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2008
Gavel, OY, SA Bursakov, G. Di Rocco, J. Trincao, I. J. Pickering, GN George, JJ Calvete, VL Shnyrov, CD Brondino, AS Pereira, J. Lampreia, P. Tavares, JJG Moura, and I. Moura. "A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774." Journal of Inorganic Biochemistry. 102 (2008): 1380-1395. AbstractWebsite

Adenylate kinase (AK) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. The AK were purified from crude extracts of two sulfate-reducing bacteria (SRB), Desulfovibrio (D.) gigas NCIB 9332 and Desulfovibrio desulfuricans ATCC 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substituted forms. These are the first reported adenylate kinases that bind either zinc or cobalt and are related to the subgroup of metal-containing AK found, in most cases, in Gram-positive bacteria. The electronic absorption spectrum is consistent with tetrahedral coordinated cobalt, predominantly via sulfur ligands, and is supported by EPR. The involvement of three cysteines in cobalt or zinc coordination was confirmed by chemical methods. Extended X-ray absorption fine structure (EXAFS) indicate that cobalt or zinc are bound by three cysteine residues and one histidine in the metal-binding site of the "LID" domain. The sequence (129)Cys-X(5)-His-X(15)-Cys-X(2)-Cys of the AK from D. gigas is involved in metal coordination and represents a new type of binding motif that differs from other known zinc-binding sites of AK. Cobalt and zinc play a structural role in stabilizing the LID domain. (C) 2008 Elsevier Inc. All rights reserved.

Morrison, J. C., S. Boyd, L. Marsano, B. Bialecki, T. Ericsson, and J. P. Santos. "Numerical methods for solving the Hartree-Fock equations of diatomic molecules I." Communications in Computational Physics. 5 (2008): 959-985. AbstractWebsite
The theory of domain decomposition is described and used to divide the variable domain of a diatomic molecule into separate regions which are solved independently. This approach makes it possible to use fast Krylov methods in the broad interior of the region while using explicit methods such as Gaussian elimination on the boundaries. As is demonstrated by solving a number of model problems, these methods enable one to obtain solutions of the relevant partial differential equations and eigenvalue equations accurate to six significant figures with a small amount of computational time. Since the numerical approach described in this article decomposes the variable space into separate regions where the equations are solved independently, our approach is very well-suited to parallel computing and offers the long term possibility of studying complex molecules by dividing them into smaller fragments that are calculated separately.
Figueiredo, Ondina M., Teresa Pereira Silva, and João Pedro Veiga. "Oxidation state and coordination of iron in red pre-soils: first results from a Fe K-edge XANES study on regoliths from Santiago Island, Cape Verde." European Geoscience Union, General Assembly 2008, Division of Soil System Science SSS-14 New Frontiers in Soil Analysis (2008). Abstract
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Fernandes, J. R., H. B. Goncalves, L. B. Oliveira, and M. M. Silva. "A pulse generator for UWB-IR based on a relaxation oscillator." Circuits and Systems II: Express Briefs, IEEE Transactions on. 55 (2008): 239-243. Abstract
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Oliveira, L. B., J. R. Fernandes, I. M. Filanovsky, C. J. M. Verhoeven, and M. M. Silva. "Quadrature LC-Oscillator." Analysis and Design of Quadrature Oscillators (2008): 81-98. Abstract
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Oliveira, L. B., J. R. Fernandes, I. M. Filanovsky, C. J. M. Verhoeven, and M. M. Silva. "Quadrature Oscillator-Mixer." Analysis and Design of Quadrature Oscillators (2008): 63-80. Abstract
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Oliveira, L. B., J. R. Fernandes, I. M. Filanovsky, C. J. M. Verhoeven, and M. M. Silva. "Quadrature Relaxation Oscillator." Analysis and Design of Quadrature Oscillators (2008): 37-61. Abstract
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Amaral, Paula, Joaquim Júdice, and Hanif D. Sherali. "A reformulation–linearization–convexification algorithm for optimal correction of an inconsistent system of linear constraints." Computers & Operations Research. 35 (2008): 1494-1509. Abstract
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Chastre, C., and M. G. Silva Reinforced Concrete Columns Jacketed with FRP Composites and Subjected to Cyclic Horizontal Loads. International Conference CCC2008 - Challenges for Civil Construction. Porto: FEUP, 2008. Abstract
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Roque, A. A., Tiago A. N. Silva, J. M. F. Calado, and J. C. Q. Dias Rolling bearing fault detection and isolation – A didactic study. 4th WSEAS/IASME International Conference on EDUCATIONAL TECHNOLOGIES (EDUTE'08). World Scientific and Engineering Academy and Society (WSEAS), 2008. Abstract
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Palma, M. L., and J. P. Santos. "Spin-rotation and nuclear shielding constants of sulfur hexafluoride." Molecular Physics. 106 (2008): 1241-1247. AbstractWebsite
We present a first theoretical determination of the hyperfine coupling constants of a spherical top molecule using ab initio methods. The scalar and tensorial contributions to the spin-rotation constants and the diamagnetic and paramagnetic contributions to the nuclear shielding constant are calculated for the 32SF6 molecule. The corrections to the spin-rotation constants due to nuclear Thomas precession are evaluated and discussed. Our results are compared with previously reported experimental values.
Palma, M. L., and J. P. Santos. "Spin-rotation and nuclear shielding constants of sulfur hexafluoride." Molecular Physics. 106 (2008): 1241-1247. AbstractWebsite

