Beyond Blender – Biology With Computers

A model of the structure of ATP synthase - found in nearly all animal and plant cells.

Since I became interested in Blender several months ago I have been convinced of the potential applications of modelling in science. Obviously communications are greatly enhanced by the 3d models we can easily make these days, but there are also people out there using modelling to investigate basic science questions relating to biological systems. One such individual is Aleksei Aksimentiev, at the University of Illinois. Check out this brief podcast (and associated article) from

University of Illinois Professor Aleksei Aksimenitev, supercomputers in tow.

I came across Aksimntiev and his work group in the first stages of research into a presentaiton I will be giving for a seminar course in cell biology later this semester. The complexity of ATP synthase and the structure of the bacterial flagellum have long been a favourite of creationists in arguing the irreducible nature of these systems. While I won’t begin to tackle these arguments, which usually rely on nuanced semantics and the inherently probabilistic approach of the natural sciences, suffice to say that my own ‘belief’ resides in the continual emergence of principles and details that help to explain that which may at first seem supernatural.

The Aksimentiev group is using computation in a number of interesting ways; modelling the nanopore/DNA system mentioned in the podcast (which could potentially be developed into a cheap and quick gene sequencer), also in exploring the mechanical properties of microtubules, and in elucidating the possible function of yet to be understood multi-subunit proteins. All of these can be found at the main page for the Aksimentiev Group. To help with my own modelling and project I hope soon to explore the tutorials available, and to begin exploring the Visual Molecular Dynamics (VMD) and associated software environments. Did I mention most of these programs are free?

Screenshot from the program described above. Click to explore photo source and remote-visualizing with VMD.


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