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2009
Martins, R., Leandro Raniero, Luis Pereira, Daniel Costa, Hugo Aguas, Sonia Pereira, Leonardo Silva, A. Gonçalves, I. Ferreira, and E. Fortunato. "Nanostructured silicon and its application to solar cells, position sensors and thin film transistors." Philosophical Magazine. 89 (2009): 2699-2721. Abstract
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Surzhykov, A., J. P. Santos, P. Amaro, and P. Indelicato. "Negative-continuum effects on the two-photon decay rates of hydrogenlike ions." Physical Review A (Atomic, Molecular, and Optical Physics). 80 (2009): 052511. AbstractWebsite
Two-photon decay of hydrogenlike ions is studied within the framework of second-order perturbation theory, based on the relativistic Dirac's equation. Special attention is paid to the effects arising from the summation over the negative-energy (intermediate virtual) states that occur in such a framework. In order to investigate the role of these states, detailed calculations have been carried out for the 2s1/2–>1s1/2 and 2p1/2–>1s1/2 transitions in neutral hydrogen H as well as for hydrogenlike xenon Xe53+ and uranium U91+ ions. We found that for a correct evaluation of the total and energy-differential decay rates, summation over the negative-energy part of Dirac's spectrum should be properly taken into account both for high-Z and low-Z atomic systems.
Surzhykov, A., J. P. Santos, P. Amaro, and P. Indelicato. "Negative-continuum effects on the two-photon decay rates of hydrogenlike ions." Physical Review A. 80 (2009): 052511. AbstractWebsite

Two-photon decay of hydrogenlike ions is studied within the framework of second-order perturbation theory, based on the relativistic Dirac's equation. Special attention is paid to the effects arising from the summation over the negative-energy (intermediate virtual) states that occur in such a framework. In order to investigate the role of these states, detailed calculations have been carried out for the 2s1/2-->1s1/2 and 2p1/2-->1s1/2 transitions in neutral hydrogen H as well as for hydrogenlike xenon Xe53+ and uranium U91+ ions. We found that for a correct evaluation of the total and energy-differential decay rates, summation over the negative-energy part of Dirac's spectrum should be properly taken into account both for high-Z and low-Z atomic systems.

Sergeeva, V., A. Alves, and AJL Phillips. "Neofusicoccum luteum associated with leaf necrosis and fruit rot of olives in New South Wales, Australia." Phytopathologia Mediterranea. 48 (2009): 294-298. Abstract
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Sousa, P., Stanimir Valtchev, Mário Neves, and A. Rodrigues. "A New Open-Loop Control Method for Stepping Motor Driving." 2nd International Conference on Power Engineering, Energy and Electrical Drives (POWERENG'2009). 2009. 605-610.
Sousa, P., S. Valtchev, M. V. Neves, and A. L. Rodrigues. "A new open-loop control method for stepping motor driving." POWERENG 2009 - 2nd International Conference on Power Engineering, Energy and Electrical Drives Proceedings (2009): 605-610. Abstract
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Polcyn, M., L. Jacobs, O. Mateus, and A. Schulp. "New specimens of Angolasaurus bocagei and comments on the early radiations of plioplatecarpine mosasaurs. Journal of Vertebrate Paleontology." Journal of Vertebrate Paleontology. 29 (2009): 165. Abstract
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Polcyn, M. J., LL Jacobs, O. Mateus, and AS Schulp. "New specimens of Angolasaurus bocagei and comments on the early radiations of plioplatecarpine mosasaurs. Journal of Vertebrate Paleontology." Journal of Vertebrate Paleontology. 29 (2009): 165. Abstract
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Louren{\c c}o, João, Nuno Pregui{\c c}a, Ricardo Dias, João Nuno Silva, João Garcia, and Lu\'ıs Veiga NGenVM: New Generation Execution Environments. Nuremberg, Germany, 2009. Abstract
This document describes a work-in-progress development of NGen-VM, a distributed infrastructure that manages execution environments with run-time and programming language support targeting applications developed in the Java programming language, deployed over clusters of many-core computers. For each running application or suite of related applications, a dedicated single-system image will be provided, regardless of the concurrent threads running on a single machine (on several cores) or scattered on different computers. Such system images rely on a single model for concurrency management (Transactional Shared Memory Model), in order fill the gap between the hardware infrastructure of clusters of many-core nodes and the application runtime that is independent from that hardware infrastructure. Interactions between threads in the same tasks will be supported by a Transactional Memory framework that provides the programming language with Atomic and Isolated code regions. Interactions between thread on different machines will also use the Transactional Memory model, but now resorting to a Distributed Shared Memory abstraction.
Silva, M. M., C. M. Leitão, and L. B. Oliveira. "Noise Performance of Transimpedance Amplifiers for Radiation Detectors." Proc. Of XXIV conference on Design of Circuits and Integrated Systems (DCIS2009) (2009): 1-6. Abstract
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Mateus, O., L. Jacobs, M. Polcyn, AS Schulp, D. Vineyard, A. Buta Neto, and M. Telles Antunes. "The oldest African eucryptodiran turtle from the Cretaceous of Angola." Acta Palaeontologica Polonica. 54 (2009): 581-588. Abstract
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Amaral, P., L. M. Fernandes, J. Júdice, and H. D. Sherali. "On optimal zero-preserving corrections for inconsistent linear systems." Journal of Global Optimization. 45 (2009): 645-666. Abstract

