F Thalmann | PubMed Health

PubMed2006

What is in a pebble shape?

We propose to characterize the shapes of flat pebbles in terms of the statistical distribution of curvatures measured along the pebble contour. This is demonstrated for the erosion of clay pebbles in a controlled laboratory apparatus. Photographs at various stages of erosion are analyzed, and compared with two models. We find that the curvature distribution complements the usual measurement of aspect ratio, and connects naturally to erosion processes that are typically faster at protruding regions of high curvature.

Journal Article↗

PubMed2003

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n2) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 105-fold for short, multistable molecules (<or=150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30% of base pairs in G+C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http://kinefold.u-strasbg.fr).

Algorithms↗