Integral equation theory based direct and accelerated systematic coarse-graining approaches.

Coarse-grained (CG) molecular dynamics (MD) simulations have become popular for investigating systems on multiple length and time scales ranging from atomistic to mesoscales. In CGMD, several atoms are mapped onto a single CG bead and the effective interactions between CG beads are determined. Iterative coarse-graining methods, such as iterative Boltzmann inversion (IBI), are computationally expensive and can have convergence issues.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics.

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics.