Folding Kinetics of Proteins and Cold Denaturation

Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The folding times are computed using Monte Carlo simulations in the region of the phase diagram where the chain occurs in the native structure. These folding times are roughly equals for the temperatures of cold and warm denaturation for a large range of solvent quality. Between these temperatures, the folding times reach maxima and thus, at low temperatures, the kinetics of the chain always speeds up as the temperature is decreased. The study of the conformational space as function of the temperature permits to elucidate this phenomenon. At low temperature, it shows that the activation barriers of the system decrease faster than the temperature as the temperature is decreased. At high temperature, the rate of the barriers over the temperature decreases as the temperature is increased because the height of the barrier is almost constant.Comment: 7 pages, 7 figure

A bijection for plane graphs and its applications

International audienceThis paper is concerned with the counting and random sampling of plane graphs (simple planar graphs embedded in the plane). Our main result is a bijection between the class of plane graphs with triangular outer face, and a class of oriented binary trees. The number of edges and vertices of the plane graph can be tracked through the bijection. Consequently, we obtain counting formulas and an efficient random sampling algorithm for rooted plane graphs (with arbitrary outer face) according to the number of edges and vertices. We also obtain a bijective link, via a bijection of Bona, between rooted plane graphs and 1342-avoiding permutations. 1 Introduction A planar graph is a graph that can be embedded in the plane (drawn in the plane without edge crossing). A pla-nar map is an embedding of a connected planar graph considered up to deformation. The enumeration of pla-nar maps has been the subject of intense study since the seminal work of Tutte in the 60's [20] showing that many families of planar maps have beautiful counting formulas. Starting with the work of Cori and Vauquelin [10] and then Schaeffer [18, 19], bijective constructions have been discovered that provide more transparent proofs of such formulas. The enumeration of planar graphs has also been the focus of a lot of efforts, culminating with the asymptotic counting formulas obtained by Giménez and Noy [16]. In this paper we focus on simple planar maps (planar maps without loops nor multiple edges), which are also called plane graphs. This family of planar maps has, quite surprisingly, not been considered until fairly recently. This is probably due to the fact that loops and multiple edges are typically allowed in studies about planar maps, whereas they are usually forbidden in studies about planar graphs. At any rate, the first result about plane graphs was an exact algebraic expressio

On the distance-profile of random rooted plane graphs

International audienceWe study the distance-profile of the random rooted plane graph Gn with n edges (by a plane graph we mean a planar map with no loops nor multiple edges). Our main result is that the profile and radius of Gn (with respect to the root-vertex), rescaled by (2n) 1/4 , converge to explicit distributions related to the Brownian snake. A crucial ingredient of our proof is a bijection we have recently introduced between rooted outer-triangular plane graphs and rooted eulerian triangulations, combined with ingredients from Chassaing and Schaeffer (2004), Bousquet-Mélou and Schaeffer (2000), and Addario-Berry and Albenque (2013). We also show that the result for plane graphs implies similar results for random rooted loopless maps and general maps

Atomic diffusion and mixing in old stars IV: Weak abundance trends in the globular cluster NGC 6752

Atomic diffusion in stars can create systematic trends of surface abundances with evolutionary stage. Globular clusters offer useful laboratories to put observational constraints on this theory as one needs to compare abundances in unevolved and evolved stars, all drawn from the same stellar population. In this paper, we show the results of an abundance study of stars in the globular cluster NGC6752 which shows weak but systematic abundances trends with evolutionary phase for Fe, Sc, Ti and Ca. The trends are best explained by a stellar structure model including atomic diffusion with efficient additional mixing. The model allows to correct for sub-primordial stellar lithium abundances of the stars on the Spite plateau, and to match it to the WMAP-calibrated Big-Bang nucleosynthesis predictions to within the mutual 1-sigma errors.Comment: 15 pages, 4 figures and 8 table

Multi-modal wave propagation in smart structures with shunted piezoelectric patches

International audienceThe propagation of wave modes in elastic structures with shunted piezoelectric patches is dealt with in this work. The wave finite element approach, which is based on the finite element method and periodical structure theory, is firstly developed as a prediction tool for wave propagation characteristics in beam like structures, and subsequently extended to consider shunted piezoelectric elements through the diffusion matrix model (DMM). With these numerical techniques, reflection and transmission coefficients of propagating waves in structures with shunted piezoelectric patches can be calculated. The performance of shunted piezoelectric patches on the control of wave propagation is investigated numerically with the DMM. Forced response of the smart structure can also be calculated, and based on which the time response of the structure can be obtained via an inverse discrete fourier transform approach. These general formulations can be applied to all types of slender structures. All these numerical tools can facilitate design modifications and systematic investigations of geometric and electric parameters of smart structures with shunted piezoelectric elements

Bayesian Credible Intervals for Online and Active Learning of Classification Trees

International audience—Classification trees have been extensively studied for decades. In the online learning scenario, a whole class of algorithms for decision trees has been introduced, called incremental decision trees. In the case where subtrees may not be discarded, an incremental decision tree can be seen as a sequential decision process, consisting in deciding to extend the existing tree or not. This problem involves an trade-off between exploration and exploitation, which is addressed in recent work with the use of Hoeffding's bounds. This paper proposes to use Bayesian Credible Intervals instead, in order to get the most out of the knowledge of the output's distribution's shape. It also studies the case of Active Learning in such a tree following the Optimism in the Face of Uncertainty paradigm. Two novel algorithms are introduced for the online and active learning problems. Evaluations on real-world datasets show that these algorithms compare positively to state-of-the-art

Generation of coherent spin-wave modes in Yttrium Iron Garnet microdiscs by spin-orbit torque

Spin-orbit effects [1-4] have the potential of radically changing the field of spintronics by allowing transfer of spin angular momentum to a whole new class of materials. In a seminal letter to Nature [5], Kajiwara et al. showed that by depositing Platinum (Pt, a normal metal) on top of a 1.3 $\mu$m thick Yttrium Iron Garnet (YIG, a magnetic insulator), one could effectively transfer spin angular momentum through the interface between these two different materials. The outstanding feature was the detection of auto-oscillation of the YIG when enough dc current was passed in the Pt. This finding has created a great excitement in the community for two reasons: first, one could control electronically the damping of insulators, which can offer improved properties compared to metals, and here YIG has the lowest damping known in nature; second, the damping compensation could be achieved on very large objects, a particularly relevant point for the field of magnonics [6,7] whose aim is to use spin-waves as carriers of information. However, the degree of coherence of the observed auto-oscillations has not been addressed in ref. [5]. In this work, we emphasize the key role of quasi-degenerate spin-wave modes, which increase the threshold current. This requires to reduce both the thickness and lateral size in order to reach full damping compensation [8] , and we show clear evidence of coherent spin-orbit torque induced auto-oscillation in micron-sized YIG discs of thickness 20 nm