhang, Feng; Ye, Zhuo; Ding, Zejun; Wang, Cai-Zhuang; Ho, Kai-Ming

2016-07-01

The atomic structure of Al90Sm10 metallic glass is studied using molecular dynamics simulations. By performing a long sub-Tg annealing, we developed a glass model closer to the experiments than the models prepared by continuous cooling. Using the cluster alignment method, we found that "3661" cluster is the dominating short-range order in the glass samples. The connection and arrangement of "3661" clusters, which define the medium-range order in the system, are enhanced significantly in the sub-Tg annealed sample as compared with the fast cooled glass samples. Unlike some strong binary glass formers such as Cu64.5Zr35.5, the clusters representing the short-range order do not form an interconnected interpenetrating network in Al90Sm10, which has only marginal glass formability.

The mechanism of transforming diamond nanowires to carbon nanostructures.

PubMed

Sorkin, Anastassia; Su, Haibin

2014-01-24

The transformation of diamond nanowires (DNWs) with different diameters and geometries upon heating is investigated with density-functional-based tight-binding molecular dynamics. DNWs of {100} and {111} oriented cross-section with projected average line density between 7 and 20 atoms Å(-1) transform into carbon nanotubes (CNTs) under gradual heating up to 3500-4000 K. DNWs with projected average line density larger than 25 atoms Å(-1) transform into double-wall CNTs. The route of transformation into CNTs clearly exhibits three stages, with the intriguing intermediate structural motif of a carbon nanoscroll (CNS). Moreover, the morphology plays an important role in the transformation involving the CNS as one important intermediate motif to form CNTs. When starting with [Formula: see text] oriented DNWs with a square cross-section consisting of two {111} facets facing each other, one interesting structure with 'nano-bookshelf' shape emerges: a number of graphene 'shelves' located inside the CNT, bonding to the CNT walls with sp(3) hybridized atoms. The nano-bookshelf structures exist in a wide range of temperatures up to 3,000 K. The further transformation from nano-bookshelf structures depends on the strength of the joints connecting shelves with CNT walls. Notably, the nano-bookshelf structure can evolve into two end products: one is CNT via the CNS pathway, the other is graphene transformed directly from the nano-bookshelf structure at high temperature. This work sheds light on the microscopic insight of carbon nanostructure formation mechanisms with the featured motifs highlighted in the pathways.

Local Crystal Structure of Antiferroelectric Bi2Mn4/3Ni2/3O6 in Commensurate and Incommensurate Phases Described by Pair Distribution Function (PDF) and Reverse Monte Carlo (RMC) Modeling.

PubMed

Szczecinski, Robert J; Chong, Samantha Y; Chater, Philip A; Hughes, Helen; Tucker, Matthew G; Claridge, John B; Rosseinsky, Matthew J

2014-04-08

The functional properties of materials can arise from local structural features that are not well determined or described by crystallographic methods based on long-range average structural models. The room temperature (RT) structure of the Bi perovskite Bi 2 Mn 4/3 Ni 2/3 O 6 has previously been modeled as a locally polar structure where polarization is suppressed by a long-range incommensurate antiferroelectric modulation. In this study we investigate the short-range local structure of Bi 2 Mn 4/3 Ni 2/3 O 6 , determined through reverse Monte Carlo (RMC) modeling of neutron total scattering data, and compare the results with the long-range incommensurate structure description. While the incommensurate structure has equivalent B site environments for Mn and Ni, the local structure displays a significantly Jahn-Teller distorted environment for Mn 3+ . The local structure displays the rock-salt-type Mn/Ni ordering of the related Bi 2 MnNiO 6 high pressure phase, as opposed to Mn/Ni clustering observed in the long-range average incommensurate model. RMC modeling reveals short-range ferroelectric correlations between Bi 3+ cations, giving rise to polar regions that are quantified for the first time as existing within a distance of approximately 12 Å. These local correlations persist in the commensurate high temperature (HT) phase, where the long-range average structure is nonpolar. The local structure thus provides information about cation ordering and B site structural flexibility that may stabilize Bi 3+ on the A site of the perovskite structure and reveals the extent of the local polar regions created by this cation.

