Peptidoglycan assembly machines: The Staphylococcus aureus Penicillin-Binding Proteins

Dissertation presented to obtain the Ph.D degree in Biology

Assessing self-organization and emergence in Evolvable Assembly Systems (EAS)

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Studies of the assembly of the Streptococcus pneumoniae capsular polysaccharide

Dissertation presented to obtain the Ph.D degree in Biology.

A semi-automatic approach to code smells detection

Eradication of code smells is often pointed out as a way to improve readability, extensibility and design in existing software. However, code smell detection remains time consuming and error-prone, partly due to the inherent subjectivity of the detection processes presently available. In view of mitigating the subjectivity problem, this dissertation presents a tool that automates a technique for the detection and assessment of code smells in Java source code, developed as an Eclipse plugin. The technique is based upon a Binary Logistic Regression model that uses complexity metrics as independent variables and is calibrated by expert‟s knowledge. An overview of the technique is provided, the tool is described and validated by an example case study.

Assembly and function of a protein cross-linking enzyme during bacterial spore morphogenesis

Sporulation in Bacillus subtilis culminates with the formation of a dormant endospore. The endospore (or spore) is one of the most resilient cell types known and can remain viable in the environment for extended periods of time. Contributing to the spore’s resistance and its ability to interact with and monitor its immediate environment is the coat, the outermost layer of B. subtilis spores. The coat is composed by over 70 different proteins, which are produced at different stages in sporulation and orderly assembled around the developing spore.(...)

EFFECT – Efficient finite element code

The theme of this dissertation is the finite element method applied to mechanical structures. A new finite element program is developed that, besides executing different types of structural analysis, also allows the calculation of the derivatives of structural performances using the continuum method of design sensitivities analysis, with the purpose of allowing, in combination with the mathematical programming algorithms found in the commercial software MATLAB, to solve structural optimization problems. The program is called EFFECT – Efficient Finite Element Code. The object-oriented programming paradigm and specifically the C ++ programming language are used for program development. The main objective of this dissertation is to design EFFECT so that it can constitute, in this stage of development, the foundation for a program with analysis capacities similar to other open source finite element programs. In this first stage, 6 elements are implemented for linear analysis: 2-dimensional truss (Truss2D), 3-dimensional truss (Truss3D), 2-dimensional beam (Beam2D), 3-dimensional beam (Beam3D), triangular shell element (Shell3Node) and quadrilateral shell element (Shell4Node). The shell elements combine two distinct elements, one for simulating the membrane behavior and the other to simulate the plate bending behavior. The non-linear analysis capability is also developed, combining the corotational formulation with the Newton-Raphson iterative method, but at this stage is only avaiable to solve problems modeled with Beam2D elements subject to large displacements and rotations, called nonlinear geometric problems. The design sensitivity analysis capability is implemented in two elements, Truss2D and Beam2D, where are included the procedures and the analytic expressions for calculating derivatives of displacements, stress and volume performances with respect to 5 different design variables types. Finally, a set of test examples were created to validate the accuracy and consistency of the result obtained from EFFECT, by comparing them with results published in the literature or obtained with the ANSYS commercial finite element code.

Code name

The present case-study concerns about the analysis of the sale of Banif Mais, the sub-holding of Banif Group for specialized credit activity, taking into account the bank’s financial situation in 2014. In 2011, Portugal was submitted to an external finance programme carried out by troika which imposed very restricted measures to the financial sector. Subsequently, Banif was not able to accomplish the required results having to appeal to Government financing, being under a recapitalization plan since 2012.

HEP-Frame: A software engineered framework to aid the development and efficient multicore execution of scientific code

This work was supported by FCT (Fundação para a Ciência e Tecnologia) within Project Scope (UID/CEC/00319/2013), by LIP (Laboratório de Instrumentação e Física Experimental de Partículas) and by Project Search-ON2 (NORTE-07-0162- FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the European Regional Development Fund.

Single line for assembly just-in-sequence multiple models

Programa Doutoral em Líderes para as Indústrias Tecnológicas

Design of bio-based supramolecular structures through self-assembly of α-lactalbumin and lysozyme

Bovine α-lactalbumin (α-La) and lysozyme (Lys), two globular proteins with highly homologous tertiary structures and opposite isoelectric points, were used to produce bio-based supramolecular structures under various pH values (3, 7 and 11), temperatures (25, 50 and 75 °C) and times (15, 25 and 35 min) of heating. Isothermal titration calorimetry experiments showed protein interactions and demonstrated that structures were obtained from the mixture of α-La/Lys in molar ratio of 0.546. Structures were characterized in terms of morphology by transmission electron microscopy (TEM) and dynamic light scattering (DLS), conformational structure by circular dichroism and intrinsic fluorescence spectroscopy and stability by DLS. Results have shown that protein conformational structure and intermolecular interactions are controlled by the physicochemical conditions applied. The increase of heating temperature led to a significant decrease in size and polydispersity (PDI) of α-La–Lys supramolecular structures, while the increase of heating time, particularly at temperatures above 50 °C, promoted a significant increase in size and PDI. At pH 7 supramolecular structures were obtained at microscale – confirmed by optical microscopy – displaying also a high PDI (i.e. > 0.4). The minimum size and PDI (61 ± 2.3 nm and 0.14 ± 0.03, respectively) were produced at pH 11 for a heating treatment of 75 °C for 15 min, thus suggesting that these conditions could be considered as critical for supramolecular structure formation. Its size and morphology were confirmed by TEM showing a well-defined spherical form. Structures at these conditions showed to be stable at least for 30 or 90 days, when stored at 25 or 4 °C, respectively. Hence, α-La–Lys supramolecular structures showed properties that indicate that they are a promising delivery system for food and pharmaceutical applications.

The entomological code. A code of nomenclature for use in entomology.

1912:May

Kinetics of methanol electrooxidation on PtRu catalysts in a membrane electrode assembly

Methanol oxidation, Kinetics, Mechanism, Rate expression, MEA, PtRu catalysts, Cyclone Flow Cell

Mechanisms of assembly and activity dependent remodelling of the presynaptic cytomatrix at the active zone

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010

Analysis and removal of code clones in software product lines

Magdeburg, Univ., Fak. für Informatik, Diss., 2013