USAGE.md

Usage of gSMFRETda

Configuration of parpmeters

The gSMFRETda can analysis multi-state dynamic systems. It uses transition rate matrix , which is shown in figure below, to represent systems' multi-state dynamic properties. The element in the matrix represent the interconversion rate constant from the state j to the state i. The cumulative distribution of dwell times from a given state, asserting exponential decay, gives as the inverse of the rate constant. When i=j, the element equal to negative numbers of sum of other elements in the column.

[](mat.jpg)

The matrix of below figure represent the dynamic system in the left subfigure above. In case you want to specify the kinetic model to be used in the calculation as shown above, you can add the argument "-k" to the pdaServ program to define the transition rate matrix as

Specifically, you need to add "-k 3 7" to set ke_zero=[3,7], in this case, to setup which element is zero in the matrix. Index starts from 1, and the matrix is RowMajor.

The Monte Carlo approach for Probability Distribution Analysis (mcPDA)

When use the Monto Carlo approach to compute PDA, the target is to minimize the probabilistic objective function F of form

in which a function f of an input variable x with structural parameters

is evaluated on average with respect to an input distribution

with distributional parameters

. In PDA, f is refer to the reduced chi-squared statistic to measure the goodness of of fit of PDA models. High-dimensional parameters

of distribution p include the kinetic parameters