Handout 1. An Overview of Molecular Simulation

Pictures and movies of modern large scale molecular simulations can be downloaded from the course web site http://micro.stanford.edu/∼me346 (click “Course Materials”). Examples include plastic deformation in metals containing a crack, phase transformation induced by shock waves, nano-indentation of metal film, laser ablation on metal surface, etc. In each of these examples, molecular simulations not only produce beautiful pictures, but they also offer new understanding on the behavior of materials at the nano-scale. Many times such understanding provides new insights on how the materials would behave at the micro-scale and nano-scale. With unique capabilities to offer, molecular simulation has become a widely used tool for scientific investigation that complements our traditional way of doing science: experiment and theory. The purpose of this course is to provide the first introduction to molecular level simulations — how do they work, what questions can they answer, and how much can we trust their results — so that the simulation tools are no longer black boxes to us. Students will develop a set of simulation codes in Matlab by themselves. (A simple Matlab tutorial written by Sigmon [5] may help you refresh your memory.) We will also give tutorial and exercise problems based on MD++, a molecular simulation package used in my research group. MD++ will be used for illustration in class as well as tools to solve homework problems.