Piezoelectric and electroacoustic properties of Ti-doped AlN thin films as a function of Ti content

In this work we present the assessment of the structural and piezoelectric properties of Al(0.5-x)TixN0.5 compounds (titanium content menor que6% atomic), which are expected to possess improved properties than conventional AlN films, such as larger piezoelectric activity, thermal stability of frequency and temperature resistance. Al:Ti:N films were deposited from a twin concentric target of Al and Ti by reactive AC sputtering, which provided films with a radial gradient of the Ti concentration. The properties of the films were investigated as a function of their composition, which was measured by electron dispersive energy dispersive X-ray spectroscopy and Rutherford backscattering spectrometry. The microstructure and morphology of the films were assessed by X-ray diffraction and infrared reflectance. Their electroacoustic properties and dielectric constant were derived from the frequency response of BAW test resonators. Al:Ti:N films properties appear to be strongly dependent on the Ti content, which modifies the AlN wurtzite crystal structure leading to greater dielectric constant, lower sound velocities, lower electromechanical factor and moderately improved temperature coefficient of the resonant frequency.

A non-perturbative Kolmogorov turbulence approach to the cosmic web structure

The Kolmogorov approach to turbulence is applied to the Burgers turbulence in the stochastic adhesion model of large-scale structure formation. As the perturbative approach to this model is unreliable, here a new, non-perturbative approach, based on a suitable formulation of Kolmogorov's scaling laws, is proposed. This approach suggests that the power-law exponent of the matter density two-point correlation function is in the range 1–1.33, but it also suggests that the adhesion model neglects important aspects of the gravitational dynamics.

Effect of Sb incorporation on the electronic structure of InAs quantum dots

On the basis of optical characterization experiments and an eight band kp model, we have studied the effect of Sb incorporation on the electronic structure of InAs quantum dots (QDs). We have found that Sb incorporation in InAs QDs shifts the hole wave function to the center of the QD from the edges of the QD where it is otherwise pinned down by the effects of shear stress. The observed changes in the ground-state energy cannot merely be explained by a composition change upon Sb exposure but can be accounted for when the change in lateral size is taken into consideration. The Sb distribution inside the QDs produces distinctive changes in the density of states, particularly, in the separation between excitation shells. We find a 50% increase in the thermal escape activation energy compared with reference InAs quantum dots as well as an increment of the fundamental transition decay time with Sb incorporation. Furthermore, we find that Sb incorporation into quantum dots is strongly nonlinear with coverage, saturating at low doses. This suggests the existence of a solubility limit of the Sb incorporation into the quantum dots during growth.

Variable structure control with chattering reduction of a generalized T-S model

In this paper, a fuzzy logic controller (FLC) based variable structure control (VSC) is presented. The main objective is to obtain an improved performance of highly non-linear unstable systems. New functions for chattering reduction and error convergence without sacrificing invariant properties are proposed. The main feature of the proposed method is that the switching function is added as an additional fuzzy variable and will be introduced in the premise part of the fuzzy rules; together with the state variables. In this work, a tuning of the well known weighting parameters approach is proposed to optimize local and global approximation and modelling capability of the Takagi-Sugeno (T-S) fuzzy model to improve the choice of the performance index and minimize it. The main problem encountered is that the T-S identification method can not be applied when the membership functions are overlapped by pairs. This in turn restricts the application of the T-S method because this type of membership function has been widely used in control applications. The approach developed here can be considered as a generalized version of the T-S method. An inverted pendulum mounted on a cart is chosen to evaluate the robustness, effectiveness, accuracy and remarkable performance of the proposed estimation approach in comparison with the original T-S model. Simulation results indicate the potential, simplicity and generality of the estimation method and the robustness of the chattering reduction algorithm. In this paper, we prove that the proposed estimation algorithm converge the very fast, thereby making it very practical to use. The application of the proposed FLC-VSC shows that both alleviation of chattering and robust performance are achieved.

