# My Research

Starting out, I'm using the LAMMPS and DynamO molecular dynamics packages to study coarse-graining schemes, and arrive at a suitable scheme to work with the intrinsically disordered protein n16N, which has been shown to be important in the biomineralisation of calcite. The coarse-graining scheme I use will need to be validated against an all-atom simulation.

## Coarse-graining proteins

Below you can see n16N in no particular conformation, realised in a coarse graining scheme due to Voth et al [1]. In this *bonds* view rendered in VMD, **green **represents the alpha carbon (backbone site), **light blue** represents a polar site, **black **is an apolar site, **dark blue** is positive and **red** is negative, i.e. an acidic group.

In this scheme, each residue (amino acid) is represented by 1 backbone site and between 0 and 4 side-chain sites. The idea is to capture as much as possible of the functional groups using the different types of sites.

## Simulation techniques

One of the first techniques I'll be employing is **statistical temperature molecular dynamics** [2], in which forces are scaled by the inverse of the statistical temperature T(U). The result is that the usual Boltzmann distribution for the probability of a state is replaced by a flat energy distribution. This makes sampling the protein energy landscape much easier since free energy barriers are no longer an issue.

[1] 2010 Multiscale Coarse-Graining of the Protein Energy Landscape. PLoS Comput Biol 6(6): e1000827. doi:10.1371/journal.pcbi.1000827

[2] Kim J, Straub JE, Keyes T, 2006 Statistical-Temperature Monte Carlo and Molecular Dynamics Algorithms. Phys. Rev. Lett. 97(5). doi:10.1103/PhysRevLett.97.050601