  Mesoscopic $N-$atom systems derive their structural and dynamical properties
from processes coupled across multiple scales in space and time. An efficient
method for understanding these systems in the friction dominated regime from
the underlying N-atom formulation is presented. The method integrates notions
of multiscale analysis, Trotter factorization, and a hypothesis that the
momenta conjugate to coarse-grained variables can be treated as a stationary
random process. The method is demonstrated for Lactoferrin, Nudaurelia Capensis
Omega Virus, and Cowpea Chlorotic Mottle Virus to assess its accuracy and
scaling with system size.
