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2000
Prudencio, M., A. Pereira, P. Tavares, S. Besson, I. Cabrito, K. Brown, B. Samyn, B. Devreese, J. VanBeeumen, F. Rusnak, G. Fauque, J. Moura, M. Tegoni, C. Cambillau, and I. Moura. "{Purification, characterization, and preliminary crystallographic study of copper-containing nitrous oxide reductase from Pseudomonas nautica 617}." Biochemistry. 39 (2000): 3899-3907.
1999
Cipriano, F. "The two dimensional Euler equation: A statistical study." COMMUNICATIONS IN MATHEMATICAL PHYSICS. 201 (1999): 139-154. Abstract

{We construct surface type measures on the level sets for the renormalized energy, which is an invariant quantity for the two dimensional periodic Euler flow, and prove the existence of weak solutions living on such level sets. Other classes of invariant measures for the motion are also introduced.}

Cipriano, F., and A. B. Cruzeiro. "Flows associated to tangent processes on the Wiener space." JOURNAL OF FUNCTIONAL ANALYSIS. 166 (1999): 310-331. Abstract

{We prove, under certain regularity assumptions on the coefficients, that tangent processes (namely semimartingales d xi(tau) = a dx(tau) + b d tau where a is an antisymmetric matrix) generate flows on the classical Wiener space. Main applications of the result can be found in the study of the geometry of path spaces. (C) 1999 Academic Press.}

Cunha, José C., João Louren{\c c}o, and Tiago Antão. "An experiment in tool integration: the DDBG parallel and distributed debugger." J. Syst. Archit.. 45 (1999): 897-907. AbstractWebsite
Most known teaching experiences focus on parallel computing courses only, but some teaching experiences on distributed computing courses have also been reported. In this paper we describe a course on Parallel and Distributed Processing that is taught at undergraduate level in the Computer Science degree of our University.This course presents an integrated approach concerning concurrency, parallelism, and distribution issues. It’s a breadth-first course addressing a wide spectrum of abstractions: the theoretical component focus on the fundamental abstractions to model concurrent systems, including process cooperation schemes, concurrent programming models, data and control distribution, concurrency control and recovery in transactional systems, and parallel processing models; the practical component illustrates the design and implementation issues involved in selected topics such as a data and control distribution problem, a distributed transaction-based support system and a parallel algorithm.We also discuss how this approach has been contributing to prepare the student to further actions regarding research and development of concurrent, distributed, or parallel systems.
Cunha, José C., João M. Lourenço, and Tiago Antão. "An experiment in tool integration: the {DDBG} parallel and distributed debugger." J. Syst. Archit.. 45 (1999): 897-907. Abstractjsa99.pdfWebsite

Most known teaching experiences focus on parallel computing courses only, but some teaching experiences on distributed computing courses have also been reported. In this paper we describe a course on Parallel and Distributed Processing that is taught at undergraduate level in the Computer Science degree of our University.This course presents an integrated approach concerning concurrency, parallelism, and distribution issues. It's a breadth-first course addressing a wide spectrum of abstractions: the theoretical component focus on the fundamental abstractions to model concurrent systems, including process cooperation schemes, concurrent programming models, data and control distribution, concurrency control and recovery in transactional systems, and parallel processing models; the practical component illustrates the design and implementation issues involved in selected topics such as a data and control distribution problem, a distributed transaction-based support system and a parallel algorithm.We also discuss how this approach has been contributing to prepare the student to further actions regarding research and development of concurrent, distributed, or parallel systems.

