Showing papers by "Instituto Superior Técnico published in 2004"

Biclustering Algorithms for Biological Data Analysis: A Survey

Abstract: A large number of clustering approaches have been proposed for the analysis of gene expression data obtained from microarray experiments. However, the results from the application of standard clustering methods to genes are limited. This limitation is imposed by the existence of a number of experimental conditions where the activity of genes is uncorrelated. A similar limitation exists when clustering of conditions is performed. For this reason, a number of algorithms that perform simultaneous clustering on the row and column dimensions of the data matrix has been proposed. The goal is to find submatrices, that is, subgroups of genes and subgroups of conditions, where the genes exhibit highly correlated activities for every condition. In this paper, we refer to this class of algorithms as biclustering. Biclustering is also referred in the literature as coclustering and direct clustering, among others names, and has also been used in fields such as information retrieval and data mining. In this comprehensive survey, we analyze a large number of existing approaches to biclustering, and classify them in accordance with the type of biclusters they can find, the patterns of biclusters that are discovered, the methods used to perform the search, the approaches used to evaluate the solution, and the target applications.

Modeling Ionic Liquids Using a Systematic All-Atom Force Field

Abstract: A new force field for the molecular modeling of ionic liquids of the dialkylimidazolium cation family was constructed. The model is based on the OPLS-AA/AMBER framework. Ab initio calculations were performed to obtain several terms in the force field not yet defined in the literature. These include torsion energy profiles and distributions of atomic charges that blend smoothly with the OPLS-AA specification for alkyl chains. Validation was carried out by comparing simulated and experimental data on fourteen different salts, comprising three types of anion and five lengths of alkyl chain, in both the crystalline and liquid phases. The present model can be regarded as a step toward a general force field for ionic liquids of the imidazolium cation family that was built in a systematic way, is easily integrated with OPLS-AA/AMBER, and is transferable between different combinations of cation−anion.

Molecular Force Field for Ionic Liquids Composed of Triflate or Bistriflylimide Anions

Abstract: A set of force field parameters is proposed for the molecular simulation of ionic liquids containing the anions trifluoromethylsufate and bis(trifluoromethylsulfonyl)imide, also known as triflate and bistriflylimide, respectively. The new set can be combined with existing force fields for cations in order to simulate common room-temperature ionic liquids, such as those of the dialkylimidazolium family, and can be integrated with the OPLS-AA or similar force fields. Ab initio quantum chemical calculations were employed to obtain molecular geometry, torsional energy profiles, and partial charge distribution in the triflate and bistriflylimide anions. One of the torsions in bistriflylimide, corresponding to the dihedral angle S−N−S−C, has a complex energy profile which is precisely reproduced by the present parameter set. A new set of partial electrostatic charges is also proposed for the pyrrolidinium and tri- and tetra-alkylammonium cations. Again, these parameters can be combined with the OPLS-AA specific...

Proton shock acceleration in laser-plasma interactions.

Abstract: The formation of strong, high Mach number (2--3), electrostatic shocks by laser pulses incident on overdense plasma slabs is observed in one- and two-dimensional particle-in-cell simulations, for a wide range of intensities, pulse durations, target thicknesses, and densities. The shocks propagate undisturbed across the plasma, accelerating the ions (protons). For a dimensionless field strength parameter ${a}_{0}=16$ ($I{\ensuremath{\lambda}}^{2}\ensuremath{\approx}3\ifmmode\times\else\texttimes\fi{}{10}^{20}\text{ }\text{ }\mathrm{W}\text{ }{\mathrm{c}\mathrm{m}}^{\ensuremath{-}2}\text{ }\ensuremath{\mu}{\mathrm{m}}^{2}$, where $I$ is the intensity and $\ensuremath{\lambda}$ the wavelength), and target thicknesses of a few microns, the shock is responsible for the highest energy protons. A plateau in the ion spectrum provides a direct signature for shock acceleration.

