Field effect and light-assisted a-Si:H sensors for detection of ions in solution

In this paper we present an amorphous silicon device that can be used in two operation modes to measure the concentration of ions in solution. While crystalline devices present a higher sensitivity, their amorphous counterpart present a much lower fabrication cost, thus enabling the production of cheap disposable sensors for use, for example, in the food industry. The devices were fabricated on glass substrates by the PECVD technique in the top gate configuration, where the metallic gate is replaced by an electrolytic solution with an immersed Ag/AgCl reference electrode. Silicon nitride is used as gate dielectric enhancing the sensitivity and passivation layer used to avoid leakage and electrochemical reactions. In this article we report on the semiconductor unit, showing that the device can be operated in a light-assisted mode, where changes in the pH produce changes on the measured ac photocurrent. In alternative the device can be operated as a conventional ion selective field effect device where changes in the pH induce changes in the transistor's threshold voltage.

: SiC Multilayer Photonic Structures with Self Optical Bias Amplification

Characteristics of tunable wavelength pi'n/pin filters based on a-SiC:H multilayered stacked cells are studied both experimental and theoretically. Results show that the device combines the demultiplexing operation with the simultaneous photodetection and self amplification of the signal. An algorithm to decode the multiplex signal is established. A capacitive active band-pass filter model is presented and supported by an electrical simulation of the state variable filter circuit. Experimental and simulated results show that the device acts as a state variable filter. It combines the properties of active high-pass and low-pass filter sections into a capacitive active band-pass filter using a changing photo capacitance to control the power delivered to the load.

Reconfigurable SiC Embedded Photonic Structures with Self Optical Bias Control

Multilayered heterostructures based on embedded a-Si:H and a-SiC:H p-i-n filters are analyzed from differential voltage design perspective using short- and long-pass filters. The transfer functions characteristics are presented. A numerical simulation is presented to explain the filtering properties of the photonic devices. Several monochromatic pulsed lights, separately (input channels) or in a polychromatic mixture (multiplexed signal) at different bit rates, illuminated the device. Steady-state optical bias is superimposed from the front and the back side. Results show that depending on the wavelength of the external background and impinging side, the device acts either as a short- or a long-pass band filter or as a band-stop filter. Particular attention is given to the amplification coefficient weights, which allow to take into account the wavelength background effects when a band or frequency needs to be filtered or the gate switch, in which optical active filter gates are used to select and filter input signals to specific output ports in wavelength division multiplexing (WDM) communication systems. This nonlinearity provides the possibility for selective removal or addition of wavelengths. A truth table of an encoder that performs 8-to-1 MUX function exemplifies the optoelectronic conversion.

SiC Multilayer Structures as Light Controlled Photonic Active Filters

Tunable wavelength division multiplexing converters based on amorphous SiC multilayer photonic active filters are analyzed. The configuration includes two stacked p-i-n structures (p(a-SiC:H)-i'(a-SiC:H)-n(a-SiC:H)-p(a-SiC:H)-i(a-Si:H)-n(a-Si:H)) sandwiched between two transparent contacts. The manipulation of the magnitude is achieved through appropriated front and back backgrounds. Transfer function characteristics are studied both theoretically and experimentally. An algorithm to decode the multiplex signal is established. An optoelectronic model supports the optoelectronic logic architecture. Results show that the light-activated device combines the demultiplexing operation with the simultaneous photodetection and self-amplification of an optical signal. The output waveform presents a nonlinear amplitude-dependent response to the wavelengths of the input channels. Depending on the wavelength of the external background and irradiation side, it acts either as a short- or a long-pass band filter or as a band-stop filter. A two-stage active circuit is presented and gives insight into the physics of the device.

Integrated photonic filters based on SiC multilayer structures

Combined tunable WDM converters based on SiC multilayer photonic active filters are analyzed. The operation combines the properties of active long-pass and short-pass wavelength filter sections into a capacitive active band-pass filter. The sensor element is a multilayered heterostructure produced by PE-CVD. The configuration includes two stacked SiC p-i-n structures sandwiched between two transparent contacts. Transfer function characteristics are studied both theoretically and experimentally. Results show that optical bias activated photonic device combines the demultiplexing operation with the simultaneous photodetection and self amplification of an optical signal acting the device as an integrated photonic filter in the visible range. Depending on the wavelength of the external background and irradiation side, the device acts either as a short- or a long-pass band filter or as a band-stop filter. The output waveform presents a nonlinear amplitude-dependent response to the wavelengths of the input channels. A numerical simulation and a two building-blocks active circuit are presented and give insight into the physics of the device. (c) 2013 Elsevier B.V. All rights reserved.

