Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in sin- g...Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in sin- gle-walled carbon nanochannels are exploited. Molecular simulations show that the density of the N2 and H2 are quite high, which is critical for the stability of the nanobubbles and may have potential applications, such as hydrogen storage, incorporated with recent experimental method to controllably produce hydrogen nanobubbles. The water molecules inside the nanochannel show an unexpected directed motion with long time period, which is indispensable in the future study of the dynamics of biological channels.展开更多
The Chinese traditional medical massage has been used as a natural therapy to eliminate some diseases. Here, the effect of the rolling massage frequency to the blood flow in the blood vessels under the rolling massage...The Chinese traditional medical massage has been used as a natural therapy to eliminate some diseases. Here, the effect of the rolling massage frequency to the blood flow in the blood vessels under the rolling massage manipulation is studied by the lattice Boltzmann simulation. The simulation results show that when the frequency is smaller than or comparable to the pulsatile frequency of the blood flow, the effect on the blood flux by the rolling massage is small. 011 the contrast, if the frequency is twice or more times of the pulsatile frequency of the blood flow, the blood flux is greatly enhanced and increases linearly with respect to the frequency. Similar behavior has also been observed on the shear stress on the blood vessel walls. The result is helpful for understanding that the rolling massage has the function of promoting the blood circulation and removing the blood stasis.展开更多
Peptide frictions in water nanofilms of various thicknesses on a mica surface are studied via molecular dynamics simulations. We find that the forced lateral motion of the peptide exhibits stick-slip behaviour at low ...Peptide frictions in water nanofilms of various thicknesses on a mica surface are studied via molecular dynamics simulations. We find that the forced lateral motion of the peptide exhibits stick-slip behaviour at low water coverage; in contrast, the smooth gliding motion is observed at higher water coverage. The adsorbed peptide can form direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds with the substrate. We propose that the stick-slip phenomenon is attributed to the overall effects of direct and indirect hydrogen bonds formed between the surface and the peptide.展开更多
Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties unde...Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation.A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter.The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs.During the compression process,firstly the hydrogen bonds between complement base pairs are broken.With the compression accumulating,the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation.This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.展开更多
A biconcave particle suspended in a Poiseuille flow is investigated by the multiple-relaxation-time lattice Boltzmann method with the Galilean-invariant momentum exchange method.The lateral migration and equilibrium o...A biconcave particle suspended in a Poiseuille flow is investigated by the multiple-relaxation-time lattice Boltzmann method with the Galilean-invariant momentum exchange method.The lateral migration and equilibrium of the particle are similar to the Segré-Silberberg effect in our numerical simulations.Surprisingly,two lateral equilibrium positions are observed corresponding to the releasing positions of the biconcave particle.The upper equilibrium positions significantly decrease with the increasing Reynolds number,whereas the lower ones are almost insensitive to the Reynolds number.Interestingly,the regular wave accompanied by nonuniform rotation is exhibited in the lateral movement of the biconcave particle.It can be attributed to the fact that the biconcave shape in various postures interacts with the parabolic velocity distribution of the Poiseuille flow.A set of contours illustrate the dynamic flow field when the biconcave particle has successive postures in a rotating period.展开更多
The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the activ...The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain,which may securely affect the original function of protein.Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.展开更多
A hydrodynamic boundary condition for the lattice Boltzmann model at impermeable boundaries is developed.This boundary condition satisfies both the no-slip condition and the fluid conservation at boundary nodes.Poiseu...A hydrodynamic boundary condition for the lattice Boltzmann model at impermeable boundaries is developed.This boundary condition satisfies both the no-slip condition and the fluid conservation at boundary nodes.Poiseuille flow and Couette flow are calculated with this technique to demonstrate the accuracy of the present boundary condition.展开更多
