bluuebunny/crossref_metadata_2025 huggingface dataset:
From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes
Authors: Heath Allison P. , Kavraki Lydia E. , Clementi Cecilia
Published: May 2007

Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time‐scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all‐atom protein structures starting from the Cα atom positions, as obtained for instance from extensive coarse‐grain simulations. The method, a reconstruction algorithm for coarse‐grain structures (RACOGS), is validated by reconstructing ensembles of coarse‐grain structures obtained during folding simulations of the proteins src‐SH3 and S6. The results show that RACOGS consistently produces low energy, all‐atom structures. A comparison of the free energy landscapes calculated using the coarse‐grain structures versus the all‐atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. © 2007 Wiley‐Liss, Inc.
FLIPDock: Docking flexible ligands into flexible receptors
Authors: Zhao Yong , Sanner Michel F.
Published: May 2007

Conformational changes of biological macromolecules when binding with ligands have long been observed and remain a challenge for automated docking methods. Here we present a novel protein–ligand docking software called FLIPDock (Flexible LIgand–Protein Docking) allowing the automated docking of flexible ligand molecules into active sites of flexible receptor molecules. In FLIPDock, conformational spaces of molecules are encoded using a data structure that we have developed recently called the Flexibility Tree (FT). While the FT can represent fully flexible ligands, it was initially designed as a hierarchical and multiresolution data structure for the selective encoding of conformational subspaces of large biological macromolecules. These conformational subspaces can be built to span a range of conformations important for the biological activity of a protein. A variety of motions can be combined, ranging from domains moving as rigid bodies or backbone atoms undergoing normal mode‐based deformations, to side chains assuming rotameric conformations. In addition, these conformational subspaces are parameterized by a small number of variables which can be searched during the docking process, thus effectively modeling the conformational changes in a flexible receptor. FLIPDock searches the variables using genetic algorithm‐based search techniques and evaluates putative docking complexes with a scoring function based on the AutoDock3.05 force‐field.

In this paper, we describe the concepts behind FLIPDock and the overall architecture of the program. We demonstrate FLIPDock's ability to solve docking problems in which the assumption of a rigid receptor previously prevented the successful docking of known ligands. In particular, we repeat an earlier cross docking experiment and demonstrate an increased success rate of 93.5%, compared to original 72% success rate achieved by AutoDock over the 400 cross‐docking calculations. We also demonstrate FLIPDock's ability to handle conformational changes involving backbone motion by docking balanol to an adenosine‐binding pocket of protein kinase A. Proteins 2007. © 2007 Wiley‐Liss, Inc.
SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles
Authors: Bueno Marta , Camacho Carlos J. , Sancho Javier
Published: May 2007

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5‐to‐40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20–30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute–solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Pactolus I‐domain: Functional switching of the Rossmann fold
Authors: Sen Mehmet , Legge Glen B.
Published: May 2007

Murine Pactolus is a neutrophil‐specific single chain glycoprotein that plays a role as an apoptosis marker for macrophages. The extracellular region of the protein shows strong sequence similarities to integrin β‐subunits. Critical sequence modifications differentiate its function when compared to the integrin family. We show experimentally that Pactolus I‐domain does not bind divalent metal ions, indicating that ligand binding is not mediated through a metal ion‐dependent adhesion site (MIDAS). NMR data was used to map secondary structure and the strand pairing within the β‐sheet to confirm an overall Rossmann fold topology. Homology modeling enhanced by the NMR data was used to determine the overall structure, with two key loop insertions/deletions (insertion 2 and SDL) that distinguish the Pactolus I‐domain from the integrin α I‐domain and β I‐domains. NMR peak exchange broadening is observed due to dimerization, correlating to the β I‐domain and β propeller heterodimerization region within the integrin headpiece. Two unique N‐linked glycosylation sites (Asn151 and Asn230) within this region disrupt dimerization and may account for why Pactolus is not found to associate with an α‐subunit. These changes in quaternary structure, ligand binding loops, glycosylation, and metal sites illustrate how evolution has rapidly and effectively altered key aspects of the integrin β‐subunit to derive a protein of novel function on an existing protein scaffold. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Ranking the factors that contribute to protein β‐sheet folding
Authors: Parisien Marc , Major François
Published: May 2007

The formation of β‐sheet domains in proteins involves five energetically important factors: the formation of networks of hydrogen bonds and hydrophobic faces, and the residue propensities, or preferences, to be found at the edges of the β‐sheet, to adopt the extended conformation, and to make contact with other residues. These relative energy contributions define a potential energy function. Here, we show how optimizing this potential energy function reveals the formation of hydrophobic faces as the utmost factor. The potential energy function was optimized to minimize the Z‐scores of the native topologies among the exhaustive sets of over 400 different β‐sheets. These results corroborate with experimental data that showed the environment of a protein is an important modulator of β‐sheet folding. The contact propensities were found to be the least important, which could explain the poor predictive power of β‐strand alignment methods based on pair‐wise contact matrices. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The relationship between N‐gram patterns and protein secondary structure
Authors: Vries John K. , Liu Xiong , Bahar Ivet
Published: May 2007