Improving quality-of-service in wireless sensor networks by mitigating “Hidden-Node Collisions”

Wireless sensor networks (WSNs) emerge as underlying infrastructures for new classes of large-scale networked embedded systems. However, WSNs system designers must fulfill the quality-of-service (QoS) requirements imposed by the applications (and users). Very harsh and dynamic physical environments and extremely limited energy/computing/memory/communication node resources are major obstacles for satisfying QoS metrics such as reliability, timeliness, and system lifetime. The limited communication range of WSN nodes, link asymmetry, and the characteristics of the physical environment lead to a major source of QoS degradation in WSNs-the ldquohidden node problem.rdquo In wireless contention-based medium access control (MAC) protocols, when two nodes that are not visible to each other transmit to a third node that is visible to the former, there will be a collision-called hidden-node or blind collision. This problem greatly impacts network throughput, energy-efficiency and message transfer delays, and the problem dramatically increases with the number of nodes. This paper proposes H-NAMe, a very simple yet extremely efficient hidden-node avoidance mechanism for WSNs. H-NAMe relies on a grouping strategy that splits each cluster of a WSN into disjoint groups of non-hidden nodes that scales to multiple clusters via a cluster grouping strategy that guarantees no interference between overlapping clusters. Importantly, H-NAMe is instantiated in IEEE 802.15.4/ZigBee, which currently are the most widespread communication technologies for WSNs, with only minor add-ons and ensuring backward compatibility with their protocols standards. H-NAMe was implemented and exhaustively tested using an experimental test-bed based on ldquooff-the-shelfrdquo technology, showing that it increases network throughput and transmission success probability up to twice the values obtained without H-NAMe. H-NAMe effectiveness was also demonstrated in a target tracking application with mobile robots - over a WSN deployment.

SiC pinpin photonic for linking the visible spectrum to the telecom gap

Expanding far beyond traditional applications at telecommunications wavelengths, the SiC photonic devices has recently proven its merits for working with visible range optical signals. Reconfigurable wavelength selectors are essential sub-systems for implementing reconfigurable WDM networks and optical signal processing. Visible range to telecom band spectral translation in SiC/Si can be accomplished using wavelength selector under appropriated optical bias, acting as reconfigurable active filters. In this paper we present a monolithically integrated wavelength selector based on a multilayer SiC/Si integrated optical filters that requires optical switches to select wavelengths. The selector filter is realized by using double pin/pin a-SiC:H photodetector with front and back biased optical gating elements. Red, green, blue and violet communication channels are transmitted together, each one with a specific bit sequence. The combined optical signal is analyzed by reading out the generated photocurrent, under different background wavelengths applied either from the front or the back side. The backgrounds acts as channel selectors that selects one or more channels by splitting portions of the input multi-channel optical signals across the front and back photodiodes. The transfer characteristics effects due to changes in steady state light, irradiation side and frequency are presented. The relationship between the optical inputs and the digital output levels is established. (C) 2014 Elsevier B.V. All rights reserved.

Chemical reaction network of flavylium ions in heterogeneous media

Dissertação apresentada para a obtenção do Grau de Doutor em Química, especialidade em Química-Física, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Protein folding, metal ions and conformational states: the case of a di-cluster ferredoxin

Dissertation presented to obtain the PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Metal ions and protein folding: conformational and functional interplay

Dissertation presented to obtain a PhD degree in Biochemistry at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Metal ions modulate the folding and stability of the tumor suppressor protein S100A2

Febs Journal (2009)276:1776-1786

Metals in proteins from sulphate-reducing bacteria: adenylate kinase and ATP sulfurylase. Proteins containing cobalt, zinc, iron (II) ions

A Thesis submitted at the Faculty Science and Technology of the New University of Lisbon for a degree in Doctor of Philosophy in Biochemistry with specialization in Physical Biochemistry

The role of halouracils in radiotherapy studied by electron transfer in atom-molecule collisions experiments

Dissertação para obtenção do Grau de Doutor em Engenharia Física

(Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review

The use of buffers to maintain the pH within a desired range is a very common practice in chemical, biochemical and biological studies. Among them, zwitterionic N-substituted aminosulfonic acids, usually known as Good’s buffers, although widely used, can complex metals and interact with biological systems. The present work reviews, discusses and updates the metal complexation characteristics of thirty one commercially available buffers. In addition, their impact on biological systems is also presented. The influences of these buffers on the results obtained in biological, biochemical and environmental studies, with special focus on their interaction with metal ions, are highlighted and critically reviewed. Using chemical speciation simulations, based on the current knowledge of the metal–buffer stability constants, a proposal of the most adequate buffer to employ for a given metal ion is presented.