Radiation sensitivity and EPR dosimetric potential of gallic acid and its esters

NASA Astrophysics Data System (ADS)

Tuner, Hasan; Oktay Bal, M.; Polat, Mustafa

2015-02-01

In the preset work the radiation sensitivities of Gallic Acid anhydrous and monohydrate, Octyl, Lauryl, and Ethyl Gallate (GA, GAm, OG, LG, and EG) were investigated in the intermediate (0.5-20 kGy) and low radiation (<10 Gy) dose range using Electron Paramagnetic Resonance (EPR) spectroscopy. While OG, LG, and EG are presented a singlet EPR spectra, their radiation sensitivity found to be very different in the intermediate dose range. At low radiation dose range (<10 Gy) only LG is found to be present a signal that easily distinguished from the noise signals. The intermediate and low dose range radiation sensitivities are compared using well known EPR dosimeter alanine. The radiation yields (G) of the interested material were found to be 1.34×10-2, 1.48×10-2, 4.14×10-2, and 6.03×10-2, 9.44×10-2 for EG, GA, GAm, OG, and LG, respectively at the intermediate dose range. It is found that the simple EPR spectra and the noticeable EPR signal of LG make it a promising dosimetric material to be used below 10 Gy of radiation dose.

Intermediate Models of Planetary Circulations in the Atmosphere and Ocean.

NASA Astrophysics Data System (ADS)

McWilliams, James C.; Gent, Peter R.

1980-08-01

Large-scale extratropical motions (with dimensions comparable to, or somewhat smaller than, the planetary radius) in the atmosphere and ocean exhibit a more restricted range of phenomena than are admissible in the primitive equations for fluid motions, and there have been many previous proposals for simpler, more phenomenologically limited models of these motions. The oldest and most successful of these is the quasi-geostrophic model. An extensive discussion is made of models intermediate between the quasi-geostrophic and primitive ones, some of which have been previously proposed [e.g., the balance equations (BE), where tendencies in the equation for the divergent component of velocity are neglected, or the geostrophic momentum approximation (GM), where ageostrophic accelerations are neglected relative to geostrophic ones] and some of which are derived here. Virtues of these models are assessed in the dual measure of nearly geostrophic momentum balance (i.e., small Rossby number) and approximate frontal structure (i.e., larger along-axis velocities and length scales than their cross-axis counterparts), since one or both of these circumstances is usually characteristic of planetary motions. Consideration is also given to various coordinate transformations, since they can yield simpler expressions for the governing differential equations of the intermediate models. In particular, a new set of coordinates is proposed, isentropic geostrophic coordinates,(IGC), which has the advantage of making implicit the advections due to ageostrophic horizontal and vertical velocities under various approximations. A generalization of quasi-geostrophy is made. named hypo-geostrophy (HG), which is an asymptotic approximation of one higher order accuracy in Rossby number. The governing equations are simplest in IGC for both HG and GM; we name the latter in these coordinates isentropic semi-geostrophy (ISG), in analogy to Hoskins' (1975) semi-geostrophy (SG). HG, GM and BE are, in our opinion, the three most valuable intermediate models for future consideration. HG and BE are superior to GM asymptotically in small Rossby number, but HG in IGC and GM are superior to HG in other coordinates and BE in frontal asymptotics. GM has global (not asymptotic) integral invariants of energy and enstrophy, which HG lacks, and this may assure physically better solutions in weakly asymptotic situations. BE has one global (energy) and one asymptotic (enstrophy) invariant. BE has difficulties of solution existence and uniqueness. Further progress in the search for intermediate models requires obtaining an extensive set of solutions for these models for comparison with quasi-geostrophic and primitive equation solutions.

Theoretical model for the discrete flexoelectric effect and a description for the sequence of intermediate smectic phases with increasing periodicity.

PubMed

Emelyanenko, A V; Osipov, M A

2003-11-01

A general phenomenological description and a simple molecular model is proposed for the "discrete" flexoelectric effect in tilted smectic liquid crystal phases. This effect defines a polarization in a smectic layer induced by a difference of director orientations in the two smectic layers adjacent to it. It is shown that the "discrete" flexoelectric effect is determined by electrostatic dipole-quadrupole interaction between positionally correlated molecules located in adjacent smectic layers, while the corresponding dipole-dipole interaction is responsible for a coupling between polarization vectors in neighboring layers. It is shown that a simple phenomenological model of a ferrielectric smectic liquid crystal, which has recently been proposed in the literature, can be used to describe the whole sequence of intermediate chiral smectic C* phases with increasing periods, and to determine the nonplanar structure of each phase without additional assumptions. In this sequence the phases with three- and four-layer periodicities have the same structure, as observed in the experiment. The theory predicts also the structure of intermediate phases with longer periods that have not been studied experimentally so far. The structures of intermediate phases with periodicities of up to nine layers are presented together with the phase diagrams, and a relationship between molecular chirality and the three-dimensional structure of intermediate phases is discussed. It is considered also how the coupling between the spontaneous polarization determined by molecular chirality and the induced polarization determined by the discrete flexoelectric effect stabilizes the nonplanar structure of intermediate phases.

Effects of eddy initial conditions on nonlinear forcing of planetary scale waves by amplifying baroclinic eddies

NASA Technical Reports Server (NTRS)

Young, Richard E.

