Temporal Variability of High Vertical Wavenumber Shear over the Izu-Ogasawara Ridge

Recent numerical studies (Hibiya et al., 1996, 1998, 2002) showed that the energy cascade across the internal wave spectrum down to small dissipation scales was under strong control of parametric subharmonic instabilities (PSI) which transfer energy from low vertical mode double-inertial frequency internal waves to high vertical mode near-inertial internal waves. To see whether or not the numerically-predicted energy cascade process is actually dominant in the real deep ocean, we examine the temporal variability of vertical profiles of horizontal velocity observed by deploying a number of expendable current profilers (XCPs) at one location near the Izu-Ogasawara Ridge. By calculating EOFs, we find the observed velocity profiles are dominated by low mode semidiurnal (∼double-inertial frequency) internal tides and high mode near-inertial internal waves. Furthermore, we find that the WKB-stretched vertical scales of the near-inertial current shear are about 250 sm and 100 sm. The observed features are reasonably explained if the energy cascade down to small dissipation scales is dominated by PSI.     

Distribution of Overturn Induced by Internal Tides and Thorpe Scale in Uchiura Bay

The vertical mixing process induced by internal tides was investigated by repeated conductivity, temperature, and depth (CTD) measurements and bottom-mounted acoustic Doppler current profiler (ADCP) in Uchiura Bay from July 24 to 25, 2001. Internal tides were observed with a wave height of 40 m and a horizontal current of 0.3 ms⁻¹. Density inversions were found in the CTD data, and the method of Galbraith and Kelley (1996) was applied to the data to identify overturns and to calculate Thorpe scale. Most of the overturns distributed in the region of low Richardson number, so that they were considered to be caused by shear instability associated with the internal tides. Thorpe scale was calculated to be 0.48 m. From the Thorpe scale, the vertical eddy diffusivity due to internal tides in Uchiura Bay was estimated as K _ρ ∼ 10⁻⁴ m²s⁻¹. This revised version was published online in July 2006 with corrections to the Cover Date.     

Numerical model of a marine chute evacuation system

A lumped-mass model of a marine evacuation chute is presented based on the equations of Kane. The effects of wind load, internal mass transport and the motions of the ends are included. A sample of predicted motions and tensions is presented for a typical extreme environmental condition. The model may be used to assess the behaviour of the chute structure under a variety of emergency evacuation scenarios.     

Internal inlet for wave generation and absorption treatment

A new method of implementing, in two-dimensional (2-D) Navier–Stokes equations, a numerical internal wave generation in the finite volume formulation is developed. To our knowledge, the originality of this model is on the specification of an internal inlet velocity defined as a source line for the generation of linear and non-linear waves. The use of a single cell to represent the source line and its transformation to an internal boundary condition proved to be an interesting alternative to the common procedure of adding a mass source term to the continuity equation within a multi-cell rectangular region. Given the reduction of the source domain to a one-dimensional region, this simple new type of source introduced less perturbation than the 2-D source type. This model was successfully implemented in the PHOENICS code (Parabolic Hyperbolic Or Elliptic Numerical Integration Code Series). In addition, the volume of fluid (VOF) fraction was used to describe the free surface displacements. A friction force term was added to the momentum transport equation in the vertical direction, in order to enhance wave damping, within relatively limited number of cells representing the sponge layers at the open boundaries. For monochromatic wave, propagating on constant water depth, numerical and analytical results showed good agreements for free surface profiles and vertical distribution of velocity components. For solitary wave simulation, the wave shape and velocity were preserved; while, small discrepancy in the tailing edge of the free surface profiles was observed. The suitability of this new numerical wave generation model for a two source lines extension was investigated and proven to be innovative. The comparisons between numerical, analytical and experimental results showed that the height of the merging waves was correctly reproduced and that the reflected waves do not interact with the source lines.     

Essential properties of Boussinesq equations for internal and surface waves in a two-fluid system

Boussinesq equations describing motions of internal waves in a two-fluid system with the presence of free surface are theoretically derived, and the associated essential properties are examined in this study. Eliminating the dependence on the vertical coordinate from all variables, four equations constitute the Boussinesq model with two flexible parameters, z_u and z_l, which indicate the specific elevations, respectively, in the upper and lower fluids. Similar to the Boussinesq model for a single-layer fluid, z_u and z_l are determined by matching the linear dispersion relation with Lamb's solution. This determines the optimal model. In the analysis stage, this problem is classified into two cases, the thicker-upper-layer case and the thicker-lower-case case, to avoid the possible divergence of wave properties as the thickness ratio grows. Since there exist two modes of motions that may be excited, cases of both modes are separately analyzed. Linear characteristics including the amplitude ratios and normalized particle velocities are analyzed. Second-order harmonic waves are examined to validate nonlinear behaviors of present model. Results of linear and nonlinear investigations show that the present model indeed extends the applicable range of traditional Boussinesq equations.     

