CHE210D: Principles of modern molecular simulation methods, S12
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Course description

The goal of this course is to equip students of a variety of backgrounds with the basic skills necessary to design and carry out molecular simulations:
  • formulation of both atomistically detailed and simplified molecular models
  • basic and advanced algorithms for computing thermodynamic and kinetic behavior
  • modern analysis techniques and visualization packages
  • physical intuition for developing and interpreting new simulation “experiments” 
  • knowledge of computational issues and methods for improving efficiency

Topics discussed in the course include: ab initio methods, classical semi-empirical force fields, energy minimization, molecular dynamics techniques, Monte Carlo methods, free energy algorithms, advanced sampling strategies, coarse-graining and multiscale methods, and rare events algorithms.   Case studies in soft condensed matter, materials, and biophysics will be presented throughout the lecture material.

This course focuses more on concepts, algorithms, and tools than on specific programming styles and languages, although enrolling students should have had at least minimal exposure to coding or mathematical software (e.g., have used any of Matlab, Mathematica, C, C++, Visual Basic, or Fortran).  From early in the course, a strong emphasis will be placed on students performing and visualizing their own simulation projects.

Coursework consists of a series of exercises in which students write their own small simulation programs based on methodologies discussed in lecture, run these, and provide analysis of results.  At the end of the course, students will complete a project in which they simulate a system of interest, based on current topics in the literature, using methodologies discussed in class.  The course will present Python as a particularly powerful and freely available programming platform for scientific computing and highly encourage its use. 

Course information

instructors Professor M. Scott Shell
shell (at)
Engineering II 3321
office hours: Tuesday 1:45-3pm and Wednesday 1-2pm, or drop by if my office door is open, or by appointment 

schedule TR 12:30-1:45pm, Engineering II 1519

textbook Understanding Molecular Simulation: From Algorithms to Applications (2nd edition)
Daan Frenkel and Berend Smit, Academic Press (2007)

grading 70% simulation exercises, 30% final project

Course syllabus and schedule

Download here.

Department of Chemical Engineering  |  University of California Santa Barbara