According to new slip effects on nanopatterned interfaces, the mechanism of enhancing water injection into hydrophobic nanomaterial SiO2 was proposed. When Hydrophobic Nanoparticles（HNPs）are adsorbed on surfaces of ...According to new slip effects on nanopatterned interfaces, the mechanism of enhancing water injection into hydrophobic nanomaterial SiO2 was proposed. When Hydrophobic Nanoparticles（HNPs）are adsorbed on surfaces of porous walls, hydrophobic nanoparticles layers are formed instead of hydrated layer, and slip effects appear on the pore wall when a driving pressure is applied to the rock cores sample. It makes fluid to move more quickly and the flow capacity increases greatly. Experiments on changing wettability of porous walls were conducted, and the phenomenon that porous walls surfaces were adsorbed by nanoparticles was validated with the Environment Scan Electron Microscopy（ESEM）. The results of displacement experiments show that flowing resistance is greatly reduced, and water-phase effective permeability is increased by 47 % averagely after being treated by nanofluid. These results indicate that the slip effect may occur on nanoparticle film of porous walls. Based on this new mechanism of enhancing water injection about hydrophobic nanomaterial SiO2, a slip velocity model in uniform porous media was introduced, and some formulas for the ratio of slip length to radius, slip length ,stream slip velocity and flux increment were deduced. and calculated results indicate that the ratio of slip length to radius is about 3.54%-6.97%, and the slip length is about 0.024 μ m -0.063 μ m. The proposed model can give a good interpretation for the mechanisms of enhancing water injection with the HNPs.展开更多
The diffusion of an ammonia molecule （NH3） in water was investigated by molecular dynamic simulations. It is found that the diffusion shows negative correlation with its dipole orientation.
基金Partly supported by One-Hundred-Talent Project from the Chinese Academy of Sciences and Shanghai Supercomputer Center of China..
文摘Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in sin- gle-walled carbon nanochannels are exploited. Molecular simulations show that the density of the N2 and H2 are quite high, which is critical for the stability of the nanobubbles and may have potential applications, such as hydrogen storage, incorporated with recent experimental method to controllably produce hydrogen nanobubbles. The water molecules inside the nanochannel show an unexpected directed motion with long time period, which is indispensable in the future study of the dynamics of biological channels.
基金supported by the National Fundamental Research Program of China under Grant No.2006CB708612Zhejiang Funding Scheme to Young College Teachers
文摘The Chinese traditional medical massage has been used as a natural therapy to eliminate some diseases. Here, the effect of the rolling massage frequency to the blood flow in the blood vessels under the rolling massage manipulation is studied by the lattice Boltzmann simulation. The simulation results show that when the frequency is smaller than or comparable to the pulsatile frequency of the blood flow, the effect on the blood flux by the rolling massage is small. 011 the contrast, if the frequency is twice or more times of the pulsatile frequency of the blood flow, the blood flux is greatly enhanced and increases linearly with respect to the frequency. Similar behavior has also been observed on the shear stress on the blood vessel walls. The result is helpful for understanding that the rolling massage has the function of promoting the blood circulation and removing the blood stasis.
基金supported by the National Natural Science Foundation of China (Grant No.10825520)the National Basic Research Program of China (Grant No.2007CB936000)the National Science Foundation for Post-Doctoral Scientists of China (Grant No.20100480645)
文摘Peptide frictions in water nanofilms of various thicknesses on a mica surface are studied via molecular dynamics simulations. We find that the forced lateral motion of the peptide exhibits stick-slip behaviour at low water coverage; in contrast, the smooth gliding motion is observed at higher water coverage. The adsorbed peptide can form direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds with the substrate. We propose that the stick-slip phenomenon is attributed to the overall effects of direct and indirect hydrogen bonds formed between the surface and the peptide.
基金Supported by the National Natural Science Foundation of China under Grant Nos 11305237 and 11174310China Post-doctoral Science Foundation Project under Grant No 2012M511159Shanghai Supercomputer Center,and Supercomputing Center of Chinese Academy of Sciences.