We present a first theoretical determination of the hyperfine coupling constants of a spherical top molecule using <i>ab initio</i> methods. The scalar and tensorial contributions to the spin-rotation constants and the diamagnetic and paramagnetic contributions to the nuclear shielding constant are calculated for the <sup>32</sup>SF<sub>6</sub> molecule. The corrections to the spin-rotation constants due to nuclear Thomas precession are evaluated and discussed. Our results are compared with previously reported experimental values.

Aguas, H., R. J. C. Silva, M. Viegas, L. Pereira, E. Fortunato, and R. Martins. "Study of environmental degradation of silver surface." physica status solidi (c). 5 (2008): 1215-1218. Abstract
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Oliveira, L. B., J. R. Fernandes, I. M. Filanovsky, C. J. M. Verhoeven, and M. M. Silva. "Transceiver Architectures and RF Blocks." Analysis and Design of Quadrature Oscillators (2008): 7-35. Abstract
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Oliveira, L. B., J. R. Fernandes, I. M. Filanovsky, C. J. M. Verhoeven, and M. M. Silva. "Two-Integrator Oscillator." Analysis and Design of Quadrature Oscillators (2008): 99-117. Abstract
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Santos, J. P., M. C. Martins, A. M. Costa, P. Indelicato, and F. Parente. "X-ray spectra emitted by Cl14+ ions in ECRIS plasmas." Vacuum. 82 (2008): 1522-1524. AbstractWebsite
We study the contribution of the most important processes leading to the creation of excited states of Cl14+ ions from the ground configurations of Cl ions in an Electron Cyclotron Resonance Ion Source (ECRIS), which lead to the emission of K X-ray lines. Theoretical values for inner-shell excitation, K and KL ionization cross-sections, and energies and transition probabilities for the de-excitation processes are calculated in the framework of the Multi-Configuration Dirac-Fock (MCDF) method. With reasonable assumptions about the electron energy distribution, a theoretical K[alpha] X-ray spectrum is obtained, which reproduces closely a recent experimental result.
Santos, J. P., M. C. Martins, A. M. Costa, P. Indelicato, and F. Parente. "X-ray spectra emitted by Cl14+ ions in ECRIS plasmas." Vacuum. 82 (2008): 1522-1524. AbstractWebsite

We study the contribution of the most important processes leading to the creation of excited states of Cl14+ ions from the ground configurations of Cl ions in an Electron Cyclotron Resonance Ion Source (ECRIS), which lead to the emission of K X-ray lines. Theoretical values for inner-shell excitation, K and KL ionization cross-sections, and energies and transition probabilities for the de-excitation processes are calculated in the framework of the Multi-Configuration Dirac-Fock (MCDF) method. With reasonable assumptions about the electron energy distribution, a theoretical K[alpha] X-ray spectrum is obtained, which reproduces closely a recent experimental result.

