A robust approach to estimating rates from time-correlation functions
  While seemingly straightforward in principle, the reliable estimation of rate constants is seldom easy in practice. Numerous issues, such as the complication of poor reaction coordinates, cause obvious approaches to yield unreliable estimates. When a reliable order parameter is available, the reactive flux theory of Chandler allows the rate constant to be extracted from the plateau region of an appropriate reactive flux function. However, when applied to real data from single-molecule experiments or molecular dynamics simulations, the rate can sometimes be difficult to extract due to the numerical differentiation of a noisy empirical correlation function or difficulty in locating the plateau region at low sampling frequencies. We present a modified version of this theory which does not require numerical derivatives, allowing rate constants to be robustly estimated from the time-correlation function directly. We compare these approaches using single-molecule force spectroscopy measurements of an RNA hairpin. 
John D. Chodera, Phillip J. Elms, William C. Swope, Jan-Hendrik Prinz,   Susan Marqusee, Carlos Bustamante, Frank No\'e, and...
cond-mat.stat-mech q-bio.BM