A new three-dimensional semi-implicit finite-volume ocean model has been developed for simulating the coastal ocean circulation, which is based on the staggered C-unstructured non-orthogonal grid in the hor- izontal d...A new three-dimensional semi-implicit finite-volume ocean model has been developed for simulating the coastal ocean circulation, which is based on the staggered C-unstructured non-orthogonal grid in the hor- izontal direction and z-level grid in the vertical direction. The three-dimensional model is discretized by the semi-implicit finite-volume method, in that the free-surface and the vertical diffusion are semi-implicit, thereby removing stability limitations associated with the surface gravity wave and vertical diffusion terms. The remaining terms in the momentum equations are discretized explicitly by an integral method. The partial cell method is used for resolving topography, which enables the model to better represent irregular topography. The model has been tested against analytical cases for wind and tidal oscillation circulation, and is applied to simulating the tidal flow in the Bohal Sea. The results are in good agreement both with the analytical solutions and measurement results.展开更多
A semi-implicit and Eulerian - Lagrangian finite difference method for three-dimensionalshallow flow has been extended to a more complete system of equations incorporating second-moment turbulence closure model and tr...A semi-implicit and Eulerian - Lagrangian finite difference method for three-dimensionalshallow flow has been extended to a more complete system of equations incorporating second-moment turbulence closure model and transport equations of salinity and temperature. The simulation for flooding and drying of mudflats has been improved. The model is applied to Xiamen waters. Based on extensive survey data, water level elevation, temperature and salinity field along the eastern open boundary and at the Jiulong River inlets and runoffs are analyzed, specified and calibrated. The computed results show good agreement with the measured data, reproduce flooding, emergence of large and complex mudflat region.展开更多
We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, a...We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.展开更多
基金The Major State Basic Research Program of China under contract No. 2012CB417002the National Natural Science Foundation of China under contract Nos 50909065 and 51109039
文摘A new three-dimensional semi-implicit finite-volume ocean model has been developed for simulating the coastal ocean circulation, which is based on the staggered C-unstructured non-orthogonal grid in the hor- izontal direction and z-level grid in the vertical direction. The three-dimensional model is discretized by the semi-implicit finite-volume method, in that the free-surface and the vertical diffusion are semi-implicit, thereby removing stability limitations associated with the surface gravity wave and vertical diffusion terms. The remaining terms in the momentum equations are discretized explicitly by an integral method. The partial cell method is used for resolving topography, which enables the model to better represent irregular topography. The model has been tested against analytical cases for wind and tidal oscillation circulation, and is applied to simulating the tidal flow in the Bohal Sea. The results are in good agreement both with the analytical solutions and measurement results.
文摘A semi-implicit and Eulerian - Lagrangian finite difference method for three-dimensionalshallow flow has been extended to a more complete system of equations incorporating second-moment turbulence closure model and transport equations of salinity and temperature. The simulation for flooding and drying of mudflats has been improved. The model is applied to Xiamen waters. Based on extensive survey data, water level elevation, temperature and salinity field along the eastern open boundary and at the Jiulong River inlets and runoffs are analyzed, specified and calibrated. The computed results show good agreement with the measured data, reproduce flooding, emergence of large and complex mudflat region.
基金supported by the National Natural Science Foundation of China(Grant No.21203178)the National Natural Science Foundation of China(Grant No.21373201)+2 种基金the National Natural Science Foundation of China(Grant No.21433014)the Science and Technological Ministry of China(Grant No.2011YQ09000505)“Strategic Priority Research Program”of the Chinese Academy of Sciences(Grant Nos.XDB10040304 and XDB100202002)
文摘We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide foldinz landscapes.
