Molecular Dynamics Basics

1
Molecular Dynamics Basics

• Aaron Wemhoff
• Multiphase Transport Laboratory
• Microscale Heat Transfer Laboratory
• Department of Mechanical Engineering
• University of California, Berkeley

2
About Molecular Dynamics

• Molecule behavior based on basic Newtonian
  mechanics of monatomic condensed gases
• Allows for bottom-up approach to
  predicting system phenomena at the nanoscale
• Newton ? Idea
• Computing Age ? Implementation
• Computationally intensive
• Advantage simple theoretical background
• Disadvantage limited system size

3
Why Monatomic Gases?

• Monatomic Gases ? van der Waals liquids and
  solids

• The van der Waals forces are weak

• Forces are sufficient at low temperatures
  (small kBT).

• It wont apply at room temperatures

• Same phenomena as common solids at room
  temperature b/c of the ratio of interatomic to
  thermal energies

• Hydrogen bonding and other polar
  interactions are not included

• Can still observe basic phenomena at the
  nanoscale more complex situations can be
  considered through complex intermolecular
  potential functions.

4
Kinetics

• Newton

5
Kinetics

• Newton

• Updated Position

6
Kinetics

• Newton

• Updated Position

• Updated Velocity

7
Kinetics

• Newton

• Updated Position

• Updated Velocity

• System Temperature

equipartition theorem
system kinetic energy
8
Intermolecular Potentials
9
Periodic Boundary Conditions

• Large systems are composed of a grid of
  equivalent smaller systems

10
Periodic Boundary Conditions

• Large systems are composed of a grid of
  equivalent smaller systems
• When molecules pass through one boundary
  another molecule enters in the opposite boundary

11
Examples

• Thin liquid film mixture density profile

12
Examples

• Thin liquid film stress distribution

13
Examples

• Molecular transport in droplets

• Bubble nucleation on solid surfaces

14
Examples

• Rayleigh-Taylor instability generation