Cavity Topology Research Articles

Numerical analysis of ventilated cavity flow over a 2-D wall mounted fence

Ventilated cavity flow over a 2-D wall mounted fence is numerically investigated using a viscous approach. An implicit unsteady compressible solver was used with a RANS k−ω SST turbulence model and VOF approach to capture the cavity interface. The simulations were carried out for a fixed fence height based Froude number and constant outlet pressure. Cavity topology, wall pressure distributions and the resulting hydrodynamic forces were determined as a function of ventilation rate, degree of fence immersion in the oncoming wall boundary layer and degree of confinement of the flow domain. It was found that with an increase in ventilation rate, lift increases and drag decreases resulting in a greater hydrodynamic efficiency (lift to drag ratio) of the fence-wall system. With increase in immersion of the fence in the boundary layer, both lift and drag decreased, while the lift to drag ratio increased. Variation in the degree of confinement had a large influence on the flow, with the reduction in lift and hydrodynamic efficiency observed for the more confined conditions.

Inverse design of high-Q wave filters in two-dimensional phononic crystals by topology optimization

Topology optimization of a waveguide-cavity structure in phononic crystals for designing narrow band filters under the given operating frequencies is presented in this paper. We show that it is possible to obtain an ultra-high-Q filter by only optimizing the cavity topology without introducing any other coupling medium. The optimized cavity with highly symmetric resonance can be utilized as the multi-channel filter, raising filter and T-splitter. In addition, most optimized high-Q filters have the Fano resonances near the resonant frequencies. Furthermore, our filter optimization based on the waveguide and cavity, and our simple illustration of a computational approach to wave control in phononic crystals can be extended and applied to design other acoustic devices or even opto-mechanical devices.

Large Eddy Simulation and investigation on the flow structure of the cascading cavitation shedding regime around 3D twisted hydrofoil

Cavitating flows are full of complex interactions between cavity evolution and vortical structures difficult to be measured in experiments. In the present work, the flow structure and dynamics of a kind of cascading cavitation shedding regime around a 3D twisted hydrofoil in full-scale water tunnel were numerically investigated using Large Eddy Simulation (LES). A homogeneous cavitation model of vapor fraction transport and a random perturbation generator based on spectral method are adopted. The mesh feasibility was carefully checked to provide an adequate capturing of the intrinsic vortical structure and the turbulence energy spectrum. The predicted cavitation behavior agrees with the experiment in primary aspects such as the cavity topology in periodic evolution, the frequency characteristics and the interlaced spanwise and streamwise vortices. Special emphasis was put on the analysis of flow details including the vortex-cavitation interaction and the pressure wave propagation. The observed convex cascading shedding is found to be caused by the particular re-entrant and side-entrant jet dynamics formed on the twisted surface. The jets reflected on the cavity closure are found to first concentrate then diverge along the minimal local slope of the foil. Another significant phenomenon is that the lift or drag has two peaks of similar magnitude in each cycle, which is analyzed to be a result of the cascading break-up and the ultimate collapse of the cavitation. An approximately linear relationship is predicted between the second-order time derivative of cavity volume and its induced pressure disturbance. The physical mechanism is clarified using a simplified analytical model.

Cavitation about a jet in crossflow

Cavitation occurrence about a jet in crossflow is investigated experimentally in a variable-pressure water tunnel using still and high-speed photography. The 0.012 m diameter jet is injected on the centreplane of a 0.6 m square test section at jet to freestream velocity ratios ranging from 0.2 to 1.6, corresponding to jet-velocity-based Reynolds numbers of$25\times 10^{3}$to$160\times 10^{3}$respectively. Measurements were made at a fixed freestream-based Reynolds number, for which the ratio of the undisturbed boundary layer thickness to jet diameter is 1.18. The cavitation number was varied from inception (up to about 10) down to 0.1. Inception is investigated acoustically for bounding cases of high and low susceptibility to phase change. The influence of velocity ratio and cavitation number on cavity topology and geometry are quantified from the photography. High-speed photographic recordings made at 6 kHz provide insight into cavity dynamics, and derived time series of spatially averaged pixel intensities enable frequency analysis of coherent phenomena. Cavitation inception was found to occur in the high-shear regions either side of the exiting jet and to be of an intermittent nature, increasing in occurrence and duration from 0 to 100 % probability with decreasing cavitation number or increasing jet to freestream velocity ratio. The frequency and duration of individual events strongly depends on the cavitation nuclei supply within the approaching boundary layer. Macroscopic cavitation develops downstream of the jet with reduction of the cavitation number beyond inception, the length of which has a power-law dependence on the cavitation number and a linear dependence on the jet to freestream velocity ratio. The cavity closure develops a re-entrant jet with increase in length forming a standing wave within the cavity. For sufficiently low cavitation numbers the projection of the re-entrant jet fluid no longer reaches the cavity leading edge, analogous to supercavitation forming about solid cavitators. Hairpin-shaped vortices are coherently shed from the cavity closure via mechanisms of shear-layer roll-up similar to those shed from protuberances and jets in crossflow in single-phase flows. These vortices are shed at an apparently constant frequency, independent of the jet to freestream velocity ratio but decreasing in frequency with reducing cavitation number and cavity volume growth. Highly coherent cavitating vortices form along the leading part of the cavity due to instability of the jet upstream shear layer for jet to freestream velocity ratios greater than about 0.8. These vortices are cancelled and condense as they approach the trailing edge in the shear layer of opposing vorticity associated with the cavity closure and the hairpin vortex formation. For lower velocity ratios, where there is decreased jet penetration, the jet upstream shear velocity gradient reverses and vortices of the opposite sense form, randomly modulated by boundary layer turbulence.