An n‐gram pattern (NP{n,m}) in a protein sequence is a set of n residues and m wildcards in a window of size n+m. Each window of n+m amino acids is associated with a collection of NP{n,m} patterns based on the combinatorics of n+m objects taken m at a time. NP{n,m} patterns that are shared between sequences reflect evolutionary relationships. Recently the authors developed an alignment‐independent protein classification algorithm based on shared NP{4,2} patterns that compared favorably to PSI‐BLAST. Theoretically, NP{4,2} patterns should also reflect secondary structure propensity since they contain all possible n‐grams for 1 ≤ n ≤ 4 and a window of 6 residues is wide enough to capture periodicities in the 2 ≤ n ≤ 5 range. This sparked interest in differentiating the information content in NP{4,2} patterns related to evolution from the content related to local propensity. The probability of α‐, β‐, and coil components was determined for every NP{4,2} pattern over all the chains in the Protein Data Bank (PDB). An algorithm exclusively based on the Z‐values of these distributions was developed, which accurately predicted 71–76% of α‐helical segments and 62–67% of β‐sheets in rigorous jackknife tests. This provided evidence for the strong correlation between NP{4,2} patterns and secondary structure. By grouping PDB chains into subsets with increasing levels of sequence identity, it was also possible to separate the evolutionary and local propensity contributions to the classification process. The results showed that information derived from evolutionary relationships was more important for β‐sheet prediction than α‐helix prediction. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Pest management programmes in vineyards using male mating disruption
Authors: Harari Ally R , Zahavi Tirtza , Gordon Dvora , Anshelevich Leonid , Harel Miriam , Ovadia Shmulik , Dunkelblum Ezra
Published: May 2007

Israeli vine growers have been reluctant to adopt the mating disruption technique for control of the European vine moth, Lobesia botrana Den. & Schiff. Since the chemically controlled honeydew moth, Cryptoblabes gnidiella Mill., coexists with the European vine moth, growers have maintained that the use of mating disruption would fail to bring about a significant reduction in pesticide use. In this study, the efficacy of mating disruption techniques against C. gnidiella was tested, as well as the effect of these methods on pesticide use and damage to clusters when the method was employed against both of the pests in wine grapes. Comparisons were made between plots treated with (1) L. botrana mating disruption pheromone, (2) L. botrana and C. gnidiella mating disruption pheromones and (3) control plots. A significant difference in the number of clusters infested with the developmental stages of the moths was seen between pheromone‐treated plots and controls, while no such difference was observed between plots treated with one versus two pheromones. A similar pattern was observed in the number of insecticide applications; the greatest number of applications was used in control plots, followed by plots treated with L. botrana mating disruption pheromone and by plots treated with pheromones against both pests, in which no pesticides were applied. Copyright © 2007 Society of Chemical Industry
Toxicity of insecticides to the sweetpotato whitefly (Hemiptera: Aleyrodidae) and its natural enemies
Authors: Bacci Leandro , Crespo André LB , Galvan Tederson L , Pereira Eliseu JG , Picanço Marcelo C , Silva Gerson A , Chediak Mateus
Published: May 2007

Efficient chemical control is achieved when insecticides are active against insect pests and safe to natural enemies. In this study, the toxicity of 17 insecticides to the sweetpotato whitefly, Bemisia tabaci (Gennadius), and the selectivity of seven insecticides to natural enemies of this insect pest were evaluated. To determine the insecticide toxicity, B. tabaci adults were exposed to abamectin, acephate, acetamiprid, cartap, imidacloprid, malathion, methamidophos, bifenthrin, cypermethrin, deltamethrin, esfenvalerate, fenitrothion, fenpropathrin, fenthion, phenthoate, permethrin and trichlorphon at 50 and 100% of the field rate (FR), and to water (untreated control). To determine the insecticide selectivity, adults of Encarsia sp., Acanthinus sp., Discodon sp. and Lasiochilus sp. were exposed to abamectin, acephate, acetamiprid, cartap, imidacloprid, malathion and methamidophos at 50 and 100% FR, and to water. Groups of each insect species were exposed to kale leaves preimmersed in each treatment under laboratory conditions. Mortality of exposed individuals was recorded 24 h after treatment. Cartap and imidacloprid at 50 and 100% FR and abamectin and acetamiprid at 100% FR showed insecticidal activity to B. tabaci adults. Abamectin at 50 and 100% FR was the least insecticidal compound to the natural enemies Acanthinus sp., Discodon sp. and Lasiochilus sp. The present results suggest that abamectin at 100% FR may decrease B. tabaci field populations but can still be harmless to predators. Implications of these results within an integrated pest management context are discussed. Copyright © 2007 Society of Chemical Industry
A review of name‐based ethnicity classification methods and their potential in population studies
Authors: Mateos Pablo
Published: May 2007

