Fractional pennes' bioheat equation: theoretical and numerical studies

In this work we provide a new mathematical model for the Pennes’ bioheat equation, assuming a fractional time derivative of single order. Alternative versions of the bioheat equation are studied and discussed, to take into account the temperature-dependent variability in the tissue perfusion, and both finite and infinite speed of heat propagation. The proposed bioheat model is solved numerically using an implicit finite difference scheme that we prove to be convergent and stable. The numerical method proposed can be applied to general reaction diffusion equations, with a variable diffusion coefficient. The results obtained with the single order fractional model, are compared with the original models that use classical derivatives.

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

Effect of the acoustic impedance in ultrasonic emitter transducers using digital modulations

In an underwater environment it is difficult to implement solutions for wireless communications. The existing technologies using electromagnetic waves or lasers are not very efficient due to the large attenuation in the aquatic environment. Ultrasound reveals a lower attenuation, and thus has been used in underwater long-distance communications. The much slower speed of acoustic propagation in water (about 1500 m/s) compared with that of electromagnetic and optical waves, is another limiting factor for efficient communication and networking. For high data-rates and real-time applications it is necessary to use frequencies in the MHz range, allowing communication distances of hundreds of meters with a delay of milliseconds. To achieve this goal, it is necessary to develop ultrasound transducers able to work at high frequencies and wideband, with suitable responses to digital modulations. This work shows how the acoustic impedance influences the performance of an ultrasonic emitter transducer when digital modulations are used and operating at frequencies between 100 kHz and 1 MHz. The study includes a Finite Element Method (FEM) and a MATLAB/Simulink simulation with an experimental validation to evaluate two types of piezoelectric materials: one based on ceramics (high acoustic impedance) with a resonance design and the other based in polymer (low acoustic impedance) designed to optimize the performance when digital modulations are used. The transducers performance for Binary Amplitude Shift Keying (BASK), On-Off Keying (OOK), Binary Phase Shift Keying (BPSK) and Binary Frequency Shift Keying (BFSK) modulations with a 1 MHz carrier at 125 kbps baud rate are compared.

Anderson localization of light in disordered superlattices containing graphene layers

We theoretically investigate light propagation and Anderson localization in one-dimensional disordered superlattices composed of dielectric stacks with graphene sheets in between. Disorder is introduced either on graphene material parameters ({\it e.g.} Fermi energy) or on the widths of the dielectric stacks. We derive an analytic expression for the localization length $\xi$, and compare it to numerical simulations using transfer matrix technique; a very good agreement is found. We demonstrate that the presence of graphene may strongly attenuate the anomalously delocalised Breswter modes, and is at the origin of a periodic dependence of $\xi$ on frequency, in contrast to the usual asymptotic decay, $\xi \propto \omega^{-2}$. By unveiling the effects of graphene on Anderson localization of light, we pave the way for new applications of graphene-based, disordered photonic devices in the THz spectral range.

To be or not to be a pseudogene: a molecular epidemiological approach to the mclx genes and its impact in tuberculosis

Tuberculosis presents a myriad of symptoms, progression routes and propagation patterns not yet fully understood. Whereas for a long time research has focused solely on the patient immunity and overall susceptibility, it is nowadays widely accepted that the genetic diversity of its causative agent, Mycobacterium tuberculosis, plays a key role in this dynamic. This study focuses on a particular family of genes, the mclxs (Mycobacterium cyclase/LuxR-like genes), which codify for a particular and nearly mycobacterial-exclusive combination of protein domains. mclxs genes were found to be pseudogenized by frameshift-causing insertion(s)/deletion(s) in a considerable number of M. tuberculosis complex strains and clinical isolates. To discern the functional implications of the pseudogenization, we have analysed the pattern of frameshift-causing mutations in a group of M. tuberculosis isolates while taking into account their microbial-, patient- and disease-related traits. Our logistic regression-based analyses have revealed disparate effects associated with the transcriptional inactivation of two mclx genes. In fact, mclx2 (Rv1358) pseudogenization appears to be primarily driven by the microbial phylogenetic background, being mainly related to the Euro-American (EAm) lineage; on the other hand, mclx3 (Rv2488c) presents a higher tendency for pseudogenization among isolates from patients born on the Western Pacific area, and from isolates causing extra-pulmonary infections. These results contribute to the overall knowledge on the biology of M. tuberculosis infection, whereas at the same time launch the necessary basis for the functional assessment of these so far overlooked genes.

