Low Electron Density Region Research Articles

Carrier recombination processes in In-polar n-InN in regions of low residual electron density

Photoluminescence (PL) spectra of In-polar n-type InN films with different dislocation and residual electron densities are investigated in the temperature range 15–300 K. The dependence of PL intensity on temperature is analyzed by using a model function that is based on rate equations for photoexcited hole density. By considering the relation between the dislocation densities estimated from the widths of the peaks of x-ray ω-rocking curves and the parameters obtained from the rate equations, two kinds of nonradiative carrier recombination processes are identified. One process is independent of threading dislocations and is thermally activated, while the other takes place in the vicinity of edge-type dislocations and requires no activation energy.

' Subunit of soybean -conglycinin forms complex with rice glutelin via a disulphide bond in transgenic rice seeds

The α′ and β subunits of soybean β-conglycinin were expressed in rice seeds in order to improve the nutritional and physiological properties of rice as a food. The α′ subunit accumulated in rice seeds at a higher level than the β subunit, but no detectable difference in mRNA transcription level between subunits was observed. Sequential extraction results indicate that the α′ subunit formed one or more disulphide bonds with glutelin. Electron microscopic analysis showed that the α′ subunit and the β subunit were transported to PB-II together with glutelin. In mature transgenic seeds, the β subunit accumulated in low electron density regions in the periphery of PB-II, whereas the α′ subunit accumulated together with glutelin in high-density regions of the periphery. The subcellular localization of mutated α′ subunits lacking one cysteine residue in the N-terminal mature region (α′ΔCys1) or five cysteine residues in the pro and N-terminal mature regions (α′ΔCys5) were also examined. Low-density regions were formed in PB-II in mature seeds of transgenic rice expressing α′ΔCys 5 and α′ΔCys1. α′ΔCys5 was localized only in the low-density regions, whereas α′ΔCys1 was found in both low- and high-density regions. These results suggest that the α′ subunit could make a complex via one or more disulphide bonds with glutelin and accumulate together in PB-II of transgenic rice seeds.

Intramembrane-cleaving Proteases

In the past decade or so, membrane-embedded proteases that carry out hydrolysis on the transmembrane region of their substrates have been discovered. These I-CLiPs2 (1) somehow create an environment for water and the hydrophilic residues needed for catalysis and bend or unwind their helical substrates to make the amide bonds susceptible to hydrolysis. Despite the distinction of being membrane-embedded and cleaving TMDs, the residues essential for catalysis by these I-CLiPs are virtually the same as those found in aqueous proteases, clear examples of convergent evolution toward a common mechanism. Described herein are the different types of I-CLiPs and an update on their structural and mechanistic features and biological roles.

New Roles for Copper Metabolism in Cell Proliferation, Signaling, and Disease

Over the past 2 decades, the molecular mechanisms by which cells acquire, distribute, and utilize copper have been under intense investigation. Significant progress has been made in the identification of genes encoding copper homeostasis proteins and in fundamental aspects of their structure, function, and mechanisms of action in copper balance. A number of more comprehensive reviews of the field with respect to the genetics, structure, function, and physiology of copper metabolism have recently appeared elsewhere (1–4). Here, we review general mechanisms for eukaryotic copper metabolism at the cellular level in the context of recent discoveries in the field, identifying potential new functions for copper and copper metabolism proteins in cell signaling, gene expression, tumor cell metastasis, and resistance to anti-neoplastic drugs.

Testing the triple network structure of the cubic Im3̄m (I) phase by isomorphous replacement and model refinement

This study provides further tests of the validity of the triple network structure of the body-centred Imm (I) cubic phase in polycatenar (phasmidic) liquid crystals, proposed by Zeng et al., Nat. Mater., 2005, 4, 562. New hemiphasmid compounds were synthesised, two of which (6 and 7) display the above phase, while 8 shows the hexagonal columnar phase. Comparison of 3-d electron density maps based on small-angle X-ray diffraction of two compounds with different proportions of high and low electron density regions (aliphatic and aromatic) helped with phasing the X-ray reflections of the cubic structure. This variant of the isomorphous replacement technique gave further support to the triple network structure proposed earlier. Furthermore, fitting calculated diffraction intensities of geometrical models to the observed ones confirmed that the oscillating segment cross-section of two of the three networks (the “octahedral networks”) are genuine structural features rather than artefacts. A rational explanation is proposed for the variable thickness of the aromatic network segments. The study has highlighted complexities of molecular packing in bicontinuous phases of thermotropic liquid crystals that are not encountered in related phases in lyotropics or block copolymers.

