Chains Of Rods Research Articles

Tunable THz Leaky-Wave Radiation from Periodic Chains of Graphene-Coated Circular Rods

Tunable THz Leaky-Wave Radiation from Periodic Chains of Graphene-Coated Circular Rods

Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum.

Three novel, anaerobic, Gram-positive bacteria were isolated from the eggshell of two separate white leghorn chicken flocks and the ileum of a healthy pig, and designated MMM721T, ISU324 and PIG517 respectively. Cells were pleomorphic and capable of forming long chains of rods or coccoid clusters. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains to be within the genus Turicibacter , of which only one species, Turicibacter sanguinis , has been formally described. However, whole genome sequencing of novel isolates returned a digital DNA–DNA hybridization value of 22.5 % and average nucleotide identity (ANI) values of 76.4 % (ANIb) and 86.0 % (ANIm), indicating divergence between the type strain MMM721T and T. sanguinis , suggesting the strains represented a novel species. The major fatty acid methyl esters of strain MMM721T were C16 : 0, C18 : 1 ω7c and C18 : 0. The strains mainly produced the volatile fatty acid lactate, along with smaller amounts of acetate and butyrate. Together, these data indicate that MMM721T, along with ISU324 and PIG517, represent a novel species within the genus Turicibacter . We propose the name Turicibacter bilis sp. nov. for the species. The type strain is MMM721T (=ATCC TSD-238T=CCUG 74757T).

Leaky-Wave Radiation From 2-D Dielectric Lattices Excited by an Embedded Electric Line Source

This article presents an analytical and numerical investigation of the radiation features of an interesting class of electromagnetic bandgap (EBG) structures excited by an electric line source. The radiation from 2-D lattices made with lossless dielectric cylinders, typically optimized by using the Bloch analysis of the corresponding 2-D photonic crystals, is originally investigated in terms of leaky waves. A thorough modal analysis of open waveguides, composed of a finite number of periodic chains of circular dielectric rods, is presented, which shows a multiplicity of bound and leaky modes. Two radiation windows are identified and the relevant directive features are described in terms of properly excited dominant leaky modes. The possible excitation of higher order leaky modes and guided modes has been carefully considered, by also capturing the relevant residue contributions in a nonspectral representation of the excited fields. The final results on radiated fields by realistic truncated structures, obtained by <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ad hoc</i> software as well as full-wave EM simulators, are in excellent agreement with those predicted by the proposed leaky-wave approach.

Modal Propagation in Periodic Chains of Circular Rods: Real and Complex Solutions

A full-wave numerical approach for the analysis of bounded and leaky modes in periodic chain composed of both lossless and lossy 2-D cylindrical inclusions is proposed. An effective method based on the lattice sums technique is adapted to the analysis of modes with complex propagation wavenumbers, thus allowing for the appropriate choice of the spectral determination for each spatial harmonic. Periodic chains of both dielectric and silver nanocylinders are studied and the relevant modal phase and attenuation constants are rigorously calculated in all the different propagation regimes, including bound and radiative regions as well as plasmonic behaviors.

Metacomposite with auxetic and in situ sign reversible thermal expansivity upon temperature fluctuation

Abstract This paper proposes a metacomposite that shrinks regardless of temperature decrease or increase, i.e. it exhibits positive and negative thermal expansions with cooling and heating, respectively, which leads to auxetic behavior. This metacomposite is constructed from rigid rods and bimaterial strips; the ends of the rigid rods are connected in series by freely-rotating pin joints while neighboring chains of rigid rods are linked by bimaterial strips that are connected to the mid-spans of the rigid rods by fixed joints. Thermal deformation results indicate that the magnitude of the coefficient of thermal expansion (CTE) of the metacomposite parallel to the rigid rod is about 3 times greater than that parallel to the bimaterial strips. Upon thermal deformation, prescription of stretching parallel to the chains of rigid rods indicate a Poisson's ratio that is approximately −1/3. Results also show that the effective in-plane CTE and Poisson's ratio are influenced by the CTE ratio of the bimaterial phases and aspect ratio of the bimaterial strip. The possibility of this auxetic metacomposite to achieve in situ sign-switching of CTE avails greater design options to the materials engineer.

