With the development of biomolecular modeling and simulation,especially implicit solvent modeling,higher requirements are set for the stability,efficiency and mesh quality of molecular mesh generation software.In this...With the development of biomolecular modeling and simulation,especially implicit solvent modeling,higher requirements are set for the stability,efficiency and mesh quality of molecular mesh generation software.In this review,we summarize the recent works in biomolecular mesh generation and molecular visualization.First,we introduce various definitions of molecular surface and corresponding meshing software.Second,as the mesh quality significantly influences biomolecular simulation,we investigate some remeshing methods in the fields of computer graphics and molecular modeling.Then,we show the application of biomolecular mesh in the boundary element method(BEM)and the finite element method(FEM).Finally,to conveniently visualize the numerical results based on the mesh,we present two types of molecular visualization systems.展开更多
Liquid argon flow along a nanochannel is studied using molecular dynamics (MD) simulation in this work.Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used as the MD simulator.The effects of redu...Liquid argon flow along a nanochannel is studied using molecular dynamics (MD) simulation in this work.Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used as the MD simulator.The effects of reduced forces at 0.5,1.0 and 2.0 on argon flow on system energy in the form of system potential energy,pressure and velocity profile are described.Output in the form of three-dimensional visualization of the system at steady-state condition using Visual Molecular Dynamics (VMD) is provided to describe the dynamics of the argon atoms.The equilibrium state is reached after 16000 time steps.The effects on system energy,pressure and velocity profile due to reduced force of 2.0 (F2) are clearly distinguishable from the other two lower forces where sufficiently high net force along the direction of the nanochannel for F2 renders the attractive and repulsive forces between the argon atoms virtually non-existent.A reduced force of 0.5 (F0.5) provides liquid argon flow that approaches Poiseuille (laminar) flow as clearly shown by the n-shaped average velocity profile.The extension of the present MD model to a more practical application affords scientists and engineers a good option for simulation of other nanofluidic dynamics processes.展开更多
基金supported by the Science Challenge Program under Grant TZ2016003by the National Key Research and Development Program of Ministry of Science and Technology under Grant 2016YFB0201304the National Natural Science Foundation of China(61772523,21573274,11771435,and 61620106003).
文摘With the development of biomolecular modeling and simulation,especially implicit solvent modeling,higher requirements are set for the stability,efficiency and mesh quality of molecular mesh generation software.In this review,we summarize the recent works in biomolecular mesh generation and molecular visualization.First,we introduce various definitions of molecular surface and corresponding meshing software.Second,as the mesh quality significantly influences biomolecular simulation,we investigate some remeshing methods in the fields of computer graphics and molecular modeling.Then,we show the application of biomolecular mesh in the boundary element method(BEM)and the finite element method(FEM).Finally,to conveniently visualize the numerical results based on the mesh,we present two types of molecular visualization systems.
基金Supported by the Academy of Sciences,Malaysia and Ministry of Science and Technology & Innovation
文摘Liquid argon flow along a nanochannel is studied using molecular dynamics (MD) simulation in this work.Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used as the MD simulator.The effects of reduced forces at 0.5,1.0 and 2.0 on argon flow on system energy in the form of system potential energy,pressure and velocity profile are described.Output in the form of three-dimensional visualization of the system at steady-state condition using Visual Molecular Dynamics (VMD) is provided to describe the dynamics of the argon atoms.The equilibrium state is reached after 16000 time steps.The effects on system energy,pressure and velocity profile due to reduced force of 2.0 (F2) are clearly distinguishable from the other two lower forces where sufficiently high net force along the direction of the nanochannel for F2 renders the attractive and repulsive forces between the argon atoms virtually non-existent.A reduced force of 0.5 (F0.5) provides liquid argon flow that approaches Poiseuille (laminar) flow as clearly shown by the n-shaped average velocity profile.The extension of the present MD model to a more practical application affords scientists and engineers a good option for simulation of other nanofluidic dynamics processes.