Gavel, Olga Yu, Sergey A. Bursakov, Giulia Di Rocco, Jose Trincao, Ingrid J. Pickering, Graham N. George, Juan J. Calvete, Valery L. Shnyrov, Carlos D. Brondino, Alice S. Pereira, Jorge Lampreia, Pedro Tavares, Jose J. G. Moura, and Isabel Moura. "{A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774}." Journal Of Inorganic Biochemistry. 102 (2008): 1380-1395. Abstract
Adenylate kinase (AK) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. The AK were purified from crude extracts of two sulfate-reducing bacteria (SRB), Desulfovibrio (D.) gigas NCIB 9332 and Desulfovibrio desulfuricans ATCC 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substituted forms. These are the first reported adenylate kinases that bind either zinc or cobalt and are related to the subgroup of metal-containing AK found, in most cases, in Gram-positive bacteria. The electronic absorption spectrum is consistent with tetrahedral coordinated cobalt, predominantly via sulfur ligands, and is supported by EPR. The involvement of three cysteines in cobalt or zinc coordination was confirmed by chemical methods. Extended X-ray absorption fine structure (EXAFS) indicate that cobalt or zinc are bound by three cysteine residues and one histidine in the metal-binding site of the "LID" domain. The sequence (129)Cys-X-5-His-X-15-Cys-X-2-Cys of the AK from D. gigas is involved in metal coordination and represents a new type of binding motif that differs from other known zinc-binding sites of AK. Cobalt and zinc play a structural role in stabilizing the LID domain. (C) 2008 Elsevier Inc. All rights reserved.
Mendes, Manuel J., Howard K. Schmidt, and Matteo Pasquali. "{Brownian dynamics simulations of single-wall carbon nanotube separation by type using dielectrophoresis}." Journal of Physical Chemistry B (2008). AbstractWebsite
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Coimbra, Patrícia, MH Gil, Herminio De C. Sousa, and Catarina M. M. Duarte. "{T O T S I U Rib N Tio T O T S I N}." (2008): 102-107. Abstract
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Duarte, A. R. C., A. Shariati, L. J. Rovetto, and C. J. Peters. "{Water cavities of sH clathrate hydrate stabilized by molecular hydrogen: Phase equilibrium measurements}." Journal of Physical Chemistry B. 112 (2008). Abstract

In this experimental phase equilibrium study, we show for the first time that it is possible to stabilize structure sH of hydrogen clathrate hydrate with the help of some selected promoters. It was established that the formation pressures of these systems are significantly higher than that of structure sII of hydrogen clathrate hydrate when tetrahydrofuran (THF) is used as a promoter. Although no experimental evidence is available yet, it is estimated that the hydrogen storage capacity of structure sH can be as high as 1.4 wt {%} of H 2 , which is about 40{%} higher compared to the hydrogen storage capacity in structure sH. © 2008 American Chemical Society.

2007
Martins, R. M. S., N. Schell, R. J. C. Silva, L. Pereira, K. K. Mahesh, and F. M. Braz Fernandes. "In-situ study of Ni-Ti thin film growth on a TiN intermediate layer by X-ray diffraction." Sensors and Actuators B-Chemical. 126.1 (2007): 332-337. Abstract
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Sampaio, José, and António Moniz Assessing Human And Technological Dimensions In Virtual Team’S Operational Competences. University Library of Munich, Germany, 2007. Abstract

Cognitive task automation may lead to over trust, complacency and loss of the necessary work environment situation awareness. This is a major constraint in complex work organizations teamwork, ending up into an operational gap, between system developments and its understanding and usability, by operators. This document presents a summary of the main results of author’s research on operational decision processes and occupational competences, applied to the air traffic control operational reality. Introducing a human/technological complementary approach to virtual team’s conceptualisation, the results show there is a dimension to be followed in human/machine integration, which stands beyond interface design, and calls for a deeper human comprehension of technological agent’s structure and functionalities, which will, ultimately, require the development of an operational cognitive framework, where work processes and technological behaviour are integrated in professional competences, as he two faces of the same coin.

Martins, R., N. Schell, R. Silva, L. Pereira, K. MAHESH, and F. FERNANDES. "{In-situ study of Ni–Ti thin film growth on a TiN intermediate layer by X-ray diffraction}." Sensors and Actuators B: Chemical. 126 (2007): 332-337. AbstractWebsite
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