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1999
Wengenack, N., H. Lopes, M. Kennedy, P. Tavares, AS Pereira, I. Moura, JJG Moura, and F. Rusnak. "Redox potential of the heme protein KatG from Mycobacterium tuberculosis." Journal of Inorganic Biochemistry. 74 (1999): 336. AbstractWebsite
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Santos, J. P., J. P. Marques, F. Parente, E. Lindroth, P. Indelicato, and J. P. Desclaux. "Relativistic 2s1/2 (L1) atomic subshell decay rates and fluorescence yields for Yb and Hg." Journal of Physics B: Atomic and Molecular Physics. 32 (1999): 2089. AbstractWebsite
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Santos, J. P., F. Mota-Furtado, M. F. Laranjeira, and F. Parente. "Rydberg states of atoms in parallel electric and magnetic fields." Physical Review A. 59 (1999): 1703-1706. AbstractWebsite

We present theoretical results for the photoabsorption spectrum of an atom in parallel electric and magnetic fields, using the R-matrix method combined with quantum-defect theory. We introduce a radial basis set which is complete and orthonormal over a semi-infinite interval [r0,(infinity)), to allow calculations to be performed for high Rydberg states in nonhydrogenic atoms without encountering problems due to linear dependence of the basis set. The nonhydrogenic character of the spectra is analyzed for Li and Rb, and a comparison is made with previous high-precision experiments which shows that the theoretical results agree very well with experiment.

Paulino, Hervé, Fernando Silva, and Luís Lopes. "Um Modelo de Programação Paralela Simples para Arquitecturas Distribuídas de Baixo-Custo." Proceedings of the 11th Symposium on Computer Architecture and High Performance Computing (SBAC-PAD'99). Eds. Philippe O. A. Navaux, Tiarajú A. Diverio, and Cláudio R. Geyer. 1999. 121-126. Abstract
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Paulino, Hervé, Fernando Silva, and Luís Lopes Um Modelo de Programação Paralela Simples para Arquitecturas Distribuíidas de Baixo-Custo. http://www.dcc.fc.up.pt/Pubs/treports.html: DCC - FC & LIACC, Universidade do Porto, 1999. Abstract
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Allain, R., P. Taquet, B. Battail, J. Dejax, P. Richir, M. Véran, F. Limon-Duparcmeur, and et al. "Un nouveau genre de dinosaure sauropode de la formation des Grès supérieurs (Aptien-Albien) du Laos." Comptes Rendus de l'Académie des Sciences-Series IIA-Earth and Planetary Science. 329 (1999): 609-616. Abstract
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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. Abstract
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.
Wengenack, N., H. Lopes, M. Kennedy, P. Tavares, AS Pereira, I. Moura, JJG Moura, and F. Rusnak. "{Redox potential of the heme protein KatG from Mycobacterium tuberculosis}." Journal Of Inorganic Biochemistry. 74 (1999): 336.
Leitão, Carlos M. M., Teresa Almeida, Gregoire Bonfait, O. M. N. D. Teodoro, and A. M. C. Moutinho. "{UHV sample holder for fast heating and cooling cycles}." Vaccum. 52 (1999): 23-26. Abstract

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1998
Volsky, S., Elena Lomonova, Ben J. Klaassens, and Stanimir Valtchev. "A Basic Computer?Aided Course on Dynamic Processes in Mechatronic Systems for Aeronautical Engineers." 9th Annual Conference of the European Association for Education in Electrical and Information Engineering (EAEEIE). 1998. 293-298.
Cunha, José C., and João Louren{\c c}o. "An integrated course on parallel and distributed processing." SIGCSE Bull.. 30 (1998): 217-221. 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.
Leite, {João Alexandre Carvalho Pinheiro}, and {José Júlio Alves} Alferes. "Dynamic Logic Programming." Declarative Programming. 1998. 393-408. Abstract
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Leite, {João Alexandre Carvalho Pinheiro}, and {José Júlio Alves} Alferes. "Dynamic Logic Programming." Representation and Reasoning. Morgan Kaufmann, 1998. 98-109. Abstract
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Paulino, Hervé, Fernando Silva, and Luís Lopes. "di_pSystem: Um Ambiente de Programação Paralela para Arquitecturas de Memória Distribuída." Actas da Primeira Conferência sobre Redes de Computadores (CRC'98). Coimbra, Portugal 1998. 143-148. Abstract

