This week we will be taking a look at a recent paper in transition path theory by Bob Skeel - Maximum Flux Transition Paths of Conformational Change [doi: 10.1021/ct900689m]. This paper introduces a novel method to compute the transition pathway. A theoretical argument and prototype implemenation are presented to justify the importance of this new approach.

Three uncontrolled approximations are used to make the maximum flux transition path computationaly feasible. First, Brownian dynamics accurately describes the movements in the collective variable space. Second, Most paths lie in a tube where isocommittors are planar. Finally, trajectories are parallel to path on average. All of these assumptions are reasonable, but may be downfalls for the method when examining larger molecules.

Bob Skeel provides two interesting test cases which demonstrate the power of his method. First is a contrived example included as an example of an extreme case which most methods can not handle. It is also convienent since once can compute the answer by hand (or at least with Mathematica). The next example is a small, but important molecule - alanine dipeptide. His tests show that other methods produce errors when a minima is introduced between the start and end state. MFTP, however, successfully avoids these errors.

The use of a contrived model to demonstrate a certain feature of the method is one idea from this paper which I will include in my future research.