All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen...All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.展开更多
An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. An...An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H- ~ ~ O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of （DMSO）m＇S=O…… HW-OW-（H20）n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.展开更多
When simulating seismic wave propagation in free space, it is essential to introduce absorbing boundary conditions to eliminate reflections from artificially trtmcated boundaries. In this paper, a damping factor refer...When simulating seismic wave propagation in free space, it is essential to introduce absorbing boundary conditions to eliminate reflections from artificially trtmcated boundaries. In this paper, a damping factor referred to as the Gaussian dmping factor is proposed. The Gaussian damping factor is based on the idea of perfectly matched layers （PMLs）. This work presents a detailed analysis of the theoretical foundations and advantages of the Gaussian damping factor. Additionally, numerical experiments for the simulation of seismic waves are presented based on two numerical models： a homogeneous model and a multi-layer model. The results show that the proposed factor works better. The Gaussian damping factor achieves a higher Signal-to-Noise Ratio （SNR） than previously used factors when using same number of PMLs, and requires less PMLs than other methods to achieve an identical SNR.展开更多
Blast wall can prevent vehicles from approaching the protective building and can reduce the destructive power of shock wave to a certain extent.However,majority of studies on blast walls have some shortcomings.The exp...Blast wall can prevent vehicles from approaching the protective building and can reduce the destructive power of shock wave to a certain extent.However,majority of studies on blast walls have some shortcomings.The explosion test data are few.Most exsiting studies focus on the propagation of shock wave and the influence of blast wall on the propagation of shock wave.Discussion on the main parameters of blast wall design is meagre,such as the design of safety distance,the distance from the blast wall to the protective building,height and width of the blast wall.This paper uses the finite element programme LS-DYNA to design the blast wall.To analyze the convergence of the finite element model and to determine the mesh size of the model,this paper establishes several finite element models with different sizes of meshes to verify the model.Then,the overpressure distribution of the shock wave on the protective building is simulated to implement the blast wall design.The geometric parameters of the blast wall are preliminarily determined.And the influence of the safety distance on the overpressure of the building surface is mainly discussed,so as to determine the final design parameters.When the overpressure is less than 2 kPa,it is considered that there will be no damage to people caused by flying fragments.Eventually,the blast wall height is 3 m,the thickness is 1 m,and the safety distance is 35 m.The proposed method is used to demonstrate the design method,and the final design parameters of the blast wall can thus be used for reference.展开更多
N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water syste...N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions （RDFs） and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.展开更多
Green-Naghdi （G-N） theory is a fully nonlinear theory for water waves. Some researchers call it a fully nonlinear Boussinesq model. Different degrees of complexity of G-N theory are distinguished by ＂levels＂ where...Green-Naghdi （G-N） theory is a fully nonlinear theory for water waves. Some researchers call it a fully nonlinear Boussinesq model. Different degrees of complexity of G-N theory are distinguished by ＂levels＂ where the higher the level, the more complicated and presumably more accurate the theory is. In the research presented here a comparison was made between two different levels of G-N theory, specifically level II and level III G-N restricted theories. A linear analytical solution for level III G-N restricted theory was given. Waves on a planar beach and shoaling waves were both simulated with these two G-N theories. It was shown for the first time that level III G-N restricted theory can also be used to predict fluid velocity in shallow water. A level III G-N restricted theory is recommended instead of a level II G-N restricted theory when simulating fullv nonlinear shallow water waves.展开更多
文摘All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.
文摘An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H- ~ ~ O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of （DMSO）m＇S=O…… HW-OW-（H20）n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.
基金supported by the National Natural Science Foundation of China(No. 61072118)
文摘When simulating seismic wave propagation in free space, it is essential to introduce absorbing boundary conditions to eliminate reflections from artificially trtmcated boundaries. In this paper, a damping factor referred to as the Gaussian dmping factor is proposed. The Gaussian damping factor is based on the idea of perfectly matched layers （PMLs）. This work presents a detailed analysis of the theoretical foundations and advantages of the Gaussian damping factor. Additionally, numerical experiments for the simulation of seismic waves are presented based on two numerical models： a homogeneous model and a multi-layer model. The results show that the proposed factor works better. The Gaussian damping factor achieves a higher Signal-to-Noise Ratio （SNR） than previously used factors when using same number of PMLs, and requires less PMLs than other methods to achieve an identical SNR.
基金This work was supported by the National Natural Science Foundation of China(No.51878507).
文摘Blast wall can prevent vehicles from approaching the protective building and can reduce the destructive power of shock wave to a certain extent.However,majority of studies on blast walls have some shortcomings.The explosion test data are few.Most exsiting studies focus on the propagation of shock wave and the influence of blast wall on the propagation of shock wave.Discussion on the main parameters of blast wall design is meagre,such as the design of safety distance,the distance from the blast wall to the protective building,height and width of the blast wall.This paper uses the finite element programme LS-DYNA to design the blast wall.To analyze the convergence of the finite element model and to determine the mesh size of the model,this paper establishes several finite element models with different sizes of meshes to verify the model.Then,the overpressure distribution of the shock wave on the protective building is simulated to implement the blast wall design.The geometric parameters of the blast wall are preliminarily determined.And the influence of the safety distance on the overpressure of the building surface is mainly discussed,so as to determine the final design parameters.When the overpressure is less than 2 kPa,it is considered that there will be no damage to people caused by flying fragments.Eventually,the blast wall height is 3 m,the thickness is 1 m,and the safety distance is 35 m.The proposed method is used to demonstrate the design method,and the final design parameters of the blast wall can thus be used for reference.
基金This work was supported by the Doctoral Scientific Research Foundation of the Natural Science Foundation of Guangdong Province, China （No.7301567） and the Research Foundation of Guangdong Pharmaceutical University, China （No.2006YKX05）.
文摘N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions （RDFs） and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.
基金Supported by the National Natural Science Foundation of China under Grant No. 50779008the 111 Project (B07019)
文摘Green-Naghdi （G-N） theory is a fully nonlinear theory for water waves. Some researchers call it a fully nonlinear Boussinesq model. Different degrees of complexity of G-N theory are distinguished by ＂levels＂ where the higher the level, the more complicated and presumably more accurate the theory is. In the research presented here a comparison was made between two different levels of G-N theory, specifically level II and level III G-N restricted theories. A linear analytical solution for level III G-N restricted theory was given. Waves on a planar beach and shoaling waves were both simulated with these two G-N theories. It was shown for the first time that level III G-N restricted theory can also be used to predict fluid velocity in shallow water. A level III G-N restricted theory is recommended instead of a level II G-N restricted theory when simulating fullv nonlinear shallow water waves.
