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A colleague here at the University of Pittsburgh recently asked me to give a guest lecture for her graduate class in scientific visualization.

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The group of Dr. Zhong Lin at Georgia Tech has recently been pumping out a range of interesting papers on the use of zinc oxide (ZnO) “nanoribbons” for energy generation. (People may be best aware of ZnO as a sunscreen material — you used to smear the white stuff on your nose.)

The basic principal is that ZnO is a piezoelectric and thus generates small amounts of charge when it is mechanically changed (stress or strain). This is the so-called direct piezoelectric effect. ZnO is also a semiconductor, so that charge from the piezoelectric effect can be used to generate actual electric current.

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On the subject of scientific visualization, Wired magazine just showcased a gallery of images on the nanoscale from scanned-probe microscopes (SPM): Scientists Scan Striking Nanoscale Images.

To me, the images are striking not just artistically, but that they really show the level of detail we can image these days. The images showcase individual atoms and molecules — real visual proof of the chemical world. Before the invention of the scanning tunneling microscope in 1986, this was basically unimaginable.

Recently, I wrote to ask for suggestions in chemistry visualizations. Rajarshi Guha wrote in with several suggestions. One of the most interesting to me was to map results or numeric data to structures themselves:

In terms of mol vis itself, I’d like to see useful ways of mapping things to structures themselves - so fragment properties could be mapped to specific parts of a molecule, effects of descriptors in a QSAR model could be mapped to parts of a molecule and so on. Some of this has been done before, but is usually quite restricted.

I mentioned this idea as to colleagues “automatic annotation.” (After all, we can do what Rajarshi describes manually.) This relates directly to some of the work I did on my Ph.D. I ran computational predictions on electronic properties of molecules and drew out key effects via statistics.

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It sits atop the cathedral Santa Maria del Fiore, and is larger than the dome of the US Capitol, St. Paul’s in London, or even St. Peter’s in Rome. It was built before any of them, in 1436. No scaffolding was used, nor does it need external support.

Filippo Brunelleschi has been celebrated as an architectural and engineering genius. There’s even a wonderful book on his design for the Florence Cathedral, which used no scaffolding and required him to invent new tools for the job.

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I’ve been asked to give a guest lecture at a computer science colleague’s graduate class on scientific visualization in February. She’s asking for a quick summary to put into her syllabus.

Her key question is this: what are problems that we are trying to solve in chemical visualization? What is the current state of visualization tools, and what would we dream of doing with them? It’s that last part which is the most interesting to me — what might we want to do if we had some ultimate tool?

Naturally I have some ideas of my own, but I’m interested in hearing some feedback. (I’ll post my ideas tomorrow.) How would you like to visualize molecules or chemical data sets? What features would you like to see in current visualization tools if you didn’t have to write the code?

Remember… the sky’s the limit!