This paper addresses the problem of finding an optimal correction of an inconsistent linear system, where only the nonzero coefficients of the constraint matrix are allowed to be perturbed for reconstructing a consistent system. Using the Frobenius norm as a measure of the distance to feasibility, a nonconvex minimization problem is formulated, whose objective function is a sum of fractional functions. A branch-and-bound algorithm for solving this nonconvex program is proposed, based on suitably overestimating the denominator function for computing lower bounds. Computational experience is presented to demonstrate the efficacy of this approach.

Capelo, J. L., R. Carreira, M. Diniz, L. Fernandes, M. Galesio, C. Lodeiro, H. M. Santos, and G. Vale. "Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques." Analytica Chimica Acta. 650 (2009): 151-159. AbstractWebsite
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Ribeiro, Celso, Paulo J. Gomes, Paulo A. Ribeiro, Maria Raposo, Hugo Águas, Pedro Mendonça dos Santos, Beatriz Borges, and Pedro Brogueira. "Polymeric Film Sensors based on PAH-PAZO Ionic Self-assembled Multi-nanolayers." BIODEVICES. 2009. 458-461. Abstract
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Martins, M. C., J. P. Marques, A. M. Costa, J. P. Santos, F. Parente, S. Schlesser, Le E. - O. Bigot, and P. Indelicato. "Production and decay of sulfur excited species in an electron-cyclotron-resonance ion-source plasma." Physical Review A (Atomic, Molecular, and Optical Physics). 80 (2009): 032501. AbstractWebsite
The most important processes for the creation of S12+ to S14+ ions excited states from the ground configurations of S9+ to S14+ ions in an electron cyclotron resonance ion source, leading to the emission of K x-ray lines, are studied. Theoretical values for inner-shell excitation and ionization cross sections, including double-KL and triple-KLL ionizations, transition probabilities and energies for the de-excitation processes, are calculated in the framework of the multiconfiguration Dirac-Fock method. With reasonable assumptions about the electron energy distribution, a theoretical Kalpha x-ray spectrum is obtained, which is compared to recent experimental data.
Martins, M. C., J. P. Marques, A. M. Costa, J. P. Santos, F. Parente, S. Schlesser, E. O. Le Bigot, and P. Indelicato. "Production and decay of sulfur excited species in an electron-cyclotron-resonance ion-source plasma." Physical Review A. 80 (2009): 032501. AbstractWebsite

The most important processes for the creation of S12+ to S14+ ions excited states from the ground configurations of S9+ to S14+ ions in an electron cyclotron resonance ion source, leading to the emission of K x-ray lines, are studied. Theoretical values for inner-shell excitation and ionization cross sections, including double-KL and triple-KLL ionizations, transition probabilities and energies for the de-excitation processes, are calculated in the framework of the multiconfiguration Dirac-Fock method. With reasonable assumptions about the electron energy distribution, a theoretical Kalpha x-ray spectrum is obtained, which is compared to recent experimental data.

