13 research outputs found
Nonlinear wave transmission and pressure on the fixed truncated breakwater using NURBS numerical wave tank
Fully nonlinear wave interaction with a fixed breakwater is investigated in a numerical wave tank (NWT). The potential theory and high-order boundary element method are used to solve the boundary value problem. Time domain simulation by a mixed Eulerian-Lagrangian (MEL) formulation and high-order boundary integral method based on non uniform rational B-spline (NURBS) formulation is employed to solve the equations. At each time step, Laplace equation is solved in Eulerian frame and fully non-linear free-surface conditions are updated in Lagrangian manner through material node approach and fourth order Runge-Kutta time integration scheme. Incident wave is fed by specifying the normal flux of appropriate wave potential on the fixed inflow boundary. To ensure the open water condition and to reduce the reflected wave energy into the computational domain, two damping zones are provided on both ends of the numerical wave tank. The convergence and stability of the presented numerical procedure are examined and compared with the analytical solutions. Wave reflection and transmission of nonlinear waves with different steepness are investigated. Also, the calculation of wave load on the breakwater is evaluated by first and second order time derivatives of the potential
The Bryopsis hypnoides Plastid Genome: Multimeric Forms and Complete Nucleotide Sequence
BACKGROUND: Bryopsis hypnoides Lamouroux is a siphonous green alga, and its extruded protoplasm can aggregate spontaneously in seawater and develop into mature individuals. The chloroplast of B. hypnoides is the biggest organelle in the cell and shows strong autonomy. To better understand this organelle, we sequenced and analyzed the chloroplast genome of this green alga. PRINCIPAL FINDINGS: A total of 111 functional genes, including 69 potential protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes were identified. The genome size (153,429 bp), arrangement, and inverted-repeat (IR)-lacking structure of the B. hypnoides chloroplast DNA (cpDNA) closely resembles that of Chlorella vulgaris. Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA. The relative amounts of the four multimeric cpDNA forms were estimated to be about 1, 1/2, 1/4, and 1/8 based on molecular hybridization analysis. Phylogenetic analyses based on a concatenated alignment of chloroplast protein sequences suggested that B. hypnoides is sister to all Chlorophyceae and this placement received moderate support. CONCLUSION: All of the results suggest that the autonomy of the chloroplasts of B. hypnoides has little to do with the size and gene content of the cpDNA, and the IR-lacking structure of the chloroplasts indirectly demonstrated that the multimeric molecules might result from the random cleavage and fusion of replication intermediates instead of recombinational events