Complex Dynamics of defective interfering baculoviruses during serial passage in insect cells

Defective interfering (DI) viruses are thought to cause oscillations in virus levels, known as the ‘Von Magnus effect’. Interference by DI viruses has been proposed to underlie these dynamics, although experimental tests of this idea have not been forthcoming. For the baculoviruses, insect viruses commonly used for the expression of heterologous proteins in insect cells, the molecular mechanisms underlying DI generation have been investigated. However, the dynamics of baculovirus populations harboring DIs have not been studied in detail. In order to address this issue, we used quantitative real-time PCR to determine the levels of helper and DI viruses during 50 serial passages of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in Sf21 cells. Unexpectedly, the helper and DI viruses changed levels largely in phase, and oscillations were highly irregular, suggesting the presence of chaos. We therefore developed a simple mathematical model of baculovirus-DI dynamics. This theoretical model reproduced patterns qualitatively similar to the experimental data. Although we cannot exclude that experimental variation (noise) plays an important role in generating the observed patterns, the presence of chaos in the model dynamics was confirmed with the computation of the maximal Lyapunov exponent, and a Ruelle-Takens-Newhouse route to chaos was identified at decreasing production of DI viruses, using mutation as a control parameter. Our results contribute to a better understanding of the dynamics of DI baculoviruses, and suggest that changes in virus levels over passages may exhibit chaos.

Integrating protein structural information

Dissertação apresentada para obtenção de Grau de Doutor em Bioquímica,Bioquímica Estrutural, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Development of procedures for the simulation of atmospheric flows over complex terrain, using OpenFOAM

The main purpose of this work was the development of procedures for the simulation of atmospheric ows over complex terrain, using OpenFOAM. For this aim, tools and procedures were developed apart from this code for the preprocessing and data extraction, which were thereafter applied in the simulation of a real case. For the generation of the computational domain, a systematic method able to translate the terrain elevation model to a native OpenFOAM format (blockMeshDict) was developed. The outcome was a structured mesh, in which the user has the ability to de ne the number of control volumes and its dimensions. With this procedure, the di culties of case set up and the high computation computational e ort reported in literature associated to the use of snappyHexMesh, the OpenFOAM resource explored until then for the accomplishment of this task, were considered to be overwhelmed. Developed procedures for the generation of boundary conditions allowed for the automatic creation of idealized inlet vertical pro les, de nition of wall functions boundary conditions and the calculation of internal eld rst guesses for the iterative solution process, having as input experimental data supplied by the user. The applicability of the generated boundary conditions was limited to the simulation of turbulent, steady-state, incompressible and neutrally strati ed atmospheric ows, always recurring to RaNS (Reynolds-averaged Navier-Stokes) models. For the modelling of terrain roughness, the developed procedure allowed to the user the de nition of idealized conditions, like an uniform aerodynamic roughness length or making its value variable as a function of topography characteristic values, or the using of real site data, and it was complemented by the development of techniques for the visual inspection of generated roughness maps. The absence and the non inclusion of a forest canopy model limited the applicability of this procedure to low aerodynamic roughness lengths. The developed tools and procedures were then applied in the simulation of a neutrally strati ed atmospheric ow over the Askervein hill. In the performed simulations was evaluated the solution sensibility to di erent convection schemes, mesh dimensions, ground roughness and formulations of the k - ε and k - ω models. When compared to experimental data, calculated values showed a good agreement of speed-up in hill top and lee side, with a relative error of less than 10% at a height of 10 m above ground level. Turbulent kinetic energy was considered to be well simulated in the hill windward and hill top, and grossly predicted in the lee side, where a zone of ow separation was also identi ed. Despite the need of more work to evaluate the importance of the downstream recirculation zone in the quality of gathered results, the agreement between the calculated and experimental values and the OpenFOAM sensibility to the tested parameters were considered to be generally in line with the simulations presented in the reviewed bibliographic sources.

Benchmarking de identificação de ano: criação de um site para benchmarking de técnicas de identificação de dano

Dissertação para obtenção do grau de Mestre em Engenharia Mecânica na Área de Manutenção e Produção

Thermodynamic and kinetic modelling of the redox properties of tetrahaem cytochromes C3

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica,especialidade Bioquímica-Física, pela Universidade Nova de Lisboa, Faculdade de Cincias e Tecnologia

What is the shape of an air bubble on a liquid surface?