A radiofrequency identification system for the 60 GHz ISM band

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Eletrónica Médica)

The influence of nitrogen and oxygen additions on the thermal characteristics of aluminium-based thin films

The ternary aluminium oxynitride (AlNxOy) system offers the possibility to obtain a wide range of properties by tailoring the ratio between pure Al, AlNx and AlOy and therefore opening a significant number of possible applications. In this work the thermal behaviour of AlNxOy thin films was analysed by modulated infrared radiometry (MIRR), taking as reference the binary AlOy and AlNx systems. MIRR is a non-contact and non-destructive thermal wave measurement technique based on the excitation, propagation and detection of temperature oscillations of very small amplitudes. The intended change of the partial pressure of the reactive gas (N2 and/or O2) influenced the target condition and hence the deposition characteristics which, altogether, affected the composition and microstructure of the films. Based on the MIRR measurements and their qualitative and quantitative interpretation, some correlations between the thermal transport properties of the films and their chemical/physical properties have been found. Furthermore, the potential of such technique applied in this oxynitride system, which present a wide range of different physical responses, is also discussed. The experimental results obtained are consistent with those reported in previous works and show a high potential to fulfil the demands needed for the possible applications of the systems studied. They are clearly indicative of an adequate thermal response if this particular thin film system is aimed to be applied in small sensor devices or in electrodes for biosignal acquisition, such as those for electroencephalography or electromyography as it is the case of the main research area that is being developed in the group.

Modelação, simulação e implementação de agitação acústica para aplicações em microfluídica

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

A study of risk-aware program transformation

In the trend towards tolerating hardware unreliability, accuracy is exchanged for cost savings. Running on less reliable machines, functionally correct code becomes risky and one needs to know how risk propagates so as to mitigate it. Risk estimation, however, seems to live outside the average programmer’s technical competence and core practice. In this paper we propose that program design by source-to-source transformation be risk-aware in the sense of making probabilistic faults visible and supporting equational reasoning on the probabilistic behaviour of programs caused by faults. This reasoning is carried out in a linear algebra extension to the standard, `a la Bird-Moor algebra of programming. This paper studies, in particular, the propagation of faults across standard program transformation techniques known as tupling and fusion, enabling the fault of the whole to be expressed in terms of the faults of its parts.

Influência do fator visão do céu na propagação do ruído em zonas urbanas

Dissertação de mestrado integrado em Engenharia Civil

Hazard assessment of storm events for the battery, New York

The environmental and socio-economic importance of coastal areas is widely recognized, but at present these areas face severe weaknesses and high-risk situations. The increased demand and growing human occupation of coastal zones have greatly contributed to exacerbating such weaknesses. Today, throughout the world, in all countries with coastal regions, episodes of waves overtopping and coastal flooding are frequent. These episodes are usually responsible for property losses and often put human lives at risk. The floods are caused by coastal storms primarily due to the action of very strong winds. The propagation of these storms towards the coast induces high water levels. It is expected that climate change phenomena will contribute to the intensification of coastal storms. In this context, an estimation of coastal flooding hazards is of paramount importance for the planning and management of coastal zones. Consequently, carrying out a series of storm scenarios and analyzing their impacts through numerical modeling is of prime interest to coastal decision-makers. Firstly, throughout this work, historical storm tracks and intensities are characterized for the northeastern region of United States coast, in terms of probability of occurrence. Secondly, several storm events with high potential of occurrence are generated using a specific tool of DelftDashboard interface for Delft3D software. Hydrodynamic models are then used to generate ensemble simulations to assess storms' effects on coastal water levels. For the United States’ northeastern coast, a highly refined regional domain is considered surrounding the area of The Battery, New York, situated in New York Harbor. Based on statistical data of numerical modeling results, a review of the impact of coastal storms to different locations within the study area is performed.

Acoustic emission analysis of the effect of a 2D wedge shaped blade on the compact bone cutting process

Surgeons may use a number of cutting instruments such as osteotomes and chisels to cut bone during an operative procedure. The initial loading of cortical bone during the cutting process results in the formation of microcracks in the vicinity of the cutting zone with main crack propagation to failure occuring with continued loading. When a material cracks, energy is emitted in the form of Acoustic Emission (AE) signals that spread in all directions, therefore, AE transducers can be used to monitor the occurrence and development of microcracking and crack propagation in cortical bone. In this research, number of AE signals (hits) and related parameters including amplitude, duration and absolute energy (abs-energy) were recorded during the indentation cutting process by a wedge blade on cortical bone specimens. The cutting force was also measured to correlate between load-displacement curves and the output from the AE sensor. The results from experiments show AE signals increase substantially during the loading just prior to fracture between 90% and 100% of maximum fracture load. Furthermore, an amplitude threshold value of 64dB (with approximate abs-energy of 1500 aJ) was established to saparate AE signals associated with microcracking (41 – 64dB) from fracture related signals (65 – 98dB). The results also demonstrated that the complete fracture event which had the highest duration value can be distinguished from other growing macrocracks which did not lead to catastrophic fracture. It was observed that the main crack initiation may be detected by capturing a high amplitude signal at a mean load value of 87% of maximum load and unsteady crack propagation may occur just prior to final fracture event at a mean load value of 96% of maximum load. The author concludes that the AE method is useful in understanding the crack initiation and fracture during the indentation cutting process.

