Matrix fractional systems

This paper addresses the matrix representation of dynamical systems in the perspective of fractional calculus. Fractional elements and fractional systems are interpreted under the light of the classical Cole–Cole, Davidson–Cole, and Havriliak–Negami heuristic models. Numerical simulations for an electrical circuit enlighten the results for matrix based models and high fractional orders. The conclusions clarify the distinction between fractional elements and fractional systems.

Assessing self-organization and emergence in Evolvable Assembly Systems (EAS)

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Ontogeny of swimming capacity in plaice (Pleuronectes platessa) larvae

Little is known regarding the swimming ability of the larvae of European plaice (Pleuronectes platessa) in relation to changes in total length (TL), dry weight (DW) and developmental stage, which is surprising given the importance of transport processes to the recruitment dynamics of this species in the North Sea and elsewhere. We investigated ontogenetic changes in the critical swimming speed (Ucrit) of plaice from hatching to the onset of metamorphosis (50 days post-hatch, dph) at 8 °C. The mean (±SD) TL and DW growth rates were 1.59 ± 0.81 and 7.7 ± 0.35 % d−1, respectively. Larvae were unable to swim at against a minimum current speed of <0.5 cm s−1 until 10 dph (7 mm TL), after which Ucrit significantly increased with increasing TL until the onset of metamorphosis and subsequent settlement. Mean (±SD) Ucrit was 0.38(0.35), 1.59(0.54), 2.27(0.49) and 2.99(0.37) cm s−1 for stage I (6.61 ± 2.64 mm TL), stage II (7.75 ± 0.60 mm TL), stage III (9.10 ± 1.00 mm TL) and stage IV (11.59 ± 0.85 mm TL) larvae, respectively. Larval TL, DW, DNA content, RNA content and Ucrit significantly increased, whereas sRD significantly declined as larvae developed from stage I to V. Although inter-individual differences in Ucrit (coefficient of variation, CV = 33 %) were as large as those in biochemical and morphological condition (CV’s of 21–42 %), differences in Ucrit were not significantly related to those in nutritional condition and larvae with lower DNA/DW had also better swimming abilities. These estimates should be useful to ongoing efforts to create individual- based models of the transport, foraging and growth of plaice larvae in the North Sea.

Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

Single molecule simulation of diffusion and enzyme kinetics

This work presents a molecular-scale agent-based model for the simulation of enzymatic reactions at experimentally measured concentrations. The model incorporates stochasticity and spatial dependence, using diffusing and reacting particles with physical dimensions. We developed strategies to adjust and validate the enzymatic rates and diffusion coefficients to the information required by the computational agents, i.e., collision efficiency, interaction logic between agents, the time scale associated with interactions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecular location (a source of biological noise) in the speed at which the reactions take place. Simulations were conducted for experimental data on the 2-hydroxymuconate tautomerase (EC 5.3.2.6, UniProt ID Q01468) and the Steroid Delta-isomerase (EC 5.3.3.1, UniProt ID P07445). Obtained results demonstrate that our approach is in accordance to existing experimental data and long-term biophysical and biochemical assumptions.

Retribution in a cheap-talk experiment

We use a two-person 3-stage game to investigate whether people choose to punish or reward another player by sacrificing money to increase or decrease the other person’s payoff. One player sends a message indicating an intended play, which is either favorable or unfavorable to the other player in the game. After the message, the sender and the receiver play a simultaneous 2x2 game. A deceptive message may be made, in an effort to induce the receiver to make a play favorable to the sender. Our focus is on whether receivers’ rates of monetary sacrifice depend on the process and the perceived sender’s intention, as is suggested by the literature on deception and procedural satisfaction. Models such as Rabin (1993), Sen (1997), and Charness and Rabin (1999) also permit rates of sacrifice to be sensitive to the sender’s perceived intention, while outcome-based models such as Fehr and Schmidt (1999) and Bolton and Ockenfels (1997) predict otherwise. We find that deception substantially increases the punishment rate as a response to an action that is unfavorable to the receiver. We also find that a small but significant percentage of subjects choose to reward a favorable action choice made by the sender.

Plataforma per a la simulació de xarxes de sensors

Aquest projecte descriu una plataforma de simulació per a xarxes de sensors des de la perspectiva dels sistemes multi-agents. La plataforma s'ha dissenyat per facilitar la simulació de diferents aplicacions concretes de xarxes de sensors. A més, s'ha entregat com a artefacte del projecte IEA (Institucions Electròniques Autònomes, TIN2006-15662-C02-0) de l'IIIACSIC. Dins l'entorn de l'IEA, aquesta és l'eina que aporta les capacitats de simulació per donar suport al disseny d'algorismes adaptatius per a xarxes de sensors.

