Grain Shape Dynamics For Molecular Simulations At The Mesoscale

Coarse-graining routines are necessary for simulating systems involving large molecules. However, their accuracy is limited by excessive simplifications that are made during the upscaling procedure. The time autocorrelation of the shape anisotropy of grains incis-polybutadiene chains is computed, and it is concluded that the image of a grain as an undeformable object is no longer valid at high level of coarse-graining. A model for the joint dynamics of the centers of mass and the shapes of grains, which are calculated from the positions of the atoms they represent, is introduced. The model reproduces the distribution and dynamics of the shape of a single-grain oligomer in various solvents, opening a route to physical modeling of complex systems such as proteins, biological cells, or realistic polymer melts.