Deformation of flexible fibers in turbulent channel flow

In this paper, we examine from a statistical point of view the deformation of flexible fibers in turbulent channel flow. Fibers are longer than the Kolmogorov length scale of the carrier flow and have finite inertia. Our aim is to examine the effect of local shear and turbulence anisotropy on fiber twisting and bending, when shape effects add to the inertial bias. To these aims, we use an Eulerian–Lagrangian approach based on direct numerical simulation of turbulence in dilute flow conditions. Fibers are modelled as chains of sub-Kolmogorov rods (referred to as elements hereinafter) interconnected by holonomic constraints that enable relative rotation of neighbouring elements. Statistics are computed from simulations at shear Reynolds number $${\text{Re}}_{\tau }=150$$, based on the channel half height, for fibers with different aspect ratio, $$\lambda _r$$ (defined as the ratio between the length $$l_r$$ of each element r composing the fiber and its cross-sectional radius, a), and different inertia, parameterized by the Stokes number of the element, $$St_r$$. We show that bending of flexible fibers is in general stronger in the bulk of the flow, where they are subject to turbulent velocity fluctuations only. Near the wall, fibers are more easily stretched by the mean shear, especially for large-enough inertia ($$St_r > 5$$ in our simulations). In spite of this different dynamics, which is connected to the anisotropy of the flow, we find that the fiber end-to-end distance reaches a steady state regardless of fiber location with respect to the wall.

Acquired immunodeficiency associated with thymoma: a case report

BackgroundAcquired immunodeficiency associated with thymoma is a rare disorder. Here we reported a case of acquired immunodeficiency with thymoma, with an unusual pattern of low CD4+ count with normal gammaglobulin levels.Case presentationA 70-year-old man presented to the emergency room of our hospital with a high-grade fever, headache, and nausea. He had a five-year history of unresectable thymoma treatment, including several cytotoxic regimens. He had received thoracic palliative radiotherapy 2 months prior to the emergent visit. During the previous month, he had experienced multiple febrile episodes, dry cough, fatigue, weight loss, and watery diarrhea. Upon admission, he had a high-grade fever, nausea, and immobility. Physical examination revealed indistinct consciousness, neck stiffness, and oropharyngeal candidiasis. Both cerebrospinal fluid and blood cultures yielded multiple short chains of Gram-positive rods later identified as Listeria monocytogenes, so he was diagnosed with Listeria meningitis. Intravenous administration of antibiotics was initiated, and the patient fully recovered and was discharged. Additional examination found normal immunoglobulin levels. Peripheral-blood cell counts revealed low CD4+ cell count (108 CD4+ cells/μl). His CD4+ cell count remained low after discharge.ConclusionsOur findings suggest that physicians need to be aware of severe infections due to immunodeficiency with thymoma.

Orientation, distribution, and deformation of inertial flexible fibers in turbulent channel flow

In this paper, we investigate the dynamics of flexible fibers in turbulent channel flow. Fibers are longer than the Kolmogorov length scale of the carrier flow, and their velocity relative to the surrounding fluid is non-negligible. Our aim is to examine the effect of local shear and turbulence anisotropy on the translational and rotational behavior of the fibers, considering different elongation (parameterized by the aspect ratio, $$\lambda $$ ) and inertia (parameterized by the Stokes number, St). To these aims, we use a Eulerian–Lagrangian approach based on direct numerical simulation of turbulence in the dilute regime. Fibers are modeled as chains of sub-Kolmogorov rods (referred to as elements hereinafter) connected through ball-and-socket joints that enable bending and twisting under the action of the local fluid velocity gradients. Velocity, orientation, and concentration statistics, extracted from simulations at shear Reynolds number $$Re_{\tau }=150$$ (based on the channel half height), are presented to give insights into the complex fiber–turbulence interactions that arise when non-sphericity and deformability add to inertial bias. These statistical observables are examined at varying aspect ratios (namely $$\lambda _{r}=l_{r}/a=2$$ and 5, with $$l_{r}$$ the semi-length of each rod-like element r composing the fiber and a its cross-sectional radius) and varying fiber inertia (considering values of the element Stokes number, $$St_{r}=1$$ , 5, 30). To highlight the effect of flexibility, statistics are compared with those obtained for fibers of equal mass that translate and rotate as rigid bodies relative to the surrounding fluid. Flexible fibers exhibit a stronger tendency to accumulate in the very-near-wall region, where they appear to be trapped by the same inertia-driven mechanisms that govern the preferential concentration of spherical particles and rigid fibers in bounded flows. In such region, the bending of flexible fibers increases as inertia decreases, and fiber deformation appears to be controlled by mean shear and turbulent Reynolds stresses. Preferential segregation into low-speed streaks and preferential orientation in the mean flow direction is also observed.