Several approaches have been proposed to classify populations into ethnic groups using people's names, as an alternative to ethnicity self‐identification information when this is not available. These methodologies have been developed, primarily in the public health and population genetics literature in different countries, in isolation from and with little participation from demographers or social scientists. The objective of this paper is to bring together these isolated efforts and provide a coherent comparison, a common methodology and terminology in order to foster new research and applications in this promising and multidisciplinary field. A systematic review has been conducted of the most representative studies that develop new name‐based ethnicity classifications, extracting methodological commonalities, achievements and shortcomings; 13 studies met the inclusion criteria and all followed a very similar methodology to create a name reference list with which to classify populations into a few most common ethnic groups. The different classifications' sensitivity varies between 0.67 and 0.95, their specificity between 0.80 and 1, their positive predicted value between 0.70 and 0.96, and their negative predicted value between 0.96 and 1.

Name‐based ethnicity classification systems have a great potential to overcome data scarcity issues in a wide variety of key topics in population studies, as is proved by the 13 papers analysed. Their current limitations are mainly due to a restricted number of names and a partial spatio‐temporal coverage of the reference population data‐sets used to produce name reference lists. Improved classifications with extensive population coverage and higher classification accuracy levels will be achieved by using population registers with wider spatio‐temporal coverage. Furthermore, there is a requirement for such new classifications to include all of the potential ethnic groups present in a society, and not just one or a few of them. Copyright © 2007 John Wiley & Sons, Ltd.
Application of microsize light‐emitting diode structure for monolithic optoelectronic integrated circuits
Authors: Moon S. Y. , Yonezu H. , Furukawa Y. , Morisaki Y. , Yamada S. , Wakahara A.
Published: May 2007

A Si/III–V–N alloys/Si structure was grown on a Si substrate by solid‐source molecular beam epitaxy (SSMBE) with an rf plasma nitrogen source and electron‐beam (EB) evaporator. A two‐dimensional (2D) growth mode was maintained during the growth of all layers. High‐resolution X‐ray diffraction (HRXRD) revealed that the structure had a small lattice mismatch to the Si substrate. InGaPN/GaPN double‐heterostructure (DH) light‐emitting diodes (LEDs) were fabricated on Si/III–V–N alloys/Si structure. The various sized LEDs were fabricated to put into the MOSFET for monolithic optoelectronic integrated circuits (OEIC). The luminescence properties of LEDs were evaluated by electroluminescence (EL). A double emission peak from all LED samples was observed at about 642 nm and 695 nm at room temperature (RT). As injection current increased, the emission peak wavelength changed from the peak wavelength of the InGaPN layer to that of the GaPN layer, likely due to carrier overflow of the active layer. A simplified fabrication process for the microsize LED of the unit circuit was proposed. The LEDs with emission areas from 5 × 5 μm2 to 20 × 20 μm2 were fabricated. The LED with an emission area of 5 × 5 μm2 can be applied to an optical device of a monolithic OEIC. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication of surface‐oxidized GaN crystallites for UV electroluminescent devices
Authors: Honda Tohru , Baba Taichi , Watanabe Makiko , Okuhata Takashi
Published: May 2007

The cathodoluminescence (CL) of GaN crystallites with and without surface oxide layers is reported. The CL intensity of the coated GaN crystallites is higher than that of the crystallites without oxide layers although the shapes of the coated GaN crystallites are similar to those of uncoated GaN crystallites. The surface coating with gallium oxide is effective for the reduction of surface recombination in GaN crystallites. Electroluminescent devices (ELDs) using GaN crystallites covered with gallium oxides were fabricated. UV light emission was observed from the GaN‐based ELDs at RT. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanotechnology applications: a driving force for R&D investment
Authors: Correia A. , Pérez M. , Sáenz J. J. , Serena P. A.
Published: May 2007

Nanoscience and nanotechnology represent scientific‐technical areas that in less than two decades have gone from being in the hands of a reduced group of researchers who glimpsed their great potential, to constitute one of the recognized pillars of the scientific advance for the next decades. This paper illustrates how the irruption of nanotechnology applications will directly affect human beings by substantially improving diagnosis and treatment of diseases, and also our capacities to interact with our surroundings. Worldwide governments realized the important role deserved to nanotechnology and during the last decade budgets allocated to R&D in nanotechnology have continuously increased. Following this global trend, Spanish scientists and institutions have gone from having a rather conservative attitude to promoting a number of different initiatives aiming at increasing the contribution of Spain to the development of nanoscience and nanotechnology. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative modelling of voltage oscillations and other oscillatory phenomena with the current burst model
Authors: Foca E. , Carstensen J. , Föll H.
Published: May 2007

