Local energy approach to the dynamic glass transition

We propose a new class of phenomenological models for dynamic glass transitions. The system consists of an ensemble of mesoscopic regions to which local energies are allocated. At each time step, a region is randomly chosen and a new local energy is drawn from a distribution that self-consistently depends on the global energy of the system. Then, the transition is accepted or not according to the Metropolis rule. Within this scheme, we model an energy threshold leading to a mode-coupling glass transition as in the p-spin model. The glassy dynamics is characterized by a two-step relaxation of the energy autocorrelation function. The aging scaling is fully determined by the evolution of the global energy and linear violations of the fluctuation dissipation relation are found for observables uncorrelated with the energies. Interestingly, our mean-field approach has a natural extension to finite dimension, that we briefly discuss.Comment: 4 pages, 5 figure

Dynamic phase diagram of the Number Partitioning Problem

We study the dynamic phase diagram of a spin model associated with the Number Partitioning Problem, as a function of temperature and of the fraction $K/N$ of spins allowed to flip simultaneously. The case K=1 reproduces the activated behavior of Bouchaud's trap model, whereas the opposite limit $K=N$ can be mapped onto the entropic trap model proposed by Barrat and M\'ezard. In the intermediate case $1 \ll K \ll N$, the dynamics corresponds to a modified version of the Barrat and M\'ezard model, which includes a slow (rather than instantaneous) decorrelation at each step. A transition from an activated regime to an entropic one is observed at temperature $T_g/2$ in agreement with recent work on this model. Ergodicity breaking occurs for $T<T_g/2$ in the thermodynamic limit, if $K/N \to 0$. In this temperature range, the model exhibits a non trivial fluctuation-dissipation relation leading for $K \ll N$ to a single effective temperature equal to $T_g/2$. These results give new insights on the relevance and limitations of the picture proposed by simple trap models.Comment: 15 pages, submitted to PR

Single-domain protein folding: a multi-faceted problem

We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape approach. As far as experiments are concerned, we focus on the recent development of single-molecule techniques. In particular, we compare the results obtained with two main techniques: single protein force measurements with optical tweezers and single-molecule fluorescence in studies on the same protein (RNase H). This allows us to point out some controversial issues such as the nature of the denatured and intermediate states and possible folding pathways. After reviewing the various numerical simulation techniques, we show that on-lattice protein-like models can help to understand many controversial issues.Comment: 26 pages, AIP Conference Proceeding

The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes. Availability: C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License. Contact: [email protected]