We have calculated the equilibrium shape of the axially symmetric meniscus along which a spherical bubble contacts a flat liquid surface by analytically integrating the Young-Laplace equation in the presence of gravity, in the limit of large Bond numbers. This method has the advantage that it provides semianalytical expressions for key geometrical properties of the bubble in terms of the Bond number. Results are in good overall agreement with experimental data and are consistent with fully numerical (Surface Evolver) calculations. In particular, we are able to describe how the bubble shape changes from hemispherical, with a flat, shallow bottom, to lenticular, with a deeper, curved bottom, as the Bond number is decreased.

Sustainability Evaluation of Biodiesel Produced from Microalgae Chlamydomonas sp Grown in Brewery Wastewater

This study performs a sustainability evaluation of biodiesel from microalga Chlamydomonas sp. grown in 20 % (v/v) of brewery’s wastewater, blended with pentose sugars (xylose, arabinose or ribose resulting from the hydrolysis of brewer’s spent grains (BSG). The life cycle steps considered for the study are: microalgae cultivation, biomass processing and lipids extraction at the brewery site, and its conversion to biodiesel at a dedicated external biofuel’s plant. Three sustainability indicators (LCEE, FER and GW) were considered and calculated using experimental data. Literature data was used, whenever necessary, to complement life cycle data, thus allowing a more accurate sustainability evaluation. A comparative analysis of the biodiesel life cycle steps was also conducted, with the main goal of identifying which steps need to be improved. Results show that biomass processing, especially cell harvesting, microalgae cultivation, and lipids extraction are the main process bottlenecks. It is also analysed the influence on the microalgae biodiesel sustainability of adding each pentose sugar to the cultivation media, concluding that it strongly influences the biomass and lipid productivity. In particular, the addition of xylose is preferable in terms of lipid productivity, but from a sustainability point of view, ribose is the best, though the difference from xylose is not significant. Nevertheless, culture without pentose addition presents the best sustainability results.

Single side damage simulations and detection in beam-like structures

Beam-like structures are the most common components in real engineering, while single side damage is often encountered. In this study, a numerical analysis of single side damage in a free-free beam is analysed with three different finite element models; namely solid, shell and beam models for demonstrating their performance in simulating real structures. Similar to experiment, damage is introduced into one side of the beam, and natural frequencies are extracted from the simulations and compared with experimental and analytical results. Mode shapes are also analysed with modal assurance criterion. The results from simulations reveal a good performance of the three models in extracting natural frequencies, and solid model performs better than shell while shell model performs better than beam model under intact state. For damaged states, the natural frequencies captured from solid model show more sensitivity to damage severity than shell model and shell model performs similar to the beam model in distinguishing damage. The main contribution of this paper is to perform a comparison between three finite element models and experimental data as well as analytical solutions. The finite element results show a relatively well performance.

Modelação do comportamento dinâmico de sistemas barragem-fundação-albufeira: análise sísmica de uma barragem de abóbadas múltiplas

Trabalho Final de Mestrado elaborado no Laboratório Nacional de Engenharia Civil (LNEC) para a obtenção do grau de Mestre em Engenharia Civil pelo Instituto Superior de Engenharia de Lisboa no âmbito do protocolo de cooperação entre o ISEL e o LNEC

Simulation of the velocity field in compound channel flow using different closure models

1st European IAHR Congress,6-4 May, Edinburg, Scotland

Estimation of rotational frequency response functions

As it is widely known, in structural dynamic applications, ranging from structural coupling to model updating, the incompatibility between measured and simulated data is inevitable, due to the problem of coordinate incompleteness. Usually, the experimental data from conventional vibration testing is collected at a few translational degrees of freedom (DOF) due to applied forces, using hammer or shaker exciters, over a limited frequency range. Hence, one can only measure a portion of the receptance matrix, few columns, related to the forced DOFs, and rows, related to the measured DOFs. In contrast, by finite element modeling, one can obtain a full data set, both in terms of DOFs and identified modes. Over the years, several model reduction techniques have been proposed, as well as data expansion ones. However, the latter are significantly fewer and the demand for efficient techniques is still an issue. In this work, one proposes a technique for expanding measured frequency response functions (FRF) over the entire set of DOFs. This technique is based upon a modified Kidder's method and the principle of reciprocity, and it avoids the need for modal identification, as it uses the measured FRFs directly. In order to illustrate the performance of the proposed technique, a set of simulated experimental translational FRFs is taken as reference to estimate rotational FRFs, including those that are due to applied moments.

