Teaching material and tools

In the fall semester of 2023 I am teaching Chem 684: Chemical Thermodynamics. See course website for details.

In the past I have I taught Chem 687: Statistical Mechanics and Chemistry. See course website for details.

In the past I have taught teaching Chem 481: Physical Chemistry I. See course website for details.

This is a very random collection which I update once in a blue moon.

Interested in using/understanding metadynamics and other enhanced sampling techniques? The PLUMED tutorials are the place to start.
An excellent introduction to good practices (thermostats, barostats, integrators, timestep etc) in classical MD simulations
Download force-field parameters for non-standard modified residues
Lecture notes on Brownian motion: I especially liked these for their clear exposition of deriving Fokker Planck equations from Langevin. Van Kampen's and Risken's books are the standard resources for these, but they can be a bit more forbidding at first read (especially the latter).
Introductory lectures on stochastic processes and stochastic differential equations: check out this MIT OCW set, especially lectures 5,7,18,21. While there is no dearth of video lectures on the web, I liked this one a lot for its clarity, content, and non-shaky camera work.
Daniel Zuckerman's blog on statistical biophysics
Entropy and the second law of thermodynamics: An explanatory essay aimed at high school students and teachers, that I originally wrote for the Teacher Plus magazine for their Physics Special issue. Full article available HERE.
Lecture notes on Stochastic processes and Brownian motion problems from a statistical physics perspective
Generating random numbers with a given distribution in MATLAB: a quick tutorial