Correia, C., E. Monzani, I. Moura, J. Lampreia, and JJG Moura. "Cross-linking between cytochrome c(3) and flavodoxin from Desulfovibrio gigas." BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 256 (1999): 367-371. Abstract
Tetraheme cytochrome c(3) (13 kDa) and flavodoxin (16 kDa), are small electron transfer proteins that have been used to mimic, in vitro, part of the electron-transfer chain that operates between substract electron donors and respiratory electron accepters partners in Desulfovibrio species (Palma, N., Moura, I., LeGall, J., Van Beeumen, J., Wampler, J., Moura, J. J. G. (1994) Biochemistry 33, 6394-6407). The electron transfer between these two proteins is believed to occur through the formation of a specific complex where electrostatic interaction is the main driving force (Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P.K. and Wampler, J.E. (1988) Biochemistry 27, 2444-2450, Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P., Wampler, J. (1989) fur. J. Biochem. 185, 695-700). In order to obtain structural information of the pre-complex, a covalent complex between the two proteins was prepared. A water-soluble carbodiimide {[}EDC (1-ethyl-3(3 dimethylaminopropyl) carbodiimide hydrochloride] was used for the cross linking reaction. The reaction was optimized varying a wide number of experimental parameters such as ionic strength, protein and cross linker concentration, and utilization of different cross linkers and reaction time between the crosslinker and proteins. (C) 1999 Academic Press.
Cabrita, E. J., SX Candeias, A. M. Ramos, CAM Afonso, and AG Santos. "Novel acid catalysed 1,4-addition-type ring-opening polymerisation of cyclic phosphorimidates." Tetrahedron Letters. 40 (1999): 137-140. Abstract
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Nunes, Isabel L., and Rita A. Ribeiro Fuzzy evaluation module of ERGO_X. Eds. C. Carlsson, and F. Tétard. Intelligent Systems and Active DSS - IFORS SPC9. Turku - Finlândia, 1999. Abstract
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Freitas, J. A. T., C. Cismasiu, and Z. M. Wang. "Comparative analysis of hybrid-Trefftz stress and displacement elements." Archives of Computational Methods in Engineering. State of the art reviews. 6.1 (1999): 35-39.
Correia, Isabel, and Maria Eugénia Captivo Different approaches for a capacitated plant location problem with several possible sizes. XXXI Simpósio Brasileiro de Pesquisa Operacional., 1999.
Cunha, José C., Pedro D. Medeiros, Vitor Duarte, João Lourenço, and Cecilia Gomes. "An Experience in Building a Parallel and Distributed Problem-Solving Environment." Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'99). CSREA Press, 1999. 1804-1809. Abstractpdpta99.pdf

We describe our experimentation with the design and implementation of specific environments, consisting of heterogeneous computational, visualization, and control components. We illustrate the approach with the design of a problem–solving environment supporting the execution of genetic algorithms. We describe a prototype supporting parallel execution, visualization, and steering. A life cycle for the development of applications based on genetic algorithms is proposed.

Freitas, J. A. T., and C. Cismaşiu. "Numerical implementation of hybrid-{T}refftz displacement elements." Computers & Structures. 73 (1999): 207-225. Abstract

The numerical implementation of the displacement model of the hybrid-{T}refftz finite element formulation is presented. The geometry of the supporting element is not constrained a priori. Unbounded, non-convex and multiply connected elements can be used. The approximation basis is naturally hierarchical and very rich. It is constructed on polynomial solutions of the governing differential equation, and extended to include the particular terms known to model accurately important local effects, namely the singular stress patterns due to cracks or point loads. Numerical and semi-analytical methods are used to compute the finite element matrices and vectors, all of which present boundary integral expressions. Appropriate procedures to store, manipulate and solve symmetric highly sparse systems are used. The characteristics of the finite element solving system in terms of sparsity and conditioning are analysed, as well as its sensitivity to the effects of mesh distortion, incompressibility and rotation of the local reference systems. Benchmark tests are used also to illustrate the performance of the element in the estimation of displacements, stresses and stress intensity factors.