Agents mòbils en situacions d'emergència: gestió dinàmica de serveis

Aquest projecte consisteix en el disseny i desenvolupament d'una arquitectura de serveis sota el paradigma dels agents inteligents. El propòsit d'ADASMI (Architecture for Dynamic Agent Service Management and Interaction) és permetre la gestió i utilització de serveis per altres agents. L'arquitectura s'ha implementat utilitzant la plataforma d'agents de JADE i es pot utilitzar amb qualsevol altra plataforma que compleixi els estàndards d'IEEE FIPA. A més, és prou flexible com per adaptar-se en entorns dinàmics, com per exemple les xarxes ad-hoc en situacions d'emergència.

Debris flow susceptibility mapping at a regional scale

Debris flow susceptibility mapping at a regional scale has been the subject of various studies. The complexity of the phenomenon and the variability of local controlling factors limit the use of process-based models for a first assessment. GISbased approaches associating an automatic detection of the source areas and a simple assessment of the debris flow spreading may provide a substantial basis for a preliminary susceptibility assessment at the regional scale. The use of a digital elevation model, with a 10 m resolution, for the Canton de Vaud territory (Switzerland), a lithological map and a land use map, has allowed automatic identification of the potential source areas. The spreading estimates are based on basic probabilistic and energy calculations that allow to define the maximal runout distance of a debris flow.

On estimation and identifiability issues of sex-linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba)

Genetic evaluation using animal models or pedigree-based models generally assume only autosomal inheritance. Bayesian animal models provide a flexible framework for genetic evaluation, and we show how the model readily can accommodate situations where the trait of interest is influenced by both autosomal and sex-linked inheritance. This allows for simultaneous calculation of autosomal and sex-chromosomal additive genetic effects. Inferences were performed using integrated nested Laplace approximations (INLA), a nonsampling-based Bayesian inference methodology. We provide a detailed description of how to calculate the inverse of the X- or Z-chromosomal additive genetic relationship matrix, needed for inference. The case study of eumelanic spot diameter in a Swiss barn owl (Tyto alba) population shows that this trait is substantially influenced by variation in genes on the Z-chromosome (sigma(2)(z) = 0.2719 and sigma(2)(a) = 0.4405). Further, a simulation study for this study system shows that the animal model accounting for both autosomal and sex-chromosome-linked inheritance is identifiable, that is, the two effects can be distinguished, and provides accurate inference on the variance components.

Creació i transmissió de coneixement als clústers empresarials: un model de simulació

Projecte de recerca elaborat a partir d’una estada a l’Snider Entrepreneurial Research Center de la Wharton School de la University of Pennsilvanya y, EUA entre juliol i desembre del 2007. L’objectiu d’aquest projecte és estudiar la relació entre les estratègies de gestió del coneixement i les tecnologies de la informació i la comunicació (TIC) en l’evolució de les poblacions d’organitzacions i els seus efectes en els patrons industrials d’aglomeració espacial. Per a això s’adopta una aproximació fonamentada en la utilització d'un model basats en agents per a obtenir hipòtesis significatives i provables sobre l’evolució de les poblacions d’organitzacions al si de clústers geogràfics. El model de simulació incorpora les perspectives i supòsits d’un marc conceptual, l’Espai de la Informació o I-Space. Això permet una conceptualització basada en la informació de l’entorn econòmic que té en compte les seves dimensions espacials i temporals. Mitjançant els paràmetres del model es dóna la possibilitat d’assignar estratègies específiques de gestió del coneixement als diversos agents i de localitzar-los en una posició de l’espai físic. La simulació mostra com l'adopció d'estratègies diverses pel que fa a la gestió del coneixement influeix en l'evolució de les organitzacions i de la seva localització espacial, i que aquesta evolució es veu modificada pel desenvolupament de les TIC. A través de la modelització de dos casos ben coneguts de clústers geogràfics d’alta tecnologia, com són Silicon Valley a Califòrnia i la Route 128 als voltants de Boston, s’estudia la interrelació entre les estratègies de gestió del coneixement adoptades per les empreses i la seva tria de localització espacial, i també com això és afectat per l’evolució de les tecnologies de la informació i de la comunicació (TIC). Els resultats obtinguts generen una sèrie d’hipòtesis de rica potencialitat sobre l’impacte del desenvolupament de les TIC en la dinàmica d’aquests clusters geogràfics. Concretament, es troba que la estructuració del coneixement i l’aglomeració espacial co-evolucionen i que aquesta coevolució es veu significativament alterada pel desenvolupament de les TIC.

