Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations

A numerical method for estimating the functional of a stochastic differential equation is evaluated for possible application to biomolecular systems. The approach uses variance reduction for stochastic trajectories to estimate relative free energy differences and define paths between initial and end points. The method shows promise as evidenced by application to simple one and two dimensional trial surfaces. This suggests that the approach may be applicable to more complex biomolecular systems.