Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
) is restricted to our local network and chosen collaborators.
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) 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.
Efficient exploration of discrete energy landscapes
Martin Mann, Konstantin Klemm
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Status: Published
Physical Review E 83: 011113 (2011)
Abstract
Many physical and chemical processes, such as folding of biopolymers,
are best described as dynamics on large combinatorial energy landscapes. A concise
approximate description of dynamics is obtained by partitioning the micro-states of
the landscape into macro-states. Since most landscapes of interest are not tractable
analytically, the probabilities of transitions between macro-states need to be extracted
numerically from the microscopic ones, typically by full enumeration of the state space.
Here we propose to approximate transition probabilities by a Markov chain Monte-
Carlo method. For landscapes of the number partitioning problem and an RNA
switch molecule we show that the method allows for accurate probability estimates
with significantly reduced computational cost.
Keywords
energy landscape, sampling algorithm