I've done one project that's followed me through the years... Also I presented the paper on it at a conference in Prague, which was pretty rad.
It's a three-dimensional modeling tool for creating nanostructures using DNA. The basic idea is, the nanoscale is mostly driven by shape, and DNA has well-defined structure. Adenine binds to thymine, cytosine to guanine, any of them can chain together, and everything bends at particular angles. Also, the technology exists to create synthetic strands of DNA with specified sequences (of A, T, C, and G), and you can also duplicate strands in large quantities with polymerase chain reaction (PCR)—an acronym that everyone knows now, because it's also one of the bases for COVID testing.
The software I wrote allows you to drag out a line in three-dimensional space, and it'll plop in a DNA helix. You can then modify the links between helices/strands to join them together, so that they can form meshes or tetrahedra or whatever else you want. Finally, it assigns types (A, T, C, or G) to all of the nucleotides, in a way that's likely to cause the DNA to assemble into your structure in the real world. This can then be verified by fabricating the sequence, amplifying it with PCR, and imaging it with atomic force microscopy. (Figure 8 of the paper shows an AFM scan of one of the generated structures.)
It's followed me through the years because it's still an active research area, so I did occasional contract work to add new features, but otherwise some researchers have asked for the source. It's a bit painful now, since it was written with Microsoft Foundation Classes and OpenGL 1.
As for the name, you know, I was in undergrad. It wasn't actually named for Final Fantasy or Dungeons and Dragons, but because in the Enuma Elish Tiamat was the mother of life. A bit extravagant, but we all did embarrassing things at that age.
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I've done one project that's followed me through the years... Also I presented the paper on it at a conference in Prague, which was pretty rad.
It's a three-dimensional modeling tool for creating nanostructures using DNA. The basic idea is, the nanoscale is mostly driven by shape, and DNA has well-defined structure. Adenine binds to thymine, cytosine to guanine, any of them can chain together, and everything bends at particular angles. Also, the technology exists to create synthetic strands of DNA with specified sequences (of A, T, C, and G), and you can also duplicate strands in large quantities with polymerase chain reaction (PCR)—an acronym that everyone knows now, because it's also one of the bases for COVID testing.
The software I wrote allows you to drag out a line in three-dimensional space, and it'll plop in a DNA helix. You can then modify the links between helices/strands to join them together, so that they can form meshes or tetrahedra or whatever else you want. Finally, it assigns types (A, T, C, or G) to all of the nucleotides, in a way that's likely to cause the DNA to assemble into your structure in the real world. This can then be verified by fabricating the sequence, amplifying it with PCR, and imaging it with atomic force microscopy. (Figure 8 of the paper shows an AFM scan of one of the generated structures.)
It's followed me through the years because it's still an active research area, so I did occasional contract work to add new features, but otherwise some researchers have asked for the source. It's a bit painful now, since it was written with Microsoft Foundation Classes and OpenGL 1.
As for the name, you know, I was in undergrad. It wasn't actually named for Final Fantasy or Dungeons and Dragons, but because in the Enuma Elish Tiamat was the mother of life. A bit extravagant, but we all did embarrassing things at that age.