Structure of intermediate shocks in collisionsless anisotropic Hall-magnetohydrodynamics plasma models

The existence of discontinuities within the double-adiabatic Hall-magnetohydrodynamics (MHD) model is discussed. These solutions are transitional layers where some of the plasma properties change from one equilibrium state to another. Under the assumption of traveling wave solutions with velocity C and propagation angle θ with respect to the ambient magnetic field, the Hall-MHD model reduces to a dynamical system and the waves are heteroclinic orbits joining two different fixed points. The analysis of the fixed points rules out the existence of rotational discontinuities. Simple considerations about the Hamiltonian nature of the system show that, unlike dissipative models, the intermediate shock waves are organized in branches in parameter space, i.e., they occur if a given relationship between θ and C is satisfied. Electron-polarized (ion-polarized) shock waves exhibit, in addition to a reversal of the magnetic field component tangential to the shock front, a maximum (minimum) of the magnetic field amplitude. The jumps of the magnetic field and the relative specific volume between the downstream and the upstream states as a function of the plasma properties are presented. The organization in parameter space of localized structures including in the model the influence of finite Larmor radius is discussed

Low Work-Function Thermionic Emission and Orbital-Motion-Limited Ion Collection at Bare-Tether Cathodic Contact

Una amarra electrodinámica (electrodynamic tether) opera sobre principios electromagnéticos intercambiando momento con la magnetosfera planetaria e interactuando con su ionosfera. Es un subsistema pasivo fiable para desorbitar etapas de cohetes agotadas y satélites al final de su misión, mitigando el crecimiento de la basura espacial. Una amarra sin aislamiento captura electrones del plasma ambiente a lo largo de su segmento polarizado positivamente, el cual puede alcanzar varios kilómetros de longitud, mientras que emite electrones de vuelta al plasma mediante un contactor de plasma activo de baja impedancia en su extremo catódico, tal como un cátodo hueco (hollow cathode). En ausencia de un contactor catódico activo, la corriente que circula por una amarra desnuda en órbita es nula en ambos extremos de la amarra y se dice que ésta está flotando eléctricamente. Para emisión termoiónica despreciable y captura de corriente en condiciones limitadas por movimiento orbital (orbital-motion-limited, OML), el cociente entre las longitudes de los segmentos anódico y catódico es muy pequeño debido a la disparidad de masas entre iones y electrones. Tal modo de operación resulta en una corriente media y fuerza de Lorentz bajas en la amarra, la cual es poco eficiente como dispositivo para desorbitar. El electride C12A7 : e−, que podría presentar una función de trabajo (work function) tan baja como W = 0.6 eV y un comportamiento estable a temperaturas relativamente altas, ha sido propuesto como recubrimiento para amarras desnudas. La emisión termoiónica a lo largo de un segmento así recubierto y bajo el calentamiento de la operación espacial, puede ser más eficiente que la captura iónica. En el modo más simple de fuerza de frenado, podría eliminar la necesidad de un contactor catódico activo y su correspondientes requisitos de alimentación de gas y subsistema de potencia, lo que resultaría en un sistema real de amarra “sin combustible”. Con este recubrimiento de bajo W, cada segmento elemental del segmento catódico de una amarra desnuda de kilómetros de longitud emitiría corriente como si fuese parte de una sonda cilíndrica, caliente y uniformemente polarizada al potencial local de la amarra. La operación es similar a la de una sonda de Langmuir 2D tanto en los segmentos catódico como anódico. Sin embargo, en presencia de emisión, los electrones emitidos resultan en carga espacial (space charge) negativa, la cual reduce el campo eléctrico que los acelera hacia fuera, o incluso puede desacelerarlos y hacerlos volver a la sonda. Se forma una doble vainas (double sheath) estable con electrones emitidos desde la sonda e iones provenientes del plasma ambiente. La densidad de corriente termoiónica, variando a lo largo del segmento catódico, podría seguir dos leyes distintas bajo diferentes condiciones: (i) la ley de corriente limitada por la carga espacial (space-charge-limited, SCL) o (ii) la ley de Richardson-Dushman (RDS). Se presenta un estudio preliminar sobre la corriente SCL frente a una sonda emisora usando la teoría de vainas (sheath) formada por la captura iónica en condiciones OML, y la corriente electrónica SCL entre los electrodos cilíndricos según Langmuir. El modelo, que incluye efectos óhmicos y el efecto de transición de emisión SCL a emisión RDS, proporciona los perfiles de corriente y potencial a lo largo de la longitud completa de la amarra. El análisis muestra que en el modo más simple de fuerza de frenado, bajo condiciones orbitales y de amarras típicas, la emisión termoiónica proporciona un contacto catódico eficiente y resulta en una sección catódica pequeña. En el análisis anterior, tanto la transición de emisión SCL a RD como la propia ley de emisión SCL consiste en un modelo muy simplificado. Por ello, a continuación se ha estudiado con detalle la solución de vaina estacionaria de una sonda con emisión termoiónica polarizada negativamente respecto a un plasma isotrópico, no colisional y sin campo magnético. La existencia de posibles partículas atrapadas ha sido ignorada y el estudio incluye tanto un estudio semi-analítico mediante técnica asintóticas como soluciones numéricas completas del problema. Bajo las tres condiciones (i) alto potencial, (ii) R = Rmax para la validez de la captura iónica OML, y (iii) potencial monotónico, se desarrolla un análisis asintótico auto-consistente para la estructura de plasma compleja que contiene las tres especies de cargas (electrones e iones del plasma, electrones emitidos), y cuatro regiones espaciales distintas, utilizando teorías de movimiento orbital y modelos cinéticos de las especies. Aunque los electrones emitidos presentan carga espacial despreciable muy lejos de la sonda, su efecto no se puede