Paracrystalline Structures Research Articles

Microstructure characterization of transition films from amorphous to nanocrocrystalline silicon

Hydrogenated silicon (Si:H) films near the threshold of crystallinity were prepared by very high-frequency plasma-enhanced chemical vapor deposition (VHF-PECVD) using a wide range of hydrogen dilution R H=[H 2]/[SiH 4] values of 2–100. The effects of H dilution R H on the structural properties of the films were investigated using micro-Raman scattering and Fourier transform infrared (FTIR) absorption spectroscopy. The obtained Raman spectra show that the H dilution leads to improvements in the short-range order and the medium-range order of the amorphous network and then to the morphological transition from amorphous to crystalline states. The onset of this transition locates between R H=30 and 40 in our case, and with further increasing R H from 40 to 100, the nanocrystalline volume fraction increases from ∼23% to 43%, and correspondingly the crystallite size enlarges from ∼2.8 to 4.4 nm. The FTIR spectra exhibit that with R H increasing, the relative intensities of both the SiH stretching mode component at 2100 cm −1and wagging mode component at 620 cm −1 increase in the same manner. We assert that these variations in IR spectra should be associated with the formation of paracrystalline structures in the low H dilution films and nanocrystalline structures in the high H dilution films.

Structural Analysis for Cellulose Fibers Treated by High Pressure Steam.

Morphology of high-pressure steamed cellulose fabrics were investigated using viscose rayon fabrics.Viscose rayon fabrics were steamed at several conditions without (dry-condition) and with (wet-condition) excess water.X-ray diffractometry revealed that the total crystallinity increased with generating cellulose Ⅳ.There were no dependences whether dry- or wet-steaming in their crystal forms.It is suggested that cellulose Ⅳ is generated from paracrystalline structure in the amorphous region.Further, steamed rayons were dyed by 5 kinds of reactive dyes to analyze the amorphous region.The relative color depths (K⁄S value) compared with the control were much decreased in dry-steamed viscose rayons whereas there was a slight difference in wet-steamed ones.The excess water at steaming showed a strong role to control the structure of the amorphous region.

Ultrastructure of spermatogenesis in the free-living marine nematodePontonema vulgare(Enoplida, Oncholaimidae)

Spermatogenesis in testes of the free-living marine nematode Pontonema vulgare was studied with electron microscopy. The nucleus of spermatocytes has a large nucleolus; the cytoplasm is filled with numerous ribosomes, mitochondria, cisternae of the rough endoplasmic reticulum (RER), Golgi bodies, and flattened osmiophilic cisternae, which are interpreted as the modified membranous organelles (MO) of the spermatozoa of other nematodes studied. After completion of the second meiotic telophase, the nucleus is surrounded by a newly formed nuclear envelope. Further nucleus transformation includes condensation of the chromatin and shrinkage of the nuclear envelope. The deep infoldings of the nuclear envelope give a starlike shape to the nuclei. The cytoplasm of the early spermatids contains the same organelles as in the late spermatocytes, including MO. Many of the latter assume a cuplike or pocketlike shape. During spermatogenesis the peripheral cytoplasm containing the ribosomes, RER, Golgi bodies, and transparent vesicles moves to one pole of the cell forming the residual body. The main cell body of the late spermatid includes the nucleus, mitochondria, and MO embedded in a dense filamentous matrix. The fibrous bodies (FB) of a paracrystalline structure occur in spermatids throughout their developmental transformations. The central part of the spermatozoa contains a starlike nucleus with a nuclear envelope. The filamentous cytoplasm of the spermatozoa includes mitochondria and MO. The spermatozoa extracted from the testes form numerous long filopodia. The dense filamentous cytoplasm of the spermatozoa is continuous with the content of the filipodia. The reconstitution of the nuclear envelope and separate development of MO and FB described in P. vulgare spermatogenesis are the special characters of enoplid nematodes. The reduced character of FB development and simplified structure of MO differentiate P. vulgare from other nematodes studied.

Sodium current modulation by a tubulin/GTP coupled process in rat neonatal cardiac myocytes.

