In silico constraint-based strain optimization methods: the quest for optimal cell factories

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.

Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

A performance-based method for seismic evaluation of masonry walls strengthened with RC layers

A conventional method for seismic strengthening of masonry walls is externally application of reinforced concrete layer (shotcrete). However, due to the lack of analytical and experimental information on the behavior of strengthened walls, the design procedures are usually followed based on the empirical relations. Using these design procedures have resulted in massive strengthening details in retrofitting projects. This paper presents a computational framework for nonlinear analysis of strengthened masonry walls and its versatility has been verified by comparing the numerical and experimental results. Based on the developed numerical model and available experimental information, design relations and failure modes are proposed for strengthened walls in accordance with the ASCE 41 standard. Finally, a sample masonry structure has been strengthened using the proposed and available conventional methods. It has been shown that using the proposed method results in lower strengthening details and appropriate (ductile) failure modes

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Affordable prefabricated modular houses using cement and polymer based materials and advanced design tools

By taking advantage of the appropriate use of cement and polymer based materials and advanced computational tools, a pre-fabricated affordable house was built in a modular system. Modular system refers to the complete structure that is built-up by assembling pre-fabricated sandwich panels composed of steel fibre reinforced self-compacting concrete (SFRSCC) outer layers that are connected by innovative glass fibre reinforced polymer (GFRP) connectors, resulting in a panel with adequate structural, acoustic, and thermal insulation properties. The modular house was prepared for a typical family of six members, but its living area can be easily increased by assembling other pre-fabricated elements. The speed of construction and the cost of the constructive elements make these houses competitive when compared to traditional solutions. In this paper the relevant research subjacent to this project (LEGOUSE) is briefly described, as well as the construction process of the built real scale prototype.

Design of a case-based reasoner for information security in military organizations

Information security is concerned with the protection of information, which can be stored, processed or transmitted within critical information systems of the organizations, against loss of confidentiality, integrity or availability. Protection measures to prevent these problems result through the implementation of controls at several dimensions: technical, administrative or physical. A vital objective for military organizations is to ensure superiority in contexts of information warfare and competitive intelligence. Therefore, the problem of information security in military organizations has been a topic of intensive work at both national and transnational levels, and extensive conceptual and standardization work is being produced. A current effort is therefore to develop automated decision support systems to assist military decision makers, at different levels in the command chain, to provide suitable control measures that can effectively deal with potential attacks and, at the same time, prevent, detect and contain vulnerabilities targeted at their information systems. The concept and processes of the Case-Based Reasoning (CBR) methodology outstandingly resembles classical military processes and doctrine, in particular the analysis of “lessons learned” and definition of “modes of action”. Therefore, the present paper addresses the modeling and design of a CBR system with two key objectives: to support an effective response in context of information security for military organizations; to allow for scenario planning and analysis for training and auditing processes.

Design of assemblies based on polymer-coated quantum dots and organic dye

During last years, photophysical properties of complexes of semiconductor quantum dots (QDs) with organic dyes have attracted increasing interest. The development of different assemblies based on QDs and organic dyes allows to increase the range of QDs applications, which include imaging, biological sensing and electronic devices.1 Some studies demonstrate energy transfer between QDs and organic dye in assemblies.2 However, for electronic devices purposes, a polymeric matrix is required to enhance QDs photostability. Thus, in order to attach the QDs to the polymer surface it is necessary to chemically modify the polymer to induce electronic charges and stabilize the QDs in the polymer. The present work aims to investigate the design of assemblies based on polymer-coated QDs and an integrated acceptor organic dye. Polymethylmethacrylate (PMMA) and polycarbonate (PC) were used as polymeric matrices, and nile red as acceptor. Additionally, a PMMA matrix modified with 2-mercaptoethylamine is used to improve the attachment between both the donor (QDs) and the acceptor (nile red), as well as to induce a covalent bond between the modified PMMA and the QDs. An enhancement of the energy transfer efficiency by using the modified PMMA is expected and the resulting assembly can be applied for energy harvesting.

Testing Nelder-Mead based repulsion algorithms for multiple roots of nonlinear systems via a two-level factorial design of experiments

This paper addresses the challenging task of computing multiple roots of a system of nonlinear equations. A repulsion algorithm that invokes the Nelder-Mead (N-M) local search method and uses a penalty-type merit function based on the error function, known as 'erf', is presented. In the N-M algorithm context, different strategies are proposed to enhance the quality of the solutions and improve the overall efficiency. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm.

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.