Antibodies and Genetically Engineered Related Molecules: Production and Purification

Abstract: Antibodies and antibody derivatives constitute 20 % of biopharmaceutical products currently in development, and despite early failures of murine products, chimeric and humanized monoclonal antibodies are now viable therapeutics. A number of genetically engineered antibody constructions have emerged, including molecular hybrids or chimeras that can deliver a powerful toxin to a target such as a tumor cell. However, the general use in clinical practice of antibody therapeutics is dependent not only on the availability of products with required efficacy but also on the costs of therapy. As a rule, a significant percentage (50-80%) of the total manufacturing cost of a therapeutic antibody is incurred during downstream processing. The critical challenges posed by the production of novel antibody therapeutics include improving process economics and efficiency, to reduce costs, and fulfilling increasingly demanding quality criteria for Food and Drug Administration (FDA) approval. It is anticipated that novel affinity-based separations will emerge from the development of synthetic ligands tailored to specific biotechnological needs. These synthetic affinity ligands include peptides obtained by synthesis and screening of peptide combinatorial libraries and artificial non-peptidic ligands generated by a de novo process design and synthesis. The exceptional stability, improved selectivity, and low cost of these ligands can lead to more efficient, less expensive, and safer procedures for antibody purification at manufacturing scales. This review aims to highlight the current trends in the design and construction of genetically engineered antibodies and related molecules, the recombinant systems used for their production, and the development of novel affinity-based strategies for antibody recovery and purification.

Ontologies: How can They be Built?

Abstract: Ontologies are an important component in many areas, such as knowledge management and organization, electronic commerce and information retrieval and extraction. Several methodologies for ontology building have been proposed. In this article, we provide an overview of ontology building. We start by characterizing the ontology building process and its life cycle. We present the most representative methodologies for building ontologies from scratch, and the proposed techniques, guidelines and methods to help in the construction task. We analyze and compare these methodologies. We describe current research issues in ontology reuse. Finally, we discuss the current trends in ontology building and its future challenges, namely, the new issues for building ontologies for the Semantic Web.

Black-hole bomb and superradiant instabilities

Abstract: A wave impinging on a Kerr black hole can be amplified as it scatters off the hole if certain conditions are satisfied, giving rise to superradiant scattering. By placing a mirror around the black hole one can make the system unstable. This is the black-hole bomb of Press and Teukolsky. We investigate in detail this process and compute the growing time scales and oscillation frequencies as a function of the mirror's location. It is found that in order for the system black hole plus mirror to become unstable there is a minimum distance at which the mirror must be located. We also give an explicit example showing that such a bomb can be built. In addition, our arguments enable us to justify why large Kerr-AdS black holes are stable and small Kerr-AdS black holes should be unstable.

Inversion of Marine Radar Images for Surface Wave Analysis

Abstract: A method to estimate sea surface elevation maps from marine radar image sequences is presented. This method is the extension of an existing inverse modeling technique to derive wave spectra from marine radar images, which assumes linear wave theory with temporal stationarity and spatial homogeneity of the observed sea surface elevation. The proposed technique to estimate wave elevation maps takes into account a modulation transfer function (MTF), which describes the radar imaging mechanisms at grazing incidence and horizontal polarization. This MTF is investigated and empirically determined by wave measurements and numerical simulations. The numerical simulations show that shadowing is the dominant effect in the radar imaging mechanism at grazing incidence and horizontal polarization. Further comparisons of wave spectra, as well as comparisons of the wave height probability distributions obtained by the wave elevation maps and the corresponding buoy measurements with the theoretical Rayleigh distribution, confirm the applicability of the proposed method.