1986-01-01

The previous study of Young and Villere concerning growth of planetary scale waves forced by wave-wave interactions of amplifying intermediate scale baroclinic eddies is extended to investigate effects of different eddy initial conditions. A global, spectral, primitive equation model is used for the calculations. For every set of eddy initial conditions considered, growth rates of planetary modes are considerably greater than growth rates computed from linear instability theory for a fixed zonally independent basic state. However, values of growth rates ranged over a factor of 3 depending on the particular set of eddy initial conditions used. Nonlinear forcing of planetary modes via wave-wave coupling becomes more important than baroclinic growth on the basic state at small values of the intermediate-scale modal amplitudes. The relative importance of direct transfer of kinetic energy from intermediate scales of motion to a planetary mode, compared to baroclinic conversion of available potential energy to kinetic energy within that planetary mode, depends on the individual case. In all cases, however, the transfer of either kinetic or available potential energy to the planetary modes was accomplished principally by wave-wave transfer from intermediate scale eddies, rather than from the zonally averaged state. The zonal wavenumber 2 planetary mode was prominent in all solutions, even in those for which eddy initial conditions were such that a different planetary mode was selectively forced at the start. General characteristics of the structural evolution of the planetary wave components of total heat and momentum flux, and modal structures themselves, were relatively insensitive to variations in eddy initial conditions, even though quantitative details varied from case to case.

German Basic Course. Volume II, Lessons 16-25. Revised.

ERIC Educational Resources Information Center

Defense Language Inst., Monterey, CA.

This is the second volume of the intermediate phase of the German Basic Course. The objective of the intermediate phase is mastery of the structural elements of the German language. Accordingly, each lesson contains the following elements: (1) introduction of new structure through "structure perception drills"; (2) a basic dialog dealing with a…

High-pressure behavior of intermediate scapolite: compressibility, structure deformation and phase transition

NASA Astrophysics Data System (ADS)

Lotti, Paolo; Comboni, Davide; Merlini, Marco; Hanfland, Michael

2018-05-01

Scapolites are common volatile-bearing minerals in metamorphic rocks. In this study, the high-pressure behavior of an intermediate member of the scapolite solid solution series (Me47), chemical formula (Na1.86Ca1.86K0.23Fe0.01)(Al4.36Si7.64)O24[Cl0.48(CO3)0.48(SO4)0.01], has been investigated up to 17.79 GPa, by means of in situ single-crystal synchrotron X-ray diffraction. The isothermal elastic behavior of the studied scapolite has been described by a III-order Birch-Murnaghan equation of state, which provided the following refined parameters: V 0 = 1110.6(7) Å3, {K_{{V_0}}} = 70(2) GPa ({β _{{V_0}}} = 0.0143(4) GPa-1) and {K_{{V}}^' = 4.8(7). The refined bulk modulus is intermediate between those previously reported for Me17 and Me68 scapolite samples, confirming that the bulk compressibility among the solid solution increases with the Na content. A discussion on the P-induced structure deformation mechanisms of tetragonal scapolite at the atomic scale is provided, along with the implications of the reported results for the modeling of scapolite stability. In addition, a single-crystal to single-crystal phase transition, which is displacive in character, has been observed toward a triclinic polymorph at 9.87 GPa. The high-pressure triclinic polymorph was found to be stable up to the highest pressure investigated.

Use of response surface methodology in a fed-batch process for optimization of tricarboxylic acid cycle intermediates to achieve high levels of canthaxanthin from Dietzia natronolimnaea HS-1.

PubMed

Nasri Nasrabadi, Mohammad Reza; Razavi, Seyed Hadi

2010-04-01

In this work, we applied statistical experimental design to a fed-batch process for optimization of tricarboxylic acid cycle (TCA) intermediates in order to achieve high-level production of canthaxanthin from Dietzia natronolimnaea HS-1 cultured in beet molasses. A fractional factorial design (screening test) was first conducted on five TCA cycle intermediates. Out of the five TCA cycle intermediates investigated via screening tests, alfaketoglutarate, oxaloacetate and succinate were selected based on their statistically significant (P<0.05) and positive effects on canthaxanthin production. These significant factors were optimized by means of response surface methodology (RSM) in order to achieve high-level production of canthaxanthin. The experimental results of the RSM were fitted with a second-order polynomial equation by means of a multiple regression technique to identify the relationship between canthaxanthin production and the three TCA cycle intermediates. By means of this statistical design under a fed-batch process, the optimum conditions required to achieve the highest level of canthaxanthin (13172 + or - 25 microg l(-1)) were determined as follows: alfaketoglutarate, 9.69 mM; oxaloacetate, 8.68 mM; succinate, 8.51 mM. Copyright 2009 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Structural short-range order of the β-Ti phase in bulk Ti-Fe-(Sn) nanoeutectic composites

NASA Astrophysics Data System (ADS)

Das, J.; Eckert, J.; Theissmann, R.