CMOS indoor light energy harvesting system for wireless sensing applications

This book discusses in detail the CMOS implementation of energy harvesting. The authors describe an integrated, indoor light energy harvesting system, based on a controller circuit that dynamically and automatically adjusts its operation to meet the actual light circumstances of the environment where the system is placed. The system is intended to power a sensor node, enabling an autonomous wireless sensor network (WSN). Although designed to cope with indoor light levels, the system is also able to work with higher levels, making it an all-round light energy harvesting system. The discussion includes experimental data obtained from an integrated manufactured prototype, which in conjunction with a photovoltaic (PV) cell, serves as a proof of concept of the desired energy harvesting system. © 2016 Springer International Publishing. All rights are reserved.

Viscosity and self-diffusion coefficients of dialkyl adipates: a correlation scheme with predictive capabilities

A correlation and predictive scheme for the viscosity and self-diffusivity of liquid dialkyl adipates is presented. The scheme is based on the kinetic theory for dense hard-sphere fluids, applied to the van der Waals model of a liquid to predict the transport properties. A "universal" curve for a dimensionless viscosity of dialkyl adipates was obtained using recently published experimental viscosity and density data of compressed liquid dimethyl (DMA), dipropyl (DPA), and dibutyl (DBA) adipates. The experimental data are described by the correlation scheme with a root-mean-square deviation of +/- 0.34 %. The parameters describing the temperature dependence of the characteristic volume, V-0, and the roughness parameter, R-eta, for each adipate are well correlated with one single molecular parameter. Recently published experimental self-diffusion coefficients of the same set of liquid dialkyl adipates at atmospheric pressure were correlated using the characteristic volumes obtained from the viscosity data. The roughness factors, R-D, are well correlated with the same single molecular parameter found for viscosity. The root-mean-square deviation of the data from the correlation is less than 1.07 %. Tests are presented in order to assess the capability of the correlation scheme to estimate the viscosity of compressed liquid diethyl adipate (DEA) in a range of temperatures and pressures by comparison with literature data and of its self-diffusivity at atmospheric pressure in a range of temperatures. It is noteworthy that no data for DEA were used to build the correlation scheme. The deviations encountered between predicted and experimental data for the viscosity and self-diffusivity do not exceed 2.0 % and 2.2 %, respectively, which are commensurate with the estimated experimental measurement uncertainty, in both cases.

Influência do tipo de adesivo em juntas híbridas soldadas-adesivas

A necessidade de utilizar métodos de ligação entre componentes de forma mais rápida, eficaz e com melhores resultados, tem causado a crescente utilização das juntas adesivas, em detrimento dos métodos tradicionais de ligação tais como a soldadura, brasagem, ligações aparafusadas e rebitadas. A utilização das juntas adesivas tem vindo a aumentar em diversas aplicações industriais por estas apresentarem vantagens das quais se destacam a redução de peso, redução de concentrações de tensões e facilidade de fabrico. No entanto, também apresentam desvantagens, como a necessidade de preparação das juntas e o descentramento da carga aplicada que provoca efeitos de flexão, os quais dão origem a tensões normais na direcção da espessura do adesivo (tensões de arrancamento), afectando assim a resistência da junta. A combinação da ligação adesiva com a soldadura por pontos permite algumas vantagens em comparação com as juntas adesivas tradicionais como a maior resistência, aumento da rigidez, melhor resistência ao corte e arrancamento e também à fadiga. Neste trabalho é apresentado um estudo experimental e numérico de juntas de sobreposição simples adesivas e híbridas (adesivas-soldadas). Os adesivos utilizados são o Araldite AV138®, apresentado como sendo frágil, e os adesivos Araldite 2015® e Sikaforce® 7752, intitulados como adesivos dúcteis. Foram considerados substratos de aço (C45E) em juntas com diferentes comprimentos de sobreposição ( ), que foram sujeitas a esforços de tracção. Foi realizada uma análise dos valores experimentais e efectuada uma comparação destes valores com os resultados obtidos por Elementos Finitos (EF) no software ABAQUS®, que incluiu uma análise de tensões na camada de adesivo e previsão do comportamento das juntas por Modelos de Dano Coesivo (MDC). A análise por MDC permitiu obter os modos de rotura, as curvas força-deslocamento e a resistência das juntas com bastante precisão, com excepção das juntas coladas com o adesivo Sikaforce® 7752. Estes resultados permitiram validar a técnica de modelação proposta para as juntas coladas e híbridas, o que representa uma base para posterior aplicação desta técnica em projecto, com as vantagens decorrentes da redução do tempo de projecto e maior facilidade de optimização.

Modelling of the kinetics of municipal solid waste composting in full-scale mechanical-biological treatment plants

A thesis submitted in fulfilment of the requirements for the Degree of Doctor of Philosophy in Sanitary Engineering in the Faculty of Sciences and Technology of the New University of Lisbon