Introduction to Computational Nanoscience

Syllabus: 

Molecular Dynamics

Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems

Interatomic Potentials

Energy Minimization and Related Methods for Exploring Energy Surfaces

Computer Simulation Methods

Molecular Dynamics Simulations Methods

Introduction to Coarse Graining Methods

Monte Carlo

Finite Difference Applications for PDEs

References:

1. A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.

2. J. M. Haile, Molecular Dynamics Simulation: Elementary Methods,  Wiley-Interscience

3. D. C. Rapaport , “The Art of Molecular Dynamics Simulation”, Cambridge University Press, 2004.

4. W. Humphrey, A. Dalke, and K. Schulten, “VMD – Visual Molecular Dynamics”, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.

5. J. C. Phillips et al., “Scalable molecular dynamics with NAMD,” Journal of computational chemistry, vol. 26, no. 16, p. 1781, 2005. “NAMD A Parallel Object-Oriented Molecular Dynamics Program”

7. “LAMMPS Molecular Dynamics Simulator”. Sandia National Laboratories. Retrieved 2010-10-03.

introductory-finite-difference-methods-for-pdes

MATLAB Primer

Codes