Elongated Rods Research Articles

Changes in metal nanoparticle shape and size induced by swift heavy-ion irradiation

Changes in the shape and size of Co, Pt and Au nanoparticles induced by swift heavy-ion irradiation (SHII) have been characterized using a combination of transmission electron microscopy, small-angle X-ray scattering and X-ray absorption near-edge structure. Elemental nanoparticles of diameters 2–15 nm were first formed in amorphous SiO 2 by ion implantation and thermal annealing and then irradiated at room temperature with 27–185 MeV Au ions as a function of fluence. Spherical nanoparticles below a minimum diameter (4–7 nm) remained spherical under SHII but progressively decreased in size as a result of dissolution into the SiO 2 matrix. Spherical nanoparticles above the minimum diameter threshold were transformed to elongated rods aligned with the ion beamdirection. The nanorod width saturated at an electronic energy deposition dependent value, progressively increasing from 4–6 to 7–10 nm (at 5–18 keV/nm, respectively) while the nanorod length exhibited a broad distribution consistent with that of the unirradiated spherical nanoparticles. The threshold diameter for spherical nanoparticle elongation was comparable to the saturation value of nanorod width. We correlate this saturation value with the diameter of the molten track induced in amorphous SiO 2 by SHII. In summary, changes in nanoparticle shape and size are governed to a large extent by the ion irradiation parameters.

Self-assembly of rodlike receptors from bulk solution

Optical waveguide lightmode spectroscopy has been used to observe the deposition of bacterial flagellar filaments of mean length 350 nm from bulk solution onto a smooth planar substratum, chemically modified to covalently bind the flagellar filaments on contact. At the highest practicable bulk concentration, the filaments follow the theoretically predicted kinetics of random sequential addition of highly elongated rigid rods to the substratum, but addition terminates with the rods almost perpendicular to the substratum. Rod-rod correlations in the bulk anomalously accelerate the rate of arrival of the filaments at the surface of the substratum, relative to spheres. At lower concentrations, this effect is absent, and the rods have time to order themselves on the substratum, forming a two-dimensional array.

Lewinella antarctica sp. nov., a marine bacterium isolated from Antarctic seawater

A marine bacterium, designated IMCC3223T, was isolated from Antarctic coastal seawater and subjected to a polyphasic taxonomic investigation. Cells of the strain were Gram-negative, short to elongated rods that were orange-coloured but negative for flexirubin-type pigments, obligately aerobic, chemoheterotrophic and devoid of gliding or flagellar motility. On the basis of 16S rRNA gene sequence comparisons, the strain was closely related to members of the genus Lewinella (86.3-93.1 %) of the family 'Saprospiraceae' in the phylum Bacteroidetes; the most closely related species was Lewinella lutea (93.1 % similarity to the type strain). The DNA G+C content of the strain was 50.3 mol% and the major respiratory quinone was MK-7. The predominant cellular fatty acids were C(16 : 1)omega7c/iso-C(15 : 0) 2-OH (39.4 %), iso-C(15 : 0) (15.9 %), C(17 : 1)omega7c (10.5 %) and C(15 : 1)omega6c (8.9 %). 16S rRNA gene sequence analyses and the phenotypic and chemotaxonomic tests allowed the differentiation of strain IMCC3223T from all recognized species of the genus Lewinella. Therefore, strain IMCC3223T represents a novel species of the genus Lewinella, for which the name Lewinella antarctica sp. nov. is proposed. The type strain is IMCC3223T (=KCCM 42688T =NBRC 103142T).

The effect of cross-sectional geometry and size on magnetostatic modes in nanorods

We study the effect of cross-sectional geometry and size on the spectrum of magnetostatic modes in dipole-coupled magnetic nanorods of circular or square cross section. The scope of this study is confined only to excitations propagating along the central axis of the nanorod; at the same time, the direction of the central axis is assumed to correspond to that of the magnetization of the sample. We find that a modification of the cross-sectional geometry results in nonuniform changes in the local field profile and the effect proves especially strong in the range of nanometer lateral dimensions. Moreover, the effect of cross-sectional geometry on the magnetostatic spectrum of a nanorod is found to be the most significant in peripheral regions of elongated rods. This is due to the occurrence of dipolar local field wells in these very regions. The shape of these peripheral wells affects first of all the bulk-dead and surface modes, which are “stuck” in them; frequencies of these modes prove to increase when the cross-sectional shape changes from square to circle.

