Nano-microscopy with Jmol

begun as a project by Rebecca Cook (UM-StL Sci. Ed.)
with inspiration from Hal Harris (UM-Stl Chem/BioChem)

Investigating nanocones from space: [seeds] [pentacone] [webercone] [hexfacet1] [hexfacet2] [dendrite2D]
Checking a buckytube nanotire: [zigzag] [btwixt] [armchair] [c60] [c70] [cap] [triple]
Discovering icosahedral twins: [1xtl-bowtie] [2xtl-butterfly] [10xtl-twin]
Locating diamond-cubic defects: [dimerows] [twinends] [facets] [fcc×2]
Lattice fingerprints: [dc vs fc] [magnetite] [apatite] [mica] [srilankite] [Pd/C] [GaInN] [ZnO]
Jmol tutorials: [unit cells] [reciprocal lattice] [unknowns] [unknown w/diffraction]
Special topics: [nanoparticle cylinder] [bicrystal interface] [RNA polymerase]

Above find links to a collection of Jmol models constructed for one-to-one comparison with experimental nanomicroscopy data. The goals are to inspire the design of classroom explorations and empirical observation challenges, as well as perhaps to help out a bit with research here and there. Check here instead for a set of related nanomicroscopy, powers-of-ten and spacetime challenges centered around a Mathematica-based applet with stronger zooming and reciprocal space capabilties, but less dedicated to atoms in direct space.

Although you can of course just "look at the pictures", the microscopy data presented in images here is intended for quantitative use e.g. for making comparative measurements on captured or printed images by hand or with image analysis programs. Hence you can assume that relative sizes and angles in the images provided are largely intact. Note: Many of the Jmol models offer a right-click menu which lets you remove perspective effects in them as well. We intend to make this model collection reliably available for as long as possible, as well as to add rubrics for application in classroom settings and new models as well. Hence suggestions on how to make them work for your applications would be most welcome.

Methanol (that red thing is an oxygen -- jmol has its own default color scheme built in and I guess oxygens are rightly viewed as hot stuff):

Pentagonal seed for a carbon nanocone (try rotating with the mouse as well):

For model set two, click here

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