Electrical characteristics related to silicon film thickness in advanced FD SOI–MOSFETs

The impact of silicon-on-insulator (SOI) thinning on electrical characteristics is investigated for various SOI impurity concentrations, and for advanced structures with TiN gates and HfO 2 gate dielectrics. It is experimentally and theoretically verified that the SOI film thickness that influences the quantum-confinement effect when the thickness decreases, clearly depends on the impurity concentration of SOI. However, once the quantum-confinement effect of the channel associated with SOI thinning occurs, the subband structure depends weakly on the SOI impurity concentration. Furthermore, the mobility in ultra-thin SOI–MOSFETs with HfO 2 gate dielectrics and TiN gates is investigated. It is shown that the mobility of both the front and back channels is reduced, particularly, in the low electron density region. In addition, the mobility exhibits considerable variations in this region. These variations do not correspond to the variations in SOI thickness or gate-oxide thickness. The results suggest that they are due to the variations in the Coulomb scattering centers.

Symmetry phase diagrams of the superconducting ground states induced by correlated hoppings interactions

The formation of p- and d-wave superconducting ground states on a square lattice is studied within the BCS formalism and a generalized Hubbard model, in which a second-neighbor correlated hopping (Δ t 3) is included in addition to the on site and nearest neighbor repulsions. The triplet superconductivity is obtained when a small distortion of the right angles in the square lattice is introduced. This distortion can be characterized by the difference between the values of Δ t 3 ± in the x ± y directions, i.e., δ 3 = ( Δ t 3 + - Δ t 3 - ) / 2 . The phase diagram is analyzed in the space of the electron density ( n) and δ 3. The results show that the p- and d-channel superconductivities are respectively enhanced in the low and high electron density regions.

Spin-triplet superconductivity in the double-chain Hubbard model with ferromagnetic exchange interaction

We study possible occurrence of spin-triplet superconductivity in the model of two Hubbard chains coupled with ferromagnetic exchange interaction. We use the analytical bozonization method as well as the numerical exact-diagonalization and density-matrix renormalization group methods. We show that, in the low electron density region, the complete ferromagnetic state occurs and the triplet pairing correlation is most dominant, where we find that the gap function behavior is p y -wave like. We also show that, in the high electron density regions, the spin-singlet superconductivity anticipated by the weak coupling analysis is most dominant, where the gap function behavior is d xy -wave like.

Construction of a cysteineless variant of the E. coli pyruvate dehydrogenase E1 subunit

The crystal structure of the E1 subunit of the pyruvate dehydrogenase complex from E. coli (PDHc-E1) revealed three regions of low electron density, spanning residues 1–55, 401–413 and 541–557 (Arjunan et al., Biochemistry 2002, 41, 5213–5221). Region 1–55 has been shown to interact with the PDHc-E2 subunit (Park et al, Biochemistry 2004, 43, 14037–14046) while region 401–413 has a role in reductive acetylation of the lipoamide of the PDHc-E2 subunit (Nemeria et al., Biochemistry 2002, 41, 15459–15467). Studies using site specific labeling (SSL) with thiol-directed probes sensitive to their local environment has immense potential to characterize the dynamics of these important regions. For this purpose five of six cysteine residues in parental PDHc-E1 (120, 259, 575, 610, 654 and 770) were converted to alanines, the sixth C259 to asparagine, by site directed mutagenesis. This PDHc-E1 variant without cysteines showed ~4-fold reduction in activity compared to parental PDHc-E1 in subunit-specific as well as overall complex activity assays. These results confirm our previous observations (Nemeria et al, Biochemistry 1998, 37, 911–922) where none of the cysteines in singly-substituted PDHc-E1 were found important for activity. Moreover, reintroduction of cysteine for SSL studies in regions 1–55 (I11C) and 401–413 (Q408C) did not result in significant reduction in PDHc-E1 activity, retaining ~40% and 80% overall activity, respectively, compared to the cysteineless PDHc-E1 variant. These results will facilitate SSL and functional characterization of these important regions in PDHc-E1. Supported by NIH grants GM62330 and GM53080.

Molecular Structures and Potential Energy Surfaces for IHI-·Arn(n= 1−7)

This study reports second-order perturbation (MP2) theory predictions of the optimized structures and relative energies for IHI-·Arn (n = 1−7) complexes. For n = 1−6, the lowest energy structure has all n Ar atoms forming a partial ring in the plane that is perpendicular to and bisects the IHI- axis. The ring is closed at n = 6, and for n = 7, one of the Ar atoms moves into a second ring. Analysis of the geometrical parameters and three-dimensional MP2 molecular electrostatic potentials (MEP) is used to determine why the ring structure is lowest in energy for n = 1−6, but not for n = 7. Based on the MEP, it is concluded that Ar atoms tend to distribute in regions of low electron density that exist in the plane perpendicular to and bisecting the IHI- axis. Hence, the global minimum for all n < 7 is a ring structure in this plane. For n = 7, steric effects force an Ar atom into a new ring.