Internal generation of waves on an arc in a rectangular grid system

This paper presents a technique to generate waves at oblique angles in finite difference numerical models in a rectangular grid system by using internal generation technique [Lee, C., Suh, K.D., 1998. Internal generation of waves for time-dependent mild-slope equations. Coast. Eng. 34, 35–57.] along an arc-shaped line source. Tests were made for four different types of wave generation layouts. Quantitative experiments were conducted under the following conditions: the propagation of waves on a flat bottom, the refraction and shoaling of waves on a planar slope, and the diffraction of waves to a semi-infinite breakwater. Numerical experiments were conducted using the extended mild-slope equations of Suh et al. [Suh, K.D., Lee, C., Park, W.S., 1997. Time-dependent equations for wave propagation on rapidly varying topography. Coast. Eng. 32, 91–117.]. The fourth layout type consisting of two parallel lines connected to a semicircle showed the best solutions, especially for a small grid size. This technique is useful for the numerical simulation of irregular waves with broad-banded directional spectrum using conventional spectral wave models for the reasonable estimation of bottom friction and wave-breaking.     

Internal wave generation in an improved two-dimensional Boussinesq model

A set of Boussinesq-type equations with improved linear frequency dispersion in deeper water is solved numerically using a fourth order accurate predictor-corrector method. The model can be used to simulate the evolution of relatively long, weakly nonlinear waves in water of constant or variable depth provided the bed slope is of the same order of magnitude as the frequency dispersion parameter. By performing a linearized stability analysis, the phase and amplitude portraits of the numerical schemes are quantified, providing important information on practical grid resolutions in time and space. In contrast to previous models of the same kind, the incident wave field is generated inside the fluid domain by considering the scattered wave field in one part of the fluid domain and the total wave field in the other. Consequently, waves leaving the fluid domain are absorbed almost perfectly in the boundary regions by employment of damping terms in the mass and momentum equations. Additionally, the form of the incident regular wave field is computed by a Fourier approximation method which satisfies the governing equations accurately in water of constant depth. Since the Fourier approximation method requires an Eulerian mean current below wave trough level or a net mass transport velocity to be specified, the method can be used to study the interaction of waves and currents in closed as well as open basins. Several computational examples are given. These illustrate the potential of the wave generation method and the capability of the developed model.     

两种鲨鱼鳃部真菌菌群的PCR-DGGE分析

以提取自东海海域两种鲨鱼(尖吻鲭鲨和噬人鲨)鳃耙组织的总DNA为模板,对其真菌菌群rDNA的基因内转录间隔区ITS1序列进行了PCR扩增,扩增产物经变性梯度凝胶电泳(DGGE)分离,电泳图谱中的7条主要条带经过二次PCR扩增后进行了克隆测序。NCBI-BLAST比对及分子系统发育分析结果表明,尖吻鲭鲨鳃部真菌菌群的优势种来自四个分类单元,其中一个来自青霉属,三个来自曲霉属;噬人鲨鳃部真菌的优势种来自四个分类单元,其中一种来自青霉属、两个来自梗孢酵母属、一个来自枝顶孢属;青霉属为两种鲨鱼鳃部共同的优势菌;另外DGGE指纹图谱显示还有种类较丰富的劣势菌存在。数据库检索显示多数真菌分类单元具有较好的产生生物活性天然产物的潜力。该PCR-DGGE分析揭示鲨鱼鳃部栖生有较丰富的真菌类群,它们的代谢产物及其与宿主之间的相互作用还有待深入研究。     

Analysis of kinematic parameters of Internal Solitary Waves in the Northern South China Sea

The monthly climatology of observed temperature and salinity from the U.S. Navy Generalized Digital Environment Model (GDEM-Version 3.0) is used to derive the geographical and seasonal distribution of kinematic parameters of nonlinear internal waves in the Northern South China Sea (NSCS). Coefficients of the Generalized Extended Korteweg-de Vries Equation (GEKdV) with a background current are investigated (phase speed, dispersion, quadratic and cubic nonlinearity parameters, normalizing factor). These parameters are used to evaluate the possible polarities, shapes of internal solitary waves, their limiting amplitudes and propagation speed. We show that the long wave phase speed and dispersion parameters mainly depend on topography characteristics and have no obvious seasonal variation. The nonlinear parameters and normalizing factor are sensitive to variations in the density stratification and topography. Background current also exerts the distinct effects on the kinematic parameters; especially the nonlinear parameter can change by an order of magnitude. The nonlinear parameters take on larger values in the summer (July), and linear internal waves are prone to become steeper and develop into large-amplitude internal solitary waves under such circumstances. This explains why nonlinear internal solitary waves occur more frequently in summer. From the kinematic viewpoint, the dispersion parameter takes on larger values in the Pacific Ocean (PO) due to deeper water depth when compared with that in the NSCS. The stronger dispersion effect in the PO hinders the formation of large amplitude internal solitary waves, explaining why nonlinear internal solitary waves are rarely found to the east of the Luzon Strait. Large near-bottom velocities dominate the shallow area and tend to increase in the warm season. The largest values are induced by internal solitary waves, indicating that internal waves are the major drivers of sediment re-suspension and erosion processes.