A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

South Atlantic Ocean cyclogenesis climatology simulated by regional climate model (RegCM3)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Exact dynamics of single-qubit-gate fidelities under the measurement-based quantum computation scheme

Measurement-based quantum computation is an efficient model to perform universal computation. Nevertheless, theoretical questions have been raised, mainly with respect to realistic noise conditions. In order to shed some light on this issue, we evaluate the exact dynamics of some single-qubit-gate fidelities using the measurement-based quantum computation scheme when the qubits which are used as a resource interact with a common dephasing environment. We report a necessary condition for the fidelity dynamics of a general pure N-qubit state, interacting with this type of error channel, to present an oscillatory behavior, and we show that for the initial canonical cluster state, the fidelity oscillates as a function of time. This state fidelity oscillatory behavior brings significant variations to the values of the computational results of a generic gate acting on that state depending on the instants we choose to apply our set of projective measurements. As we shall see, considering some specific gates that are frequently found in the literature, the fast application of the set of projective measurements does not necessarily imply high gate fidelity, and likewise the slow application thereof does not necessarily imply low gate fidelity. Our condition for the occurrence of the fidelity oscillatory behavior shows that the oscillation presented by the cluster state is due exclusively to its initial geometry. Other states that can be used as resources for measurement-based quantum computation can present the same initial geometrical condition. Therefore, it is very important for the present scheme to know when the fidelity of a particular resource state will oscillate in time and, if this is the case, what are the best times to perform the measurements.

Comments, with reply on 'Continuous time relay-controlled model reference adaptive-system' by A. Abdulkareem and R. Nagarajam

An adaptive scheme is shown by the authors of the above paper (ibid. vol. 71, no. 2, pp. 275-276, Feb. 1983) for continuous time model reference adaptive systems (MRAS), where relays replace the usual multipliers in the existing MRAS. The commenter shows an error in the analysis of the hyperstability of the scheme, such that the validity of this configuration becomes an open question.

A steady-state model for heat pipes of circular or rectangular cross-sections

The objective of this paper is to present a generalized analytical-numerical model of the internal flow in heat pipes. The model formulation is based on two-dimensional formulation of the energy and momentum equations in the vapour and liquid regions and also in the metallic tube. The numerical solution of the model is obtained by using the descretization scheme LOAD and the SIMPLE numerical code. The flow fields, as well as the pressure fields, for different geometries were obtained and discussed. Copyright © 1996 Elsevier Science Ltd.

Quasi-Dirac neutrinos in a model with local B - L symmetry

In a model with B - L gauge symmetry, right-handed neutrinos may have exotic local B - L charge assignments: two of them with B - L = -4 and the other one having B - L = 5. Then, it is natural to accommodate the right-handed neutrinos with the same B - L charge in a doublet of the discrete S3 symmetry, and the third one in a singlet. If the Yukawa interactions involving right-handed neutrinos are invariant under S3, the quasi-Dirac neutrino scheme arises naturally in this model. However, we will show how in this scheme it is possible to give a value for θ13 in agreement with the Daya Bay results. For example the S3 symmetry has to be broken in the Yukawa interactions involving right-handed charged leptons. © 2013 IOP Publishing Ltd.

Braneworlds scenarios in a gravity model with higher order spatial three-curvature terms

In this work we study a Hořava-like 5-dimensional model in the context of braneworld theory. The equations of motion of such model are obtained and, within the realm of warped geometry, we show that the model is consistent if and only if λ takes its relativistic value 1. Furthermore, we show that the elimination of problematic terms involving the warp factor second order derivatives are eliminated by imposing detailed balance condition in the bulk. Afterwards, Israel's junction conditions are computed, allowing the attainment of an effective Lagrangian in the visible brane. In particular, we show that the resultant effective Lagrangian in the brane corresponds to a (3 + 1)-dimensional Hořava-like model with an emergent positive cosmological constant but without detailed balance condition. Now, restoration of detailed balance condition, at this time imposed over the brane, plays an interesting role by fitting accordingly the sign of the arbitrary constant β, insuring a positive brane tension and a real energy for the graviton within its dispersion relation. Also, the brane consistency equations are obtained and, as a result, the model admits positive brane tensions in the compactification scheme if, and only if, β is negative and the detailed balance condition is imposed. © 2013 Springer-Verlag Berlin Heidelberg and Società Italiana di Fisica.

Climate estimates for Eastern Amazon with OLAM model

O modelo OLAM tem como característica a vantagem de representar simultaneamente os fenômenos de escala global e regional através de um esquema de refinamento de grades. Durante o projeto REMAM o modelo foi aplicado para alguns estudos de caso com objetivo de avaliar o desempenho do modelo na estimativa do clima da região leste da Amazônia em períodos de El Niño e La Niña. Estudos de caso foram feitos para os períodos chuvosos dos anos 2010 e 2011que apresentaram condições oceânicas distintas. Inicialmente, os resultados do modelo foram comparados com dados observados da região de estudo. Os resultados mostraram que o modelo consegue representar bem os principais centros convectivos da região e adjacências, da evolução local do ciclo diurno de temperatura, e da dinâmica dos ventos. Posteriormente, a análise dos resultados mostrou que, se tivermos bons dados de condição inicial e boa representação da evolução das condições de temperatura da superfície do mar, o modelo consegue prever com antecedência de dois e três meses se uma estação chuvosa será mais seca ou úmida.

