TREEKIN

treekin − Calculate a macrostate dynamics of biopolymers

treekin [options] < foo.bar

treekin computes a reduced dynamics of biopolymer folding by means of a Markov process that (generally) operates at the level of macrostates, i.e. basins of attraction in the underlying energy landscapes.
treekin reads a barfile foo.bar and (optionally) a file rates.out in the current working directory (both computed by barriers).

−a, −−absorb i

Make a state i absorbing (default none)

−m, −−method m

Select method to build transition matrix. Possible values for m are:
A ==> Arrhenius−like macrostate kinetics (default)
F ==> Full process kinetics (consider all states from subopt)
I ==> Apply microscrates from barriers
N.B.: A rates.out file must be present in the current working directory

−−p0 s=x

Set the start population probability of state s to x. This option can be given multiple times. Note that the sum of all population probabilities must be 1.

−−t0 time

Set simulation start time in internal units (default 0.1)

−−t8 time

Set simulation stop time in internal units (default 1e+09)

−−tinc increment

Time scaling factor for logarithmic time scale (default 1.02)

−T, −−Temp temp

Set the simulation temperature in Celsius to temp (default 37.0)

−−info

Show all settings (default off)

−h −−help

Output help information and exit.

−V −−version

Output version information and exit.

−b, −−bin

read binary input (default= off)

−d, −−degeneracy

Consider degeracy in transition rates (default= off)

−e, −−exponent

Use matrix−expontent routines, NO diagonalization (default off)

−−fpt

calculate first passage times (default=off)

−n, −−nstates num

Read num states

−r, −−recover

Recover from pre−calculated Eigenvalues and Eigenvectors (default=off)

−w −−wrecover

Write recovery file containing Eigenvalues and Eigenvectors (default=off)

−u, −−umatrix

Dump transition matrix U to a binary file mx.bin (default= off)

−x, −−mathematicamatrix

Dump transition matrix U to Mathematica−readable file mxMat.txt (default=off)

Typically, the first step is to compute an energy landscape by barriers:

barriers −−saddle −−bsize −−rates < foo.sub > foo.bar

the resulting barfile (foo.bar) and rates file (rates.out) are then processed by:

treekin −−p0 2=1 −m I < foo.bar

Here, the simulation starts with 100% of the initial population in macrostate 2(second lowest local minimum in the barrier tree). The transition matrix is constructed from a set of microscopic rates (as computed by barriers). Generally, the microstate dynamics is much more accurate than the simple Arrhenius−like dynamics.
The first column in the output is the time, all other columns list the population of the individual (macro)states in the simulation.

If you use this program in your work you might want to cite:

M.T. Wolfinger, W.A. Svrcek−Seiler, Ch. Flamm, I.L. Hofacker, P.F. Stadler (2004) Efficient Folding Dynamics of RNA Secondary Structures J.Phys.A: Math.Gen. 37: 4731−4741

I.L. Hofacker, Ch. Flamm, M.T. Wolfinger, P.F. Stadler (2004) Approximation of RNA Folding Kinetics Using Sequences of Barrier Trees. in preparation

Michael Wolfinger, Ivo Hofacker, Christoph Flamm, Andreas Svrcek−Sailer, Peter Stadler. Send comments to <ivo@tbi.univie.ac.at>

barriers(1)