Optical Absorption Measurements of Sputtered Ti Ion Density and Discussion of Ionization Mechanisms in Inductively Coupled Plasma-Assisted DC Sputtering

This study discusses the ionization mechanisms of sputtered titanium (Ti) in inductively coupled plasma (ICP)-assisted dc magnetron sputtering based on measurements and model analyses. Ionic and atomic densities of sputtered titanium were measured using an optical absorption method under an Ar pressure of 3.5 Pa against rf(13.56MHz) power applied to the inserted coil. A Langmuir probe provided measurements of electron densities against coil rf power, giving input parameters for model analyses. We adopted a model analysis method presented by J. Hopwood and F. Qian [J. Appl. Phys. 78, 758 (1995)]. Variations of ionic and atomic densities and ionization fractions against electron density from model calculation agreed with those obtained by measurements. The results showed clearly that electron impact ionization dominates ionization of sputtered titanium in high er electron density regions compared to Penning ionization through Ar metastable atoms. Penning ionization played an important role at the lower electron density region because of the longer time for radiative decay of Ar metastable atoms.

Thermal activation of the trapped proton in diamond crystal: direct molecular dynamics calculation

For simulation of thermal behavior of the proton in the tetrahedral (T) trapping site of a C 26H 32 diamond cluster model, a direct molecular dynamics calculation was accomplished in a temperature range from 100 to 800 K based on the newly developed methodology at the PM3 molecular orbital (MO) level. The proton vibrating around only the T site below 550 K, diffuses to the next T site through the hexagonal (H) site in low electron density region at 600 K. However, at 800 K the proton transfers through the H site to the bond center (BC) site and the middle (M) site designated as a middle point between two neighboring centers of the rhombuses composed of three carbon atoms and the T site on the same level for each. The proton–carbon bond formation (C–H +–C) is occurred at the M site followed by decrease in the potential energy. Finally, the proton is vibrating between the M site and the BC site in high electron density region.

Comparison of edge pedestal parameters for JT-60U and DIII-D H-mode plasmas

Edge pedestal parameters (pedestal temperature and density, pedestal width)for JT-60U and DIII-D are studied and compared. For the discharges used in thestudy,the JT-60U H-mode operation space is in the high edge ion temperature and low edge electron density region, whereas DIII-D discharges have higher edgeelectron density and lower electron temperature. The pedestal width scalinghas been studied separately in each machine. We tested these pedestal scalingsagainst each other using JT-60U ion temperature pedestal width data andDIII-D electron temperature pedestal width data. Three previous scalings forpedestal width (Δ∝ε0.5ρpi,Δ/R∝(ρpi/R)0.66,Δ/R∝(βpPED)0.4) are tested usingtemperature pedestal widths from bothmachines. The relations between pedestal width and dimensionless parametersare examined. We propose a new pedestal width scaling for Te and Ti based onthis study of the two machines. The new scaling includes normalized poloidalgyroradius and Greenwald density: Δ∝aρ*0.4nG*0.3κ-1.5. The result of the comparison ofthese scalings is that the new scaling and Δ/R∝(βpPED)0.4 are well fitted and thefitting errors are almost the same as experimental error. However, furtherstudy is necessary for scaling parameters.

Sequence-related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures

RP4 TrbB, an essential component of the conjugative transfer apparatus of the broad-host-range plasmid RP4, is a member of the PulE protein superfamily involved in multicomponent machineries transporting macromolecules across the bacterial envelope. PulE-like proteins share several well conserved motifs, most notable a nucleoside triphosphate binding motif (P-loop). Helicobacter pylori HP0525 also belongs to the PulE superfamily and is encoded by the pathogenicity island cag, involved in the inflammatory response of infected gastric epithelial cells in mammals. The native molecular masses of TrbB and HP0525 as determined by gel filtration and glycerol gradient centrifugation suggested a homohexameric structure in the presence of ATP and Mg(2+). In the absence of nucleotides and bivalent cations, TrbB behaved as a tetramer whereas the hexameric state of HP0525 remained unaffected. Electron microscopy and image processing demonstrated that TrbB and HP0525 form ring-shaped complexes (diameter: 12 nm) with a central region (diameter: 3 nm) of low electron density when incubated in the presence of ATP and Mg(2+). However, the TrbB average image appeared to be more elliptical with strong twofold rotational symmetry whereas HP0525 complexes are regular hexagons. Six well defined triangle-shaped areas of high electron density were distinguishable in both cases. Covalent crosslinking of TrbB suggests that the hexameric ring is composed from a trimer of dimers, because only dimeric, tetrameric, and hexameric species were detectable. The toroidal structure of TrbB and HP0525 suggests that both proteins catalyze a repetitive process, most probably translocating a cognate substrate across the inner membrane.