A high-intensity highly coherent soft X-ray femtosecond laser seeded by a high harmonic beam

Abstract: Synchrotrons have for decades provided invaluable sources of soft X-rays, the application of which has led to significant progress in many areas of science and technology. But future applications of soft X-rays--in structural biology, for example--anticipate the need for pulses with much shorter duration (femtoseconds) and much higher energy (millijoules) than those delivered by synchrotrons. Soft X-ray free-electron lasers should fulfil these requirements but will be limited in number; the pressure on beamtime is therefore likely to be considerable. Laser-driven soft X-ray sources offer a comparatively inexpensive and widely available alternative, but have encountered practical bottlenecks in the quest for high intensities. Here we establish and characterize a soft X-ray laser chain that shows how these bottlenecks can in principle be overcome. By combining the high optical quality available from high-harmonic laser sources (as a seed beam) with a highly energetic soft X-ray laser plasma amplifier, we produce a tabletop soft X-ray femtosecond laser operating at 10 Hz and exhibiting full saturation, high energy, high coherence and full polarization. This technique should be readily applicable on all existing laser-driven soft X-ray facilities.

Revival of the unified dark energy–dark matter model?

Abstract: We consider the generalized Chaplygin gas (GCG) proposal for unification of dark energy and dark matter and show that it admits an unique decomposition into dark energy and dark matter components once phantomlike dark energy is excluded. Within this framework, we study structure formation and show that difficulties associated to unphysical oscillations or blowup in the matter power spectrum can be circumvented. Furthermore, we show that the dominance of dark energy is related to the time when energy density fluctuations start deviating from the linear $\ensuremath{\delta}\ensuremath{\sim}a$ behavior.

Small Kerr-anti-de Sitter black holes are unstable

Abstract: Superradiance in black hole spacetimes can trigger instabilities. Here we show that, due to superradiance, small Kerr-anti-de Sitter black holes are unstable. Our demonstration uses a matching procedure, in a long wavelength approximation.

Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics

Abstract: To gain insight into the global mechanism underlying phenol toxicity and tolerance in bacteria, we have generated a two-dimensional protein reference map and used it to identify variations in protein expression levels in Pseudomonas putida KT2440 following exposure to sub-lethal inhibitory concentrations of this solvent. Inspection of the two-dimensional gel electrophoresis gels revealed that 1 h following sudden cell exposure to two different concentrations of phenol, leading to the inhibition of exponential growth (600 mg/L) or to growth arrest for, at least, 4 h before inhibited growth resumption (800 mg/L), the amount of 68 proteins was increased while the amount of 13 proteins was reduced. The up-regulated proteins include proteins involved in the: (i) oxidative stress response (AhpC, SodB,Tpx and Dsb); (ii) general stress reponse (UspA, HtpG, GrpE and Tig); (iii) energetic metabolism (AcnB, AtpH, Fpr, AceA, NuoE, and MmsA-1); (iv) fatty acid biosynthesis (FabB, AccC-1 and FabBx1); (v) inhibition of cell division (MinD); (vi) cell envelope biosynthesis (LpxC, VacJ, and MurA); (vii) transcription regulation (OmpR and Fur); and (viii) transport of small molecules (TolC, BraC, AotJ, AapJ, FbpA and OprQ). Among the down-regulated proteins are those involved in nucleotide biosynthesis (PurM, PurL, PyrH and Dcd) and cell motility (FliC). The information emerging from this genome expression profiling and the detailed investigation of the biological role of candidate genes, as targets of phenol toxicity or as determinants of phenol resistance in P. putida KT2440, will allow more rationale strategies for developing bacteria with greater solvent tolerance with impact in bioremediation and whole-cell biotransformations in media with organic solvents.