Torosantucci, Antonella, Paola Chiani, Carla Bromuro, Flavia De Bernardis, Angelina S. Palma, Yan Liu, Giuseppina Mignogna, Bruno Maras, Marisa Colone, Annarita Stringaro, Silvia Zamboni, Ten Feizi, and Antonio Cassone. "Protection by Anti-beta-Glucan Antibodies Is Associated with Restricted beta-1,3 Glucan Binding Specificity and Inhibition of Fungal Growth and Adherence." Plos One. 4 (2009). Abstract
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Chaves, I., C. Pinheiro, JAP Paiva, S. Planchon, K. Sergeant, J. Renaut, JA Graca, G. Costa, AV Coelho, and CPP Ricardo. "Proteomic evaluation of wound-healing processes in potato (Solanum tuberosum L.) tuber tissue." PROTEOMICS. 9 (2009): 4154-4175. Abstract
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Chaves, I., C. Pinheiro, JAP Paiva, S. Planchon, K. Sergeant, J. Renaut, JA Graca, G. Costa, AV Coelho, and CPP Ricardo. "Proteomic evaluation of wound-healing processes in potato (Solanum tuberosum L.) tuber tissue." PROTEOMICS. 9 (2009): 4154-4175. Abstract
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Viciosa, M. T., N. T. Correia, M. Salmeron Sanchez, AL Carvalho, MJ Romao, J. L. Gomez Ribelles, and M. Dionisio. "Real-Time Monitoring of Molecular Dynamics of Ethylene Glycol Dimethacrylate Glass Former." Journal of Physical Chemistry B. 113 (2009): 14209-14217. Abstract
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Santos, JM, and AJL Phillips. "Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal." Fungal Diversity. 34 (2009): 111-125. Abstract
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Amaro, P., J. P. Santos, F. Parente, A. Surzhykov, and P. Indelicato. "Resonance effects on the two-photon emission from hydrogenic ions." Physical Review A (Atomic, Molecular, and Optical Physics). 79 (2009): 062504. AbstractWebsite
A theoretical study of the all two-photon transitions from initial bound states with ni=2,3 in hydrogenic ions is presented. High-precision values of relativistic decay rates for ions with nuclear charge in the range 1<=Z<=92 are obtained through the use of finite basis sets for the Dirac equation constructed from B splines. We also report the spectral (energy) distributions of several resonant transitions, which exhibit interesting structures, such as zeros in the emission spectrum, indicating that two-photon emission is strongly suppressed at certain frequencies. We compare two different approaches (the line profile approach and the QED approach based on the analysis of the relativistic two-loop self-energy) to regularize the resonant contribution to the decay rate. Predictions for the pure two-photon contributions obtained in these approaches are found to be in good numerical agreement.
Amaro, P., J. P. Santos, F. Parente, A. Surzhykov, and P. Indelicato. "Resonance effects on the two-photon emission from hydrogenic ions." Physical Review A. 79 (2009): 062504. AbstractWebsite

A theoretical study of the all two-photon transitions from initial bound states with ni=2,3 in hydrogenic ions is presented. High-precision values of relativistic decay rates for ions with nuclear charge in the range 1<=Z<=92 are obtained through the use of finite basis sets for the Dirac equation constructed from B splines. We also report the spectral (energy) distributions of several resonant transitions, which exhibit interesting structures, such as zeros in the emission spectrum, indicating that two-photon emission is strongly suppressed at certain frequencies. We compare two different approaches (the line profile approach and the QED approach based on the analysis of the relativistic two-loop self-energy) to regularize the resonant contribution to the decay rate. Predictions for the pure two-photon contributions obtained in these approaches are found to be in good numerical agreement.

Honzí?ek, J., A. Mukhopadhyay, T. Santos-Silva, MJ Romão, and C. C. Romão. "Ring-functionalized molybdenocene complexes." Organometallics. 28 (2009): 2871-2879. Abstract
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Santos, S., Alberto Cardoso, A. Santos, and P. Gil Robust Monitoring and Fault Tolerance in Wireless Sensor Networks. n/a, 2009. Abstract
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