Statistical Analysis of Native Contact Formation in the Folding of Designed Model Proteins

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein, b) non-local bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds, c) the rest of the native bonds whose behaviour is subordinated, to a large extent, to that of the local- and non-local native contacts

Eye movement desensitisation and reprocessing (EMDR) treatment associated with parent management training (PMT) for the acute symptoms in a patient with PANDAS syndrome: a case report

BACKGROUND: The purpose of this report was to present the results of eye movement desensitisation and reprocessing (EMDR) therapy associated with parent management training (PMT) in a child with paediatric autoimmune neuropsychiatric disorder associated with streptococcus (PANDAS), who had previously only been treated with pharmacological treatment. CASE PRESENTATION: The case concerns an 11-year-old boy who presented with simple and complex vocal tics, motor tics, obsessive-compulsive traits and irritability from the age of 6 years, in addition to a positive result for streptococcal infection. The course of symptoms followed a relapsing-remitting trend with acute phases that were contingent on the infectious episodes. CONCLUSIONS: Following eight sessions of EMDR, preceded by training sessions with the parents, the child showed a significant reduction in symptoms and disappearance of the exacerbation. These results indicate the possibility of improving the treatment outcomes of patients with PANDAS by a combined approach using both antibiotic and EMDR therapies

Coherent Adiabatic Spin Control in the Presence of Charge Noise Using Tailored Pulses

We study finite-time Landau-Zener transitions at a singlet-triplet level crossing in a GaAs double quantum dot, both experimentally and theoretically. Sweeps across the anticrossing in the high driving speed limit result in oscillations with a small visibility. Here we demonstrate how to increase the oscillation visibility while keeping sweep times shorter than T2* using a tailored pulse with a detuning dependent level velocity. Our results show an improvement of a factor ~2.9 for the oscillation visibility. In particular, we were able to obtain a visibility of ~0.5 for St\"uckelberg oscillations, which demonstrates the creation of an equally weighted superposition of the qubit states.Comment: Related papers at http://pettagroup.princeton.ed

Spin exchange interaction with tunable range between graphene quantum dots

We study the spin exchange between two electrons localized in separate quantum dots in graphene. The electronic states in the conduction band are coupled indirectly by tunneling to a common continuum of delocalized states in the valence band. As a model, we use a two-impurity Anderson Hamiltonian which we subsequently transform into an effective spin Hamiltonian by way of a two-stage Schrieffer-Wolff transformation. We then compare our result to that from a Coqblin-Schrieffer approach as well as to fourth order perturbation theory.Comment: 8 pages, 3 figure

Fractional and noncommutative spacetimes

We establish a mapping between fractional and noncommutative spacetimes in configuration space. Depending on the scale at which the relation is considered, there arise two possibilities. For a fractional spacetime with log-oscillatory measure, the effective measure near the fundamental scale determining the log-period coincides with the non-rotation-invariant but cyclicity-preserving measure of \kappa-Minkowski. At scales larger than the log-period, the fractional measure is averaged and becomes a power-law with real exponent. This can be also regarded as the cyclicity-inducing measure in a noncommutative spacetime defined by a certain nonlinear algebra of the coordinates, which interpolates between \kappa-Minkowski and canonical spacetime. These results are based upon a braiding formula valid for any nonlinear algebra which can be mapped onto the Heisenberg algebra.Comment: 15 pages. v2: typos correcte

Fair Loss-Tolerant Quantum Coin Flipping

Coin flipping is a cryptographic primitive in which two spatially separated players, who in principle do not trust each other, wish to establish a common random bit. If we limit ourselves to classical communication, this task requires either assumptions on the computational power of the players or it requires them to send messages to each other with sufficient simultaneity to force their complete independence. Without such assumptions, all classical protocols are so that one dishonest player has complete control over the outcome. If we use quantum communication, on the other hand, protocols have been introduced that limit the maximal bias that dishonest players can produce. However, those protocols would be very difficult to implement in practice because they are susceptible to realistic losses on the quantum channel between the players or in their quantum memory and measurement apparatus. In this paper, we introduce a novel quantum protocol and we prove that it is completely impervious to loss. The protocol is fair in the sense that either player has the same probability of success in cheating attempts at biasing the outcome of the coin flip. We also give explicit and optimal cheating strategies for both players.Comment: 12 pages, 1 figure; various minor typos corrected in version

