Simulating soft matter self-assembly using deformable nanoscale building blocks

Most computational studies of soft matter assembly focus on coarse-grained models which employ rigid building blocks that do not exhibit shape adaptation during the self-assembly. We study the self-assembly of elastic building blocks using the virus capsid system as an example. A coarse-grained model of protein subunits that incorporates their stretching and bending energies is developed while retaining many features of the rigid-body models including a truncated pyramid shape favorable to icosahedral capsid assembly. Molecular dynamics simulations show that flexible protein subunits can reproduce the rich assembly diagram associated with the T1 Minute Virus of Mice (MVM) system including fully-formed 20-subunit capsids, kinetically-trapped disordered structures, and non-assembled configurations. In addition to traditional control parameters such as steric attraction between proteins and salt concentration, the model enables the study of using elasticity as a knob to change assembly behavior. The pronounced effects of changing protein flexibility on the capsid assembly and assembly-competent pathway products are discussed.