III - Contribuição para o estudo biológico e ecológico das Podostemaceae do salto do Piracicaba

1 - The Author, in this 3 thd. contribution, concludes the study of the biology and ecology of the species Tristicha trifaria (Willd.) Spreng. and Mourera aspera (Bong.) Tul., both of the Piracicaba Fall. 2 - According to the results of Dr. Peter van Royen (State Herbarium of Leiden, Holland), who made a complete revision of Podostemaceae of the Piracicaba Fall, the species Tristicha hypnoides (St. Hil.) Spreng. var. Hilarii Tul. and Mnioppsis Glazioviana Warm, correspond, respectively, to theTristicha trifaria (Willd.) Spreng. and Mniopsis weddelliana Tul. Apinagia Accorsii Toledo was transferred by Royen to the genus Wettsteiniola. So, its new name is Wettsteiniola accorsii (Toledo) v. Royen. 3 - Propagation by seeds may occur in the following places: a) placenta of partially open fruits; b) external and internal walls of the open capsules; c) pedicels of the fruits; d) remains of rhizomes, branches, etc. e) organic residues accumulated in water holes in the fall; f) clean rocks, in which the little groups of seedlings seems to be a colony of algae. Seeds adhere to the substrata above by means, of a mucilage produced by the transformation of the external integuments in contact with water. 4 - In the growth of the four species below it was found in Piracicaba Fall conspicuous zoning so scattered: a) Wettsteiniola accorsii (Toledo) v. Royen, in rocks situated just within the water fall, where velocity of the current and aeration of the water are very high. b) Tristicha trifaria (Willd.) Spreng. and Mniopsis weddelliana Tul., in rocks at some distance (100 m more or less) upstream until near the bridge across the river. c) Mourera aspera (Bong.) Tul., 300 m upwards the bridge. 5- During 1949, the ecological conditions of the Piracicaba Fall were changed due to the following factors: a) dry season very long, begining from last period of June until 30 november; b) stopping, during four months, of water from the Atibaia river (one of the components of Piracicaba river) near to the city of Americana, in the place where a new station of the Companhia Paulista de Força e Luz was build. In consequence, most of the Podostemaceae died. On the dry rocks there were only fruits and dried plants. 6 - Tristicha trifaria has the same biological and ecological behavior as the Mniopsis weddelliana,. 7 - The vegetative propagation of Tristicha trifaria is made by increasing of its branches, production of stolons with vegetatives buds and regeneration of old parts in especial conditions of water and aeration. 8 - Mourera aspera has the same vegetative propagation as the Wettsteiniola accorsii; it produces stolons (in very little percentage) with vegetative buds, branches of the rhizomes and regeneration of active old parts. 9 - Frequently, there is, on the plants an accumulation of sand, silt, loam, organic substances, and so on. The quantity of material stored depends of the purity of the water, of the morphology of the plants and of the situation on the fall. 10 - In extrem conditions of dry heat, the surviving of the species in its habitat depends exclusively from germination of seeds in the mentioned substrata. Exceptionally, some plants survive in a few water pockets full with the weak remaining current.

Memòria justificativa de l'estada de recerca

Estudi elaborat a partir d’una estada a l’Associação para o Desenvolvimento da Aerodinânica Industrial (ADAI) de la Universitat de Coimbra, Portugal, entre març i juliol de 2006. Aquesta disposa d'un laboratori d'assaigs i té medis suficients per a cremar de manera controlada parcel•les prèviament delimitades en terreny forestal. Això permet observar el fenomen dels incendis forestals a dues escales de treball diferents. L’objectiu ha estat l’obtenció de dades experimentals sobre la propagació de fronts de flames que avancen sobre combustible tractat amb retardants sota l’efecte del pendent o el vent. S’ha participat en proves experimentals de camp i se n’han realitzat dues en instal•lacions de laboratori en què l’efecte del pendent o de la velocitat del vent podia ser variat. Degut a l’elevat nombre de variables que entren en joc l’anàlisi acurada de les dades encara està en procés.

Molluscicide activity of the "Avelós" plant (Euphorbia tirucalli, L. ) on Biomphalaria glabrata, the mollusc vector of schistosomiasis

An aqueous solution of the latex of Euphorbia tirucalli collected at sites receiving large amounts of sunlight showed molluscicide action on Biomphalaria glabrata, with LD50 obtained at the concentration of 28,0 ppm and LD90 at the concentration of 85,0 ppm. The toxicity of the product for fish was similar to that of Bayluscide and of copper sulfate used for comparison. However, the wide distribution of the plant, its easy propagation and the simple procedure for extraction of the active substance, which is biodegradable, favor "avelós" as a promising agent in the control of schistosomiasis.