Elucidation of the disulfide folding pathway of hirudin by a topology-based approach

A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional approaches based on native topology, not all native bonds are treated in the same way; in particular, a suitable energy term is introduced to account for the special strength of disulfide bonds (irrespective of whether they are native or not) as well as their ability to undergo intra-molecular reshuffling. The model thus possesses the minimal ingredients necessary to investigated the much debated issue of whether the re-folding process occurs through partially structured intermediates with native or non-native disulfide bonds. This strategy is applied to a context of particular interest, the re-folding process of Hirudin, a thrombin-specific protease inhibitor, for which conflicting folding pathways have been proposed. We show that the only two parameters in the model (temperature and disulfide strength) can be tuned to reproduce well a set of experimental transitions between species with different number of formed disulfide. This model is then used to provide a characterisation of the folding process and a detailed description of the species involved in the rate-limiting step of Hirudin refolding.Comment: 14 pages, 9 figure

Spectral properties and infrared absorption in manganites

Within a recently proposed variational approach it has been shown that, in $La_{1-x}A_xMnO_3$ perovskites with $0<x<0.5$, near the metal-insulator transition, the combined effect of the magnetic and electron-phonon interactions pushes the system toward a regime of two coexisting phases: a low electron density one made by itinerant large polarons forming ferromagnetic domains and a high electron density one made by localized small polarons giving rise to paramagnetic or antiferromagnetic domains depending on temperature. Employing the above-mentioned variational scheme, in this paper spectral and optical properties of manganites are derived for $x=0.3$ at different temperatures. It is found that the phase separation regime induces a robust pseudogap in the excitation spectrum of the system. Then the conductivity spectra are characterized by a transfer of spectral weight from high to low energies, as the temperature $T$ decreases. In the metallic ferromagnetic phase, at low $T$ two types of infrared absorption come out: a Drude term and a broad absorption band due respectively to the coherent and incoherent motion of large polarons. The obtained results turn out in good agreement with experiments.Comment: 9 figure

Non-local composite spin-lattice polarons in high temperature superconductors

The non-local nature of the polaron formation in t-t'-t"-J model is studied in large lattices up to 64 sites by developing a new numerical method. We show that the effect of longer-range hoppings t' and t" is a large anisotropy of the electron-phonon interaction (EPI) leading to a completely different influence of EPI on the nodal and antinodal points in agreement with the experiments. Furthermore, nonlocal EPI preserves polaron's quantum motion, which destroys the antiferromagnetic order effectively, even at strong coupling regime, although the quasi-particle weight in angle-resolved-photoemission spectroscopy is strongly suppressed.Comment: 5 pages, 4 figure

Steps toward a classifier for the Virtual Observatory. I. Classifying the SDSS photometric archive

Modern photometric multiband digital surveys produce large amounts of data that, in order to be effectively exploited, need automatic tools capable to extract from photometric data an objective classification. We present here a new method for classifying objects in large multi-parametric photometric data bases, consisting of a combination of a clustering algorithm and a cluster agglomeration tool. The generalization capabilities and the potentialities of this approach are tested against the complexity of the Sloan Digital Sky Survey archive, for which an example of application is reported.Comment: To appear in the Proceedings of the "1st Workshop of Astronomy and Astrophysics for Students" - Naples, 19-20 April 200

Ballistic transport in one-dimensional loops with Rashba and Dresselhaus spin-orbit coupling

We discuss the combined effect of Rashba and Dresselhaus spin-orbit interactions in polygonal loops formed by quantum wires, when the electron are injected in a node and collected at the opposite one. The conditions that allow perfect localization are found. Furthermore, we investigate the suppression of the Al'tshuler--Aronov--Spivak oscillations that appear, in presence of a magnetic flux, when the electrons are injected and collected at the same node. Finally, we point out that a recent realization of a ballistic spin interferometer can be used to obtain a reliable estimate of the magnitude ratio of the two spin-orbit interactions.\bigskipComment: 6 figure

Two channel model for optical conductivity of high mobility organic crystals

We show that the temperature dependence of conductivity of high mobility organic crystals Pentacene and Rubrene can be quantitatively described in the framework of the model where carriers are scattered by quenched local impurities and interact with phonons by Su-Schrieffer-Hegger (SSH) coupling. Within this model, we present approximation free results for mobility and optical conductivity obtained by world line Monte Carlo, which we generalize to the case of coupling both to phonons and impurities. We find fingerprints of carrier dynamics in these compounds which differ from conventional metals and show that the dynamics of carriers can be described as a superposition of a Drude term representing diffusive mobile particles and a Lorentz term associated with dynamics of localized charges.Comment: 6 pages, 5 figure