Pinheiro-Pita, HJ, F. Coito, A. Steiger-Garção, R. Gonçalves, and L. Palma. "O projecto OCTOPUS: Modelo da Arquitectura de Software." Jornadas de Engenharia de Telecomunicações e Computadores – JETC99. 1999. Abstract

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Camarinha-Matos, L. M., H. Afsarmanesh, and T. Cardoso. "Partners search and quality-related information exchange in a virtual." Global Production Management: IFIP WG5. 7 International Conference on Advances in Production Management Systems September 6–10, 1999, Berlin, Germany. Vol. 24. Springer, 1999. 76. Abstract

Partners search and selection is an important activity in the life cycle of a Virtual Enterprise. Among other factors, the commitment of the potential partners to fulfil quality requirements is a major decision criterion during the selection phase. An approach to search suppliers in suppliers’ directories available on Internet is presented and the major negotiation steps leading to an adequate selection of partners are introduced. The quality-related information management functionalities required in a virtual enterprise support platform are also discussed.

Camarinha-Matos, L. M., and T. Cardoso. "Selection of Partners for a Virtual Enterprise." Infrastructures for Virtual Enterprises: Networking Industrial Enterprises IFIP TC5 WG5. 3/PRODNET Working Conference on Infrastructures for Virtual Enterprises (PRO-VE’99) October 27–28, 1999, Porto, Portugal. Vol. 27. Springer, 1999. 259. Abstract

Electronic procurement of partners is an important functionality during the life cycle of a virtual enterprise. A prototype implementation, featuring selection based on both internal or Internet-based suppliers’ directories, is discussed. The generation of call for tenders and support for management of received bids is introduced and directions for contract negotiation and decision support system are discussed.

Cunha, José C., Pedro D. Medeiros, Vitor Duarte, João Louren{\c c}o, and Cecilia Gomes. "An Experience in Building a Parallel and Distributed Problem-Solving Environment." PDPTA 1999: Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications. CSREA Press, 1999. 1804-1809. Abstract
We describe our experimentation with the design and implementation of specific environments, consisting of heterogeneous computational, visualization, and control components. We illustrate the approach with the design of a problem–solving environment supporting the execution of genetic algorithms. We describe a prototype supporting parallel execution, visualization, and steering. A life cycle for the development of applications based on genetic algorithms is proposed.
Godinho, M. H., C. Costa, and J. L. Figueirinhas. "Liquid crystal and cellulose derivatives composites used in electro-optical applications." Molecular Crystals and Liquid Crystals. 331.1 (1999): 173-179. Abstract
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Mateus, O. "Monofilia dos dinossauros e Origem das Aves: Serão as aves dinossauros?" Actas do II Congresso de Ornitologia. Eds. P, P. Catry, and F. Moreira. Lisboa: SPEA- Sociedade Portuguesa para o Estudo das Aves, 1999. 184-185. Abstract
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Mateus, O. "Monofilia dos dinossauros e Origem das Aves: Serão as aves dinossauros?" Actas do II Congresso de Ornitologia. Eds. Spea- Sociedade Portuguesa Estudo para o das Aves, P, P. Catry, and F. Moreira. Lisboa 1999. 184-185. Abstract
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Almendra, MJ, CD Brondino, O. Gavel, AS Pereira, P. Tavares, S. Bursakov, R. Duarte, J. CALDEIRA, JJG Moura, and I. Moura. "Purification and characterization of a tungsten-containing formate dehydrogenase from Desulfovibrio gigas." Biochemistry. 38 (1999): 16366-16372. AbstractWebsite

An air-stable formate dehydrogenase (FDH), an enzyme that catalyzes the oxidation of formate to carbon dioxide, was purified from the sulfate reducing organism Desulfovibrio gigas (D. gigas) NCIB 9332. D. gigas FDH is a heterodimeric protein [alpha (92 kDa) and beta (29 kDa) subunits] and contains 7 +/- 1 Fe/protein and 0.9 +/- 0.1 W/protein, Selenium was not detected. The UV/visible absorption spectrum of D, gigas FDH is typical of an iron-sulfur protein. Analysis of pterin nucleotides yielded a content of 1.3 +/- 0.1 guanine monophosphate/mol of enzyme, which suggests a tungsten coordination with two molybdopterin guanine dinucleotide cofactors. Both Mossbauer spectroscopy performed on D. gigas FDH grown in a medium enriched with Fe-57 and EPR studies performed in the native and fully reduced state of the protein confirmed the presence of two [4Fe-4S] clusters. Variable-temperature EPR studies showed the presence of two signals compatible with an atom in a d(1) configuration albeit with an unusual relaxation behavior as compared to the one generally observed for W(V) ions.

