Mechanical Unfolding of a Simple Model Protein Goes Beyond the Reach of One-Dimensional Descriptions

We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we also provide a quantitative description of the unfolding pathways followed by the system. Our study shows a complex dynamical scenario. In particular, we see that the usual one-dimensional picture: free-energy vs end-to-end distance representation, gives a misleading description of the process. Unfolding can occur following different pathways and configurations which seem to play a central role in one-dimensional pictures are not the intermediate states of the unfolding dynamics.Comment: 10 pages, 6 figure

Nonparametric maximum likelihood estimation of probability densities by penalty function methods

When it is known a priori exactly to which finite dimensional manifold the probability density function gives rise to a set of samples, the parametric maximum likelihood estimation procedure leads to poor estimates and is unstable; while the nonparametric maximum likelihood procedure is undefined. A very general theory of maximum penalized likelihood estimation which should avoid many of these difficulties is presented. It is demonstrated that each reproducing kernel Hilbert space leads, in a very natural way, to a maximum penalized likelihood estimator and that a well-known class of reproducing kernel Hilbert spaces gives polynomial splines as the nonparametric maximum penalized likelihood estimates

Anisotropic friction: assessment of force components and resulting trajectories

International audienceWe report on an experimental device that makes it possible to assess the frictional properties of the contact between a slider and a horizontal surface, and to study the resulting trajectories of the slider when pulled across the surface by means of a flexible link. First, we show experimentally that, when the frictional properties are anisotropic, the slider is subjected, in addition to the dissipative frictional force oriented along the trajectory, to a force, perpendicular to the trajectory, which thus does not contribute to energy dissipation. Therefore, the slider does not necessarily moves in the pulling direction. Second, we show that the trajectories of the slider, when in continuous motion, in absence of inertial effects, can be recovered by assuming that, at all time, the friction force compensates the pulling force. We point out that we prove experimentally that the normal component of the friction force is given as the derivative, with respect to the sliding direction, of the tangential component. This result is particularly interesting as the relation between the normal and the tangential components is compatible with " the maximum of energy release rate " criterion used in the theory of fracture

Cooper pairs as bosons

Although BCS pairs of fermions are known not to obey Bose-Einstein (BE) commutation relations nor BE statistics, we show how Cooper pairs (CPs), whether the simple original ones or the CPs recently generalized in a many-body Bethe-Salpeter approach, being clearly distinct from BCS pairs at least obey BE statistics. Hence, contrary to widespread popular belief, CPs can undergo BE condensation to account for superconductivity if charged, as well as for neutral-atom fermion superfluidity where CPs, but uncharged, are also expected to form.Comment: 8 pages, 2 figures, full biblio info adde

Tracing the Evolution of Agglomeration Economies: Spain, 1860-1991

This article attempts to quantify how the effect of agglomeration economies on population growth has evolved over time. Using district population in Spain between 1860 and 1991, recorded approximately every decade, this article examines whether initial population affects subsequent population growth. Our results show that, while the relationship between these two variables hardly existed during the second half of the 19th century, this link increased significantly between 1910 and 1970, although this trend was abruptly interrupted by the Civil War and the autarkic period that followed. The intensity of this relationship debilitated in the 1970s, a process that continued during the 1980s as rural out-migration diminished and de-industrialisation hit traditional manufacturing sectors. Our findings also stress that agglomeration economies were stronger in medium-size districts, especially from 1960 onwards, thus suggesting that congestion costs began to mitigate the benefits arising from agglomeration economies in the largest locations

Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.Comment: 7 pages, 5 figures, 1 tabl

Entanglement assisted alignment of reference frames using a dense covariant coding

We present a procedure inspired by dense coding, which enables a highly efficient transmission of information of a continuous nature. The procedure requires the sender and the recipient to share a maximally entangled state. We deal with the concrete problem of aligning reference frames or trihedra by means of a quantum system. We find the optimal covariant measurement and compute the corresponding average error, which has a remarkably simple close form. The connection of this procedure with that of estimating unitary transformations on qubits is briefly discussed.Comment: 4 pages, RevTeX, Version to appear in PR