The current burst model (CBM) has been extended to include more complex oscillatory phenomena of the Si electrode in aqueous HF. In particular it accounts for additional effects inherent to the voltage oscillations, i.e. capacitive effects, very small oxide thickness, etc. A powerful Monte‐Carlo implementation now allows to simulate all presently known aspects of electrodes. Besides current oscillations under potentiostatic conditions, the CBM can now quantitatively produce voltage oscillations and other more complex phenomena like driven oscillations in close agreement with experiments. New data extraction routines provide information about, e.g., correlation lengths and thus bridge the gap to general non‐linear pattern formation theories. The CBM is far simpler than competing theories, but is nevertheless the only model presently capable of quantitatively simulating all aspects of oscillatory phenomena of the Si electrode. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Different deposition behavior of copper on silicon and porous silicon surfaces during immersion plating
Authors: Kurokawa A. , Kawamura Y. L. , Sakka T. , Ogata Y. H.
Published: May 2007

The deposition behavior of Cu during immersion plating was investigated on Si and porous Si (PS) surfaces. The deposition of Cu could be observed on the PS surface, but not on the native Si surface. In the electrochemical characterization of the two surfaces in HF solution, a plateau of anodic current was observed at the PS structure, but not at the Si surface. The potential region of the plateau was more negative than the potential at which Si dissolution or PS formation takes place. The electrochemical measurements of the PS samples in HF solution revealed that oxidation of hydrogen remaining in the PS layer can not participate in the appearance of the anodic plateau. The different deposition behavior on the Si and PS surfaces enables selective deposition of Cu on a PS pattern drawn on n ‐type Si by laser scanning. A new patterning method of Cu on n ‐type Si by utilizing this behavior was successfully achieved. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thermal conductivity features of nanostructured CdS/Al2O3 composites
Authors: Nosova L. , Igamberdiev Kh. , Sokolov V. , Yuldashev Sh. , Shashkov A. G. , Khabibullaev P. K.
Published: May 2007

Highly ordered porous alumina (Al2O3) structures with pore diameter of 60 nm were fabricated by two‐step anodization process. CdS‐nanoparticles were grown into porous alumina template kept on Al‐substrate by using SILAR (successive ion layer adsorption and reaction) technique. The temperature dependences (10–300 K) of thermal conductivity of CdS/Al2O3 nanocomposites have been measured by pulsed method of periodical heating (3ω) which is one of the most sensitive tools for nanostructure investigation. It was shown that temperature dependences of thermal conductivity of CdS/Al2O3 nanocomposites are determined by infill degree of alumina pores. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In situ electrochemical characterization of porous n ‐InP (100)
Authors: Santinacci L. , Gonçalves A.‐M. , David C. , Eb A. , Gerard I. , Mathieu C. , Herlem M. , Etcheberry A.
Published: May 2007

Porous structures have been anodically grown onto n ‐InP (100) in HCl. Surface chemistry and pore morphology have been respectively studied by X‐ray photoelectron spectroscopy and scanning electron microscopy but in situ electrochemical investigations have been emphasized. Capacitance and photocurrent experiments have been performed while the porous etching occurred. No modifications of the electronic structure (flat band potential remains constant) are observed during the pore formation. However, for high dissolution charges, the photocurrent spectra are sharpened because the porous films behave like electrically “dead layers”. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Porous screen printed indium tin oxide (ITO) for NOx gas sensing
Authors: Mbarek H. , Saadoun M. , Bessaïs B.
Published: May 2007

Tin‐doped Indium Oxide (ITO) films were prepared by the screen printing method. Transparent and conductive ITO thin films were obtained from an organometallic based paste fired in an Infrared furnace. The Screen printed ITO films were found to be granular and porous. This specific morphology was found to be suitable for sensing different gaseous species. This work investigates the possibility of using screen printed (ITO) films as a specific material for efficient NOx gas sensing. It was found that screen printed ITO is highly sensitive and stable towards NOx, especially for gas concentration higher than 50 ppm and starting from a substrate working temperature of about 180 °C. The sensitivity of the ITO films increases with increasing NOx concentration and temperature. The sensitivity and stability of the screen printed ITO based sensors were studied within time. The ITO crystallite grain size dimension was found to be a key parameter that influencesè the gas response characteristics. Maximum gas sensitivity and minimum response time were observed for ITO films having lower crystallite size dimensions. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Single crystalline GaN grown on porous Si(111) by MOVPE
Authors: Cheng Kai , Degroote S. , Leys M. , Van Daele B. , Germain M. , Van Tendeloo G. , Borghs G.
Published: May 2007

