Binding of antioxidant flavone isovitexin to human serum albumin investigated by experimental and computational assays

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

An improved interolog mapping-based computational prediction of protein protein interactions with increased network coverage

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Cogeneration design problem Computational complexity analysis and solution through an expert system

Purpose - The purpose of this paper is twofold: to analyze the computational complexity of the cogeneration design problem; to present an expert system to solve the proposed problem, comparing such an approach with the traditional searching methods available.Design/methodology/approach - The complexity of the cogeneration problem is analyzed through the transformation of the well-known knapsack problem. Both problems are formulated as decision problems and it is proven that the cogeneration problem is np-complete. Thus, several searching approaches, such as population heuristics and dynamic programming, could be used to solve the problem. Alternatively, a knowledge-based approach is proposed by presenting an expert system and its knowledge representation scheme.Findings - The expert system is executed considering two case-studies. First, a cogeneration plant should meet power, steam, chilled water and hot water demands. The expert system presented two different solutions based on high complexity thermodynamic cycles. In the second case-study the plant should meet just power and steam demands. The system presents three different solutions, and one of them was never considered before by our consultant expert.Originality/value - The expert system approach is not a "blind" method, i.e. it generates solutions based on actual engineering knowledge instead of the searching strategies from traditional methods. It means that the system is able to explain its choices, making available the design rationale for each solution. This is the main advantage of the expert system approach over the traditional search methods. On the other hand, the expert system quite likely does not provide an actual optimal solution. All it can provide is one or more acceptable solutions.

Computational speed-up with a single qudit

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

A graphical tool for the tomographic characterisation of microstructural features on metal matrix composites

Research on the micro-structural characterization of metal-matrix composites uses X-ray computed tomography to collect information about the interior features of the samples, in order to elucidate their exhibited properties. The tomographic raw data needs several steps of computational processing in order to eliminate noise and interference. Our experience with a program (Tritom) that handles these questions has shown that in some cases the processing steps take a very long time and that it is not easy for a Materials Science specialist to interact with Tritom in order to define the most adequate parameter values and the proper sequence of the available processing steps. For easing the use of Tritom, a system was built which addresses the aspects described before and that is based on the OpenDX visualization system. OpenDX visualization facilities constitute a great benefit to Tritom. The visual programming environment of OpenDX allows an easy definition of a sequence of processing steps thus fulfilling the requirement of an easy use by non-specialists on Computer Science. Also the possibility of incorporating external modules in a visual OpenDX program allows the researchers to tackle the aspect of reducing the long execution time of some processing steps. The longer processing steps of Tritom have been parallelized in two different types of hardware architectures (message-passing and shared-memory); the corresponding parallel programs can be easily incorporated in a sequence of processing steps defined in an OpenDX program. The benefits of our system are illustrated through an example where the tool is applied in the study of the sensitivity to crushing – and the implications thereof – of the reinforcements used in a functionally graded syntactic metallic foam.

NUMERICAL AND ANALYTICAL VERIFICATION OF A MULTISCALE COMPUTATIONAL MODEL FOR IMPACT PROBLEMS IN HETEROGENEOUS VISCOELASTIC MATERIALS WITH EVOLVING DAMAGE

Composites are engineered materials that take advantage of the particular properties of each of its two or more constituents. They are designed to be stronger, lighter and to last longer which can lead to the creation of safer protection gear, more fuel efficient transportation methods and more affordable materials, among other examples. This thesis proposes a numerical and analytical verification of an in-house developed multiscale model for predicting the mechanical behavior of composite materials with various configurations subjected to impact loading. This verification is done by comparing the results obtained with analytical and numerical solutions with the results found when using the model. The model takes into account the heterogeneity of the materials that can only be noticed at smaller length scales, based on the fundamental structural properties of each of the composite’s constituents. This model can potentially reduce or eliminate the need of costly and time consuming experiments that are necessary for material characterization since it relies strictly upon the fundamental structural properties of each of the composite’s constituents. The results from simulations using the multiscale model were compared against results from direct simulations using over-killed meshes, which considered all heterogeneities explicitly in the global scale, indicating that the model is an accurate and fast tool to model composites under impact loads. Advisor: David H. Allen