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

Protein cavities and tunnels are critical in determining phenomena such as ligand binding, molecular transport, and enzyme catalysis. Molecular dynamics (MD) simulations enable the exploration of the flexibility and conformational plasticity of protein cavities, extending the information available from static experimental structures relevant to, for example, drug design. Here, we present a new tool (trj_cavity) implemented within the GROMACS ( www.gromacs.org ) framework for the rapid identification and characterization of cavities detected within MD trajectories. trj_cavity is optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, for example, protein channels. Its novel grid-based algorithm performs an efficient neighbor search whose calculation time is linear with system size, and a comparison of performance with other widely used cavity analysis programs reveals an orders-of-magnitude improvement in the computational cost. To demonstrate its potential for revealing novel mechanistic insights, trj_cavity has been used to analyze long-time scale simulation trajectories for three diverse protein cavity systems. This has helped to reveal, respectively, the lipid binding mechanism in the deep hydrophobic cavity of a soluble mite-allergen protein, Der p 2; a means for shuttling carbohydrates between the surface-exposed substrate-binding and catalytic pockets of a multidomain, membrane-proximal pullulanase, PulA; and the structural basis for selectivity in the transmembrane pore of a voltage-gated sodium channel (NavMs), embedded within a lipid bilayer environment. trj_cavity is available for download under an open-source license ( http://sourceforge.net/projects/trjcavity ). A simplified, GROMACS-independent version may also be compiled.

Detection of faults position and possible crushed zones by using electrical resistivity and microgravity methods: Application to the Lar Dam area, Iran

The main purposes of this study are to determine the fault position and possible crushed zones, general position and qualitative image of injection curtain, topology of cavities, and weak areas, and also examine deep extension of existing cracks in Berm. Geophysical examinations were performed by using the combination of electrical resistivity and microgravimetry data in Lar Dam. These studies include measurements of 420 electrical soundings with 1,000 m maximum length of current transmitter and measuring 1,081 microgravimetry stations. Also, in order to examine the possible density contrasts, this study discussed three-dimensional modeling by microgravimetry method to obtain Bouguer anomaly and residual anomaly, and determine the edge of residual anomaly. The result of these studies identified four crushed and weak areas with maximum water flight potential. Due to priority and importance degree of geological anomalies, these four weak areas are in the south part of the dam body, north of Berm, south of Berm, and west and southwest of Berm. The observed cracks in Berm are results of Berm subsidence that is due to fault activities or falling developed cavities along faults. It is presented that these cavities which are extended to depth of 70 m can have significant effect on the stability of the dam body.

All-fiber lasers through photonic crystal fibers

AbstractA review on all-fiber lasers based on photonic crystal fibers is presented. Photonic crystal fibers present improved features beyond what conventional optical fibers can offer. Due to their geometric versatility, photonic crystal fibers can present special properties and abilities which can lead to enhanced lasing structures. A brief description of photonic crystal fibers and fiber laser’s properties is presented. All-fiber laser structures developed using photonic crystal fibers are described and divided in two groups, depending on the cavity topology: ring cavity fiber lasers and linear cavity fiber lasers. All-fiber lasers applications in the photonic crystal fiber related sensing field are described.

Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1–3 mutant

Nitrophorins (NPs) are nitric oxide (NO)-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. Though NP7 exhibits a large sequence resemblance with other NPs, two major differential features are the ability to interact with negatively charged cell surfaces and the presence of a specific N-terminus composed of three extra residues (Leu1-Pro2-Gly3). The aim of this study is to examine the influence of the N-terminus on the ligand binding, and the topological features of inner cavities in closed and open states of NP7, which can be associated to the protein structure at low and high pH, respectively. Laser flash photolysis measurements of the CO rebinding kinetics to NP7 and its variant NP7(Δ1–3), which lacks the three extra residues at the N-terminus, exhibit a similar pattern and support the existence of a common kinetic mechanism for ligand migration and binding. This is supported by the existence of a common topology of inner cavities, which consists of two docking sites in the heme pocket and a secondary site at the back of the protein. The ligand exchange between these cavities is facilitated by an additional site, which can be transiently occupied by the ligand in NP7, although it is absent in NP4. These features provide a basis to explain the enhanced internal gas hosting capacity found experimentally in NP7 and the absence of ligand rebinding from secondary sites in NP4. The current data allow us to speculate that the processes of docking to cell surfaces and NO release may be interconnected in NP7, thereby efficiently releasing NO into a target cell. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications

Genome of the model dicot flowering plant, Arabidopsis thaliana, a popular tool for understanding molecular biology of plant physiology, encodes all three classes of plant hemoglobins that differ in their sequence, ligand binding and spectral properties. As such these globins are of considerable attention. Crystal structures of few members of plant class I nonsymbiotic hemoglobin have been described earlier. Here we report the crystal structure of Arabidopsis class I hemoglobin (AHb1) to 2.2Ǻ and compare its key features with the structures of similar nonsymbiotic hemoglobin from other species. Crystal structure of AHb1 is homologous to the related members with similar globin fold and heme pocket architecture. The structure is homodimeric in the asymmetric unit with both distal and proximal histidines coordinating to the heme iron atom. Residues lining the dimeric interface are also conserved in AHb1 with the exception of additional electrostatic interaction between H112 and E113 of each subunit and that involving Y119 through two water molecules. In addition, differences in heme pocket non-covalent interactions, a novel Ser residue at F7 position, Xe binding site variability, internal cavity topology differences, CD loop conformation and stability and other such properties might explain kinetic variability in AHb1. Detailed cavity analysis of AHb1 showed the presence of a novel long tunnel connecting the distal pockets of both the monomers. Presence of such tunnel, along with conformational heterogeneity observed in the two chains, might suggest cooperative ligand binding and support its role in NO scavenging. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Microscopic theory of superconductivity in MgB2-type systems in a magnetic field: A neighborhood of H c2

We calculate the upper critical magnetic field H c2 in the framework of a microscopic superconductivity theory with two energy bands of different dimensions on the Fermi surface with the cavity topology typical of the compound MgB2 taken into account (an anisotropic system). We assume an external magnetic field parallel to the crystallographic z axis. We obtain analytic formulas in the low-temperature range (T/Tc ≪ 1) and also near the critical temperature ((T-Tc)/Tc ≪ 1). We compare the temperature dependence of Hc2 for a two-band anisotropic system with that of H c2 0 corresponding to a two-band isotropic system (with Fermi-surface cavities of the same topology). We determine the role of the band-structure anisotropy, the positive curvature of the upper critical field near the critical temperature, and the important role of the ratio v1/v2 of the velocities on the Fermi surface in determining Hc2. We also obtain the values of the parameters Δ1 and Δ2 along the line of the critical magnetic field.

A Novel Multilayer Aperture-Coupled Cavity Resonator for Millimeter-Wave CMOS RFICs

A novel millimeter-wave cavity resonator, completely compatible with commercial CMOS fabrication techniques, has been designed and fabricated in a 0.25-mum CMOS process and tested. The resonator employs a capacitively loaded cavity topology effectively implemented using the CMOS multimetal-layer and via-hole structure. The CMOS capacitively loaded cavity resonator, including two coupling apertures and microstrip feed lines, occupies an area of 2 mmtimes1.4 mmtimes6.28 mum, which is much smaller than the cavity resonator designed without a capacitive load at the same resonant frequency. It resonates at 30 GHz with a corresponding insertion loss of 2 dB and unloaded quality factor of 22.2. The resonant-frequency reduction is approximately 50%, as compared to that without the capacitive load. The design and performance of a new CMOS coupling aperture, which is useful as a coupling mechanism and a vertical interconnect for highly dense millimeter-wave CMOS RF integrated circuits (RFICs) are also presented. The developed low-loss and compact CMOS cavity resonator can be used to realize various millimeter-wave on-chip passive components such as wideband bandpass filters and diplexers and is suitable for direct integration with other CMOS circuits on a single chip. It is attractive for CMOS RFIC design at millimeter-wave frequencies

Design techniques for dual-passband filters

This paper introduces two possible approaches to the design of microwave filters presenting two passbands separated by one rejection band, which is created by suitably placing transmission zeros in the stopband. In the first method, the two passbands have almost equal extension and the transmission zeros are symmetrically placed in the stopband; the second method instead allows the synthesis of filters with different passbands width and all the transmission zeros in the stopband placed at the same frequency. Both design methods are based on suitably defined frequency transformations and employ well-established prototype synthesis techniques; the practical implementation is performed through the classical multiple-coupled cavity topology. Two test filters operating in the global system for mobile communication 800-MHz band, designed with the described procedures and actually fabricated, have validated the novel design methods.

