Saturday, September 26, 2009

Tunneling and STM

A few weeks ago, I gave a guest lecture (read: "I am at a conference that day, could you do it for me?") in a course entitled Unifying Concepts in Nanoscience. The topic was basic quantum mechanics (chapter 9 and a bit of 10 in Atkin's Physical Chemistry): particle in a box, etc.

These days, the first thing I do when preparing a lecture is to scour Molecular Workbench for useful animations, as I have discussed in a previous post. True to form MW did not disappoint, and I put together the following set of MW slides (note: you need to install MW first before clicking on it).

The screencast above shows how I used four of the slides to illustrate the concept of tunneling and and how it applies to STM.

Once again, I found animated simulations in general, and MW in particular, invaluable in bringing across complex concepts. And once again MW did all the hard work.

2012.09.01 UpdateI made a few more screencasts of parts of my lecture

Sunday, September 13, 2009

The Computational Chemistry Movie

Last week I presented the Computational Chemistry group to the new graduate students, and made the above movie for the occasion. As I mentioned in previous posts (here and here) I think molecular animation is a powerful but overlooked recruiting tool.

Most of the movie is one long Jmol script, but it took some post-editing of the resulting recording to smooth the transitions, i.e. remove the lag time when Jmol is computing the surfaces. The coordinates of the reaction and the large nanostructure is taken from Chemtube3D and this site, respectively. I have described how to extract the coordinates from a site using Jmol in a previous post. The orbitals and vibrational modes were computed using GAMESS and RHF/STO-3G.

The molecular dynamics animation towards the end is done with Molecular Workbench. You can find the simulation here, but you need to install Molecular Workbench to see it.

The equation animation and final credits are done with Powerpoint.

I hope you find the movie entertaining and useful, and feel free to use it (i.e. link to it, embed it, use in a Powerpoint presentation, etc.) if you do. Here is the page in where you can find the link and the source file in .mov and .flv formats.

Tuesday, September 8, 2009

Hearing voices

While looking for something completely different, I came across this online presentation by Martin Head-Gordon on computational quantum chemistry. The link is here and you click on View Presentation on the right.

The lecture is part of a series on modeling within nanoscience, and the hosting site,, has many other interesting things.