This project, started in mid July 2018, models collagen fibrils as cylinders with radius R and length L.

Rod-like (collagen) molecules within the fibrils are represented as by a continuous twist angle with respect to the z axis, i.e. it is a continuum theory, and constrained to be a double-twist form. For more details on the double-twist, see the paper 'polymorphism of stable collagen fibrils' (doi:10.1039/C8SM00377G) for previous work.

The fibrils also have density fluctuations along the length of the fibril, of the form rho(z)=rho_{ref}+deltacos(etaz). There is a preferred period observed in experiment, which is known as the d-band. It is hypothesized that the twist and the maximal d-band length d0 are coupled together as d0*cos(twist) to give the actual spacing of the density fluctuations. This couples the fluctuations and the twist field together.

The goal of this project is to see how density fluctuations along the z-direction modify the double-twist configuration, and the free energy of the fibrils.

TEsting. Double check. Triple check.