The Role of Non-native Interactions in the Folding of Knotted Proteins

Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein show a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavoring early knotting events.Comment: Accepted for publication on PLOS Computational Biolog

Study of psi' and chi_c decays as feed-down sources of J/psi hadro-production

The interpretation of the J/psi suppression patterns observed in nuclear collisions, at CERN and RHIC, as a signature of the formation of a deconfined phase of QCD matter, requires knowing which fractions of the measured J/psi yields, in pp collisions, are due to decays of heavier charmonium states. From a detailed analysis of the available mid-rapidity charmonium hadro-production cross sections, or their ratios, we determine that the J/psi feed-down contributions from psi' and chi_c decays are, respectively, (8.1 +/- 0.3) % and (25 +/- 5) %. These proton-proton values are derived from global averages of the proton-nucleus measurements, assuming that the charmonium states are exponentially absorbed with the length of matter they traverse in the nuclear targets.Comment: 12 pages, 4 figures, 3 table

The Effect of Interactions on the Conductance of Graphene Nanoribbons

We study the effects of the interaction between electrons and holes on the conductance G of quasi-one-dimensional graphene systems. We first consider as a benchmark the limit in which all interactions are negligible, recovering the predictions of the tight-binding approximation for the spectrum of the system, and the well-known result G=4 e^2/h for the lowest conductance quantum. Then we consider an exactly solvable field theoretical model in which the electro-magnetic interactions are effectively local. Finally, we use the effective field theory formalism to develop an exactly solvable model in which we also include the effect of non-local interactions. We find that such interactions turn the nominally metallic armchair graphene nanoribbon into a semi-conductor, while the short-range interactions lead to a correction to the G=4 e^2/h formula.Comment: 9 pages, 1 figur

RR Lyrae in XSTPS: The halo density profile in the North Galactic Cap

We present a catalog of RR Lyrae stars (RRLs) observed by the Xuyi Schmidt Telescope Photometric Survey (XDSS). The area we consider is located in the North Galactic Cap, covering 376.75 sq deg at RA $\approx$ 150 deg and Dec $\approx$ 27 deg down to a magnitude limit of i $\approx$ 19. Using the variability information afforded by the multi-epoch nature of our XDSS data, combined with colors from the Sloan Digital Sky Survey, we are able to identify candidate RRLs. We find 318 candidates, derive distances to them and estimate the detection efficiency. The majority of our candidates have more than 12 observations and for these we are able to calculate periods. These also allows us to estimate our contamination level, which we predict is between 30% to 40%. Finally we use the sample to probe the halo density profile in the 9-49 kpc range and find that it can be well fitted by a double power law. We find good agreement between this model and the models derived for the South Galactic Cap using the Watkins et al. (2009) and Sesar et al. (2010) RRL data-sets, after accounting for possible contamination in our data-set from Sagittarius stream members. We consider non-spherical double power law models of the halo density profile and again find agreement with literature data-sets, although we have limited power to constrain the flattening due to our small survey area. Much tighter constraints will be placed by current and future wide-area surveys, most notably ESA's astrometric Gaia mission. Our analysis demonstrates that surveys with a limited number of epochs can effectively be mined for RRLs. Our complete sample is provided as accompanying online material.Comment: 14 pages, ApJ (in press

Numerical Modelling Approaches for the Analysis of Earthquake Triggered Landslides

Different numerical approaches for the analysis of earthquake triggered landslides are studied. Improved simplified models are developed and their performance for evaluating the response of natural slopes subjected to earthquakes is studied. Using more sophisticated numerical techniques the influence of several factors such as the hydro mechanical behavior assumptions, 1D vs. 2D geometry, and the input motion are assessed. 2D computations have shown that the kinematics of the slope motion is largely affected by the geometry of the slope. As far as the soil behavior is concerned, the results indicate that introduction of progressive yielding in the soil model provides larger displacement, progressive pore-pressure generation and more diffuse deformation. For the input motion, the number of peaks and their amplitudes have been identified as being the mains factors for irreversible displacements

Exploring the Chiral Regime of QCD in the Interacting Instanton Liquid Model

Since contemporary lattice QCD calculations have highlighted the need to understand the dependence of QCD observables on the quark mass, this paper presents the framework to investigate this dependence in the context of the Interacting Instanton Liquid Model (IILM). By computing the nucleon and pion masses for a wide range of quark masses, we show that the IILM reproduces the existing lattice data for pion masses in the range 450 - 730 MeV. We also show that in the low-pion mass regime, the nucleon mass dependence in this model is consistent with O(p^4) Chiral Perturbation Theory and O(p^3) Baryon Chiral Perturbation theory. The nucleon sigma-term extracted from this analysis is in qualitative agreement with but slightly below the result from recent lattice calculations. To further explore this model in the chiral regime, we show that the spectral density of the Dirac operator and the three-point scalar correlation function agree with the behavior expected from chiral perturbation theory for two flavors. In the IILM, we identify a characteristic quark energy scale, m*= 80 MeV, which governs the zero mode zone and thus the scale for instanton mediated chiral symmetry breaking, and discuss its physical significance

Protótipo de um lisímetro de pesagem automático para estudos em casa de vegetação.

Um prototipo de lisimetro de pesagem automatico foi desenvolvido para medicoes do requerimento de agua das culturas. O sistema e operado com o auxilio de apenas um computador, na forma de placa, e basicamente, feito de um conjunto extenso metros de precisao ("strain gages"), um regulador de voltagem, um conversor de sinal analogico para digital e um conjunto de amplificadores operacionais. Os extenso metros transdutores foram colados, com adesivo epoxy, sobre uma lamina de aluminio e conectados em um circuito de "ponte de wheatstone" para a medicao de variaveis, tais como peso. Um sistema de aquisicao automatica de dados foi criado. Os principios, esboco, montagem e funcionamento da instrumentacao estao descritos. O sistema foi calibrado atraves de carregamento e descarregamento de pesos padrao pre-selecionados na plataforma de pesagem e testado e avaliado em plantas de milho e feijoeiro que foram cultivadas em vasos, em condicoes de casa de vegetacao, na EMBRAPA-CNPMS. Um programa de computador foi desenvolvido para adquirir os dados dos sensores, permitindo os registros de local, data, horario e dados para posicoes especificas da memoria e orientando o usuario para a entrada dos intervalos de tempo. Uma linguagem residente BASIC, contida no microprocessador, foi utilizada na programacao