Publications - Published papers

Please find below publications of our group. Currently, we list 508 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

BarMap: RNA folding on dynamics energy landscapes

Ivo L. Hofacker, Christoph Flamm, Christian Heine, Michael T. Wolfinger, Gerik Scheuermann, and Peter F. Stadler.


PREPRINT 09-048: [ PDF ]
[ Publishers's page ]  paperID




Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, in particularly in time-variable and externally triggered systems are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we described the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyse the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on indidividual landscapes and to model external triggers and and environmental changes as small but discrete changes in the landscapes. A "barmap" links macrostates of temporally adjacent landscapes and defines the transfer of population densities from ``snapshot&#039;&#039; to the next. Implemented in the <tt>BarMap</tt> software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many non-stationary scenaria, including temperature changes, co-transcriptional folding, re-folding in consequence to degradation, and mechanically constrained kinetics as in the case of pulling polymers through a pore.


RNA folding kinetics, barrier tree, dynamic energy landscape, co-transcriptional folding


doi: 10.1261/rna.2093310