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.
  1. J. M. Haile, Molecular Dynamics Simulation: Elementary Methods,  Wiley-Interscience
  1. D. C. Rapaport , “The Art of Molecular Dynamics Simulation”, Cambridge University Press, 2004.
  1. W. Humphrey, A. Dalke, and K. Schulten, “VMD – Visual Molecular Dynamics”, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.
  1. 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”
  1. “LAMMPS Molecular Dynamics Simulator”. Sandia National Laboratories. Retrieved 2010-10-03.

introductory-finite-difference-methods-for-pdes

MATLAB Primer


Codes

Parabolic PDE

ode_RK4

Hyperbolic PDE

Elliptic PDE


Slides:

Chapter1

Chapter2

Chapter3

Chapter4

Chapter5_2

Chapter6 – Monte Carlo1


 

HW:

HW1

HW2_N

HW3_Nano

HW4: VMD_HM

HW 5: HW5_N

HW 6: HW6N_MD

HW7: HW7_NAMD

HW8: LAMMPS

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