In this work, GaN growth on porous Si(111) will be reported. The porosity of the substrates was 30% or 50%. In the latter case, various thicknesses, from 0.6 μm to 10 μm, were investigated. The morphology of the GaN surfaces was analyzed by optical interference microscopy. The crystalline quality of the epitaxial layers was characterized by High Resolution X‐Ray Diffraction (HR‐XRD) and cross‐sectional Transmission Electron Microscopy (TEM). A Full Width at Half Maximum (FWHM) of the X‐ray symmetric rocking curve (0002) 2θ – ω scan of 290 arc sec was obtained for a 1 μm thick GaN layer, which is comparable with that of GaN grown on bulk Si(111) substrates. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology and photoluminescence of anodized aluminium‐coated 6H‐SiC samples
Authors: Keffous A. , Bourenane K. , Gabouze N. , Kechouane M. , Kerdja T. , Manseri A. , Guerbous L. , Oudjaout D.
Published: May 2007

In this work, we report the effect of surface modification by aluminum metallization, prior to anodization in a solution of HF/Ethylene glycol, on the morphology and photoluminescence of p‐type porous SiC. For this purpose, a thin metallic film of aluminum has been deposited on a highly resistive 6H‐SiC. The morphology of the porous SiC layer has been investigated by Scanning Electron Microscopy (SEM). The results show that aluminum play a crucial role on the dissolution of SiC; it initiates and facilitates the electrochemical etching. The photoluminescence spectra of the anodized Al‐coated samples exhibit two emission bands centered at about 430 nm and 560 nm. While for the uncoated samples, a strong luminescence with a peak located at 560 nm is observed. Finally, the role of Al on the photoluminescence mechanism is discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical characterization of self‐ordered porous alumina membranes of various thicknesses
Authors: Marsal L. F. , Vojkuvka L. , Ferré‐Borrull J. , Trifonov T. , Pallarès J.
Published: May 2007

We present the fabrication and optical characterization of self‐ordered porous alumina membranes (PAM). The samples were fabricated by using a two‐step anodization process in 0.3 M oxalic acid at 40 V and 20 °C. PAMs of different thickness (9 μm, 24 μm and 45 μm) were obtained by applying different anodization lengths. The morphology of the PAMs was examined using a Scanning Electron Microscope in order to estimate their thickness and porosity. The optical transmission spectra of such PAMs of different thicknesses were measured by using UV‐VIS spectrometer in the range of 300–1000 nm. The refraction index and the extinction coefficient for the studied range were determined from the fitting of the measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gravimetric method to find internal surface of macroporous silicon membranes
Authors: Nechitailov A. A. , Astrova E. V. , Kukushkina Yu. A.
Published: May 2007

A simple method to evaluate the internal surface area, porosity, pore diameter and pore density of macroporous silicon membranes has been proposed and tested. The porosity p is obtained from the mass loss under anodizing, and the surface area per unit volume Sv is determined from the mass of SiO2 formed on the pore surface as a result of thermal oxidation. The average pore diameter d and pore density N can be easily calculated from the obtained Sv and p. Experimental verification of d and N was performed by means of SEM and optical microscope images; Sv was checked by BET technique. Surface area and porosity on the resistivity of initial n‐Si in the range ρ = 3–25 Ohm · cm have been studied for the samples with regular and self‐organized macropore “lattices”. The obtained values are within the limits p = 27–50%, Sv = 2800–6000 cm2/cm3, d = 1.9–6.5 μm, N = 1.4–10 × 106 cm–2, and in a good agreement with the data of microscopic characterization. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Anodisation of branched and columnar macropores in n‐type silicon under front‐side illumination
Authors: Depauw V. , Kim H. J. , Beaucarne G. , Poortmans J. , Celis J.‐P. , Mertens R.
Published: May 2007

The growth of well‐defined regular columnar macropores under front‐side illumination on medium doped n‐type silicon has been investigated. The various morphologies observed, with branched or columnar pores, differ from those reported so far on substrates of both higher and lower resistivities. Unlike stated by the macropore growth model, current density is found to influence the pore growth rate. These observations indicate that, under the conditions used in this work, the pore growth is at the border between meso‐ and macroporous mechanism. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Commercial applications of porous Si: optical filters and components
Authors: Kochergin V. , Foell H.
Published: May 2007

It is shown that porous Silicon in various geometries and morphologies can be used for novel optical elements by combining theoretical insights with suitable porous structures and some pre‐ and post‐processing of the Silicon. The paper restricts itself to light propagation in the pore direction. Theoretical and experimental results will be presented for the following novel optical elements: environmentally stable optical components from mesoporous Silicon, long wave pass filters, macroporous Silicon UV Filters, and polarization components for the UV range. Either new components are presented, mostly with first experimental results, or the state‐of‐the art for previously discussed elements is considerably improved upon. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative measurements of hydro‐alcoholic binary mixtures by porous silicon optical microsensors
Authors: De Stefano Luca , Rotiroti Lucia , Rea Ilaria , Moretti Luigi , Rendina Ivo
Published: May 2007