文摘Using a simple sphere-tip compression system,the local radial mechanical properties of DNA are systematically studied by changing the tip size.When the tip size decreases,the radial compression elastic properties under external loads become sensitive to the tip size and the local DNA conformation.A sudden force break appears in the compression-force curve when the tip size is less than or equal to 12 nm in diameter.The analysis of the hydrogen bonds and the base stacking interaction shows that a local unwinding process occurs.During the compression process,firstly the hydrogen bonds between complement base pairs are broken.With the compression accumulating,the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation.This local unwinding behavior deduced by external loads is helpful to understand the biological process and is important to DNA-based nanomechanical devices.
基金Supported by the National Natural Science Foundation of China under Grant Nos 10825520 and 11162002the National Basic Research Program of China under Grant No 2012CB932400.
文摘A biconcave particle suspended in a Poiseuille flow is investigated by the multiple-relaxation-time lattice Boltzmann method with the Galilean-invariant momentum exchange method.The lateral migration and equilibrium of the particle are similar to the Segré-Silberberg effect in our numerical simulations.Surprisingly,two lateral equilibrium positions are observed corresponding to the releasing positions of the biconcave particle.The upper equilibrium positions significantly decrease with the increasing Reynolds number,whereas the lower ones are almost insensitive to the Reynolds number.Interestingly,the regular wave accompanied by nonuniform rotation is exhibited in the lateral movement of the biconcave particle.It can be attributed to the fact that the biconcave shape in various postures interacts with the parabolic velocity distribution of the Poiseuille flow.A set of contours illustrate the dynamic flow field when the biconcave particle has successive postures in a rotating period.
基金Supported by the Chinese Academy of Sciencesthe National Natural Science Foundation of China under Grant Nos 10825520 and 11104308.
文摘The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain,which may securely affect the original function of protein.Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.
基金Supported in part by Exxon R&E company,the Chinese Postdoctoral Foundation,and ShanghaiPostdoctoral Foundation.
文摘A hydrodynamic boundary condition for the lattice Boltzmann model at impermeable boundaries is developed.This boundary condition satisfies both the no-slip condition and the fluid conservation at boundary nodes.Poiseuille flow and Couette flow are calculated with this technique to demonstrate the accuracy of the present boundary condition.
基金Project supported by the National Nature Science Foundation of China(Grant No. 50674065) Shanghai Leading Academic Discipline Project(Grant No.Y0103).
文摘According to new slip effects on nanopatterned interfaces, the mechanism of enhancing water injection into hydrophobic nanomaterial SiO2 was proposed. When Hydrophobic Nanoparticles（HNPs）are adsorbed on surfaces of porous walls, hydrophobic nanoparticles layers are formed instead of hydrated layer, and slip effects appear on the pore wall when a driving pressure is applied to the rock cores sample. It makes fluid to move more quickly and the flow capacity increases greatly. Experiments on changing wettability of porous walls were conducted, and the phenomenon that porous walls surfaces were adsorbed by nanoparticles was validated with the Environment Scan Electron Microscopy（ESEM）. The results of displacement experiments show that flowing resistance is greatly reduced, and water-phase effective permeability is increased by 47 % averagely after being treated by nanofluid. These results indicate that the slip effect may occur on nanoparticle film of porous walls. Based on this new mechanism of enhancing water injection about hydrophobic nanomaterial SiO2, a slip velocity model in uniform porous media was introduced, and some formulas for the ratio of slip length to radius, slip length ,stream slip velocity and flux increment were deduced. and calculated results indicate that the ratio of slip length to radius is about 3.54%-6.97%, and the slip length is about 0.024 μ m -0.063 μ m. The proposed model can give a good interpretation for the mechanisms of enhancing water injection with the HNPs.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.10825520,11175230)
文摘The diffusion of an ammonia molecule （NH3） in water was investigated by molecular dynamic simulations. It is found that the diffusion shows negative correlation with its dipole orientation.