Increasing renewable energy sources in island energy supply : case study Porto Santo

Abstract: While the energy supply of most islands depends mainly on expensive oil derivatives’ importation, the others are linked by usually a weak electricity grid connection to the mainland. Due to high energy costs the islands are proving to be excellent test beds for the introduction of new technologies, and some islands are trying to become so-called renewable islands, to satisfy their energy demand mainly or entirely from indigenous and renewable sources, thus increasing the security of supply, and employment opportunities, without necessarily increasing the costs. Islands that have energy sources, such as hydro or geothermal energy, can easily integrate them into the power system, but those with mainly intermittent renewable energy sources are confronted with the necessity of energy storage. The most promising technologies are reversible hydro where geography allows, and storing hydrogen where it does not. The stored hydrogen can later be used for electricity production, and also for transport. This paper describes the H2RES model for optimisation of integration of hydrogen usage with intermittent renewable energy sources on the example of an isolated island in the Madeira archipelago, Porto Santo. It shows that it is possible to significantly increase the penetration of renewable energy sources, albeit at a relatively high cost, with hydrogen storage technology. The H2RES model, which includes reversible hydro and batteries as storage technologies, can serve as a valuable tool for island energy planning.

Dynamic Analysis for Planar Multibody Mechanical Systems with Lubricated Joints

Abstract: The dynamic analysis of planar multibody systems with revolute clearance joints, including dry contact and lubrication effects is presented here. The clearances are always present in the kinematic joints. They are known to be the sources for impact forces, which ultimately result in wear and tear of the joints. A joint with clearance is included in the multibody system much like a revolute joint. If there is no lubricant in the joint, impacts occur in the system and the corresponding impulsive forces are transmitted throughout the multibody system. These impacts and the eventual continuous contact are described here by a force model that accounts for the geometric and material characteristics of the journal and bearing. In most of the machines and mechanisms, the joints are designed to operate with some lubricant fluid. The high pressures generated in the lubricant fluid act to keep the journal and the bearing surfaces apart. Moreover, the lubricant provides protection against wear and tear. The equations governing the dynamical behavior of the general mechanical systems incorporate the impact force due to the joint clearance without lubricant, as well as the hydrodynamic forces owing to the lubrication effect. A continuous contact model provides the intra-joint impact forces. The friction effects due to the contact in the joints are also represented. In addition, a general methodology for modeling lubricated revolute joints in multibody mechanical systems is also presented. Results for a slider-crank mechanism with a revolute clearance joint between the connecting rod and the slider are presented and used to discuss the assumptions and procedures adopted.

Plasma based charged-particle accelerators

Abstract: Studies of charged-particle acceleration processes remain one of the most important areas of research in laboratory, space and astrophysical plasmas. In this paper, we present the underlying physics and the present status of high gradient and high energy plasma accelerators. We will focus on the acceleration of charged particles to relativistic energies by plasma waves that are created by intense laser and particle beams. The generation of relativistic plasma waves by intense lasers or electron beams in plasmas is important in the quest for producing ultra-high acceleration gradients for accelerators. With the development of compact short pulse high brightness lasers and electron positron beams, new areas of studies for laser/particle beam-matter interactions is opening up. A number of methods are being pursued vigorously to achieve ultra-high acceleration gradients. These include the plasma beat wave accelerator mechanism, which uses conventional long pulse (~100 ps) modest intensity lasers (I ~ 1014–1016 W cm−2), the laser wakefield accelerator (LWFA), which uses the new breed of compact high brightness lasers ( 1018 W cm−2, the self-modulated LWFA concept, which combines elements of stimulated Raman forward scattering, and electron acceleration by nonlinear plasma waves excited by relativistic electron and positron bunches. In the ultra-high intensity regime, laser/particle beam–plasma interactions are highly nonlinear and relativistic, leading to new phenomena such as the plasma wakefield excitation for particle acceleration, relativistic self-focusing and guiding of laser beams, high-harmonic generation, acceleration of electrons, positrons, protons and photons. Fields greater than 1 GV cm−1 have been generated with particles being accelerated to 200 MeV over a distance of millimetre. Plasma wakefields driven by positron beams at the Stanford Linear Accelerator Center facility have accelerated the tail of the positron beam. In the near future, laser plasma accelerators will be producing GeV particles.