Biogenic Origin of Polymetallic Nodules from the Clarion-Clipperton Zone in the Eastern Pacific Ocean: Electron Microscopic and EDX Evidence

Polymetallic/ferromanganese nodules (Mn-nodules) have been assigned a huge economic potential since they contain considerable concentrations of manganese, copper, nickel, iron, and cobalt. It has been assumed that they are formed by, besides hydrogenous, nonbiogenic processes, biogenic processes based on metabolic processes driven by microorganisms. In the present study, we applied the techniques of digital optical microscopy and high-resolution scanning electron microscopy to search for microorganisms in Mn-nodules. They were collected from the Clarion-Clipperton Zone in the Eastern Pacific Ocean and are composed of Mn (23.9%), Cu (0.69%), Ni (1.02%), Fe (10.9%), and Co (0.29%). These Mn-nodules, between 2.3 and 4.8 cm, show a distinct lamination; they are composed of small-sized micronodules, 100 to 450 microm in size, which are bound together by an interstitial whitish material. In the micronodules, a dense accumulation of microorganisms/bacteria could be visualized. Only two morphotypes exist: (1) round-shaped cocci and (2) elongated rods. The cocci (diameter: approximately 3.5 microm) are arranged in bead-like chains, while the rods (approximately 2 x 0.4 microm) are arranged either as palisades or in a linear row. Energy-dispersive X-ray spectroscopy analyses showed that the areas rich in microorganisms/bacteria are also rich in Mn, while in regions where no microorganisms are found, the element Si is dominant. We suggest that growth of the Mn-nodules starts with the formation of "micronodules." The formation of micronodules is assumed to be mediated by microorganisms. After accretion of biogenic and additional nonbiogenic minerals, the micronodules assemble to large nodules on the sea floor through additional inclusion of nonbiogenic material.

New insights into the formation of textures through spray-drying and self-assembly

New insights into the formation of textures result from a detailed characterisation of spray-dried mesoporous silica-based microspheres by Nuclear Magnetic Resonance (NMR), Small Angle X-Ray Scattering (SAXS), Transmission Electron Microscopy (TEM), and Scanning Electron Microscopy (SEM). Representative samples are obtained from sols of different chemical composition and containing surfactant molecules (cetyltrimethylammonium bromide, CTAB) and siloxane oligomers. The study of the morphological and textural properties leads us to complete the previous knowledge on these materials. We have shown that there is always a phase separation between the surfactant aggregates and the siloxane network at the nanometric level, but not at a microscopic or macroscopic level. In addition, the characteristics of the small interacting colloids (CTAB micelles and siloxane oligomers) determine the morphology of the samples, the proportions of non-ordered and ordered domains, as well as the spatial extent and the nature of the ordered phases. Two kinds of constrains exist at this respect: the rate of solidification during spray-drying, and the steric constrains imposed by the geometry of the ordered phases. From our results, we propose a mechanism of texture formation during spray-drying through two main steps: the evolution from an isotropic liquid to a non-ordered phase made of micelles and siloxane oligomers; and the transition from this non-ordered phase to an ordered phase by the spatial reorganisation of the micelles and their concomitant fusion into elongated rods.

Effect of a cowpea mild mottle virus isolate on growth and yield of bambara groundnut (<i>Vigna subterranea</i> L.)

Effect of a cowpea mild mottle virus isolate on growth and yield of bambara groundnut (<i>Vigna subterranea</i> L.)

Multiple Distinct Assemblies Reveal Conformational Flexibility in the Small Heat Shock Protein Hsp26

Small heat shock proteins are a superfamily of molecular chaperones that suppress protein aggregation and provide protection from cell stress. A key issue for understanding their action is to define the interactions of subunit domains in these oligomeric assemblies. Cryo-electron microscopy of yeast Hsp26 reveals two distinct forms, each comprising 24 subunits arranged in a porous shell with tetrahedral symmetry. The subunits form elongated, asymmetric dimers that assemble via trimeric contacts. Modifications of both termini cause rearrangements that yield a further four assemblies. Each subunit contains an N-terminal region, a globular middle domain, the alpha-crystallin domain, and a C-terminal tail. Twelve of the C termini form 3-fold assembly contacts which are inserted into the interior of the shell, while the other 12 C termini form contacts on the surface. Hinge points between the domains allow a variety of assembly contacts, providing the flexibility required for formation of supercomplexes with non-native proteins.

Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new event-driven algorithm that takes the excluded volume interactions between particles into account as instantaneous collisions, but neglects the hydrodynamic interactions. This algorithm is applied to dense systems of highly elongated rods and proves to be efficient. The calculated isotropic-nematic spinodals lie between the previously established binodals in the phase diagram and extrapolate for infinitely long rods to Onsager's [Ann. N. Y. Acad. Sci. 51, 627 (1949)] theoretical predictions. Moreover, we investigate the shear induced shifts of the spinodals, qualitatively confirming the theoretical prediction of the critical shear rate at which the two spinodals merge and the isotropic-nematic phase transition ceases to exist.

