Unit 2 — Advanced Molecular Simulation

Overview

Molecular Dynamics (MD) and Density Functional Theory (DFT) applied to nanostructured materials.

Topics

• Molecular Dynamics with EMT, Lennard-Jones, and Tersoff potentials
• Density Functional Theory (DFT) with GPAW
• Electronic structure and band gap calculation
• Computational nanofabrication: surface passivation, doping

Key Technologies

• ASE + GPAW — DFT calculations
• OpenMM — GPU-accelerated MD
• Matplotlib / Plotly — Results visualization

Learning Outcomes

1. Run MD simulations with different interatomic potentials
2. Calculate electronic properties via DFT
3. Analyze thermodynamic properties (temperature, pressure, energy)
4. Simulate nanofabrication processes computationally

Notebooks

Open in GitHub