A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data

In [1], the authors proposed a framework for automated clustering and visualization of biological data sets named AUTO-HDS. This letter is intended to complement that framework by showing that it is possible to get rid of a user-defined parameter in a way that the clustering stage can be implemented more accurately while having reduced computational complexity

Gas-phase reactivity of protonated 2-oxazoline derivatives: mass spectrometry and computational studies

RATIONALE: Oxazolines have attracted the attention of researchers worldwide due to their versatility as carboxylic acid protecting groups, chiral auxiliaries, and ligands for asymmetric catalysis. Electrospray ionization tandem mass spectrometric (ESI-MS/MS) analysis of five 2-oxazoline derivatives has been conducted, in order to understand the influence of the side chain on the gas-phase dissociation of these protonated compounds under collision-induced dissociation (CID) conditions. METHODS: Mass spectrometric analyses were conducted in a quadrupole time-of-flight (Q-TOF) spectrometer fitted with electrospray ionization source. Protonation sites have been proposed on the basis of the gas-phase basicity, proton affinity, atomic charges, and a molecular electrostatic potential map obtained on the basis of the quantum chemistry calculations at the B3LYP/6-31 + G(d, p) and G2(MP2) levels. RESULTS: Analysis of the atomic charges, gas-phase basicity and proton affinities values indicates that the nitrogen atom is a possible proton acceptor site. On the basis of these results, two main fragmentation processes have been suggested: one taking place via neutral elimination of the oxazoline moiety (99 u) and another occurring by sequential elimination of neutral fragments with 72 u and 27 u. These processes should lead to formation of R+. CONCLUSIONS: The ESI-MS/MS experiments have shown that the side chain could affect the dissociation mechanism of protonated 2-oxazoline derivatives. For the compound that exhibits a hydroxyl at the lateral chain, water loss has been suggested to happen through an E2-type elimination, in an exothermic step. Copyright (C) 2012 John Wiley & Sons, Ltd.

Error Upper Bounds for a Computational Method for Nonlinear Boundary and Initial-Value Problems

This work develops a computational approach for boundary and initial-value problems by using operational matrices, in order to run an evolutive process in a Hilbert space. Besides, upper bounds for errors in the solutions and in their derivatives can be estimated providing accuracy measures.

Computational tools for comparing asymmetric GARCH models via Bayes factors

In this paper we use Markov chain Monte Carlo (MCMC) methods in order to estimate and compare GARCH models from a Bayesian perspective. We allow for possibly heavy tailed and asymmetric distributions in the error term. We use a general method proposed in the literature to introduce skewness into a continuous unimodal and symmetric distribution. For each model we compute an approximation to the marginal likelihood, based on the MCMC output. From these approximations we compute Bayes factors and posterior model probabilities. (C) 2012 IMACS. Published by Elsevier B.V. All rights reserved.

A multiple time scale survival model with a cure fraction

Many recent survival studies propose modeling data with a cure fraction, i.e., data in which part of the population is not susceptible to the event of interest. This event may occur more than once for the same individual (recurrent event). We then have a scenario of recurrent event data in the presence of a cure fraction, which may appear in various areas such as oncology, finance, industries, among others. This paper proposes a multiple time scale survival model to analyze recurrent events using a cure fraction. The objective is analyzing the efficiency of certain interventions so that the studied event will not happen again in terms of covariates and censoring. All estimates were obtained using a sampling-based approach, which allows information to be input beforehand with lower computational effort. Simulations were done based on a clinical scenario in order to observe some frequentist properties of the estimation procedure in the presence of small and moderate sample sizes. An application of a well-known set of real mammary tumor data is provided.