Arctic warming will promote Atlantic-Pacific fish interchange

Throughout much of the Quaternary Period, inhospitable environmental conditions above the Arctic Circle have been a formidable barrier separating most marine organisms in the North Atlantic from those in the North Pacific(1,2). Rapid warming has begun to lift this barrier(3), potentially facilitating the interchange of marine biota between the two seas(4). Here, we forecast the potential northward progression of 515 fish species following climate change, and report the rate of potential species interchange between the Atlantic and the Pacific via the Northwest Passage and the Northeast Passage. For this, we projected niche-based models under climate change scenarios and simulated the spread of species through the passages when climatic conditions became suitable. Results reveal a complex range of responses during this century, and accelerated interchange after 2050. By 2100 up to 41 species could enter the Pacific and 44 species could enter the Atlantic, via one or both passages. Consistent with historical and recent biodiversity interchanges(5,6), this exchange of fish species may trigger changes for biodiversity and food webs in the North Atlantic and North Pacific, with ecological and economic consequences to ecosystems that at present contribute 39% to global marine fish landings.

Debris flow hazard modelling on medium scale: Valtellina di Tirano, Italy

Debris flow hazard modelling at medium (regional) scale has been subject of various studies in recent years. In this study, hazard zonation was carried out, incorporating information about debris flow initiation probability (spatial and temporal), and the delimitation of the potential runout areas. Debris flow hazard zonation was carried out in the area of the Consortium of Mountain Municipalities of Valtellina di Tirano (Central Alps, Italy). The complexity of the phenomenon, the scale of the study, the variability of local conditioning factors, and the lacking data limited the use of process-based models for the runout zone delimitation. Firstly, a map of hazard initiation probabilities was prepared for the study area, based on the available susceptibility zoning information, and the analysis of two sets of aerial photographs for the temporal probability estimation. Afterwards, the hazard initiation map was used as one of the inputs for an empirical GIS-based model (Flow-R), developed at the University of Lausanne (Switzerland). An estimation of the debris flow magnitude was neglected as the main aim of the analysis was to prepare a debris flow hazard map at medium scale. A digital elevation model, with a 10 m resolution, was used together with landuse, geology and debris flow hazard initiation maps as inputs of the Flow-R model to restrict potential areas within each hazard initiation probability class to locations where debris flows are most likely to initiate. Afterwards, runout areas were calculated using multiple flow direction and energy based algorithms. Maximum probable runout zones were calibrated using documented past events and aerial photographs. Finally, two debris flow hazard maps were prepared. The first simply delimits five hazard zones, while the second incorporates the information about debris flow spreading direction probabilities, showing areas more likely to be affected by future debris flows. Limitations of the modelling arise mainly from the models applied and analysis scale, which are neglecting local controlling factors of debris flow hazard. The presented approach of debris flow hazard analysis, associating automatic detection of the source areas and a simple assessment of the debris flow spreading, provided results for consequent hazard and risk studies. However, for the validation and transferability of the parameters and results to other study areas, more testing is needed.

Structural Validity of the Wechsler Intelligence Scale for Children (WISC-IV) in a French-speaking Swiss sample

The Wechsler Intelligence Scale for Children-fourth edition (i.e. WISC-IV) recognizes a four-factor scoring structure in addition to the Full Scale IQ (FSIQ) score: Verbal Comprehension (VCI), Perceptual Reasoning (PRI), Working Memory (WMI), and Processing Speed (PSI) indices. However, several authors suggested that models based on the Cattell-Horn-Carroll (CHC) theory with 5 or 6 factors provided a better fit to the data than does the current four-factor solution. By comparing the current four-factor structure to CHC-based models, this research aimed to investigate the factorial structure and the constructs underlying the WISC-IV subtest scores with French-speaking Swiss children (N = 249). To deal with this goal, confirmatory factor analyses (CFAs) were conducted. Results showed that a CHC-based model with five factors better fitted the French-Swiss data than did the current WISC-IV scoring structure. All together, these results support the hypothesis of the appropriateness of the CHC model with French-speaking children.

New tools for epidemiology: a space odyssey

Geographical Information Systems (GIS) facilitate access to epidemiological data through visualization and may be consulted for the development of mathematical models and analysis by spatial statistics. Variables such as land-cover, land-use, elevations, surface temperatures, rainfall etc. emanating from earth-observing satellites, complement GIS as this information allows the analysis of disease distribution based on environmental characteristics. The strength of this approach issues from the specific environmental requirements of those causative infectious agents, which depend on intermediate hosts for their transmission. The distribution of these diseases is restricted, both by the environmental requirements of their intermediate hosts/vectors and by the ambient temperature inside these hosts, which effectively govern the speed of maturation of the parasite. This paper discusses the current capabilities with regard to satellite data collection in terms of resolution (spatial, temporal and spectral) of the sensor instruments on board drawing attention to the utility of computer-based models of the Earth for epidemiological research. Virtual globes, available from Google and other commercial firms, are superior to conventional maps as they do not only show geographical and man-made features, but also allow instant import of data-sets of specific interest, e.g. environmental parameters, demographic information etc., from the Internet.