Molecular Dynamics Simulation: Fundamentals and Applications

Front Cover
Molecular Dynamics Simulation
Copyright Page
Contents
List of symbols
Preface
1 Fundamentals of classical molecular dynamics simulation
	1.1 Introduction
		1.1.1 Atomistic simulation
		1.1.2 Molecular dynamics simulation
		1.1.3 Applications of molecular dynamics simulation
		1.1.4 Limitations of molecular dynamics simulation
	1.2 Fundamentals of molecular dynamics simulation
		1.2.1 Procedure
		1.2.2 System initialization
		1.2.3 Periodic boundary conditions
		1.2.4 Energy minimization and structure optimization
		1.2.5 Force calculation
		1.2.6 Time integration algorithms
		1.2.7 Neighbor list
		1.2.8 Ensemble and statistical observables
		1.2.9 Accuracy of MD simulation
	1.3 Hardware and software for MD simulation
	References
2 Potential energy functions
	2.1 The Born–Oppenheimer assumption
		2.1.1 Construction of potential energy functions
		2.1.2 Two-body potentials
		2.1.3 Many-body potentials
	2.2 Potential energy functions for different materials
		2.2.1 Ionic materials
		2.2.2 Metals
		2.2.3 Covalent materials
		2.2.4 Molecular systems
	References
3 Control techniques of molecular dynamics simulation
	3.1 Types of constraints in molecular dynamics simulation
	3.2 Thermodynamic ensembles
	3.3 Temperature control
		3.3.1 Thermostat based on simple velocity rescaling
		3.3.2 Gaussian thermostat
		3.3.3 Berendsen thermostat
		3.3.4 Bussi–Donadio–Parrinello thermostat
		3.3.5 Andersen thermostat
		3.3.6 Langevin thermostat
		3.3.7 Nosé–Hoover thermostat
		3.3.8 Thermostat effects in equilibrium molecular dynamics simulations
		3.3.9 Temperature control in nonequilibrium molecular dynamics simulations
	3.4 Pressure control
		3.4.1 Berendsen barostat
		3.4.2 Andersen barostat
		3.4.3 Parrinello–Rahman barostat
		3.4.4 Martyna–Tuckerman–Tobias–Klein barostat
	3.5 Boundary conditions
	3.6 Rigid bond constraints
	References
4 Advanced ab initio molecular dynamics and coarse-grained molecular dynamics
	4.1 Motivations for the development of advanced molecular dynamics simulation methods
	4.2 Ab initio molecular dynamics
		4.2.1 Quantum mechanics foundation of classical molecular dynamics
		4.2.2 Born–Oppenheimer molecular dynamics
		4.2.3 Car–Parrinello molecular dynamics
	4.3 Coarse-grained molecular dynamics
		4.3.1 Theoretical formulation
		4.3.2 Iterative Boltzmann inversion method
		4.3.3 Multiscale coarse-grained method
		4.3.4 Relative entropy optimization method
		4.3.5 Challenges
	References
5 Application of molecular dynamics simulation in mechanical problems
	5.1 Role of molecular dynamics simulation in modeling the mechanical properties of materials
	5.2 Tensile, compressive, and shear tests
		5.2.1 Tensile tests
		5.2.2 Compressive tests
		5.2.3 Shear tests
	5.3 Nanoindentation and nanoscratching tests
		5.3.1 Nanoindentation tests
		5.3.2 Nanoscratching tests
	5.4 Tribological behaviors
		5.4.1 Nanofriction
		5.4.2 Nanowear
		5.4.3 Nanolubrication
	5.5 Interfacial effects in nanocomposites
		5.5.1 Polymer-based nanocomposites
		5.5.2 Metal-based nanocomposites
	5.6 Defect effects
	References
6 Application of molecular dynamics simulation in thermal problems
	6.1 Demand for understanding the thermal properties of nanomaterials
	6.2 Molecular dynamics simulation methods for thermal conductivity calculation
		6.2.1 Direct method
		6.2.2 Green–Kubo method
	6.3 Molecular dynamics simulation of interfacial thermal transport
		6.3.1 Interfacial thermal transport models
		6.3.2 Interfacial thermal transport of a silicene/graphene hybrid monolayer
			6.3.2.1 Simulation model
			6.3.2.2 Interfacial thermal conductance
			6.3.2.3 Temperature effect
			6.3.2.4 Strain effect
			6.3.2.5 Heat flux effect
		6.3.3 Interfacial thermal transport of a silicene/graphene hybrid bilayer
			6.3.3.1 Simulation model
			6.3.3.2 Interface thermal conductance
			6.3.3.3 Temperature and interface coupling strength effects
			6.3.3.4 GE hydrogenation effect
	6.4 Thermal rectification effects
	References
7 Application of molecular dynamics simulation in mass transport problems
	7.1 Fluids in nanoconfinement
		7.1.1 Fluid-driven methods
			7.1.1.1 Pressure-driven method
			7.1.1.2 Temperature-gradient driven method
			7.1.1.3 Electric-field driven method
			7.1.1.4 Surface-wave driven method
		7.1.2 Water flow in carbon nanotubes
		7.1.3 Water flow in porous monolayer graphene
		7.1.4 Water flow in multilayer graphene and graphene oxide membranes
	7.2 Nanofiltration with porous thin films
		7.2.1 Reverse osmosis process
		7.2.2 Forward osmosis process
		7.2.3 Capacitive deionization
	7.3 Liquid–vapor phase transition
		7.3.1 Droplet evaporation in a gaseous environment
		7.3.2 Liquid evaporation on a substrate
	References
8 Application of molecular dynamics simulation in other problems
	8.1 Reactive molecular dynamics simulations
		8.1.1 ReaxFF force field
		8.1.2 Application of ReaxFF in reactive MD simulations
	8.2 Irradiation processes
	8.3 Material crystallization
	References
Index
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