An Efficient Model of Tethers for Tethered Satellite Systems

This paper concerns about modeling of tethered satellites systems (TSS). In this paper, tethers of TSS are modeled as chains of elastic rods connected by rigid joints. A group of spatial vectors are used to describe displacement, orientation and deformation of the rods, which can avoid the coupling of trigonometric functions of Euler angles. The coordinates of spatial vectors are chosen as the generalized coordinates of system. Equations of motion are derived and written in explicit form. A computationally efficient algorithm is developed to solve equations of motion. Computational complexity of the developed algorithm is reduced to O(n) (n denotes the number of rods). A numerical experiment is performed. Results about energy show energy conservation principle is obeyed. The same numerical experiment is also performed utilizing multibody software ADAMS. Validity of the presented algorithm is demonstrated by comparing numerical results of the two methods.

Competition and protist predation are important regulators of riverine bacterial community composition and size distribution

ABSTRACTAmong the bacterivorous protists, heterotrophic nanoflagellates (HNFs) are considered to be the main grazers of bacteria in freshwaters due to their size-selective grazing. In this work, we assessed the change of a riverine bacterial community in controlled incubations, where HNFs’ predation pressure was initially released through filtration. Filtration did not prevent the passage of cysts, which grew in the enrichments afterwards. Data on the composition of the bacterial community were gathered by Catalyzed Reporter Deposition Fluorescent In situ Hybridization (CARD-FISH) using 16S probes targeting phylogenetic groups. Bacterial cell size was also examined using image analysis. Overall, the initial filtration directly (through release of predation pressure) or indirectly (through competition among bacterial groups) affected the bacterial community composition. When nanoflagellate abundance rose, a reduction of bacterial abundance and changes in cell size distribution were observed. Gamma-Proteobacteria and Actinobacteria were the groups showing the greatest reduction in abundance. Beta-Proteobacteria showed a reduction of cell size and were found in aggregates. Alpha-Proteobacteria and Actinobacteria developed two distinct filamentous morphotypes: short, segmented rods and long chains of rods. Our results showed that the release of the predation pressure and the successive rise of the nanoflagellates changed the bacterial community in terms of composition at large phylogenetic scale. HNF grazing is highly group-specific and seems to reconstruct the community based on cell size, and thus, not only drastically changing the bacterial community composition, but also increasing its functional diversity.

Density and Shape Effects in the Acoustic Propulsion of Bimetallic Nanorod Motors

Bimetallic nanorods are propelled without chemical fuels in megahertz (MHz) acoustic fields, and exhibit similar behaviors to single-metal rods, including autonomous axial propulsion and organization into spinning chains. Shape asymmetry determines the direction of axial movement of bimetallic rods when there is a small difference in density between the two metals. Movement toward the concave end of these rods is inconsistent with a scattering mechanism that we proposed earlier for acoustic propulsion, but is consistent with an acoustic streaming model developed more recently by Nadal and Lauga ( Phys. Fluids 2014 , 26 , 082001 ). Longer rods were slower at constant power, and their speed was proportional to the square of the power density, in agreement with the acoustic streaming model. The streaming model was further supported by a correlation between the disassembly of spinning chains of rods and a sharp decrease in the axial speed of autonomously moving motors within the levitation plane of the cylindrical acoustic cell. However, with bimetallic rods containing metals of different densities, a consistent polarity of motion was observed with the lighter metal end leading. Speed comparisons between single-metal rods of different densities showed that those of lower density are propelled faster. So far, these density effects are not explained in the streaming model. The directionality of bimetallic rods in acoustic fields is intriguing and offers some new possibilities for designing motors in which shape, material, and chemical asymmetry might be combined for enhanced functionality.

Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer.

BackgroundArchaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2.ResultsBiofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method.ConclusionsThe developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-014-0065-5) contains supplementary material, which is available to authorized users.

Mesoscale simulation study of the structure and rheology of dilute solutions of flexible micelles

Mesoscale Brownian dynamics simulations were performed to study the structures and rheological properties of dilute solutions of flexible micelles. The micelles were modelled by chains of rigid rods. The scission energy and bending potential were introduced to model the interactions of micellar rods. The spatial distributions and orientations under shear flow were investigated. The transient stresses after the start-up of shear flow and steady-state rheological properties were also investigated. The simulation results showed that the transitions of the structure under shear flow and the rheological properties vary with the scission energy and flexibility of the micelles.

Analysis of the phylogenetic diversity of estrone-degrading bacteria in activated sewage sludge using microautoradiography–fluorescence in situ hybridization

In situ uptake of [2,4,6,7- 3H( N)]estrone ([ 3H]E1) by the major phylogenetic groups present in activated sludge samples from two different municipal wastewater treatment plants was investigated using microautoradiography–fluorescence in situ hybridization (MAR–FISH). Approximately 1–2% of the total cells confined in the samples by an EUB probe mix contributed to E1 assimilation. Almost all the detected E1-assimilating cells involved in the early phase of E1 degradation were affiliated with the Beta- and Gammaproteobacteria. In the early phase of E1 degradation, no E1-assimilating cells affiliated with the Alphaproteobacteria, Actinobacteria, the Cytophaga–Flavobacterium cluster of phylum Bacteroidetes, or the phyla Chloroflexi, Nitrospira and Planctomycetes were detected. Bacteria affiliated with the Betaproteobacteria in the shape of long rods or chains of rods were found to contribute most to in situ E1 degradation. They contributed 61% and 82% of total E1-assimilating cells in cultures from two sources of activated sludge spiked with [ 3H]E1. The E1-degrading bacteria related to the Betaproteobacteria differed phylogenetically from the aerobic E1-degrading bacterial isolates reported in previous studies. In addition, MAR–FISH revealed the significant contribution of E1-degrading bacteria affiliated with the Gammaproteobacteria in the degradation of E1 in activated sludge.

Isotropic-to-nematic transition in liquid-crystalline heteropolymers: I. Formalism andmain-chain liquid-crystalline polymers

We formulate a density functional approach for arbitrarily branched liquid-crystalline (LC)heteropolymers consisting of elongated rigid rods coupled through elastic joints. The theoryexactly accounts for the energetic and entropic single-chain effects, whereas the interchainexcluded volume effects are treated within the Onsager approximation. We apply thetheory to finite-length main-chain LC polymers composed of rigid mesogens coupled byflexible spacers of finite length, modelled initially as chains of thin rods. The theory thenallows an easy passage to the wormlike chain limit for the spacers. Employing a bifurcationanalysis we analytically obtain the stability boundaries of the isotropic phasetowards the nematic liquid crystalline phase, as a function of the relative size of themesogens with respect to the spacers and the spacer flexibility. From the sameanalysis we also obtain the distribution of the incipient nematic ordering at thespinodal density as a function of position along the chain, including the end-effects.

Selective growth of metal tips onto semiconductor quantum rods and tetrapods.