despreciar en el análisis global de la estructura de la vaina y de dos capas finas entre la vaina y la región cuasi-neutra. El análisis proporciona las condiciones paramétricas para que la corriente sea SCL. También muestra que la emisión termoiónica aumenta el radio máximo de la sonda para operar dentro del régimen OML y que la emisión de electrones es mucho más eficiente que la captura iónica para el segmento catódico de la amarra. En el código numérico, los movimientos orbitales de las tres especies son modelados para potenciales tanto monotónico como no-monotónico, y sonda de radio R arbitrario (dentro o más allá del régimen de OML para la captura iónica). Aprovechando la existencia de dos invariante, el sistema de ecuaciones Poisson-Vlasov se escribe como una ecuación integro-diferencial, la cual se discretiza mediante un método de diferencias finitas. El sistema de ecuaciones algebraicas no lineal resultante se ha resuelto de con un método Newton-Raphson paralelizado. Los resultados, comparados satisfactoriamente con el análisis analítico, proporcionan la emisión de corriente y la estructura del plasma y del potencial electrostático. ABSTRACT An electrodynamic tether operates on electromagnetic principles and exchanges momentum through the planetary magnetosphere, by continuously interacting with the ionosphere. It is a reliable passive subsystem to deorbit spent rocket stages and satellites at its end of mission, mitigating the growth of orbital debris. A tether left bare of insulation collects electrons by its own uninsulated and positively biased segment with kilometer range, while electrons are emitted by a low-impedance active device at the cathodic end, such as a hollow cathode, to emit the full electron current. In the absence of an active cathodic device, the current flowing along an orbiting bare tether vanishes at both ends and the tether is said to be electrically floating. For negligible thermionic emission and orbital-motion-limited (OML) collection throughout the entire tether (electron/ion collection at anodic/cathodic segment, respectively), the anodic-to-cathodic length ratio is very small due to ions being much heavier, which results in low average current and Lorentz drag. The electride C12A7 : e−, which might present a possible work function as low as W = 0.6 eV and moderately high temperature stability, has been proposed as coating for floating bare tethers. Thermionic emission along a thus coated cathodic segment, under heating in space operation, can be more efficient than ion collection and, in the simplest drag mode, may eliminate the need for an active cathodic device and its corresponding gas-feed requirements and power subsystem, which would result in a truly “propellant-less” tether system. With this low-W coating, each elemental segment on the cathodic segment of a kilometers-long floating bare-tether would emit current as if it were part of a hot cylindrical probe uniformly polarized at the local tether bias, under 2D probe conditions that are also applied to the anodic-segment analysis. In the presence of emission, emitted electrons result in negative space charge, which decreases the electric field that accelerates them outwards, or even reverses it, decelerating electrons near the emitting probe. A double sheath would be established with electrons being emitted from the probe and ions coming from the ambient plasma. The thermionic current density, varying along the cathodic segment, might follow two distinct laws under different con ditions: i) space-charge-limited (SCL) emission or ii) full Richardson-Dushman (RDS) emission. A preliminary study on the SCL current in front of an emissive probe is presented using the orbital-motion-limited (OML) ion-collection sheath and Langmuir’s SCL electron current between cylindrical electrodes. A detailed calculation of current and bias profiles along the entire tether length is carried out with ohmic effects considered and the transition from SCL to full RDS emission is included. Analysis shows that in the simplest drag mode, under typical orbital and tether conditions, thermionic emission provides efficient cathodic contact and leads to a short cathodic section. In the previous analysis, both the transition between SCL and RDS emission and the current law for SCL condition have used a very simple model. To continue, considering an isotropic, unmagnetized, colissionless plasma and a stationary sheath, the probe-plasma contact is studied in detail for a negatively biased probe with thermionic emission. The possible trapped particles are ignored and this study includes both semianalytical solutions using asymptotic analysis and complete numerical solutions. Under conditions of i) high bias, ii) R = Rmax for ion OML collection validity, and iii) monotonic potential, a self-consistent asymptotic analysis is carried out for the complex plasma structure involving all three charge species (plasma electrons and ions, and emitted electrons) and four distinct spatial regions using orbital motion theories and kinetic modeling of the species. Although emitted electrons present negligible space charge far away from the probe, their effect cannot be neglected in the global analysis for the sheath structure and two thin layers in between the sheath and the quasineutral region. The parametric conditions for the current to be space-chargelimited are obtained. It is found that thermionic emission increases the range of probe radius for OML validity and is greatly more effective than ion collection for cathodic contact of tethers. In the numerical code, the orbital motions of all three species are modeled for both monotonic and non-monotonic potential, and for any probe radius R (within or beyond OML regime for ion collection). Taking advantage of two constants of motion (energy and angular momentum), the Poisson-Vlasov equation is described by an integro differential equation, which is discretized using finite difference method. The non-linear algebraic equations are solved using a parallel implementation of the Newton-Raphson method. The results, which show good agreement with the analytical results, provide the results for thermionic current, the sheath structure, and the electrostatic potential.

