It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is ...It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is sufficient to get the temperature with high accuracy and small computational cost based on the generalized canonical ensemble(GCE).Lennard–Jones fluids,the atomic water models,such as TIP4P/2005,TIP4P/ICE,and the mW water models are applied to illustrate the method.We start from the coexistent system of the two phases with a plane interface,then equilibrate the system under the GCE,which can stabilize the coexistence of the phases,to directly derive the phase transition temperature without sensitive dependence on the applied parameters of the GCE and the size of the simulation systems.The obtained result is in excellent agreement with that in literatures.These features make the GCE approach in determining the phase transition temperature of systems be robust,easy to use,and particularly good at working on computationally expensive systems.展开更多
Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of frict...Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction(COF)because of the transformation in bond structure from sp^(3)-C to sp^(2)-C during friction processes.However,the mechanism for such a transformation during friction is not well understood.This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics(MD)simulation.Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear,resulting in a decrease in growth rate of the wear rate after the running-in stage.It is worth noting that the sp^(3)-C atoms were increased during the running-in stage when the films contained lower sp^(3)/sp^(2) ratios.However,the formed sp^(3)-C atoms could only be short-lived and gradually transformed to sp^(2)-C atoms with the graphitization generated on the wearing surface of the films.The radial distribution function and translational order parameter indicated that the films'high sp^(3)/sp^(2) ratio led to an increased sp^(2)-C proportion on the wear scar after friction,which caused an increased structural ordering.展开更多
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensem- ble dynamics （RED） method to more efficiently sample complex （biopolymer） systems, and to explore thei...Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensem- ble dynamics （RED） method to more efficiently sample complex （biopolymer） systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.展开更多
基金the National Natural Science Foundation of China(Grant Nos.11574310,11674345,and 21733010)Beijing National Laboratory for Molecular Sciences,China(Grant No.BNLMS201835).
文摘It is very important to determine the phase transition temperature,such as the water/ice coexistence temperature in various water models,via molecular simulations.We show that a single individual direct simulation is sufficient to get the temperature with high accuracy and small computational cost based on the generalized canonical ensemble(GCE).Lennard–Jones fluids,the atomic water models,such as TIP4P/2005,TIP4P/ICE,and the mW water models are applied to illustrate the method.We start from the coexistent system of the two phases with a plane interface,then equilibrate the system under the GCE,which can stabilize the coexistence of the phases,to directly derive the phase transition temperature without sensitive dependence on the applied parameters of the GCE and the size of the simulation systems.The obtained result is in excellent agreement with that in literatures.These features make the GCE approach in determining the phase transition temperature of systems be robust,easy to use,and particularly good at working on computationally expensive systems.
基金This work was co-supported by the National Natural Science Foundation of China(No.51905466)Aeronautical Science Foundation of China(No.201945099002)+1 种基金Natural Science Foundation of Hebei Province,China(Nos.E2021203191 and E2020203184)Youth Top Talent Project of Hebei Province Higher Education,China(No.BJ2019058).
文摘Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction(COF)because of the transformation in bond structure from sp^(3)-C to sp^(2)-C during friction processes.However,the mechanism for such a transformation during friction is not well understood.This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics(MD)simulation.Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear,resulting in a decrease in growth rate of the wear rate after the running-in stage.It is worth noting that the sp^(3)-C atoms were increased during the running-in stage when the films contained lower sp^(3)/sp^(2) ratios.However,the formed sp^(3)-C atoms could only be short-lived and gradually transformed to sp^(2)-C atoms with the graphitization generated on the wearing surface of the films.The radial distribution function and translational order parameter indicated that the films'high sp^(3)/sp^(2) ratio led to an increased sp^(2)-C proportion on the wear scar after friction,which caused an increased structural ordering.
基金Project supported by the National Natural Science Foundation of China(Grant No.11175250)
文摘Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensem- ble dynamics （RED） method to more efficiently sample complex （biopolymer） systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.
