The Moncznik Biomatics Series
In 2009 I started tinkering with JAVA3d (http://en.wikipedia.org/wiki/Java_3D). Since then I have created several steps in a process. The applets could be many things, but one common thread ,so far, seems to be as tools for understanding and exploring the dynamics of protein-folding or vibrations. They could also be used as living demonstrations of mathematical principles, specifically abstract algebra; Lagrange's theorem, group theory. The field is also ripe for computer generated art and physics.
This is an animation of what a 6 carbon chain would look like if you grabbed it at one end and used this point as the origin.
Carbon is considered the basis of life as we know it. We are carbon life forms. Arginine is a JAVA3d app that is simply an animation of a chain of 6 carbon atoms. Perhaps this is what Hawking considers a "String"? If there do exist fundamental particles of any sort then they too surely will have geometric properties, possibly similar to the tetrahedrtal geometry of carbon.
An interactive 3d tool or toy for exploring the intra-molecular relationships amongst the 400 possible dipeptides.
An interactive 3d tool or toy for exploring the intra-molecular relationships amongst any chosen sequence of peptides. All bonds are of uniform length thus this applet is more for purely mathematical exploration of a given sequence. In real life no two bonds are exactly the same, but analysis should start from this stage.
A tool to help analyze RCSB PDB files
An interactive 3d drawing program for exploring possible vibrational patterns of proteins. These are 2 dimensional snapshots of 3 dimensional structures which can be thought of as what would happen if one could grab a polypeptide by one end and hold it in place then stick a paintbrush on the other end.