Microtubule disassembly by colchicine increases spontaneous beating of neonatal cardiac myocytes by an unknown mechanism. Here, we measure drug effects on spontaneous calcium transients and whole cell ionic currents to define the route between microtubule depolymerization and the increase in the rate of contraction. Colchicine treatment disassembles microtubules resulting in free tubulin dimers, thereby increasing the spontaneous beating frequency and changing both the rates of rise and decay of calcium transients. In addition, colchicine treatment produces an increase of the sodium current (I(Na)) while I(Ca) is not modified. The colchicine-enhanced I(Na) was blocked by the addition of 10 microM TTX. In addition, the colchicine-induced increase of I(Na) was prevented when GTP was omitted from the patch pipette. Vinblastine also depolymerizes microtubules but re-aggregates tubulin into paracrystalline structures. Free tubulin dimers are not increased with vinblastine treatment. We found no modification in calcium transients or I(Na) in the presence of vinblastine. Action potential durations measured at 50 % and 90 % repolarization were shorter, and the dV/dt was larger, in colchicine-treated cells compared to untreated cells. The resting membrane potential and overshoot of the action potentials were comparable in both kinds of cells. Our data suggest that release of free tubulin dimers may activate G proteins, which in turn modulate the sodium channel. An increase in whole cell I(Na) changes the spontaneous firing rate and this may be the underlying cause of the increase in the frequency of contraction in neonatal cardiac myocytes. We suggest a new role for dimeric tubulin in regulating membrane excitability.

Hepatitis C Virus Nonstructural Proteins Are Localized in a Modified Endoplasmic Reticulum of Cells Expressing Viral Subgenomic Replicons

For many years our knowledge on hepatitis C virus (HCV) replication has been based on in vitro experiments or transfection studies. Recently, the first reliable system for studying viral replication in tissue culture cells was developed. Taking advantage of this system, we examined in detail the localization of viral nonstructural (NS) proteins in cells containing functional replication complexes. By fractionation experiments and immunomicroscopy, we observed that all NS proteins were associated with the endoplasmic reticulum (ER) membranes, confirming the hypothesis that the ER is the site of membrane-associated HCV RNA replication. Interestingly, NS3 and NS4A were preferentially localized in endoplasmic reticulum cisternae surrounding mitochondria, suggesting additional subcellular compartment-related functions for these viral proteins. Furthermore, the immunoelectron microscopy revealed the loss of the organization and other morphological alterations of the ER (convoluted cisternae and paracrystalline structures), resembling alterations observed in liver biopsies of HCV-infected individuals and in flavivirus-infected cells.

Fine structure of the external nasal gland of two lizards (Podarcis sicula campestris and Chalcides chalcides).

In this study, we describe the ultrastructural features of the external nasal gland in two lizards: ruin lizard (Podarcis sicula campestris) and seps (Chalcides chalcides). Two secretory cell types, which differ interspecifically, have been found in the secretory endpieces of the glandular tubules in both species examined. An unusual morphological observation was the presence of paracrystalline structures in the secretory granules of the seromucous cells of the external nasal gland of the seps. These structures may be related to the packaging mechanism of glycoproteins or to their macromolecular structure. They may also reflect segregation of heterogeneous subcomponents within the same secretory granule. The striated cells are located in the distal segment of the glandular tubules, and have the typical ultrastructural features of the cells which in some species of reptiles, but not in these two lizards, are known to be capable of elaborating a hyperosmotic saline solution.

Immunoelectron microscopical detection of tubulins during spermiogenesis in phytophagous bugs (Hemiptera: Pentatomidae)

Summary Ultrastructural and immunocytochemical studies were carried out in the tail region of spermatids and spermatozoa of the phytophagous bugs, Acrosternum aseadum and Euchistus heros. The axoneme presented a 9+9+2 microtubule pattern and bridges occurred between axonemal microtubules 1, 5, and mitochondrial derivatives. Two paracrystalline structures, embedded in an amorphous matrix, were observed in the mitochondrial derivatives. The axonemal microtubules contained alpha, acetylated and tyrosinated tubulin. Cytoplasmic microtubules contained alpha, beta and gamma tubulin. Moreover, the gamma tubulin was detected near the electron dense rod, an element associated with the centriole, suggesting that this structure may be a microtubule organizing center.