Analysis of energy dissipation in stirred suspension polymerisation reactors using computational fluid dynamics

This work evaluates the spatial distribution of normalised rates of droplet breakage and droplet coalescence in liquidliquid dispersions maintained in agitated tanks at operation conditions normally used to perform suspension polymerisation reactions. Particularly, simulations are performed with multiphase computational fluid dynamics (CFD) models to represent the flow field in liquidliquid styrene suspension polymerisation reactors for the first time. CFD tools are used first to compute the spatial distribution of the turbulent energy dissipation rates (e) inside the reaction vessel; afterwards, normalised rates of droplet breakage and particle coalescence are computed as functions of e. Surprisingly, multiphase simulations showed that the rates of energy dissipation can be very high near the free vortex surfaces, which has been completely neglected in previous works. The obtained results indicate the existence of extremely large energy dissipation gradients inside the vessel, so that particle breakage occurs primarily in very small regions that surround the impeller and the free vortex surface, while particle coalescence takes place in the liquid bulk. As a consequence, particle breakage should be regarded as an independent source term or a boundary phenomenon. Based on the obtained results, it can be very difficult to justify the use of isotropic assumptions to formulate particle population balances in similar systems, even when multiple compartment models are used to describe the fluid dynamic behaviour of the agitated vessel. (C) 2011 Canadian Society for Chemical Engineering

Spectral fluctuation and 1/f(alpha) noise in the energy level statistics of interacting trapped bosons

It has been recently shown numerically that the transition from integrability to chaos in quantum systems and the corresponding spectral fluctuations are characterized by 1/f(alpha) noise with 1 <= alpha <= 2. The system of interacting trapped bosons is inhomogeneous and complex. The presence of an external harmonic trap makes it more interesting as, in the atomic trap, the bosons occupy partly degenerate single-particle states. Earlier theoretical and experimental results show that at zero temperature the low-lying levels are of a collective nature and high-lying excitations are of a single-particle nature. We observe that for few bosons, the P(s) distribution shows the Shnirelman peak, which exhibits a large number of quasidegenerate states. For a large number of bosons the low-lying levels are strongly affected by the interatomic interaction, and the corresponding level fluctuation shows a transition to a Wigner distribution with an increase in particle number. It does not follow Gaussian orthogonal ensemble random matrix predictions. For high-lying levels we observe the uncorrelated Poisson distribution. Thus it may be a very realistic system to prove that 1/f(alpha) noise is ubiquitous in nature.

Describing some of the Dimensions that comprise the Profile of the Faculty Staff of Statistics Departments in Brazil

Statistics is a required course in virtually all undergraduate programs in Brazilian universities. In addition, undergraduate programs in Statistics are offered in many public universities. However, despite the importance of this science, there are no systematic studies in the national literature regarding the characterization of the faculty staff, which is responsible for the teaching of statistics in the country. In this context, this paper presents a description of the faculty members of undergraduate courses in Statistics. This description was based on a descriptive sample, related to aspects of their education and scientific production. A prediction of future demand for PhDs in Statistics to fill the vacancies is also provided based on the retirement of faculty members in undergraduate courses in Statistics in the country.

Computational and experimental characterization of a low-cost piezoelectric valveless diaphragm pump

Flow pumps act as important devices in areas such as Bioengineering, Medicine, and Pharmacy, among other areas of Engineering, mainly for delivering liquids or gases at small-scale and precision flow rate quantities. Principles for pumping fluids based on piezoelectric actuators have been widely studied, since they allow the construction of pump systems for displacement of small fluid volumes with low power consumption. This work studies valveless piezoelectric diaphragm pumps for flow generation, which uses a piezoelectric ceramic (PZT) as actuator to move a membrane (diaphragm) up and down as a piston. The direction of the flow is guaranteed by valveless configuration based on a nozzle-diffuser system that privileges the flow in just one pumping direction. Most research efforts on development of valveless flow pump deal either with computational simulations based on simplified models or with simplified physical approaches based on analytical models. The main objective of this work is the study of a methodology to develop a low-cost valveless piezoelectric diaphragm flow pump using computational simulations, parametric study, prototype manufacturing, and experimental characterization. The parametric study has shown that the eccentricity of PZT layer and metal layer plays a key role in the performance of the pump.