Sequence-related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures.

RP4 TrbB, an essential component of the conjugative transfer apparatus of the broad-host-range plasmid RP4, is a member of the PulE protein superfamily involved in multicomponent machineries transporting macromolecules across the bacterial envelope. PulE-like proteins share several well conserved motifs, most notable a nucleoside triphosphate binding motif (P-loop). Helicobacter pylori HP0525 also belongs to the PulE superfamily and is encoded by the pathogenicity island cag, involved in the inflammatory response of infected gastric epithelial cells in mammals. The native molecular masses of TrbB and HP0525 as determined by gel filtration and glycerol gradient centrifugation suggested a homohexameric structure in the presence of ATP and Mg(2+). In the absence of nucleotides and bivalent cations, TrbB behaved as a tetramer whereas the hexameric state of HP0525 remained unaffected. Electron microscopy and image processing demonstrated that TrbB and HP0525 form ring-shaped complexes (diameter: 12 nm) with a central region (diameter: 3 nm) of low electron density when incubated in the presence of ATP and Mg(2+). However, the TrbB average image appeared to be more elliptical with strong twofold rotational symmetry whereas HP0525 complexes are regular hexagons. Six well defined triangle-shaped areas of high electron density were distinguishable in both cases. Covalent crosslinking of TrbB suggests that the hexameric ring is composed from a trimer of dimers, because only dimeric, tetrameric, and hexameric species were detectable. The toroidal structure of TrbB and HP0525 suggests that both proteins catalyze a repetitive process, most probably translocating a cognate substrate across the inner membrane.

VLA Observations of Carbon Radio Recombination Lines toward the HiiRegion Complex S88B

We present high angular resolution VLA observations of the C92α, C110α, and C166α radio recombination lines of carbon from the region of massive star formation known as S88B. The observations reveal that the carbon emission arises from two distinct components that are intimately associated with the compact (S88B2) and cometary (S88B1) regions of ionized gas within the complex. The brighter carbon component has an angular size of ~66, an average line-center velocity of 21.0 ± 0.5 km s-1, and an average line width of 5.1 ± 1.0 km s-1; it is associated with the compact H II region. The second component has an angular size of ~16'' and is found projected toward the head of the cometary-like H II region. The average center velocity and width of the carbon line emission are 21.1 ± 0.7 km s-1 and 5.1 ± 1.7 km s-1, respectively. The spatial location and velocity of both carbon regions suggest that the emission arises in layers of photodissociated gas at the interface between the molecular cloud and the regions of ionized gas that are undergoing a champagne phase. From a model analysis of the dependence of the recombination line intensity with principal quantum number, we conclude that the carbon emission originates in warm photodissociated regions. The electron temperatures and electron densities of the photodissociated gas range between 400 and 600 K and between 40 and 80 cm-3, respectively. Further, we find that stimulated amplification of the background H II region continuum radiation contributes significantly to the carbon emission in both components. We also detected emission in sulfur radio recombination lines from both components. We find that the ratios of sulfur to carbon line intensities are considerable larger than the [S/C] cosmic abundance ratio and that they vary with principal quantum number, with values in the range between 0.3 and 0.6. We attribute the large values of the intensity ratios to depletion of carbon in the gas phase by a factor of ~5 and the variations with principal quantum number to stimulated emission effects in a region of low electron density (ne ~ 3 cm-3) and low temperature (Te ~ 50 K) that surrounds the C+ region.

