Computer simulation of polyrotaxanes

A polyrotaxane is a polymer chain which is threaded with molecular rings.   Stoppers at the end of the chain keep the rings from falling off the chain. These polyrotaxanes have been formulated into soft gels, but the connection between the measured properties of the gel depend upon the architecture of the chain are not understood.  Here we will amend a stochastic simulation, test it, and use it to produce data that will help us to correlate dynamic properties with the molecular architecture of the chain.  The simulation will be done at the mesoscale:  the unit of length will be a statistical monomer of the chain, the unit time will be the smallest relaxation time, and the energy will be thermal energy or $k_BT.$
This is primarily a non-experimental project, focussing upon programming code (no packages),  and generating & analysing lots of data in the aim to understand polyrotaxane dynamics.