The inhibitory activity of synthetic compounds and ions against transporters of multi-drug resistant bacteria

RESUMO: Sessenta e três derivados de hidantoína foram utilizados para avaliar possíveis efeitos de modulação na actividade das bombas de efluxo (BE) na Salmonella NCTC 13349 utilizando um método fluorimétrico semi-automático. Nenhum dos compostos apresentaram actividade anti-bacteriana até concentrações de 240 mg/L. Entre todos os compostos, SZ-7 demonstrou possuir propriedades de modulação de effluxo na presença de glucose. Para testar esta actividade, estirpes de Salmonella resistentes à ciprofloxacina, induzidas a elevados níveis de resistência com sobre-expressão de BE, foram expostas ao SZ-7. Este derivado afectou a susceptibilidade das estirpes à ciprofloxacina. Uma vez que os 63 compostos estudados apresentaram pouco efeito inibitório /cumulativo, apesar de serem conhecidos pelos seus efeitos moduladores de BE-dependentes de iões em eucariotas, foi questionado o papel dos iões na regulação de BE bacterianas, que poderão influenciar a eficácia de novos compostos. Para este estudo, utilizamos a Escherichia coli AG100 como modelo, devido ao extenso conhecimento no que respeita a estrutura e actividade das BE. Devido à importância de iões de cálcio (Ca2+) nos canais de transporte membranar e na actividade de ATPases, a sua actividade na modulação do efluxo foi investigada. De resultados anteriormente obtidos concluiu-se que a pH 5 o efluxo é independente de energia metabólica; contudo, a pH 8 é absolutamente dependente, sendo que o Ca2+ é indispensável para manter a actividade das ATPases bacterianas. A acumulação/effluxo de EtBr pela E. coli AG100 foi determinada na presença/ausência de Ca2+, clorpromazina (inibidor de ligação de Ca2+ a proteínas), e ácido etilenodiamino tetra-acético (quelante de Ca2+). Acumulação/effluxo aumentou a pH 8, contudo o Ca2+ reverte estes efeitos evidenciando a sua importância no funcionamento das BE bacterianas. Em resumo este trabalho colocou em evidência que muitos aspectos bioquímicos e bioenergéticos devem ser tomados em consideração no estudo da resistência bacteriana mediada por BE.------- ABSTRACT: Sixty-three hydantoin derivatives were evaluated for their modulating effects on efflux pump (EP) activity of Salmonella NCTC 13349 utilizing a semi-automatic fluorometric method. None of the compounds presented antibacterial activities at concentrations as high as 240 mg/L. Among all compounds, SZ-7 showed possible efflux modulating activity in the presence of glucose, indicative of a potential EP inhibitor. To verify its potential effects, ciprofloxacin-resistant Salmonella strains, induced to high level resistance with over-expressing EPs, were exposed to SZ-7. This derivative affected the susceptibility of the ciprofloxacin-resistant strains. Since the 63 compounds studied had very low inhibitory/accumulative effects, even though their known for being efficient in modulating ion-driven eukaryotic EPs, we questioned whether ions had a leading role in regulating bacterial EPs, influencing the effectiveness of new compounds. For this study we used Escherichia coli AG100 as a model, due to the extensive knowledge on its EPs structure and activity. Owing the importance of calcium ions (Ca2+) for membrane transport channels and activity of ATPases, the role of Ca2+ was investigated. From previous results we concluded that at pH 5 efflux is independent of metabolic energy; however, at pH 8 it is entirely dependent of metabolic energy and the Ca2+ ions are essential to maintain the activity of bacterial ATPases. Accumulation and efflux of ethidium bromide (EtBr) by E. coli AG100 was determined in the presence and absence of Ca2+, chlorpromazine (inhibitor of Ca2+-binding to proteins), and ethylenediaminetetraacetic acid (Ca2+ chelator). Accumulation of EtBr increased at pH 8; however Ca2+ reversed these effects providing information as to the importance of this ion in the regulation of bacterial EP systems. Overall this work puts in evidence that many biochemical and bioenergetic aspects related to the strains physiology need to be taken into consideration in bacterial drug resistance mediated by EPs.