An evolutionary approach to the use of Petri net based models: from parallel controllers to HW/SW co-design

"A workshop within the 19th International Conference on Applications and Theory of Petri Nets - ICATPN’1998"

Acellular Gellan-gum based bilayered structures for the regeneration of osteochondral defects: a preclinical study

 In orthopaedics, the management and treatment of osteochondral (OC) defects remains an ongoing clinical challenge. Autologous osteochondral mosaicplasty has been used as a valid option for OC treatments although donor site morbidity remains a source of concern [1]. Engineering a whole structure capable of mimicking different tissues (cartilage and subchondral bone) in an integrated manner could be a possible approach to regenerate OC defects. In our group we have been proposing the use of bilayered structures to regenerate osteochondral defects [2,3]. The present study aims to investigate the pre-clinical performance of bilayered hydrogels and spongy-like hydrogels in in vivo  models (mice and rabbit, respectively), in both subcutaneous and orthotopic models. The bilayered structures were produced from Low Acyl Gellan Gum (LAGG) from Sigma-Aldrich, USA. Cartilage-like layers were obtained from a 2wt% LAGG solution. The bone-like layers were made of 2wt% LAGG with incorporation of hydroxyapatite at 20% and 30% (w/v). Hydrogels and spongy-like were subcutaneouly implanted in mice to evaluate the inflammatory response. Then, OC defects were induced in rabbit knee to create a critical size defect (4 mm diameter and 5 mm depth), and then hydrogels and sponges implanted. Both structures followed different processing methods. The hydrogels were injected allowing in situ  crosslinking. Unlike, the spongy-like were pre-formed by freeze-drying. The studies concerning subcutaneous implantation and critical size OC defect were performed for 2 and 4 weeks time, respectively. Cellular behavior and inflammatory responses were assessed by means of histology staining and biochemical function and matrix deposition by immunohistochemistry. Additionally, both OC structures stability and new cartilage and bone formation were evaluated by using vivo- computed tomography (Scanco 80). The results showed no acute inflammatory response for both approaches. New tissue formation and integration in the adjacent tissues were also observed, which present different characteristic behaviors when comparing hydrogels and sponges response. As future insights, a novel strategy for regeneration of OC defects can be designed encompassing both, hydrogels and spongy-like structures and cellular approaches. References: 1. Espregueira-Mendes J. et al. Osteochondral transplantation using autografts from the upper tibio-fibular joint for the treatment of knee cartilage lesions. Knee Surgery, Sports Traumatology, Arthroscopy 20,1136, 2012. 2. Oliveira JM. et al, Novel hydroxyapatite/chitosan bilayered scaffold for osteochondral tissue-engineering applications: Scaffold design and its performance when seeded with goat bone marrow stromal cells. Biomaterials 27, 6123, 2006. 3. Pereira D R. et al. Gellan Gum-Based Hydrogel Bilayered Scaffolds for Osteochondral Tissue Engineering. Key Engineering Materials 587, 255, 2013.

A GIS extension model to calculate urban heat island intensity based on urban geometry

This paper presents a simulation model, which was incorporated into a Geographic Information System (GIS), in order to calculate the maximum intensity of urban heat islands based on urban geometry data. The method-ology of this study stands on a theoretical-numerical basis (Okeâ s model), followed by the study and selection of existing GIS tools, the design of the calculation model, the incorporation of the resulting algorithm into the GIS platform and the application of the tool, developed as exemplification. The developed tool will help researchers to simulate UHI in different urban scenarios.

Assessment of the effectiveness of steel fibre reinforcement for the punching resistance of flat slabs by experimental research and design approach

The present paper deals with the experimental assessment of the effectiveness of steel fibre reinforcement in terms of punching resistance of centrically loaded flat slabs, and to the development of an analytical model capable of predicting the punching behaviour of this type of structures. For this purpose, eight slabs of 2550 x 2550 x 150 mm3 dimensions were tested up to failure, by investigating the influence of the content of steel fibres (0, 60, 75 and 90 kg/m3) and concrete strength class (50 and 70 MPa). Two reference slabs without fibre reinforcement, one for each concrete strength class, and one slab for each fibre content and each strength class compose the experimental program. All slabs were flexurally reinforced with a grid of ribbed steel bars in a percentage to assure punching failure mode for the reference slabs. Hooked ends steel fibres provided the unique shear reinforcement. The results have revealed that steel fibres are very effective in converting brittle punching failure into ductile flexural failure, by increasing both the ultimate load and deflection, as long as adequate fibre reinforcement is assured. An analytical model was developed based on the most recent concepts proposed by the fib Mode Code 2010 for predicting the punching resistance of flat slabs and for the characterization of the behaviour of fibre reinforced concrete. The most refined version of this model was capable of predicting the punching resistance of the tested slabs with excellent accuracy and coefficient of variation of about 5%.

Systematic design analysis and risk management on engineered nanoparticles occupational exposure

The production of nanotechnology-based products is increasing, along with the conscience of the possible harmful effects of some nanomaterials. The “safety-by-design” approaches are getting attention as helpful tools to develop safer products and production processes. The Systematic Design Analysis Approach could help to identify the solutions to control the workplace risks by defining the emission and exposure scenarios and the possible barriers to interrupt them. By applying this approach in a photocatalytic ceramic tiles development project it was possible to identify relevant nanoparticles emission scenarios and related barriers, and defining possible ways to reduce it.