New magnetostatic modes in small nonellipsoidal magnetic particles

AbstractMagnetostatic normal modes are investigated here in elongated rods. The dipolar field resulting from the dipole–dipole interactions is calculated numerically in points of the axis connecting opposite rod face centers (central axis ) by collecting individual contributions to this field coming from each of the atomic planes perpendicular to the central axis. The applied magnetic field is assumed to be oriented along the central axis, and the magnetization to be uniform throughout the sample. The frequency spectrum of magnetostatic waves propagating in the direction of the applied field is found numerically by solving the Landau–Lifshitz equation of motion with the spatially nonhomogeneous dipolar field taken into account; the mode amplitude profiles are depicted as well. While energetically highest modes have bulk‐extended character, the modes forming the lower part of the spectrum are localized in the subsurface region (bulk‐dead modes ). Between these two mode types, magnetostatic modes of a new type (comb modes ) are found to occur, characterized by two clearly discernible regions: a zone of fast amplitude oscillations inside the rod, and narrow slow‐oscillation regions at the borders. Absorbing virtually no energy from an applied alternating field, comb modes will have no significant contribution to the magnetic noise. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Jiangella gansuensis gen. nov., sp. nov., a novel actinomycete from a desert soil in north-west China

A novel actinomycete strain, designated YIM 002(T), was isolated from a desert soil sample in Gansu Province, north-west China. This actinomycete isolate formed well-differentiated aerial and substrate mycelia. In the early stages of growth, the substrate mycelia fragmented into short or elongated rods. Chemotaxonomically, it contained ll-2,6-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose and glucose. Phospholipids present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. MK-9(H(4)) was the predominant menaquinone. The major fatty acids were anteiso C(15 : 0) (35.92 %), anteiso C(17 : 0) (15.84 %), iso C(15 : 0) (10.40 %), iso C(16 : 0) (7.07 %) and C(17 : 1)omega8c (9.37 %). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002(T) is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002(T) be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002(T) (=DSM 44835(T)=CCTCC AA 204001(T)=KCTC 19044(T)).

Dynamics of elongated magnetic droplets and elastic rods in magnetic field

The physics of viscous and elastic magnetic filaments is considered. It is shown that the normal stresses arising due to the magnetic torques cause very interesting peculiarities in the dynamics of the filaments in rotating fields; the formation and the propagation of the shock wave of a tangent angle, development of S like steady shapes if the frequency is beyond the critical and other. Elastic magnetic filaments due to the buckling instability have hairpin shapes. The models developed are applied for the description of the magnetosomes in the magnetotactic bacteria.

Formation of Cr–germanide nanoparticles during growth of epitaxial Ge–Cr thin films

Microstructural evolution has been investigated as a function of substrate temperature in Ge–4 at.%Cr films grown by molecular beam epitaxy (MBE), by employing transmission electron microscopy (TEM); the TEM results have been correlated to the magnetic properties. Magnetometry measurements show that samples grown at substrate temperatures of 200 °C and above are paramagnetic. Significantly different microstructures have been shown to evolve, depending on the substrate temperature ( T s) during MBE growth. For T s=200 °C, the film consists of elongated rods, or “noodles” of the equilibrium Cr 11Ge 19 phase. For T s=400 °C, a nanodispersion of metastable Cr 11Ge 8 equiaxed precipitates form within the Ge-matrix. It is thus proposed that for T s=400 °C a supersaturated Ge–Cr solid-solution is initially formed from the vapor phase, followed by solid-state precipitation. At T s=200 °C, precipitation analogous to a cellular/discontinuous transformation results in the formation of cooperatively grown rod-like or noodle shaped microstructures.

Excitation of dipole oscillons in a dusty plasmacontaining elongated dust rods

The dispersion properties and excitation mechanisms of `dipole oscillons' in a dusty plasma containing charged elongated rod-like dust grainsare investigated in the presence of streaming plasma particles for cases without and with an external static magnetic field.In a magnetized dusty plasma, a new `oscillon-ion lower-hybrid' mode is found, which can be excited by the equilibrium energy of cross-field drifting ions.

Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments

Three novel strains of cold-adapted bacteria, ST-82T, ST-10 and ST-92, were isolated from freshwater sediments. These three isolates were very similar to each other in phenotypic and chemotaxonomic traits, as well as in 16S rDNA sequence. The strains were Gram-negative, elongated filament-like rods that formed bright yellow colonies. They showed neither flexirubin pigments nor gliding motility. The strains were able to hydrolyse casein, gelatin, starch, agar, aesculin, urea, uric acid and tyrosine. They also lysed cells of Escherichia coil and Pseudomonas putida. The temperature range for growth was 0-25 degrees C, with optimum growth occurring at 15-20 degrees C. For all isolates, protease secretion increased as temperature decreased. Sodium chloride inhibited their growth, although the strains tolerated up to 1.5% (w/v) NaCl. Menaquinone-6 was the major respiratory quinone. The major cellular fatty acids were C15 : 0, iso-C15 : 0, anteiso-C15 : 0, C15:1, iso-C15:1, C16 : 1omega7cis, iso-C16 : 1, iso-C17 : 1, iso-C15 : 3-OH and iso-C16 : 0 3-OH. The DNA G + C content was 34.0-34.8 mol%. Phylogenetic analysis based on 16S rDNA sequences suggested that the strains belonged to the genus Flavobacterium and were closely related to Flavobacterium xanthum and Flavobacterium frigidarium, with sequence similarities of 96.9 and 96.3%, respectively. In physiological and biochemical analyses, the isolates were differentiated from all known members of the genus Flavobacterium. The name Flavobacterium limicola is proposed for these novel strains, and the type strain is ST-82T (=JCM 11473T =DSM 15094T).

Density functional for anisotropic fluids

We propose a density functional for anisotropic fluids of hard body particles. Itinterpolates between the well established geometrically based Rosenfeld functionalfor hard spheres and the Onsager functional for elongated rods. We test the newapproach by calculating the location of the nematic–isotropic transition insystems of hard spherocylinders and hard ellipsoids. The results are comparedwith existing simulation data. Our functional predicts the location of thetransition much more accurately than the Onsager functional, and almost as wellas the theory by Parsons and Lee. We argue that it might be suited to studyinhomogeneous systems.

Hongia gen. nov., a new genus of the order Actinomycetales.

An aerobic, nocardioform actinomycete, named LM 161T, was isolated from a soil sample obtained from a gold mine in Kongiu, Republic of Korea. This organism formed well-differentiated aerial and substrate mycelia and produced branched hyphae that fragmented into short or elongated rods. The cell wall contains major amounts of LL-diaminopimelic acid, alanine, glycine, glutamic acid, mannose, glucose, galactose, ribose and acetyl muramic acid. The major phospholipids of this isolate are phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and the major isoprenologue is a tetrahydrogenated menaquinone with nine isoprene units. The whole-cell hydrolysate of strain LM 161T contains 12-methyltetradecanoic and 14-methylpentadecanoic acids as the predominant fatty acids, but does not contain mycolic acids. The G+C content of the DNA is 71.3 mol%. The phylogenetic position of the test strain was investigated using an almost complete 16S rDNA sequence. The isolate formed the deepest branch in the clade encompassing the members of the suborder Propionibacterineae Rainey et al. 1997. On the basis of chemical, phenotypic and genealogical data, it is proposed that this isolate be classified within a new genus as Hongia koreensis gen. nov., sp. nov. in the order Actinomycetales. The type strain is LM 161T (= IMSNU 50530T).

Critical adsorption on curved objects.

A systematic field-theoretical description of critical adsorption on curved objects such as spherical or rodlike colloidal particles immersed in a fluid near criticality is presented. The temperature dependence of the corresponding order parameter profiles and of the excess adsorption are calculated explicitly. Critical adsorption on elongated rods is substantially more pronounced than on spherical particles. It turns out that, within the context of critical phenomena in confined geometries, critical adsorption on a microscopically thin "needle" represents a distinct universality class of its own. Under favorable conditions the results are relevant for the flocculation of colloidal particles.

Phase diagram of Onsager crosses

Onsager crosses are hard nonconvex bodies formed by rigidly connecting three elongated rods, equally thick but not necessarily equally long, to form perpendicular crosses. We study the phase behavior of systems of such particles, focusing on their ability to form spatially homogeneous orientationally ordered phases with a symmetry lower than that of the standard uniaxial nematic. We treat these systems in the Onsager, second virial coefficient, approximation. We apply bifurcation analysis to build up a global picture of the phase diagram, which is then refined using approximate numerical calculations. Finally, we generalize the Gaussian approximation for the nematic orientational distribution function, to deal with the more ordered phases encountered here, and compare with the results from the previous techniques to see whether it is feasible to reliably predict the phase diagrams from a computationally cheaper technique.

RESEARCH NOTE Virial coefficients of Onsager crosses

Onsager crosses are particles formed by rigidly connecting three perpendicular, elongated rods of length L and diameter D. We have investigated the behaviour of the virial coefficients of Onsager crosses as a function of the aspect ratio L/D of the rods. The interest in these particles stems from the fact that they should exhibit a cubatic liquid crystalline phase in the limit (L/D) →∞. It is shown that in order for the theory predicting this phase to be strictly valid, the rod aspect ratio should be extremely large ((L/D) ≳ 1000).