S. Typhimurium sseJ gene decreases the S. Typhi cytotoxicity toward cultured epithelial cells

<p>Abstract</p> <p>Background</p> <p><it>Salmonella enterica </it>serovar Typhi and Typhimurium are closely related serovars as indicated by >96% DNA sequence identity between shared genes. Nevertheless, <it>S</it>. Typhi is a strictly human-specific pathogen causing a systemic disease, typhoid fever. In contrast, <it>S</it>. Typhimurium is a broad host range pathogen causing only a self-limited gastroenteritis in immunocompetent humans. We hypothesize that these differences have arisen because some genes are unique to each serovar either gained by horizontal gene transfer or by the loss of gene activity due to mutation, such as pseudogenes. <it>S</it>. Typhi has 5% of genes as pseudogenes, much more than <it>S</it>. Typhimurium which contains 1%. As a consequence, <it>S</it>. Typhi lacks several protein effectors implicated in invasion, proliferation and/or translocation by the type III secretion system that are fully functional proteins in <it>S</it>. Typhimurium. SseJ, one of these effectors, corresponds to an acyltransferase/lipase that participates in SCV biogenesis in human epithelial cell lines and is needed for full virulence of <it>S</it>. Typhimurium. In <it>S</it>. Typhi, <it>sseJ </it>is a pseudogene. Therefore, we suggest that <it>sseJ </it>inactivation in <it>S</it>. Typhi has an important role in the development of the systemic infection.</p> <p>Results</p> <p>We investigated whether the <it>S</it>. Typhi <it>trans</it>-complemented with the functional <it>sseJ </it>gene from <it>S</it>. Typhimurium (STM) affects the cytotoxicity toward cultured cell lines. It was found that <it>S</it>. Typhi harbouring <it>sseJ_STM</it>presents a similar cytotoxicity level and intracellular retention/proliferation of cultured epithelial cells (HT-29 or HEp-2) as wild type <it>S</it>. Typhimurium. These phenotypes are significantly different from wild type <it>S</it>. Typhi</p> <p>Conclusions</p> <p>Based on our results we conclude that the mutation that inactivate the <it>sseJ </it>gene in <it>S</it>. Typhi resulted in evident changes in the behaviour of bacteria in contact with eukaryotic cells, plausibly contributing to the <it>S</it>. Typhi adaptation to the systemic infection in humans.</p

Naturwall: active timber wall for renovation of existent buildings

The renovation of old buildings is actually the challenge to cope with increased effort in order to reduce climate global change, channeling more investment and awareness in this sense, defining more experimentations and find innovative solutions. The difficulty of carrying out an intervention on the existing buildings necessarily arise from the lack of information on the existing structure and the lack of coordinated processes between the multidisciplinary skills involved, as well as a difficulty to optimize the process that would make it even more competitive on the renovation work instead on the new construction. Naturwall is an innovative energy saving system for existent buildings by using wood in multifunctional components able to mitigate the environmental effort in building management. The project meant to introduce an industrialized design method in the renovation of existing build environment that highlights opportunities gave by "off site" production and parametric design approach, without neglecting the aesthetical values and the possibility to change the architectural image of residential and non residential constructions. The project aims to create a representative model of solution that will be promoted in Italy and widespread in other similar contex

Analogue neural networks on correlated random graphs

We consider a generalization of the Hopfield model, where the entries of patterns are Gaussian and diluted. We focus on the high-storage regime and we investigate analytically the topological properties of the emergent network, as well as the thermodynamic properties of the model. We find that, by properly tuning the dilution in the pattern entries, the network can recover different topological regimes characterized by peculiar scalings of the average coordination number with respect to the system size. The structure is also shown to exhibit a large degree of cliquishness, even when very sparse. Moreover, we obtain explicitly the replica symmetric free energy and the self-consistency equations for the overlaps (order parameters of the theory), which turn out to be classical weighted sums of 'sub-overlaps' defined on all possible sub-graphs. Finally, a study of criticality is performed through a small-overlap expansion of the self-consistencies and through a whole fluctuation theory developed for their rescaled correlations: Both approaches show that the net effect of dilution in pattern entries is to rescale the critical noise level at which ergodicity breaks down.Comment: 34 pages, 3 figure