First-principles study of electric-field gradients at the Cd site for neutral hydrogen-cadmium complexes in crystalline silicon

In the present work, a first-principles investigation of electric-field gradients (EFG's) at the Cd site for possible neutral complexes of Cd-H in crystalline silicon has been performed. This was motivated by experimental results observed by perturbed angular correlation spectroscopy, and with the aim of trying to establish the validity of the configurational models proposed in the literature. We use the full-potential linear-muffin-tin-orbital method, within the local-density functional theory, and the supercell approach. We have allowed local relaxations of the Cd and Si nearest and next-nearest neighbors for different positions of H in the high and low electron-density regions. We have found that H in an intrabond site is unstable (saddle point), and that a bridgelike configuration is the energetically favorable one, where the Cd atom and the nearest silicon suffer relaxations along the [111] direction. The antibond positions of low electronic density regions were also studied, and have been found to be also local minima. The calculated EFG's in these configurations that locally minimize the total energy of the supercell (H at bridgelike and H in antibond sites to Cd and ${\mathrm{Si}}_{1}$) give quadrupolar coupling constants which are in agreement with the experimental results.

Role of ceramide 1 in the molecular organization of the stratum corneum lipids

The main barrier of the skin is formed by the lipids in the apical skin layer, the stratum corneum (SC). In SC mainly ceramides (CER), free fatty acids (FFA) and cholesterol (CHOL) are present. The CER are composed of at least six different fractions. CER 1 has an exceptional molecular structure as it contains a linoleic acid linked to a long-chain ω-hydroxy acid (C > 30). The SC lipids are organized in two lamellar phases with periodicities of approximately 6 and 13 nm, respectively. Recent studies revealed that ceramides isolated from pig SC mixed with cholesterol in confined ratios mimic stratum corneum lipid phase behavior closely (Bouwstra, J.A., et al. 1996. J. Lipid Res. 37: 999–1011). In this paper the role of CER 1 for the SC lipid lamellar organization was studied. For this purpose lipid phase behavior of mixtures of CHOL and total ceramide fraction was compared with that of mixtures of CHOL and a ceramide mixture lacking CER 1. These studies showed that in the absence of CER 1 almost no long periodicity phase was formed over a wide CHOL/CER molar ratio. A model is proposed for the molecular arrangement of the two lamellar phases. This model is based on the dominant role CER 1 plays in the formation of the long periodicity phase, electron density distribution calculations, and observations, such as i) the bimodal distribution of the fatty acid chain lengths of the ceramides, ii) the phase separation between long-chain ceramides and short-chain ceramides in a monolayer approach, and iii) the absence of swelling of the lamellae upon increasing the water content organization in SC. In this molecular model the short periodicity phase is composed of only two high electron density regions indicating the presence of only one bilayer, similar to that often found in phospholipid membranes. The molecular arrangement in the long periodicity phase is very exceptional. This phase most probably consists of two broad and one narrow low electron density regions. The two broad regions are formed by partly interdigitating ceramides with long-chain fatty acids of approximately 24–26 C atoms, while the narrow low-electron density region is formed by fully interdigitating ceramides with a short free fatty acid chain of approximately 16 to 18 C atoms.—Bouwstra, J. A., G. S. Gooris, F. E. R. Dubbelaar, A. M. Weerheim, A. P. IJzerman, and M. Ponec. Role of ceramide 1 in the molecular organization of the stratum corneum lipids. J. Lipid Res. 1998. 39: 186–196.

Using a structure envelope to facilitate structure solution from powder diffraction data

Given just a few strong low-index reflections, a periodic nodal surface (PNS), which divides the unit cell into regions of high and low electron density, can be generated. Fourteen known zeolite structures were examined to verify the validity of the procedure developed and in all cases the framework atoms were found to lie on just one side of the calculated curved surface. In other words, the surface defines a structure envelope. The same approach was applied to a few ionic and organic structures and was found to be equally valid. Since these reflections, with large d spacings, are precisely the ones that are least likely to be involved in overlap in a powder diffraction pattern, such a PNS can also be calculated using powder data. The resulting restriction in the region of the asymmetric unit in which atoms are likely to be found has immediate implications for any of the direct-space methods of structure determination from powder data. The use of this structure envelope as a mask in a straightforward grid search procedure reduced the computer time required to solve several framework structures by as much as two orders of magnitude.

Low density electron pairs in the extended Hubbard model

We study the extended Hubbard model in the parameter region where it exhibits superconducting instabilities. The model is defined by onsite and nearest-neighbor Coulomb interactions U and V, and hopping integral t. We calculate pair binding energies for various finite clusters by performing exact diagonalization of the Hamiltonian. We show results for one-dimensional chains and discuss results for 4 × 4, 6 × 6, and 8 × 8 two-dimensional square lattices. Results of solving the BCS equation for the pair binding energy as functions of carrier density n, and Coulomb interactions U and V, are compared with the exact diagonalization results. In the dilute concentration limit ( n → 0), the BCS equation is expected to be exact and, in the low electron density region, the results for the pair binding energy are found to be in fairly good agreement with the exact solutions.