Structure and physical properties of paracrystalline atomistic models of amorphous silicon

We have examined the structure and physical properties of paracrystalline molecular dynamics models of amorphous silicon. Simulations from these models show qualitative agreement with the results of recent mesoscale fluctuation electron microscopy experiments on amorphous silicon and germanium. Such agreement is not found in simulations from continuous random network models. The paracrystalline models consist of topologically crystalline grains which are strongly strained and a disordered matrix between them. We present extensive structural and topological characterization of the medium range order present in the paracrystalline models and examine their physical properties, such as the vibrational density of states, Raman spectra, and electron density of states. We show by direct simulation that the ratio of the transverse acoustic mode to transverse optical mode intensities ITA/ITO in the vibrational density of states and the Raman spectrum can provide a measure of medium range order. In general, we conclude that the current paracrystalline models are a good qualitative representation of the paracrystalline structures observed in the experiment and thus provide guidelines toward understanding structure and properties of medium-range-ordered structures of amorphous semiconductors as well as other amorphous materials.

The Structure of Mast Cell Secretory Granules in the Blind Mole Rat (Spalax ehrenbergi)

Eosinophils, basophils, and mast cells produce and secrete active substances whose role is to attack invading parasites and protect the host. In this study we use morphometric methods to study mast cells in the blind mole rat (Spalax ehrenbergi). The subterranean and solitary way of life of this species has led to the evolutionary development of special anatomical, morphological, behavioral, and physiological adaptations. Because of its particular lifestyle, the mole rat is less exposed to parasites than other rodents. This could provide a unique model for research into the pathobiology of mast cells. The paracrystalline structure of the mast cell granule content is composed of parallel plates. Diffraction analysis of electron micrographs of thin sections of araldite-embedded tissues indicated that each crystal line plate is a periodic array of parallelograms. The crystal unit cell volume is approximately 930 nm3, suggesting that each unit cell is composed of one heparin molecule and one to three additional adsorbed proteins. Morphometric data show that characteristics of the secretory granules of mast cells of the blind mole rat resemble those of other rodents. The mast cell unit granule volume in the present study was calculated to be 0.055 μm3, similar to that of rat peritoneal mast cells.

Paracrystalline structure of activated carbons

Structural studies by means of neutron diffraction of activated carbons,prepared from a polymer of phenol formaldehyde resin by carbonization and activation processes, with variable porosity, arepresented. The neutron scattering data were recorded over the rangeof the scattering vector Q from 2.5 to 500 nm-1. Thestructure of activated carbons has been described in terms ofdisordered graphite-like layers with very weak interlayercorrelations. The model has been generated by computer simulationsand its validity has been tested by comparison of the experimentaland calculated intensity functions. Modelling studies have shownthat the model containing 3-4 layers each about 2 nm in diameteraccounts for the experimental data and that graphite layers arerandomly translated and rotated, according to the turbostraticstructure. Near-neighbour carbon-carbon distances of about0.139 nm and 0.154 nm have been determined. The Debye-Waller factorexp (-Q2σ2/2) with σ = σ0(r)1/2 suggestsa paracrystalline structure within a single layer. The value ofthe interlayer spacing of 0.36 nm has been found from paracrystalline simulations of the layer arrangement in the c-axisdirection. The high quality of the experimental data has enableddetermination of the coordination numbers, the interatomic distancesand their standard deviations using a curve-fitting procedure overthe Q-range from 250 nm to 500 nm, providing structuralinformation about short- and intermediate-range ordering.

Progressive Langerhans’ cell histiocytosis in a puppy

A 8‐month‐old, female miniature Dachshund dog was presented for the complaint of pruritic, generalized, multiple nodules and plaques. Two months previously, a nodule on the left pinna was excised and diagnosed as a cutaneous histiocytoma. One month post‐excision, a nodule reappeared at the same site and, shortly thereafter, additional nodules developed. Histopathological examination revealed a diffuse proliferation of histiocytic cells, which reacted strongly to antibodies for vimentin and lysozyme. Immunophenotypic analysis showed that most of the cells expressed CD1a, CD1c, CD11c, CD18, CD45 and MHC class II markers. Electron microscopic examination revealed cytoplasmic filopodia and paracrystalline structures. These findings indicated that the cells originated from Langerhans’ cell. The disease progressed despite glucocorticoid therapy and griseofulvin was administered as an immunomodulating drug. All lesions resolved completely after 7 weeks of griseofulvin treatment. The dog, however, died three months later after discontinuation of griseofulvin therapy and a necropsy was not performed. It is considered that the present canine dermatosis corresponds with a severe form of Langerhans’ cell histiocytosis in humans rather than canine cutaneous histiocytoma.

