Some things to look at: (including two books in the Canisius Library)
0. On EASEL:
Meera Sitharam: email@example.com https://www.cise.ufl.edu/~sitharam/bio.html
she gave a talk at Canisius several years ago on modular assembly of biological structures.
- An October 2014 workshop: Configuration spaces of linkages, organized by Brigitte Servatius and Meera Sitharam.
Report from the workshop https://aimath.org/pastworkshops/linkagesrep.pdf
3-trees are glued together tetrahedra, as a first approximation of a molecule. The 3-tree is viewed as a rigid graph or framework. A partial 3-tree has edges removed so that it is flexible. The EASEL program keeps track of allowable lengths of the edges which can added back in to make it rigid. This is the idea behind Convex Cayley Configuration Space.
I also saw a reference to work by Richard Pollack, with some title like “convexifying a polygon” 1999? His website is at http://www.math.nyu.edu/faculty/, but I didn’t see a link to this work.
- Other references that might discuss topology and geometry of biological molecules:
Protein Geometry, Classification, Topology and Symmetry: A Computational Analysis of Structure, by William R. Taylor, Andras Aszodi (I have a pdf of this book).
Monastyrsky, M.I. Topology in Molecular Biology. Springer (2007). Is it available at canisius as an ebook?
Roald Hoffmann on the philosophy, art, and science of chemistry QD6 .H64 2012
Solids and surfaces : a chemist’s view of bonding in extended structures Hoffmann, Roald. QD471 .H83 1988
- A nice undergraduate thesis on Linkages
- Some photocopied articles that I have (listed in my bibliographies):
- a link to youtube video of recent lecture on knotted graphs (by Topology and Chemistry author);