# Analysis of Energy Landscapes with Barriers and Friends

### The barriers program

The program
` barriers `

reads an energy sorted list of conformations
of a landscape, and computes local minima and energy barriers of the
landscape. For RNA secondary structures, suitable input is produced by
` RNAsubopt `

For each local minimum found it prints to stdout, the
conformation of the minimum, its energy, the number of the "parent"-minimum
it merges with, and the height of the energy barrier. Additional
information on each minimum, such as saddle point conformation and basin
sizes can be included via options. A PostScript drawing of the resulting
tree is written to "tree.ps" in the current directory.

For detailed instructions see the man page.

### Download

source code
of program `barriers`

release 1.5.2

### The treekin program

The program ` treekin `

computes folding
dynamics on coarse grained version of an energy landscape, where all
conformations belonging to the same local minimum have been contracted
into a single macro-state. `treekin`

reads in the a list of
local minima (macro-states) and effective refolding rates between these
minima as computed by `barriers --rates`

. Since the
the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of
the master equation conformations (i.e. diagonalization of the rate matrix).
For detailed instructions see the man page.

### Download

source code of program ` treekin `

release 0.3.1

### The bar_map program

The program ` bar_map `

computes a mapping
between a series of barrier trees as computed by the `barriers`

program. This of interest in particular in the context of co-transcriptional
folding, where the one can compute barrier trees corresponding to different
length partial transcripts; or for dynamic landscapes produced e.g. when
varying the temperature.

The mapping produced by `bar_map`

can be used in conjunction
with `treekin`

to compute folding dynamics on time-varying
landscape. In the case of co-transcriptional folding, for
example, `treekin`

is used to compute folding dynamics for the
length of 1 elongation step, the `bar_map`

mapping is then used
to transfer the final population onto the next (longer) landscape and thus to
obtain the initial condition for the next `treekin`

computation.

For detailed instructions see the man page.

To simplify using `bar_map`

in conjunction with treekin,
the `barmap_simulator`

utility produces shell script containing
treekin commands for a complete simulation run.

### Download

bar_map
and barmap_simulator Perl code.