Topological derivative for the inverse scattering of elastic waves

To establish an alternative analytical framework for the elastic-wave imaging of underground cavities, the focus of this study is an extension of the concept of topological derivative, rooted in elastostatics and shape optimization, to three-dimensional elastodynamics involving semi-infinite and infinite solids. The main result of the proposed boundary integral approach is a formula for topological derivative, explicit in terms of the elastodynamic fundamental solution, obtained by an asymptotic expansion of the misfit-type cost functional with respect to the creation of an infinitesimal hole in an otherwise intact (semi-infinite or infinite) elastic medium. Valid for an arbitrary shape of the infinitesimal cavity, the formula involves the solution of six canonical exterior elastostatic problems, and becomes fully explicit when the vanishing cavity is spherical. A set of numerical results is included to illustrate the potential of topological derivative as a computationally efficient tool for exposing an approximate cavity topology, location, and shape via a grid-type exploration of the host solid. For a comprehensive solution to three-dimensional inverse scattering problems involving elastic waves, the proposed approach can be used most effectively as a pre-conditioning tool for more refined, albeit computationally intensive minimization-based imaging algorithms. To the authors' knowledge, an application of topological derivative to inverse scattering problems has not been attempted before; the methodology proposed in this paper could also be extended to acoustic problems.

Solution 1H NMR study of the heme cavity and folding topology of the abbreviated chain 118-residue globin from the cyanobacterium Nostoc commune.

The globin from the cyanobacterium Nostoc commune, abbreviated GlbN, which appears to serve as a part of a terminal oxidase rather than as a respiratory pigment, displays relatively normal O2 binding properties, despite the highly abbreviated polypeptide chain, (118 residues) relative to more conventional globins [Thorsteinsson, M. V. , Bevan, D. R., Potts, M., Dou, Y., Eich, R. F., Hargrove, M. S., Gibson, Q. H., and Olson, J. S. (1999) Biochemistry 38, 2117-2126]. The nature of the heme cavity and the general folding topology of this cyanoglobin were investigated by solution 1H NMR to establish the extent to which, and the manner in which, this compact globin adheres to the standard globin fold. This represents by far the smallest globin subjected to structural analysis. The paramagnetic cyanomet derivative was selected because its characteristically large magnetic anisotropy imparts significant dipolar shifts which both improve resolution to greatly facilitate assignments and serve as indicators of the folding topology of the globin. Identification of the axial His 70 and highly conserved Phe 35 (CD1) determined the absolute orientation of the heme and proximal His. Sequential assignments of four helical and one loop segments, which exhibit dipolar contacts to the heme and among each other, confirm the presence of well-conserved F, G, and H helices and the FG corner. The majority of the abbreviation of the chain relative to the more conventional length globins is accommodated in the A-D helices, of which the last is completely missing. The distal residue which provides a H-bond to bound ligand is identified as Gln 43, but the expected helical position E7 could not be confirmed. His 46, placed at position E10, is found to adopt alternate orientations into, and out of, the heme cavity depending on protonation state, suggesting the presence of a Bohr effect at low pH. It is shown that the dipolar shifts exhibited by backbone protons for the assigned residues conform well to those observed for other cyanomet globins and further support a conserved Mb fold. Perturbed medium-range dipolar contacts and the pH-independent backbone proton lability of the F helix are interpreted in terms of a holoprotein which is less stable than a conventional length globin.

Effects of cavity topology on the nonlinear dynamics of additive-pulse mode-locked lasers

We study the effect of cavity topology on the nonlinear dynamics of additive-pulse mode-locked (APM) lasers configured in the Fabry–Perot and Michelson geometries. In experiments the Fabry–Perot laser often exhibits such behaviors as period doubling and quasiperiodicity as the nonlinearity is increased, whereas the Michelson APM (M-APM) exhibits none of these effects. Numerical studies confirm that the M-APM appears to be more resistant to such behavior and thus is more tolerant to excessive nonlinearity in the control cavity. Using the concepts of intensity- and phase-dependent two-beam and multiple-beam interference, we obtain a general empirical rule connecting cavity topology to pulse train instabilities for fast saturable absorber mode-locked lasers employing coupled cavities.