Coufal, DE, P. Tavares, AS Pereira, BH Hyunh, and SJ Lippard. "Reactions of nitric oxide with the reduced non-heme diiron center of the soluble methane monooxygenase hydroxylase." Biochemistry. 38 (1999): 4504-4513. AbstractWebsite

The soluble methane monooxygenase system from Methylococcus capsulatus (Bath) catalyzes the oxidation of methane to methanol and water utilizing dioxygen at a non-heme, carboxylate-bridged diiron center housed in the hydroxylase (H) component. To probe the nature of the reductive activation of dioxygen in this system, reactions of an analogous molecule, nitric oxide, with the diiron(II) form of the enzyme (H-red) Were investigated by both continuous and discontinuous kinetics methodologies using optical, EPR, and Mossbauer spectroscopy. Reaction of NO with H-red affords a dinitrosyl species, designated H-dinitrosyl, with optical spectra (lambda(max) = 450 and 620 nm) and Mossbauer parameters (delta = 0.72 mm/s, Delta E-Q = 1.55 mm/s) similar to those of synthetic dinitrosyl analogues and of the dinitrosyl adduct of the reduced ribonucleotide reductase R2 (RNR-R2) protein. The H-dinitrosyl species models features of the H-peroxo intermediate formed in the analogous dioxygen reaction. In the presence of protein B, H-dinitrosyl builds up with approximately the same rate constant as H-peroxo (similar to 26 s(-1)) at 4 degrees C. In the absence of protein B, the kinetics of H-dinitrosyl formation were best fit with a biphasic A –> B –> C model, indicating the presence of an intermediate species between H-red and H-dinitrosyl. This result contrasts with the reaction of H-red with dioxygen, in which the H-peroxo intermediate forms in measurable quantities only in the presence of protein B. These findings suggest that protein B may alter the positioning but not the availability of coordination sites on iron for exogenous ligand binding and reactivity.

Archer, M., AL Carvalho, S. Teixeira, I. Moura, JJG Moura, F. Rusnak, and MJ Romao. "Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein." Protein Science. 8 (1999): 1536-1545. Abstract
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Almendra, MJ, CD Brondino, O. Gavel, AS Pereira, P. Tavares, S. Bursakov, R. Duarte, J. CALDEIRA, JJG Moura, and I. Moura. "{Purification and characterization of a tungsten-containing formate dehydrogenase from Desulfovibrio gigas}." Biochemistry. 38 (1999): 16366-16372. Abstract
An air-stable formate dehydrogenase (FDH), an enzyme that catalyzes the oxidation of formate to carbon dioxide, was purified from the sulfate reducing organism Desulfovibrio gigas (D. gigas) NCIB 9332. D. gigas FDH is a heterodimeric protein [alpha (92 kDa) and beta (29 kDa) subunits] and contains 7 +/- 1 Fe/protein and 0.9 +/- 0.1 W/protein, Selenium was not detected. The UV/visible absorption spectrum of D, gigas FDH is typical of an iron-sulfur protein. Analysis of pterin nucleotides yielded a content of 1.3 +/- 0.1 guanine monophosphate/mol of enzyme, which suggests a tungsten coordination with two molybdopterin guanine dinucleotide cofactors. Both Mossbauer spectroscopy performed on D. gigas FDH grown in a medium enriched with Fe-57 and EPR studies performed in the native and fully reduced state of the protein confirmed the presence of two [4Fe-4S] clusters. Variable-temperature EPR studies showed the presence of two signals compatible with an atom in a d(1) configuration albeit with an unusual relaxation behavior as compared to the one generally observed for W(V) ions.