Mycorrhizal preferences and fine spatial structure of the epiphytic orchid Epidendrum rhopalostele

• Premise of the study: The presence of compatible fungi is necessary for epiphytic orchid recruitment. Thus, identifying associated mycorrhizal fungi at the population level is essential for orchid conservation. Recruitment patterns may also be conditioned by factors such as seed dispersal range and specific environmental characteristics. • Methods: In a forest plot, all trees with a diameter at breast height >1 cm and all individuals of the epiphytic orchid Epidendrum rhopalostele were identified and mapped. Additionally, one flowering individual of E. rhopalostele per each host tree was randomly selected for root sampling and DNA extraction. • Key results: A total of 239 E. rhopalostele individuals were located in 25 of the 714 potential host trees. Light microscopy of sampled roots showed mycorrhizal fungi in 22 of the 25 sampled orchids. Phylogenetic analysis of ITS1-5.8S-ITS2 sequences yielded two Tulasnella clades. In four cases, plants were found to be associated with both clades. The difference between univariate and bivariate K functions was consistent with the random labeling null model at all spatial scales, indicating that trees hosting clades A and B of Tulasnella are not spatially segregated. The analysis of the inhomogenous K function showed that host trees are not clustered, suggesting no limitations to population-scale dispersal. χ2 analysis of contingency tables showed that E. rhopalostele is more frequent on dead trees than expected. • Conclusions: Epidendrum rhopalostele establishes mycorrhizal associations with at least two different Tulasnella species. The analysis of the distribution patterns of this orchid suggests a microsite preference for dead trees and no seed dispersal limitation.

