Current Challenges in Modeling Cellular Metabolism

Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.

A modular traffic sampling architecture for flexible network measurements

Dissertação de Mestrado (Programa Doutoral em Informática)

Fundamental concepts in multibody dynamics

In this chapter, the fundamental ingredients related to formulation of the equations of motion for multibody systems are described. In particular, aspects such as degrees of freedom, types of coordinates, basic kinematics joints and types of analysis in multibody systems are briefly characterized. Illustrative examples of application are also presented to better clarify the fundamental issues for spatial rigid multibody systems, which are of crucial importance in the formulation development of mathematical models of mechanical systems, as well as its computational implementation.

Vector of coordinates, velocities and accelerations

This chapter describes the how the vector of coordinates are defined in the formulation of spatial multibody systems. For this purpose, the translational motion is described in terms of Cartesian coordinates, while rotational motion is specified using the technique of Euler parameters. This approach avoids the computational difficulties associated with the singularities in the case of using Euler angles or Bryant angles. Moreover, the formulation of the velocities vector and accelerations vector is presented and analyzed here. These two sets of vectors are defined in terms of translational and rotational coordinates.

The role of marine anaerobic bacteria and archaea in bioenergy production

The development of products from marine bioresources is gaining importance in the biotechnology sector. The global market for Marine Biotechnology products and processes was, in 2010, estimated at 2.8 billion with a cumulative annual growth rate of 510% (Børresen et al., Marine biotechnology: a new vision and strategy for Europe. Marine Board Position Paper 15. Beernem: Marine Board-ESF, 2010). Marine Biotechnology has the potential to make significant contributions towards the sustainable supply of food and energy, the solution of climate change and environmental degradation issues, and the human health. Besides the creation of jobs and wealth, it will contribute to the development of a greener economy. Thus, huge expectations anticipate the global development of marine biotechnology. The marine environment represents more than 70% of the Earths surface and includes the largest ranges of temperature, light and pressure encountered by life. These diverse marine environments still remain largely unexplored, in comparison with terrestrial habitats. Notwithstanding, efforts are being done by the scientific community to widespread the knowledge on oceans microbial life. For example, the J. Craig Venter Institute, in collaboration with the University of California, San Diego (UCSD), and Scripps Institution of Oceanography have built a state-of-the-art computational resource along with software tools to catalogue and interpret microbial life in the worlds oceans. The potential application of the marine biotechnology in the bioenergy sector is wide and, certainly, will evolve far beyond the current interest in marine algae. This chapter revises the current knowledge on marine anaerobic bacteria and archaea with a role in bio-hydrogen production, syngas fermentation and bio-electrochemical processes, three examples of bioenergy production routes.

Glazing daylighting performance and Trombe wall thermal performance of a modular façade system in four different Portuguese cities

This paper reports on a new façade system that uses passive solutions in the search for energy efficiency. The differentials are the versatility and flexibility of the modules, which are important advantages of the system. The thermal performance of Trombe walls and glazings and the daylighting performance of glazing were the key aspects analyzed in the results. Computational simulations were accomplished for the thermal performance of different arrangements of the modules with DesignBuilder software. The glazing daylighting performance was studied by means of Ecotect and Desktop Radiance programs and compared with the transmittance curves of glazings. Occupancy profile and internal gains were fixed according to the Portuguese reality for both studies. The main characteristics considered in this research were the use of two double glazings, four different climates in Portugal and one and two Trombe walls in the façade. The results show an important reduction in the energy consumption with the use of Trombe walls and double self-cleaning glazing in the façade, which also presented better daylighting performance.

On the frictional contacts in multibody system dynamics

"Series title: Computational methods in applied sciences, ISSN1871-3033, vol. 42"

FISHji: new ImageJ macros for the quantification of fluorescence in epifluorescence images

Fluorescence in situ hybridization (FISH) is based on the use of fluorescent staining dyes, however, the signal intensity of the images obtained by microscopy is seldom quantified with accuracy by the researcher. The development of innovative digital image processing programs and tools has been trying to overcome this problem, however, the determination of fluorescent intensity in microscopy images still has issues due to the lack of precision in the results and the complexity of existing software. This work presents FISHji, a set of new ImageJ methods for automated quantification of fluorescence in images obtained by epifluorescence microscopy. To validate the methods, results obtained by FISHji were compared with results obtained by flow cytometry. The mean correlation between FISHji and flow cytometry was high and significant, showing that the imaging methods are able to accurately assess the signal intensity of fluorescence images. FISHji are available for non-commercial use at http://paginas.fe.up.pt/nazevedo/.

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.

O desenvolvimento do pensamento abstrato através de game-based learning e do Scratch

Relatório de estágio de mestrado em Ensino de Informática

Desenvolvimento do pensamento computacional com recurso ao Scratch: uma experiência com alunos do 8ºano

Relatório de estágio de mestrado em Ensino de Informática

A aprendizagem do léxico na compreensão leitora

Relatório de estágio de mestrado em Ensino do Português no 3.º Ciclo do Ensino Básico e no Ensino Secundário e do Espanhol nos Ensinos Básico e Secundário

Descodificação do De re aedificatoria de Alberti: gramáticas de forma para a análise e geração de edifícios sagrados

Teses de Doutoramento em Arquitectura.

Single molecule simulation of diffusion and enzyme kinetics

This work presents a molecular-scale agent-based model for the simulation of enzymatic reactions at experimentally measured concentrations. The model incorporates stochasticity and spatial dependence, using diffusing and reacting particles with physical dimensions. We developed strategies to adjust and validate the enzymatic rates and diffusion coefficients to the information required by the computational agents, i.e., collision efficiency, interaction logic between agents, the time scale associated with interactions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecular location (a source of biological noise) in the speed at which the reactions take place. Simulations were conducted for experimental data on the 2-hydroxymuconate tautomerase (EC 5.3.2.6, UniProt ID Q01468) and the Steroid Delta-isomerase (EC 5.3.3.1, UniProt ID P07445). Obtained results demonstrate that our approach is in accordance to existing experimental data and long-term biophysical and biochemical assumptions.

Insights on the mechanical behavior of keratin fibrils

Supplementary data associated with this article can be found,in the online version, at http://dx.doi.org/10.1016/j.ijbiomac.2016.05.018.