From continuum Fokker-Planck models to discrete kinetic models.

Two theoretical formalisms are widely used in modeling mechanochemical systems such as protein motors: continuum Fokker-Planck models and discrete kinetic models. Both have advantages and disadvantages. Here we present a "finite volume" procedure to solve Fokker-Planck equations. The procedure relates the continuum equations to a discrete mechanochemical kinetic model while retaining many of the features of the continuum formulation. The resulting numerical algorithm is a generalization of the algorithm developed previously by Fricks, Wang, and Elston through relaxing the local linearization approximation of the potential functions, and a more accurate treatment of chemical transitions. The new algorithm dramatically reduces the number of numerical cells required for a prescribed accuracy. The kinetic models constructed in this fashion retain some features of the continuum potentials, so that the algorithm provides a systematic and consistent treatment of mechanical-chemical responses such as load-velocity relations, which are difficult to capture with a priori kinetic models. Several numerical examples are given to illustrate the performance of the method.