Two dimensional array of magnetoferritin on quartz surface

The conditions for producing linear arrays of magnetoferritin on quartz surface are described. Two-dimensional ordered array of mFT on a quartz surface can be formed by spreading a concentrated solution of mFT on quartz and evaporating the film at 90% relative humidity and at room temperature. Under these conditions, mFT forms a close packed linear arrays with hexagonal symmetry. Drying at 50% relative humidity and at room temperature produced structures containing both hexagonal and orthogonal symmetries. A surface loading of 5–10 μg/cm 2 was found to be ideal for forming a paracrystalline structure with a large crystal size.

A Damage Model for Disordered Structures in Ion Irradiated Silicon

AbstractMedium-range order has been observed in ion-implanted amorphous silicon, suggesting a paracrystalline structure for this material. The origin of a paracrystalline structure may be due to an energy spike phenomenon. To evaluate the influence of energy spikes on a particular process, we have attempted to calculate the characteristic energy in a spike. However, the observed depth dependence of amorphous structures in as-implanted silicon is puzzling. To explain this, we simulated the depth distribution of cascade events in a particular energy range. We found a great increase of point defect concentration and cascade events as the depth increases. This result could explain the experimental depth dependence.

A Damage Model for Disordered Structures in Ion Irradiated Silicon

ABSTRACTMedium-range order has been observed in ion-implanted amorphous silicon, suggesting a paracrystalline structure for this material. The origin of a paracrystalline structure may be due to an energy spike phenomenon. To evaluate the influence of energy spikes on a particular process, we have attempted to calculate the characteristic energy in a spike. However, the observed depth dependence of amorphous structures in as-implanted silicon is puzzling. To explain this, we simulated the depth distribution of cascade events in a particular energy range. We found a great increase of point defect concentration and cascade events as the depth increases. This result could explain the experimental depth dependence.

Comparative Fluctuation Microscopy Study of Medium-Range Order in Hydrogenated Amorphous Silicon Deposited by Various Methods

ABSTRACTWe have characterized by fluctuation electron microscopy the medium-range order of hydrogenated amorphous silicon thin films deposited by a variety of methods. Films were deposited by reactive magnetron sputtering, hot-wire chemical vapor deposition, and plasma enhanced chemical vapor deposition with and without H2 dilution of the SiH4 precursor gas. All of the films show the signature of the paracrystalline structure typical of amorphous Si. There are small variations in the degree of medium-range order with deposition method and H content. The PECVD film grown with high H2 dilution contains Si crystals ∼5 nm in diameter at a density of ∼109 cm−2. The amorphous matrix surrounding these crystals shows no difference in mediumrange order from the standard PECVD film. This supports explanations of the resistance of the H-dilution material to light-induced degradation that depend only on the presence of crystalline grains without modifications of the amorphous matrix.

Paracrystalline structures in the epithelial principal cells of the epididymis of water buffalo (Bubalus bubalis)

The ultrastructure of many principal cells in the cauda epididymis of water buffaloes with ages varying between 4, 18, 24, 30 and 36 months, revealed, in many cells, the presence of long, curved paracrystalline structures that are quite large and frequently encountered in the cytoplasm, usually near the nucleus. Concomitantly or not, smaller rod-like, hexagonal or curled structures can be found in the nucleus. Both structures, cytoplasmic and intranuclear, are made up of a sheath of parallel filaments. These paracrystals may appear as thin, regularly spaced filaments that are associated with fine, evenly spaced subunits. Occasionally, the association of paracrystalline structures with membranes similar to the endoplasmic reticulum was observed, but no membranes were consistently found in close contact with the nuclear crystalloids. It is postulated that both structures are proteinaceous and may represent stored enzymes or substances present in the intraluminal fluid, which are absorbed and initially stored in numerous intraepithelial vacuoles of the corpus and cauda of the buffalo epididymis.

