__Software__

**Analysis of finite-length two state trajectories **

(Download a free version of the Software RDF, NOW)

RDF - Our software for analyzing, noisy, finite length, two-state trajectories finds

a unique mechanism of Reduced Dimensions (RD form) from the actual noisy data,

and translates it to a set of possible kinetic schemes.
*
Our complete toolbox for solving two-state trajectories takes the data, *

creates the noisy trajectory from it, filters noise, and analyzes the trajectory.

The output includes: all the mechanism-free information contained in the data,

the reduced dimensions form that best fits the data,

and a set of possible kinetic schemes that are built from the RD form.
Read more.

The software is useful in the following fields of research:

(1) Dynamics of DNA and RNA on the single molecule level

(2) Dynamics of proteins on the single molecule level

(3) Enzymatic activity

(4) Ion channel recordings

(5) Single molecule force measurements

(6) Quantum dots

(7) Diffusion of individual objects (bio-molecules, beads, etc.)

*Our complete toolbox for analyzing two-state trajectories takes two conjugated column vectors of random times (or any other kind of non-negative observations) and the associated time increment, and gives as an output all the mechanism-free information contained in the data, and the reduced dimensions form that best fits the data. The subroutine works in Matlab environment and uses the optimization toolbox. *

Read more on the subroutine.

Now we develop an independent interface that analysis the time trajectory.

In addition, we release commands that are part of the software, yet are useful independently.

Each command comes in an interface.

- Exponential fit

*
Our routine takes as an input a vector of random times (or any other kind of non-negative observations) and the associated time increment, *

and gives as an output the optimal exponential expansion of the probability density function that is constructed from the random times:

that is, the output is a set of L amplitudes and L conjugated rates.

The method is based on the Pade approximation method with Longman recursion relation, and a maximum likelihood technique.
Read more.

- Rank estimation of a 2D WT-PDF

*Our subroutine takes two column vectors of random times (or any other kind of non-negative observations) and the associated time increment,*

and gives as an output the rank of the two-dimensional waiting time probability density function (2D WT-PDF) built from these random times.

The subroutine is based on singular value decomposition of the second order cumulative WT-PDF,

and on noise-analysis of the ratios of successive singular values.

Read more.
- 2D WT-PDFs
*Our subroutine takes two column vectors of random times *

(or any other kind of non-negative observations) and the associated time increment,

and gives as an output the eigenvalues and the matrices of coefficients,

in the exponential expansions of all four two-dimensional WT-PDFs.

Read more.

* Future projects*

Still, there are (at least) two other software that we intend

to develop. These are in the fields of expertise of O.Flomenbom.

(*****) *Dynamics* - software for the simulations and the analysis of Fokker-Planck

and Langevin equations with many arguments.

(*****) *Proteins* - software for simulations and analysis of the dynamics of proteins.