Kinetic modeling of low-pressure nitrogen discharges and post-discharges

Abstract: The kinetic modeling of low-pressure (p ∼ 1−10 torr) stationary nitrogen discharges and the corresponding afterglows is reviewed. It is shown that a good description of the overall behavior of nitrogen plasmas requires a deep understanding of the coupling between different kinetics. The central role is played by ground-state vibrationally excited molecules, N2(X 1 Σ + g ,v ), which have a strong influence on the shape of the electron energy distribution function, on the creation and destruction of electronically excited states, on the gas heating, dissociation and on afterglow emissions. N2(X 1 Σ + ,v ) molecules are actually the hinge ensuring a strong link between the various kinetics. The noticeable task done by electronically excited metastable molecules, in particular N2(A 3 Σ + u )a nd N2(a � 1 Σ − u ), is also pointed out. Besides contributing to the same phenomena as vibrationally excited molecules, these electronic metastable states play also a categorical role in ionization. Furthermore, vibrationally excited molecules in high v levels are in the origin of the peaks observed in the flowing afterglow for the concentrations of several species, such as N2(A 3 Σ + ), N2(B 3 Πg), N + 2 (B 2 Σ + u ) and electrons, which occur downstream from the discharge after a dark zone as a consequence of the V-V up-pumping mechanism.

Caring for Agents and Agents that Care: Building Empathic Relations with Synthetic Agents

Abstract: When building agents and synthetic characters, and in order to achieve believability, we must consider the emotional relations established between users and characters, that is, we must consider the issue of "empathy". Defined in broad terms as "An observer reacting emotionally because he perceives that another is experiencing or about to experience an emotion", empathy is an important element to consider in the creation of relations between humans and agents. In this paper we will focus on the role of empathy in the construction of synthetic characters, providing some requirements for such construction and illustrating the presented concepts with a specific system called FearNot!. FearNot! was developed to address the difficult and often devastating problem of bullying in schools. By using role playing and empathic synthetic characters in a 3D environment, FearNot! allows children from 8 to 12 to experience a virtual scenario where they can witness (in a third-person perspective) bullying situations. To build empathy into FearNot! we have considered the following components: agentýs architecture; the charactersý embodiment and emotional expression; proximity with the user and emotionally charged situations.We will describe how these were implemented in FearNot! and report on the preliminary results we have with it.

ELM pace making and mitigation by pellet injection in ASDEX Upgrade

Abstract: In ASDEX Upgrade, experimental efforts aim to establish pace making and mitigation of type-I edge localized modes (ELMs) in high confinement mode (H-mode) discharges. Injection of small size cryogenic deuterium pellets (~(1.4?mm)2 ? 0.2?mm ? 2.5 ? 1019?D) at rates up to 83?Hz imposed persisting ELM control without significant fuelling, enabling for investigations well inside the type-I ELM regime. The approach turned out to meet all required operational features. ELM pace making was realized with the driving frequency ranging from 1 to 2.8 times the intrinsic ELM frequency, the upper boundary set by hardware limits. ELM frequency enhancement by pellet pace making causes much less confinement reduction than by engineering means like heating, gas bleeding or plasma shaping. Confinement reduction is observed in contrast to the typical for engineering parameters. Matched discharges showed triggered ELMs ameliorated with respect to intrinsic counterparts while their frequency was increased. No significant differences were found in the ELM dynamics with the available spatial and temporal resolution. By breaking the close correlation of ELM frequency and plasma parameters, pace making allows the establishment of fELM as a free parameter giving enhanced operational headroom for tailoring H-mode scenarios with acceptable ELMs. Use was made of the pellet pace making tool in several successful applications in different scenarios. It seems that further reduction of the pellet mass could be possible, eventually resulting in less confinement reduction as well.