In this communication, we present a simple, completely reversible and well performing optical microsensor for the quantitative determination in liquid hydro‐alcoholic binary mixtures, based on the simple and low cost porous silicon (PSi) nanotechnology. In our sensor device, the transducer element is a PSi optical microcavity (PSMC) which is constituted by a Fabry‐Pérot layer between two distributed Bragg reflectors. When the device is exposed to the mixture, the partial substitution of air in the pores changes the average refractive index of PSMC, causing a red shift of its reflectivity spectrum, characteristic of the concentration of each component. We have characterized, in the 0‐100% composition range, three hydro‐alcoholic binary mixtures (water‐Ethanol, water‐ Methanol and water‐ Isopropanol) which exhibit very different behaviour. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An integrated hybrid optical device for sensing applications
Authors: De Stefano L. , Rea I. , Rotiroti L. , Fragomeni L. , Della Corte F. G. , Rendina I.
Published: May 2007

We present the design and the fabrication of an integrated hybrid optical sensor for liquid and gas sensing based on the anodic bonding technique. The device is composed by three distinct elements separately realised and then joined together: a planar SOI waveguide, a porous silicon micro‐chamber and a glass slide. The presence of a liquid or gaseous substance in the reaction chamber is revealed as a change in the propagation characteristic of the guided mode. In case of exposure to methanol, the preliminary experimental results show that the propagation of the laser beam, coupled into the SOI waveguide, has been efficiently modulated. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Composite structures of porous silicon and polyaniline for optoelectronic applications
Authors: Urbach B. , Korbakov N. , Bar‐david Y. , Yitzchaik S. , Sa'ar A.
Published: May 2007

Composite structures of p‐type meso‐porous silicon (PS) and polyaniline (PAN) have been fabricated by electrochemical polymerization process. The composite structure provides a unique way to control the conduction either through the porous silicon matrix or via the polyaniline, by changing the polarity of the applied bias voltage. In addition, photoluminescence (PL) experiments revealed enhanced PL emission at the green wavelengths that are originated from the polyaniline network, rather than the porous silicon. The above composite structure can be used as a building block for improved electroluminescence and light emitting devices in a wide range of applications. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication of UV filters from porous silicon at low temperatures
Authors: Becerra D. , Agarwal V.
Published: May 2007

In the present work we study the influence of the anodization temperature on the morphology and optical properties of porous silicon monolayers and multilayers. UV filters for the wavelength range of 200– 400 nm were fabricated at low temperatures and their optical response was compared with the metallic mirrors as well as with the filters made at room temperature. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tunable one‐dimensional photonic crystal structures based on grooved Si infiltrated with liquid crystal E7
Authors: Perova T. S. , Tolmachev V. A. , Astrova E. V. , Zharova Yu. A. , O'Neill S. M.
Published: May 2007

Tuning of a photonic band gap in a composite one‐dimensional photonic crystal structure infiltrated with nematic liquid crystal E7 has been evaluated by simulations. It has been found that a sufficient shift of the short wavelength edge, λ edge of a main photonic band gap can be obtained in structures with a pronounced initial alignment of the liquid crystal director in the grooves of a single crystalline Si matrix. The largest effect is predicted for the reorientation of liquid crystal molecules from planar homogeneous alignment along the grooves to homeotropic alignment with respect to the Si walls due to an electro‐optical effect. The shift in photonic band gap due to thermal tuning, resulting from the transition of liquid crystal from the mesophase to the isotropic phase, is less than for electric tuning. Thermo‐tuning has been demonstrated experimentally. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of porous silicon Thue‐Morse structures
Authors: De Stefano Luca , Rea Ilaria , Rotiroti Lucia , Moretti Luigi , Rendina Ivo
Published: May 2007

Dielectric aperiodic Thue‐Morse structures up to 128 layers have been realized by the porous silicon technology. Normal incidence reflectivity measurements have been performed to investigate the photonic properties of the devices. A partial photonic band gap region, centered at 1100 nm and 70 nm wide has been observed for the S6 and S7 Thue‐Morse structures. The S6 multilayer has been studied as sensor device on exposure to several chemical substances. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A new approach based on transfer matrix formalism to characterize porous silicon layers by reflectometry
Authors: Pirasteh P. , Boucher Y. G. , Charrier J. , Dumeige Y.
Published: May 2007

We use reflectometry coupled to transfer matrix formalism in order to investigate the comparative effect of surface (localized) and volume (distributed) losses inside a porous silicon monolayer. Both are modeled as fictive absorption. Surface losses are described as a Dirac‐like singularity of permittivity localized at an interface whereas volume losses are described trough the imaginary part of the porous silicon complex permittivity. A good agreement with experimental data is determined by this formalism. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Capacitance method for determination of basic parameters of porous silicon
Authors: Adamyan A. , Adamian Z. , Aroutiounian V.
Published: May 2007