Weather forecasting for Eastern Amazon with OLAM model

O modelo OLAM tem como característica a vantagem de representar simultaneamente os fenômenos meteorológicos de escala global e regional através de um esquema de refinamento de grades. Durante o projeto REMAM, o modelo foi aplicado para alguns estudos de caso com objetivo de avaliar o desempenho do modelo na previsão numérica de tempo para a região leste da Amazônia. Estudos de caso foram feitos para os doze meses do ano de 2009. Os resultados do modelo para estes casos foram comparados com dados observados na região de estudo. A análise dos dados de precipitação mostrou que o modelo consegue representar a distribuição média da precipitação acumulada e os aspectos da sazonalidade da ocorrência dos eventos, mas não consegue prever individualmente a acumulação de precipitação local. No entanto, avaliação individual de alguns casos mostrou que o modelo OLAM conseguiu representar dinamicamente e prever, com alguns dias de antecedência, o desenvolvimento de fenômenos meteorológicos costeiros como as linhas de instabilidade, que são um dos mais importantes sistemas precipitantes da Amazônia.

Numerical solution of the FENE-CR model in complex flows

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Constrained least square pre-distortion scheme for multiuser ultra-wideband

The study proposes a constrained least square (CLS) pre-distortion scheme for multiple-input single-output (MISO) multiple access ultra-wideband (UWB) systems. In such a scheme, a simple objective function is defined, which can be efficiently solved by a gradient-based algorithm. For the performance evaluation, scenarios CM1 and CM3 of the IEEE 802.15.3a channel model are considered. Results show that the CLS algorithm has a fast convergence and a good trade-off between intersymbol interference (ISI) and multiple access interference (MAI) reduction and signal-to-noise ratio (SNR) preservation, performing better than time-reversal (TR) pre-distortion.

New Isomers in the Full Seniority Scheme of Neutron-Rich Lead Isotopes: The Role of Effective Three-Body Forces

The neutron-rich lead isotopes, up to Pb-216, have been studied for the first time, exploiting the fragmentation of a primary uranium beam at the FRS-RISING setup at GSI. The observed isomeric states exhibit electromagnetic transition strengths which deviate from state-of-the-art shell-model calculations. It is shown that their complete description demands the introduction of effective three-body interactions and two-body transition operators in the conventional neutron valence space beyond Pb-208.

A General Latent Class Model for Performance Evaluation of Diagnostic Tests in the Absence of a Gold Standard: An Application to Chagas Disease

We propose a new general Bayesian latent class model for evaluation of the performance of multiple diagnostic tests in situations in which no gold standard test exists based on a computationally intensive approach. The modeling represents an interesting and suitable alternative to models with complex structures that involve the general case of several conditionally independent diagnostic tests, covariates, and strata with different disease prevalences. The technique of stratifying the population according to different disease prevalence rates does not add further marked complexity to the modeling, but it makes the model more flexible and interpretable. To illustrate the general model proposed, we evaluate the performance of six diagnostic screening tests for Chagas disease considering some epidemiological variables. Serology at the time of donation (negative, positive, inconclusive) was considered as a factor of stratification in the model. The general model with stratification of the population performed better in comparison with its concurrents without stratification. The group formed by the testing laboratory Biomanguinhos FIOCRUZ-kit (c-ELISA and rec-ELISA) is the best option in the confirmation process by presenting false-negative rate of 0.0002% from the serial scheme. We are 100% sure that the donor is healthy when these two tests have negative results and he is chagasic when they have positive results.

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.

Probabilistic crack growth analyses using a boundary element model: Applications in linear elastic fracture and fatigue problems

This paper addresses the numerical solution of random crack propagation problems using the coupling boundary element method (BEM) and reliability algorithms. Crack propagation phenomenon is efficiently modelled using BEM, due to its mesh reduction features. The BEM model is based on the dual BEM formulation, in which singular and hyper-singular integral equations are adopted to construct the system of algebraic equations. Two reliability algorithms are coupled with BEM model. The first is the well known response surface method, in which local, adaptive polynomial approximations of the mechanical response are constructed in search of the design point. Different experiment designs and adaptive schemes are considered. The alternative approach direct coupling, in which the limit state function remains implicit and its gradients are calculated directly from the numerical mechanical response, is also considered. The performance of both coupling methods is compared in application to some crack propagation problems. The investigation shows that direct coupling scheme converged for all problems studied, irrespective of the problem nonlinearity. The computational cost of direct coupling has shown to be a fraction of the cost of response surface solutions, regardless of experiment design or adaptive scheme considered. (C) 2012 Elsevier Ltd. All rights reserved.