Unless you have been living under a rock for the last week, I am sure everyone has seen the latest images of a molecule produced by IBM.  I got curious as to what could be revealed by projecting the images in 3D, so I wrote an app to do just that.  The results turned out to be so good, that I decided to release the app for everyone to use.

The app is called 'DeepThought's Atomic Force Microscopy Viewer v1.0' or 'DAFMV'.  Its an OpenGL app that takes specially prepared images and converts them into 3D representations.  Simple controls allow you to fly around the 3D model and access different visualizations of the data.  To use this software you will need at least a 64-bit version of Windows 7 (it may work on 64-bit Vista, but I have not checked, the same for WINE).

You can download the zip file from here.  Just copy the contents to your desktop and read the file called README.txt.  Everything is explained in this file.  If you have any issues, leave a comment below.  This a prototype version of the software, so don't expect to much from it at this stage, but it does produce some wonderful images.  Have a look at this image below:

This image is a 3D representation of this image produced by IBM.  This image is of a Buckyball, a Carbon-60 structure that looks like a football, only this is drawn flat and the bottom is removed:

This image is a representation of the forces detected.  Lighter colors are areas of less dense forces and darker colors are areas of dense forces.  These forces are a mixture of mechanical contact force, van der Waals forces, capillary forces, chemical bonding, electrostatic forces, magnetic forces, Casimir forces, solvation forces, etc.  For a more technical explanation we have this statement from Leo Gross of IBM:

"We found two different contrast mechanisms to distinguish bonds. The first one is based on small differences in the force measured above the bonds. We expected this kind of contrast but it was a challenge to resolve," said IBM scientist Leo Gross. "The second contrast mechanism really came as a surprise: Bonds appeared with different lengths in AFM measurements. With the help of ab initio calculations we found that the tilting of the carbon monoxide molecule at the tip apex is the cause of this contrast."

Thus, you cannot view this image as 3D representations of what a molecule looks like, but rather only the density of forces.  Using the method, we can visualize these forces in 3D by giving them particular heights, but it should always be remembered that real molecule should be thought of similar to a gas.  That is, the 3D heights represent areas where the gas is densest.  Its not a scientifically valid viewpoint, but it is the best way to think about it.

In the first image above, I have the output set to line mode.  This provides a very good sense of what we means by a wavefunction, or the wave nature of particles.  I really like this view as the fine detail is revealed.  With a click of the mouse, we can switch to a solid view as below:

This view is better for examining larger structures.  For example, the Carbon atoms at the corners.  In this next image, we can see that the structure is not as pronounced as the angle of the detector has changed and we lose some length information.  It could also relate to the images I used.  If IBM release better quality images, I will supply them as an update for everyone.  For now, this will need to do.

In the above image, we get a very good sense of just how a molecule holds itself together.  The arrangement of forces provides an interlocking mechanism that keeps the atoms in place.  These interlocking forces can occur in different ways, some having more strength or stability than others.

In this next image we get a close up of less dense set of forces in the center of an area of a dense arrangement of forces.  If we think of this like a football, then we can almost see how this would be an area leading to the center of the ball and why it can be found in each of the depressions.  It would be where the fields end.  We can also see that the forces are elongated when we come to the edge of the molecule, most likely due to the detector being at a steeper angle and being able to determine more length information from the Buckyball.

As I mentioned earlier, these images are based upon the density of the forces in a given area.  The lightest densities are raised and the densest are lowered.  We can reverse this with a click of a mouse, to provide an alternative view of the data which looks like this:

In this view, our peaks now become depressions.  This is useful for looking at particles.  Let's take a look at those red towers, which appear to be the atoms at the corners and the forces that surround them.

The black holes in the red are most likely the atoms themselves.  So, again, let's take a closer look:

Now, this is interesting.  What exactly is that small depression beside the bottom atom?  Is it an artifact, some weird effect of forces, an electron not captured properly, or a new particle?  I have been puzzling over this one for quite some time now, so if you have an answer, please post it below.

Well, have fun and if you have any questions, comments or issues then please post below.