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Cunha, José C., Pedro D. Medeiros, João M. Lourenço, Vítor Duarte, João Vieira, Bruno Moscão, Daniel Pereira, and Rui Vaz. "The DOTPAR Project: Towards a Framework Supporting Domain Oriented Tools for Parallel and Distributed Processing." Proceedings of the International Conference and Exhibition on High-Performance Computing and Networking (HPCN'98). HPCN Europe 1998. London, UK: Springer-Verlag, 1998. 952-954. Abstractdotpar98.pdf

We discuss the problem of building domain oriented environments by a composition of heterogeneous application components and tools. We describe several individual tools that support such environments, namely a distributed monitoring and control tool (DAMS), a process-based distributed debugger (PDBG) and a heterogeneous interconnection model (PHIS). We discuss our experience with the development of a Problem Oriented Environment in the domain of genetic algorithms, obtained by a composition of heterogeneous tools and application components.

Cunha, José C., João M. Lourenço, João Vieira, Bruno Moscão, and Daniel Pereira. "A Framework to Support Parallel and Distributed Debugging." Proceedings of the International Conference and Exhibition on High-Performance Computing and Networking (HPCN'98). HPCN Europe 1998. London, UK: Springer-Verlag, 1998. 708-717. Abstracthpcn98.pdf

We discuss debugging prototypes that can easily support new functionalities, depending on the requirements of high-level computational models, and allowing a coherent integration with other tools in a software engineering environment. Concerning the first aspect, we propose a framework that identifies two distinct levels of functionalities that should be supported by a parallel and distributed debugger using: a process and thread-level, and a coordination level concerning sets of processes or threads. An incremental approach is used to effectively develop prototypes that support both functionalities. Concerning the second aspect, we discuss how the interfacing with other tools has influenced the design of a process-level debugging interface (PDBG) and a distributed monitoring and control layer called (DAMS).

Mendes, B., P. Urbano, C. Alves, J. Morais, N. Lapa, and J. F. Oliveira. "Fungi as environmental microbiological indicators." Water Science and Technology. 38.12 (1998): 155-162. AbstractWebsite

An evaluation of the mycological quality of the sand beaches of the Lisboa and Vale do Tejo coastal area in Portugal was undertaken in May-October 1994. The keratinolytic fungi, yeasts, potential pathogenic and allergic and/or environmental saprophytic fungi were analysed. The results for the yeast Candida were evaluated according to the “Proposed Guidelines for the Microbiological Quality of Sand” (Mendes et al., 1993). The data showed good/satisfactory quality of the sand beaches for the genus Candida. The results indicate that the allergic and/or environmental saprophytic fungi were the most common in sand beaches. The fungi Scopulariopsis and the yeast Candida could be used as specific indicator organisms of sand beaches quality. A new quality objective is introduced that will contribute to improve the sand beaches quality.

Cunha, José C., and João M. Lourenço. "An Integrated Course on Parallel and Distributed Processing." SIGCSE Bull.. 30 (1998): 217-221. Abstractsigcse98.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.

Lourenço, João M., and José C. Cunha. "The PDBG Process-Level Debugger for Parallel and Distributed Programs." Proceedings of the SIGMETRICS symposium on Parallel and Distributed Tools. {SPDT}'98. New York, NY, USA: ACM, 1998. 154. Abstractspdt-asbt98.pdf

In this paper we discuss several issues concerning the design and implementation of a debugger for parallel and distributed applications. This debugger uses a client-server approach to isolate the debugging user-interface from the debugging services, by way of a two-level structured approach: the component-level to observe and act upon individual processes; and the coordination-level to observe the interprocess relations and act upon them.

Lourenço, João M., and José C. Cunha. "Replaying Distributed Applications with RPVM." Proceeding of the 2nd Austrian-Hungarian Workshop on Distributed and Parallel Systems (DAPSYS'98). University of Vienna, 1998. Abstractdapsys98.pdf

Parallel debugging is complex and difficult. Complex because the programmer has to deal with multiple program flows and process interactions, and difficult due to the very limited choice on effective and easy-to-use debugging tools for parallel programming. Simple and necessary features for parallel debugging are absent even from commercial debuggers, such as a record-replay feature, that allows to re-execute multiple times a parallel application assuring that during each re-execution the internal race conditions are solved in the same way they were in the first time. Some work has been done on record-replay techniques for parallel and distributed applications, but just a few have been applied to specific systems (such as PVM or MPI), and even less have produced working prototypes. In this paper we describe a method designed to work with the PVM system and how it was implemented to provide a working prototype.