Structure of thin films of poly(3,4-ethylenedioxythiophene)

Thin films (50–400 nm) of tosylate-doped poly(3,4-ethylene-dioxy-thiophene) (PEDOT) on various substrates have been studied by grazing incidence X-ray diffraction, using synchrotron radiation. The material was found to be highly anisotropic. This is correlated with a strong anisotropy observed in its optical and electronic properties. The crystalline order is limited, and evidence is found for a paracrystalline structure. A structural model is presented, which corroborates with the optical anisotropy. The effect of heating the material to 200 °C was studied. Unlike the situation for other substituted polythiophenes, heating PEDOT increases the crystalline order.

Ion-Implanted Amorphous Silicon Studied by Variable Coherence TEM

AbstractAmorphous silicon formed by ion-implantation of crystalline silicon is investigated with the use of VC-TEM (variable-coherence transmission electron microscopy). This technique is sensitive to medium-range-order structures. The results from high-energy Si implanted samples showed a striking similarity to sputtered amorphous silicon. We found that both ion-implanted and sputtered samples have paracrystalline structures, rather than the expected continuous random network (CRN). We also observed the structural relaxation of the ion-implanted amorphous silicon after ex-situ thermal annealing towards the random network. The more disordered structures are favored and a large heat of relaxation is released as the temperature increases. Finally, we show some preliminary results on the structural variation with the sample depth.

Ge- and sn-containing poly(p-xylylene): synthesis, structure and thermal behavior

Block copolymers of unsubstituted poly(p-xylylene)(PPX) and Ge- or Sn-organic bridged PPX (GePPX and SnPPX) were prepared by pyrolysis of specially synthesized organometallic p-cyclophane precursors followed by deposition and polymerization of the thus produced p-xylylene monomers. The copolymer structure and thermal behavior were investigated depending on deposition temperature (10 and −196°C). The copolymer PPX-GePPX obtained from solid monomers deposited at −196°C (2a) consists of long quasi-independent PPX and GePPX blocks and has paracrystalline structure. Thermal treatment of 2a near 160°C yields crystalline regions of PPX along with paracrystalline aggregates of GePPX. Pyrolysis of this system near 300°C in an inert atmosphere results in the formation of Ge crystals in PPX matrix. In contrast, the copolymer PPX-GePPX produced by simultaneous deposition and polymerization at 10°C (2a′) contains shorter blocks of PPX and GePPX than the copolymer deposited at −196°C. Copolymer 2a′ turns to the amorphous state during thermal treatment, and its pyrolysis does not lead to Ge-crystal formation; hence the supramolecular structure of the polymer plays an important role in inorganic phase formation. The copolymer PPX-SnPPX (2b) is formed only at a deposition temperature of −196°C; deposition at 10°C yields oligomeric resins. The structure of 2b is nearly the same as that of 2a; pyrolysis of 2b in air results in SnO2-crystal formation in a PPX matrix.

Ge- and Sn-containing poly(p-xylylene): synthesis, structure and thermal behavior

Block copolymers of unsubstituted poly(p-xylylene)(PPX) and Ge- or Sn-organic bridged PPX (GePPX and SnPPX) were prepared by pyrolysis of specially synthesized organometallic p-cyclophane precursors followed by deposition and polymerization of the thus produced p-xylylene monomers. The copolymer structure and thermal behavior were investigated depending on deposition temperature (10 and −196°C). The copolymer PPX-GePPX obtained from solid monomers deposited at −196°C (2a) consists of long quasi-independent PPX and GePPX blocks and has paracrystalline structure. Thermal treatment of 2a near 160°C yields crystalline regions of PPX along with paracrystalline aggregates of GePPX. Pyrolysis of this system near 300°C in an inert atmosphere results in the formation of Ge crystals in PPX matrix. In contrast, the copolymer PPX-GePPX produced by simultaneous deposition and polymerization at 10°C (2a′) contains shorter blocks of PPX and GePPX than the copolymer deposited at −196°C. Copolymer 2a′ turns to the amorphous state during thermal treatment, and its pyrolysis does not lead to Ge-crystal formation; hence the supramolecular structure of the polymer plays an important role in inorganic phase formation. The copolymer PPX-SnPPX (2b) is formed only at a deposition temperature of −196°C; deposition at 10°C yields oligomeric resins. The structure of 2b is nearly the same as that of 2a; pyrolysis of 2b in air results in SnO2-crystal formation in a PPX matrix.