Microstructure and physical characteristics of porous silicon (PS), such as thickness, bulk porosity, dielectric permittivity, and refractive index depend directly on the production conditions, e.g., on the electrolyte composition, anodizing current density, duration of etching etc. Many various possibilities of applications of PS generate high interest towards elaboration of new or modified operative nondestructive methods for testing the microstructure characteristics of PS layer for the adjustment of its processing regimes. According to the mechanism of formation of porous silicon and experimental data on the morphology of PS layers, a porous layer represented as a structure with cylindrical pores of equal lengths piercing the silicon frame. This approximation allows considering the structure using the parallel plate model with in parallel connected capacitances of the silicon frame and the air or liquid dielectric filled pores. A method for obtaining information on the volume porosity, thickness, and dielectric permittivity of a PS layer by means of two measurements of the structure capacitance – in dry air and when the pores are filled by a condensed medium having a dielectric permittivity strongly differing from that of air (e.g., methanol) is described. Sufficiently good agreement has been revealed between the data calculated from the capacitance measurements and obtained by other methods. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Impedance spectroscopy of in‐plane anisotropic porous silicon films
Authors: Forsh P. A. , Martyshov M. N. , Timoshenko V. Yu. , Kashkarov P. K.
Published: May 2007

Free‐standing porous silicon films prepared from heavily boron‐doped (110) Si wafers are investigated by means of the impedance spectroscopy in the frequency range from 5 Hz to 10 MHz. The AC electrical conductivity of the films is found to be significantly larger along the [1$ \bar 1 $0] in‐plane crystallographic direction than that along the [001] one. While the AC conductivity anisotropy decreases with increasing frequency, the capacity anisotropy exhibits non‐monotonic frequency dependence. The experimental results are explained by considering potential barriers for charge carrier transport between anisotropic Si nanocrystals in porous silicon films. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of form anisotropy of silicon nanocrystals on birefringence and dichroism in porous silicon
Authors: Efimova A. I. , Krutkova E. Yu. , Golovan L. A. , Timoshenko V. Yu. , Kashkarov P. K.
Published: May 2007

Artificial anisotropic optical media based on nanostructured silicon formed by electrochemical porosifying of Si substrates are investigated. Strong birefringence and dichroism of surface silicon‐hydrogen bonds vibrations are found in the infrared spectral range. A comprehensive analysis of the absorption bands corresponding to the deformation and stretching modes is performed. The experimental results are discussed in terms of an effective medium model, taking into account the morphological anisotropy of Si nanocrystals in porous Si layers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The birefringence level of anisotropically nanostructured silicon
Authors: Diener J. , Künzner N. , Gross E. , Kovalev D. , Timoshenko V. Yu. , Fujii M.
Published: May 2007

We present a detailed study of the anisotropic optical properties of mesoporous silicon layers prepared from substrates having different doping levels under various preparation conditions. It is demonstrated that the morphology of the layers strongly depends on the preparation conditions. The experimental data are explained in the framework of an effective medium model which takes into account different morphologies of the layers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An investigation of an etch‐through process on porous silicon
Authors: Kan P. Y. Y. , Finstad T. G.
Published: May 2007

An etch–through process on porous silicon (PS) has been investigated. A macro‐(>50 nm) and meso‐(10‐50 nm) PS were fabricated by electrochemical anodisation process. A normal electrochemical etching from the front‐side will only yield some parts of the area being etched all the way through the wafer, due to the statistical process which leads to an uneven etch front towards the back‐side of the wafer. A new method has been tried in which a thin PS layer was fabricated at the back‐side before etching. The etch‐through PS apparently shows that all the pores were past through the wafer for the whole etching area (1 cm2). The etch data were recorded and were plotted as voltage and temperature against time. An etch‐through thin meso PS membrane (10‐50 nm diameter, 50‐100 µm thick) has also been investigated. The PS were characterized by scanning electron microscopy. A proposed model for the etch‐through PS is discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pressure mediated release of hydrogen from silicon co‐implanted with H2+ and He+
Authors: Misiuk Andrzej , Barcz Adam
Published: May 2007

Hydrogen out‐diffusion from porous‐like buried layers prepared in single crystalline Si by implantation with hydrogen (Si:H) or hydrogen and helium (Si:H, He) depends, among others, on the sequence of layers enriched with H and He and on implantation conditions. Hydrogen loss at 720–920 K decreases, increases or does not depend on hydrostatic pressure of ambient (HP, up to 1.1 GPa). This unusual effect is related to specific microstructure of Si:H, He induced under HP and to the He‐mediated energy of creation of vacancies as well as of the strength of H–Si bonds. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Formation of Ag‐Cu nanoparticles in SiO2 films by sol‐gel process and their effect on the film properties
Authors: Díaz‐Flores L. L. , Garníca‐Romo M. G. , González‐Hernández J. , Yáñez‐Limón J. M. , Vorobiev P. , Vorobiev Y. V.
Published: May 2007