2006-12-01

The authors report lattice distortion and "ω-like" structural short-range order (SRO) of the β-Ti phase in a Ti-Fe-(Sn) bulk nanoeutectic composite prepared by slow cooling from the melt. The nanoeuetctic phases are chemically homogeneous, but the addition of Sn releases the local lattice strain, modifies the structural SRO, and prevents the formation of stacking faults in the body centered cubic (bcc) β-Ti phase resulting in improved plastic deformability. The elastic properties and the structural SRO of the β-Ti phase are proposed to be important parameters for developing advanced high strength, ductile Ti-base nanocomposite alloys.

Isothermal fatigue mechanisms in Ti-based metal matrix composites

NASA Technical Reports Server (NTRS)

Majumdar, Bhaskar S.; Newaz, Golam M.

1993-01-01

Stress-controlled isothermal fatigue experiments were performed at room temperature (RT) and 548 C (in argon) on (0)8 SCS6/Ti 15-3 metal matrix composites (MMC's) with 15 and 41 volume percent SCS6 (SiC) fibers. The primary objectives were to evaluate the mechanical responses, and to obtain a clear understanding of the damage mechanisms leading to failure of the MMC's. The mechanical data indicated that strain ranges attained fairly constant values in the stress-controlled experiments at both RT and 538 C, and remained so for more than 85 percent of life. The fatigue data for MMC's with different volume fraction fibers showed that MMC life was controlled by the imposed strain range rather than the stress range. At RT, and at low and intermediate strain ranges, the dominant fatigue mechanism was matrix fatigue, and this was confirmed metallurgically from fractographic evidence as well as from observations of channel type dislocation structures in the matrix of fatigued MMC specimens. Reaction-zone cracks acted as important crack initiating sites at RT, with their role being to facilitate slip band formation and consequent matrix crack initiation through classical fatigue mechanisms. MMC life agreed with matrix life at the lower strain ranges, but was smaller than matrix life at higher strain ranges. Unlike the case of monotonic deformation, debonding damage was another major damage mechanism during fatigue at RT, and it increased for higher strain ranges. At high strain ranges at RT, fractography and metallography showed an absence of matrix cracks, but long lengths of debonds in the outer layers of the SCS6 fibers. Such debonding and consequent rubbing during fatigue is believed to have caused fiber damage and their failure at high strain ranges. Thus, whereas life was matrix dominated at low and intermediate strain ranges, it was fiber dominated at high strain ranges. At 538 C, the mean stain constantly increased (ratchetting) with the number of cycles. At high strain ranges, such ratchetting led to overload failure of the fibers, and debonding of the type at RT was very small. At intermediate strain ranges, fractography showed large areas of matrix cracks. However, in spite of this matrix dominated mechanism, the MMC life at elevated temperatures was significantly less than the matrix fatigue life at all strain ranges. The reason for this difference is still unclear, although metallographic and fractographic evidences suggest that internal crack initiation sites at Mo-ribbons and reaction-zone cracks may have played a critical role, with the former tending to dominate.

Template-directed synthesis of MS (M=Cd, Zn) hollow microsphere via hydrothermal method

NASA Astrophysics Data System (ADS)

Wang, Shi-Ming; Wang, Qiong-Sheng; Wan, Qing-Li

2008-05-01

CdS, ZnS hollow microspheres were prepared with chitosan as the synthesis template at 140 and 150 °C, respectively, by hydrothermal method. The resultant products were characterized by X-ray diffraction (XRD) measurements in order to determine the crystalline phase of the products. The structural and morphological features of the nanoparticles were investigated by transmission electron microscopy (TEM) and ultraviolet-visible diffuse reflection spectroscopy (DRS). The experimental results indicated that all the nanoparticles aggregated into hollow microspheres and chitosan as a template played an important role in the formation of hollow microspheres. In addition, an intermediate complex structure-controlling possible reaction mechanism was proposed in this paper.

Emergence and stability of intermediate open vesicles in disk-to-vesicle transitions.

PubMed

Li, Jianfeng; Zhang, Hongdong; Qiu, Feng; Shi, An-Chang

2013-07-01

The transition between two basic structures, a disk and an enclosed vesicle, of a finite membrane is studied by examining the minimum energy path (MEP) connecting these two states. The MEP is constructed using the string method applied to continuum elastic membrane models. The results reveal that, besides the commonly observed disk and vesicle, open vesicles (bowl-shaped vesicles or vesicles with a pore) can become stable or metastable shapes. The emergence, stability, and probability distribution of these open vesicles are analyzed. It is demonstrated that open vesicles can be stabilized by higher-order elastic energies. The estimated probability distribution of the different structures is in good agreement with available experiments.