Low work-function thermionic emission and orbital-motion-limited ion collection at bare-tether cathodic contact

With a thin coating of low-work-function material, thermionic emission in the cathodic segment of bare tethers might be much greater than orbital-motion-limited (OML) ion collection current. The space charge of the emitted electrons decreases the electric field that accelerates them outwards, and could even reverse it for high enough emission, producing a potential hollow. In this work, at the conditions of high bias and relatively low emission that make the potential monotonic, an asymptotic analysis is carried out, extending the OML ion-collection analysis to investigate the probe response due to electrons emitted by the negatively biased cylindrical probe. At given emission, the space charge effect from emitted electrons increases with decreasing magnitude of negative probe bias. Although emitted electrons present negligible space charge far away from the probe, their effect cannot be neglected in the global analysis for the sheath structure and two thin layers in between sheath and the quasineutral region. The space-charge-limited condition is located. It is found that thermionic emission increases the range of probe radius for OML validity and is greatly more effective than ion collection for cathodic contact of tethers.

Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius

Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 Å resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA–protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this “closed” conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.

The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand

The normal function of human intercellular adhesion molecule-1 (ICAM-1) is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 binds to leukocyte function-associated antigen (LFA-1) or macrophage-1 antigen (Mac-1). However, ICAM-1 is also used as a receptor by the major group of human rhinoviruses and is a catalyst for the subsequent viral uncoating during cell entry. The three-dimensional atomic structure of the two amino-terminal domains (D1 and D2) of ICAM-1 has been determined to 2.2-Å resolution and fitted into a cryoelectron microscopy reconstruction of a rhinovirus–ICAM-1 complex. Rhinovirus attachment is confined to the BC, CD, DE, and FG loops of the amino-terminal Ig-like domain (D1) at the end distal to the cellular membrane. The loops are considerably different in structure to those of human ICAM-2 or murine ICAM-1, which do not bind rhinoviruses. There are extensive charge interactions between ICAM-1 and human rhinoviruses, which are mostly conserved in both major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is known to be mediated by a divalent cation bound to the insertion (I)-domain on the α chain of LFA-1 and the carboxyl group of a conserved glutamic acid residue on ICAMs. Domain D1 has been docked with the known structure of the I-domain. The resultant model is consistent with mutational data and provides a structural framework for the adhesion between these molecules.

The underlying pathway structure of biochemical reaction networks

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function.

Structure-based conformational preferences of amino acids

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for α-helices and β-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.

The lipid bilayer determines helical tilt angle and function in lactose permease of Escherichia coli

The structure of lactose permease from Escherichia coli in its lipid environment was studied by attenuated total reflection Fourier transform infrared spectroscopy. The protein exhibits an α-helical content of about 65% and about 25% β-sheet. Unusually fast hydrogen/deuterium (H/D) exchange to 90–95% completion suggests a structure that is highly accessible to the aqueous phase. An average tilt angle of 33° for the helices was found with respect to the bilayer normal at a lipid-to-protein ratio of ≈800:1 (mol/mol), and the permease exhibits optimal activity under these conditions. However, upon decreasing the lipid-to-protein ratio, activity decreases continuously in a manner that correlates with the decrease in the lipid order parameter and the increase in the average helical tilt angle. Taken together, the data indicate that the structure and function of the permease are strongly dependent on the order and integrity of the lipid bilayer.

Genetic definition of a protein-splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution

Inteins are protein-splicing elements, most of which contain conserved sequence blocks that define a family of homing endonucleases. Like group I introns that encode such endonucleases, inteins are mobile genetic elements. Recent crystallography and computer modeling studies suggest that inteins consist of two structural domains that correspond to the endonuclease and the protein-splicing elements. To determine whether the bipartite structure of inteins is mirrored by the functional independence of the protein-splicing domain, the entire endonuclease component was deleted from the Mycobacterium tuberculosis recA intein. Guided by computer modeling studies, and taking advantage of genetic systems designed to monitor intein function, the 440-aa Mtu recA intein was reduced to a functional mini-intein of 137 aa. The accuracy of splicing of several mini-inteins was verified. This work not only substantiates structure predictions for intein function but also supports the hypothesis that, like group I introns, mobile inteins arose by an endonuclease gene invading a sequence encoding a small, functional splicing element.

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-Å crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.