I recently developed a novel minimization method for the elastic energy of DNA at the base-pair level. The method makes it possible to obtain the optimal pathways of DNA fragments in which the terminal base pairs are spatially constrained. Moreover, the method accounts for the presence of proteins on the DNA and therefore can be used to study the shaping of DNA induced by the presence of proteins.
Optimized DNA plasmid of 1280 bp containing 64 Hbb proteins regularly spaced by 5-bp spacers
Since my PhD I have been studying elastic rod theory and its application to biopolymers. Part of my work led to an accurate description of the geometry and the mechanics of a knotted rod. I also successfully applied elastic rod theory to single-molecule experiments performed on DNA (extension-rotation measurements). I recently started to work on how normal mode analysis applied to elastic rods can be used to conveniently describe the dynamics of DNA.
Examples of vibrational modes for a clamped ring under torsional stress.