DNA ropes (24th of March 2016)

Here it is - after too much time, I finally packed, at least a part of research which deals with shapes of DNA "ropes" condensed in a "virus" (actually cylinders of different sizes, but OK ... you know how it is with us physicists - the cows can be spherical as is well known). Manuscript has been sent "in the wild", for review so we'll see what happens. On 17th of March at the invitation of Bojan Žagrović I held a seminar in Biocenter in Vienna. The lecture contains a good part of the results from the manuscript. You can listen to the seminar by clicking on the arrow in the window above (streaming from YouTube).

Shape 2

Concerning scientific visualization, the challenge was to present the shapes of condensed DNA molecule, actually thick ropes with closed centroid curve. I opted for line representation, i.e. a drawing (above and below). Such a representation has several advantages, first of all easy vectorization, and sometimes it is even more readable than full 3D representation with shadows and changes of tone depending on the position on the object surface.

Shape 4

The manuscript deals exclusively with theory and explains possible DNA shapes within a virus using a simplified physical model. Still, it is very interesting that some of the shapes I found in my calculations were proposed in the literature quite some time ago. For example, the shape which was proposed by Nick Hud on the basis of his experimental results (below) ...

Hud's shape

... appeared also as an optimal shape in my theoretical approach (below).

Shape 1

This is not the only "coincidence". Depending on the parameters of the system and on the elongation of the cylinder (height vs. diameter) confining the "DNA rope", I also get some other shapes previously proposed. For example, in 1978 Earnshaw and coworkers have proposed the shape of DNA molecule in T4 bacteriophage (below) ...

Earnshaw's shape

... which is quite similar to the shape I found in my calculations (below).

Shape 3

Some of the shapes I wanted to present were so complex that their three-dimensional nature could be seen only with additional "interventions", e.g. by virtually "cutting out" pieces of the shape (below).

Shape 5

When and if the paper appears, I'll make an update to this page.

UPDATE: (02.07.2016.) The paper was just published in Scientific Reports. >> Here is the link to it. And here is the link to the >> paper in PDF.

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Last updated on 24th of March 2016.