Open-source software in operations research in engineering teaching

ENEGI 2013: Atas do 2º Encontro Nacional de Engenharia e Gestão Industrial, Universidade de Aveiro, 17 e 18 de maio de 2013, Aveiro, Portugal.

Utilization of remote experimentation in mobile devices for education

In this paper the authors intend to demonstrate the utilization of remote experimentation (RE) using mobile computational devices in the Science areas of the elementary school, with the purpose to develop practices that will help in the assimilation process of the subjects taught in classroom seeking to interlink them with the daily students? activities. Allying mobility with RE we intend to minimize the space-temporal barrier giving more availability and speed in the information access. The implemented architecture utilizes technologies and freely distributed softwares with open code resources besides remote experiments developed in the Laboratory of Remote Experimentation (RExLab) of Federal University of Santa Catarina (UFSC), in Brazil, through the physical computation platform of the ?open hardware of construction of our own. The utilization of open code computational tools and the integration of hardware to the 3D virtual worlds, accessible through mobile devices, give to the project an innovative face with a high potential for reproducibility and reusability.

Sistema de Torre de Refrigeração

Mestrado em Engenharia Química - Ramo Optimização Energética na Indústria Química

Constraint-based modelling of mixed microbial populations: Application to polyhydroxyalkanoates production

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Dispersion of fillers in viscoelastic polymer matrices using Eulerian-Lagrangian approaches

Understanding the behavior of c omplex composite materials using mixing procedures is fundamental in several industrial processes. For instance, polymer composites are usually manufactured using dispersion of fillers in polymer melt matrices. The success of the filler dispersion depends both on the complex flow patterns generated and on the polymer melt rheological behavior. Consequently, the availability of a numerical tool that allow to model both fluid and particle would be very useful to increase the process insight. Nowadays there ar e computational tools that allow modeling the behavior of filled systems, taking into account both the behavior of the fluid (Computational Rheology) and the particles (Discrete Element Method). One example is the DPMFoam solver of the OpenFOAM ® framework where the averaged volume fraction momentum and mass conservation equations are used to describe the fluid (continuous phase) rheology, and the Newton’s second law of motion is used to compute the particles (discrete phase) movement. In this work the refer red solver is extended to take into account the elasticity of the polymer melts for the continuous phase. The solver capabilities will be illustrated by studying the effect of the fluid rheology on the filler dispersion, taking into account different fluid types (generalized Newtonian or viscoelastic) and particles volume fraction and size. The results obtained are used to evaluate the relevance of considering the fluid complex rheology for the prediction of the composites morphology

An integrated model for simulation of construction phasing of arch concrete dams

Dissertação de mestrado integrado em Civil Engineering

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

A novel ABCG-like transporter of Trypanosoma cruziis involved in natural resistance to benznidazole

Benznidazole (BZ) is one of the two drugs used for Chagas disease treatment. Nevertheless therapeutic failures of BZ have been reported, which were mostly attributed to variable drug susceptibility among Trypanosoma cruzistrains. ATP-binding cassette (ABC) transporters are involved in a variety of translocation processes and some members have been implicated in drug resistance. Here we report the characterisation of the first T. cruzi ABCG transporter gene, named TcABCG1, which is over-expressed in parasite strains naturally resistant to BZ. Comparison ofTcABCG1 gene sequence of two TcI BZ-resistant strains with CL Brener BZ-susceptible strain showed several single nucleotide polymorphisms, which determined 11 amino acid changes. CL Brener transfected with TcI transporter genes showed 40-47% increased resistance to BZ, whereas no statistical significant increment in drug resistance was observed when CL Brener was transfected with the homologous gene. Only in the parasites transfected with TcI genes there was 2-2.6-fold increased abundance of TcABCG1transporter protein. The analysis in wild type strains also suggests that the level of TcABCG1transporter is related to BZ natural resistance. The characteristics of untranslated regions of TcABCG1genes of BZ-susceptible and resistant strains were investigated by computational tools.

An adaptive multiscale method for density-driven instabilities

Accurate modeling of flow instabilities requires computational tools able to deal with several interacting scales, from the scale at which fingers are triggered up to the scale at which their effects need to be described. The Multiscale Finite Volume (MsFV) method offers a framework to couple fine-and coarse-scale features by solving a set of localized problems which are used both to define a coarse-scale problem and to reconstruct the fine-scale details of the flow. The MsFV method can be seen as an upscaling-downscaling technique, which is computationally more efficient than standard discretization schemes and more accurate than traditional upscaling techniques. We show that, although the method has proven accurate in modeling density-driven flow under stable conditions, the accuracy of the MsFV method deteriorates in case of unstable flow and an iterative scheme is required to control the localization error. To avoid large computational overhead due to the iterative scheme, we suggest several adaptive strategies both for flow and transport. In particular, the concentration gradient is used to identify a front region where instabilities are triggered and an accurate (iteratively improved) solution is required. Outside the front region the problem is upscaled and both flow and transport are solved only at the coarse scale. This adaptive strategy leads to very accurate solutions at roughly the same computational cost as the non-iterative MsFV method. In many circumstances, however, an accurate description of flow instabilities requires a refinement of the computational grid rather than a coarsening. For these problems, we propose a modified iterative MsFV, which can be used as downscaling method (DMsFV). Compared to other grid refinement techniques the DMsFV clearly separates the computational domain into refined and non-refined regions, which can be treated separately and matched later. This gives great flexibility to employ different physical descriptions in different regions, where different equations could be solved, offering an excellent framework to construct hybrid methods.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

O ensino de reações orgânicas usando química computacional: I. reações de adição eletrofílica a alquenos

Basic concepts that play an important role in some organic reactions are revisited in this paper, which reports a pedagogical experience involving undergraduate and graduate students. A systematic procedure has been applied in order to use widespread available computational tools. This paper aims to discuss the use of computers in teaching electrophilic addition reactions to alkenes. Two classical examples have been investigated: addition to non-conjugated alkenes and addition to conjugated dienes. The results were compared with those normally discussed in organic textbooks. Several important concepts, such as conformational analysis and energy control (kinetic and thermodynamic) involved in reaction mechanisms can be taught more efficiently if one connects theoretical and practical tools.

Un método para enseñar el porqué suceden las reacciones químicas

A methodology is proposed for explaining one of the central questions in the teaching of general chemistry courses to freshman students: why do chemical transformations occur? The answer to this question is based on thermodynamics but we propose arriving at an answer in a more intuitive way by using computational tools in a bid to increase the motivation of students for learning chemistry.

Object-oriented Programming Applied to the Development of Structural Analysis and Optimization Software

This paper presents the development of a two-dimensional interactive software environment for structural analysis and optimization based on object-oriented programming using the C++ language. The main feature of the software is the effective integration of several computational tools into graphical user interfaces implemented in the Windows-98 and Windows-NT operating systems. The interfaces simplify data specification in the simulation and optimization of two-dimensional linear elastic problems. NURBS have been used in the software modules to represent geometric and graphical data. Extensions to the analysis of three-dimensional problems have been implemented and are also discussed in this paper.