Sol‐gel thin films and microcrystalline powders of SiO2 doped with Ag and Cu were obtained under environmental conditions of pressure and temperature. The precursor material was a mixture of water, tetraethyl‐orthosilicate, ethanol and aqueous solutions of Ag and Cu salts, the components were taken in ratios known to provide SiO2 matrix material with good structure. The annealing was performed in oxidizing and reducing atmosphere, the temperature varied in the range of 100–800 °C. Formation of metal particles of 100 nm order of magnitude was confirmed by X‐ray, optical and SEM analysis. In presence of metal particles, the SiO2 matrix was crystallized in α‐cristobalite at annealing temperature as low as 500 °C, and in quartz form at 800 °C. A simple model treating the metal‐induced low‐temperature crystallization is presented. The material obtained is promising for the use as optical filter, gas sensing element and antibacterial agent. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Regular patterning of PS substrates by a self‐assembled mask
Authors: Nagy N. , Pap A. E. , Deák A. , Volk J. , Horváth E. , Hórvölgyi Z. , Bársony I.
Published: May 2007

Regularly ordered porous structures were fabricated in ion‐implanted p‐ and n‐type silicon. Mono‐layered Langmuir‐Blodgett (LB) films and a double‐layered film from Stöber silica spheres of 350 nm diameter were used as masking layers in the boron and phosphorus ion‐implantation step, providing the laterally periodic doping structure. The various ordered porous structures are obtained after the anodic etch process. The PS layer can be removed by alkaline etching. The masking LB silica layer and the resulting structures are shown in the SEM images. Using the self‐assembled nanoparticles, regular patterns of high resolution can easily be prepared in an inexpensive manner on large area silicon. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gradient‐porous structure of silicon
Authors: Starkov V. , Gavrilin E.
Published: May 2007

Silicon membranes with through pores have been manufactured based on silicon plates with a gradient‐porous structure (GPSi), in which the pore cross section and structure varies with depth. The obtained structure can serve a basis for the development of electrodes for solid polymer fuel cells. The developed technology allows to change porosity and porous morphology on all thickness of a porous membrane. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polymer supported porous TiO2: application to photo‐catalysis
Authors: Saadoun M. , Chorfi H. , Bousselmi L. , Bessaïs B.
Published: May 2007

This work concerns the preparation and characterization of polymer supported adhesive TiO2 films starting from the P25 TiO2 powder. For this purpose, we prepared a TiO2 based paste and used the screen printing method. The annealing temperature of the screen printed layers was chosen taking into account the variation of the composition ratio and morphology of the TiO2 powder. X‐Ray Diffraction (XRD) analyses show that the TiO2 powder conserves the same anatase/rutile composition at annealing temperatures below 600 °C, beyond the rutile TiO2 phase increases. Annealing dependence of the morphological features of the TiO2 powder was investigated by Atomic Force Microscopy (AFM). XRD and AFM investigations enabled us preparing flexible polymer supported porous TiO2 films (mostly anatase), just by choosing temperatures that allow elimination of the organic inks forming the screen printing paste. Scanning Electron Microscopy (SEM) shows that polymer supported TiO2 films are inhomogeneous and porous, which make them highly suitable for photo‐catalysis applications. The photo‐catalytic performances of the polymer supported porous TiO2 films were experienced on a typical textile dye by absorbance measurements using UV‐Visible spectroscopy. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Low refractive index porous silicon multilayer with a high reflection band
Authors: Xifré Pérez E. , Pallarès J. , Ferré‐Borrull J. , Trifonov T. , Marsal L. F.
Published: May 2007

We present the fabrication and characterization of a one‐dimensional photonic crystal consisting of the periodic repetition of two porous silicon layers with different refractive index. The refractive indices of the single layers have been determined from experimental measurements using two different methods. Both methods lead to the same results: the obtained average refractive index for a current density of J = 30 mA/cm2 is 1.7 and for J = 70 mA/cm2 is 1.3. The reflectivity spectrum of the studied multilayer for different angles of incidence has been measured and a good agreement with the simulation of the structure has been achieved. It has been observed that it presents a high reflectivity band in the NIR. Besides, we show that the projected band structure of the multilayer can be used for the analysis of the reflectivity results. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of duty cycle and frequency on the morphology of porous silicon formed by alternating square pulse anodic etching
Authors: Escorcia J. , Agarwal V.
Published: May 2007

In this work we report the fabrication and characterization of porous silicon formed by alternating square pulse anodization. The effect of duty cycle (5–100%) and frequency was studied for porous silicon samples made with highly doped silicon wafers, under the same equivalent charge condition. The high resolution scanning electron microscopy images reveal that, under the same conditions of current and frequency, there exists an optimum value of duty cycle (20%), at which the structure exhibits superior characteristics. Maintaining the same charge supplied during the positive square pulse for the total anodization time, with a 10 mA/cm2 current density and 5% duty cycle, samples were fabricated at different frequencies (from constant current to 100 Hz) and the etching rate/thickness of the PSL formed at a 10 Hz frequency is found to be maximum, indicating that the response of the electrochemical reaction is maximum at this frequency. However, a reduction in the interface roughness between porous silicon and crystalline Si is obtained only at high frequencies. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)