Code for "A numerical algorithm for investigating the role of
the motor-cargo linkage in molecular motor driven
transport." by John Fricks,  Hongyun Wang, and Tim Elston

In this directory, you will find the Matlab scripts corresponding to the examples in "A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor driven transport" by Fricks, Wang, and Elston. There are three subdirectories corresponding to each of the three examples--"flashingratchet", "tiltedperiodicpotential", and "twostate". Each of these has a number of Matlab helper functions, the function which implements the method ("asymptotic.m"), and a main.m program to illustrate how to call the function. The "asymptotic.m" files implement the numerical method given the parameters and return the asymptotic velocity and the effective diffusion. The helper functions are "bx.m", "fx.m", "by.m", and "fy.m" which determine the forward and backward rates for the x and y coordinates respectively and also "phi.m" which gives the potential function given a certain (x,y) pair and the parameters("flashing" has an extra file "phia.m" which contains the second potential function). Below are links to the subdirectories.