We show the anisotropic selective growth of gold tips onto semiconductor (cadmium selenide) nanorods and tetrapods by a simple reaction. The size of the gold tips can be controlled by the concentration of the starting materials. The new nanostructures display modified optical properties caused by the strong coupling between the gold and semiconductor parts. The gold tips show increased conductivity as well as selective chemical affinity for forming self-assembled chains of rods. Such gold-tipped nanostructures provide natural contact points for self-assembly and for electrical devices and can solve the difficult problem of contacting colloidal nanorods and tetrapods to the external world.

PH stress can cause cell elongation in Bacillus and Clostridium species: a research note

Spoilage of low pH products by a wide range of sporeformers is often observed. Work was done to isolate these organisms and establish the minimum pH allowing growth. At low pH values (below 4.3), a haziness or slight turbidity was noted in the broths which did not correspond to an increase in cell numbers determined by plate count. Microscopic investigations revealed the presence of elongated cells or chains of rods in the lower pH broths which were not present in the higher pH broths. The elongated cell morphology disappeared when cells were returned to optimum pH conditions. Phillips, L. E., Humphrey, T. J., & Lappin-Scott, H. M. (1998). [Journal of Applied Microbiology, 84 (5), 820–826] illustrated this with Salmonella when chilled. It is concluded that cell elongation is a stress response to sub-optimal pH conditions, which can revert and give a rapid apparent increase in cell numbers when conditions become more favourable.

Simulations of fiber flocculation: Effects of fiber properties and interfiber friction

Non-Brownian fibers commonly flocculate in flowing suspensions at relatively low concentrations (<1% by weight). We have developed a particle-level simulation technique modeling fibers as chains of rods connected by hinges to probe fiber flocculation. The model incorporates fiber flexibility, irregular fiber equilibrium shapes, and frictional fiber interactions. Model fibers reproduce known orbits of isolated rigid and flexible fibers in shear flow. Simulation predictions of first normal stress differences in homogeneously dispersed, dilute flexible fiber suspensions agree with experimental data. Fiber features such as flexibility and irregular equilibrium shapes strongly impact single fiber and suspension behavior. Fibers aggregate in simulations with interfiber friction, in the absence of attractive forces between fibers. Strong flocculation is observed in suspensions of stiff fibers with irregular equilibrium shapes. Flocs contain many fibers with three or more contact points, and derive cohesiveness from elastic energy held in fibers—consistent with the elastic interlocking mechanism of flocculation. At higher concentrations (nL3≈100, where n is the fiber number density and L is the fiber length), coherent fiber networks form in simulations. Average numbers of contacts per fiber and contact force magnitudes in sheared and static networks are compared with existing fiber network theory predictions.

Mechanical flocculation in flowing fiber suspensions

Non-Brownian fibers commonly flocculate in flowing suspensions. A particle level simulation technique modeling fibers as chains of rods connected by hinges is developed to probe flocculation. Simulations show that flocculation can be induced solely by interfiber friction-attractive forces between fibers are not necessary. Simulated mechanical floc characteristics are consistent with experimental observations. In contrast, simulations of flocs formed by attractive forces behave qualitatively differently.

Nonlinear Dynamics of a Flexible Multirod (Multibeam) System

The paper presents a general nonlinear numerical model for the dynamic analysis of a spatial structure that includes chains of flexible rods, with rigid bodies between them, and different kinds of connections between all these components. Such a system is denoted a multirod or multibeam system. The model is derived using a multibody system approach. The motion of each rod includes elastic deformations that are superimposed on finite rigid body motions. The elastic model of each rod is nonlinear and includes bending in two perpendicular directions, torsion, axial motion, and warping. Any distribution of the rod properties can be considered. Finite elements are used to describe the deformations. Although the elastic derivation is confined to moderate deformations, any level of nonlinearity can be addressed by dividing each rod into sub-rods. The joints between the rods are general and may include springs and dampers. A new formulation of Lagrange method is used in order to derive the equations of motion. It offers various advantages concerning the accuracy, stability of the constraints, and the modeling of constraints. The model is validated by comparing its results with new experimental results. Good agreement is shown between the experimental and numerical results.