Lourenço, João M., and José C. Cunha. "A Thread-Level Distributed Debugger." Proceedings of the 3rd International Conference on Vector and Parallel Processing (VecPar'98). Porto, Portugal: Universidade do Porto, 1998. 359-366. Abstractvecpar98.pdf

In order to address the diversity of existing parallel programming models, it is important to provide development environments that can be incrementally extended with new services. Concerning the debugging of process based models, we have previously designed and implemented a basic interface that can be accessed by other tools as well as by debugging modules associated with high-level programming languages.

Cunha, José C., João M. Lourenço, and Vitor Duarte. "Tool Integration Issues for Parallel and Distributed Debugging." Proceedings of the 3rd SEIHPC Workshop. Braga, Portugal: University of Westminster, 1998. Abstractseihpc98.pdf

This paper describes our experience with the design and implementation of a distributed debugger for C/PVM programs within the scope of the SEPP and HPCTI Copernicus projects. These projects aimed at the development of an integrated parallel software engineering environment based on a high-level graphical parallel programming model (GRAPNEL) and a set of associated tools supporting graphical edition, compilation, simulated and real parallel execution, testing, debugging, performance monitoring, mapping, and load balancing. We discuss how the development of the debugging tool was strongly influenced by the requirements posed by other tools in the environment, namely support for high-level graphical debugging of GRAPNEL programs, and support for the integration of static and dynamic analysis tools. We describe the functionalities of the DDBG debugger and its internal architecture, and discuss its integration with two separate tools in the SEPP/HPCTI environment: the GRED graphical editor for GRAPNEL programs, and the STEPS testing tool for C/PVM programs.

Cunha, José C., João Lourenço, and Vitor Duarte. "Using DDBG to Support Testing and High-level Debugging Interfaces." Computers and Artificial Intelligence. 17 (1998). Abstractcaij98.pdfWebsite

This paper describes our experience with the design and implementation of a distributed debugger for C/PVM programs within the scope of the SEPP and HPCTI Copernicus projects. These projects aimed at the development of an integrated parallel software engineering environment based on a high-level graphical parallel programming model (GRAPNEL) and a set of associated tools supporting graphical edition, compilation, simulated and real parallel execution, testing, debugging, performance monitoring, mapping, and load balancing. We discuss how the development of the debugging tool was strongly influenced by the requirements posed by other tools in the environment, namely support for high-level graphical debugging of GRAPNEL programs, and support for the integration of static and dynamic analysis tools. We describe the functionalities of the DDBG debugger and its internal architecture, and discuss its integration with two separate tools in the SEPP/HPCTI environment: the GRED graphical editor for GRAPNEL programs, and the STEPS testing tool for C/PVM programs.

Valentine, AM, P. Tavares, AS Pereira, R. Davydov, C. Krebs, BM Koffman, DE Edmondson, BH HUYNH, and SJ Lippard. "{Generation of a mixed-valent Fe(III)Fe(IV) form of intermediate Q in the reaction cycle of soluble methane monooxygenase, an analog of intermediate X in ribonucleotide reductase R2 assembly}." Journal Of The American Chemical Society. 120 (1998): 2190-2191.
Cunha, José C., Pedro D. Medeiros, João Louren{\c c}o, V\'ıtor Duarte, João Vieira, Bruno Moscão, Daniel Pereira, and Rui Vaz. "The DOTPAR Project: Towards a Framework Supporting Domain Oriented Tools for Parallel and Distributed Processing." HPCN 1998: Proceedings of the International Conference and Exhibition on High-Performance Computing and Networking. HPCN Europe 1998. London, UK: Springer-Verlag, 1998. 952-954. Abstract
We discuss the problem of building domain oriented environments by a composition of heterogeneous application components and tools. We describe several individual tools that support such environments, namely a distributed monitoring and control tool (DAMS), a process-based distributed debugger (PDBG) and a heterogeneous interconnection model (PHIS). We discuss our experience with the development of a Problem Oriented Environment in the domain of genetic algorithms, obtained by a composition of heterogeneous tools and application components.