The dynamic effect of pipe-wall viscoelasticity in hydraulic transients. Part I—experimental analysis and creep characterization

Abstract: The mechanical behaviour of the pipe material determines the pressure response of a fluid system during the occurrence of transient events. in viscoelastic pipes, typically made of polyethylene (pe), maximum or minimum transient pressures are rapidly attenuated and the overall pressure wave is delayed in time. this is a result of the retarded deformation of the pipe-wall. this effect has been observed in transient data collected in a high-density pe pipe-rig, at imperial college (london, uk). several transient tests were carried out to collect pressure and circumferential strain data. the pipe material presented a typical viscoelastic mechanical behaviour with a sudden pressure drop immediately after the fast valve closure, a major dissipation and dispersion of the pressure wave, and transient mechanical hysteresis. the creep-function of the pipe material was experimentally determined by creep tests, and, its order-of-magnitude was estimated based on pressure-strain data collected from the pipe-rig. a goo...

Latest supernova data in the framework of the generalized Chaplygin gas model

Abstract: We use the most recent Type Ia supernova data in order to study the dark energy–dark matter (XCDM) unification approach in the context of the generalized Chaplygin gas (GCG) model. Rather surprisingly, we find that data allow models with α > 1. We have studied how the GCG adjusts flat and non-flat models, and our results show that GCG is consistent with a flat case up to 68 per cent confidence level. Actually this holds even if one relaxes the flat prior assumption. We have also analysed what one should expect from a future experiment such as the Supernova/Acceleration Probe (SNAP). We find that there is a degeneracy between the GCG model and an XCDM model with a phantom-like dark energy component.

Near-GeV-energy laser-wakefield acceleration of self-injected electrons in a centimeter-scale plasma channel.

Abstract: The first three-dimensional, particle-in-cell (PIC) simulations of laser-wakefield acceleration of self-injected electrons in a 0.84 cm long plasma channel are reported. The frequency evolution of the initially 50 fs (FWHM) long laser pulse by photon interaction with the wake followed by plasma dispersion enhances the wake which eventually leads to self-injection of electrons from the channel wall. This first bunch of electrons remains spatially highly localized. Its phase space rotation due to slippage with respect to the wake leads to a monoenergetic bunch of electrons with a central energy of 0.26 GeV after 0.55 cm propagation. At later times, spatial bunching of the laser enhances the acceleration of a second bunch of electrons to energies up to 0.84 GeV before the laser pulse intensity is significantly reduced.

Analysis of consensus partition in cluster ensemble

Abstract: In combination of multiple partitions, one is usually interested in deriving a consensus solution with a quality better than that of given partitions. Several recent studies have empirically demonstrated improved accuracy of clustering ensembles on a number of artificial and real-world data sets. Unlike certain multiple supervised classifier systems, convergence properties of unsupervised clustering ensembles remain unknown for conventional combination schemes. In this paper, we present formal arguments on the effectiveness of cluster ensemble from two perspectives. The first is based on a stochastic partition generation model related to re-labeling and consensus function with plurality voting. The second is to study the property of the "mean" partition of an ensemble with respect to a metric on the space of all possible partitions. In both the cases, the consensus solution can be shown to converge to a true underlying clustering solution as the number of partitions in the ensemble increases. This paper provides a rigorous justification for the use of cluster ensemble.

Simple Continuous-Time Formulation for Short-Term Scheduling of Batch and Continuous Processes

Abstract: A new and simple general mathematical formulation for scheduling multipurpose plants involving batch and/or continuous processes, based on the resource−task network (RTN) representation, is presented. The formulation uses a uniform-time-grid continuous-time representation and results in a very efficient mixed integer linear programming model that can be solved to optimality for a given number of event points. The performance of the formulation is illustrated through the solution of two case studies that have been thoroughly examined in the literature: the first involves a continuous plant and is solved for three different storage policies, and the second concerns a batch plant. The formulation is shown to compare favorably to existing continuous-time formulations. More specifically, a new optimal solution is obtained for the finite intermediate storage scenario of the first case that is also a global optimal solution.