Letter to the Editor: BDpack, an open source parallel Brownian dynamics simulation package

Hydrodynamic interactions (HI), polymer-solvent interactions, and finite extensibility effects (or force-extension relation) are the physical phenomena that are central in determining macromolecular dynamics under equilibrium and nonequilibrium settings [1–6]. Brownian Dynamics (BD) is a mesoscale simulation technique which is used to study the dynamics and material properties of synthetic and biological polymeric solutions, with different architectures [1,2,4–11]. In BD, the Itô stochastic differential equation (SDE) is integrated to determine the configurational evolution of the system. The influence of the solvent on the mesoscopic scale solutes is implicitly considered via random Brownian and hydrodynamic drag forces. The hydrodynamic coupling between different parts of the chains is explicitly considered using the diffusion tensor [1,2]. Exact calculation of HI is an important advantage of BD over other mesoscale simulation techniques. Moreover, the polymer-solvent effective interactions are incorporated using excluded volume (EV)...