Computation of transit times using the milestoning method with applications to polymer translocation.
Milestoning is an efficient approximation for computing long-time kinetics and thermodynamics of large molecular systems, which are inaccessible to brute-force molecular dynamics simulations. A common use of milestoning is to compute the mean first passage time (MFPT) for a conformational transition of interest. However, the MFPT is not always the experimentally observed timescale. In particular, the duration of the transition path, or the mean transit time, can be measured in single-molecule experiments, such as studies of polymers translocating through pores and fluorescence resonance energy transfer studies of protein folding. Here we show how to use milestoning to compute transit times and illustrate our approach by applying it to the translocation of a polymer through a narrow pore.
Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA. ahawk@physics.utexas.edu
Alexander T
AT
Hawk
Sai Sriharsha M
SS
Konda
Dmitrii E
DE
Makarov
D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011108:Polymers / Q000737:chemistry*; D017510:Protein Folding; D013816:Thermodynamics
D011108:Polymers