Rui Faria

A strain-based plastic viscous-damage model for massive concrete structures

Within the framework of continuum damage mechanics, a new constitutive damage model for massive concrete is presented, mainly intended for the seismic analysis of gravity and arch dams. Consistent with thermodynamic requirements, a straindriven formalism is adopted, improving the algorithmic efficiency as much as required for the analysis of large scale problems to become feasible. Two scalar damage variables are introduced as internal variables, as well as a plastic-strain tensor. An extension to account for the concrete strain-rate dependency, suitable for seismic analysis, is presented at the end. The efficiency of numerical predictions from the constitutive model is illustrated through numerical applications and algorithmic implementation is also detailed.

Chromosomal speciation revisited: rearranging theory with pieces of evidence.

The suggestion that chromosomal rearrangements play a role in speciation resulted from the observation that heterokaryotypes are often infertile. However, the first chromosomal speciation models were unsatisfactory and data available to test them was scarce. Recently, large amounts of data have become available and new theoretical models have been developed explaining how rearrangements facilitate speciation in the face of gene flow. Here, we re-examine theoretical predictions and revisit different sources of data. Although rearrangements are often associated with increased levels of divergence, unequivocal demonstration that their role in suppressing recombination results in speciation is often lacking. Finally, we question some previous predictions and suggest new empirical and theoretical approaches to understanding the relevance of rearrangements in the origin of species.

Numerical modelling of concrete curing, regarding hydration and temperature phenomena

A numerical model that accounts for the hydration and aging phenomena during the early ages of concrete curing is presented in a format suitable for a finite element implementation. Assuming the percolation of water through the hydrates already formed as the dominant mechanism of cement hydration, the model adopts an internal variable called hydration degree, whose evolution law is easily calibrated and allows an accurate prediction of the hydration heat production. Compressive strength evolution is related to the aging degree, a concept that accounts for the influences of the hydration and curing temperature on the final mechanical properties of concrete. The model capabilities are illustrated by means of a wide set of experimental tests involving ordinary and high performance concretes, and through the simulation of the concrete curing on a viaduct deck of the Oresund Link.

Advances in Ecological Speciation: an integrative approach

The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference ‘Advances in Ecological Speciation’ organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.

A prominent role of KRAB-ZNF transcription factors in mammalian speciation?

The mechanisms of speciation have been one of the most debated topics in evolutionary biology. Among all reproductive barriers, postzygotic reproductive isolation is perhaps the one that has attracted the most attention from geneticists. Despite remarkable advances in the identification of loci involved in Drosophila speciation, little is known about the genes, functions, and biochemical interactions of the molecules underlying hybrid sterility and inviability in mammals. Here, we discuss the main evolutionary and molecular features that make transcription factors (TFs), especially the family of zinc finger proteins with a Krüppel-associated box domain (KRAB-ZNF), strong candidates to play an important role in postzygotic reproductive isolation. Motivated by the recent identification of the gene encoding PR domain zinc finger protein 9 (Prdm9; a KRAB-ZNF gene) as the first hybrid sterility gene identified in mammals, we further propose integrative approaches to study KRAB-ZNF genes with the main goal of characterizing the molecular pathways and interactions involved in hybrid incompatibilities.

SIMULATION OF THE CYCLIC BEHAVIOUR OF R/C RECTANGULAR HOLLOW SECTION BRIDGE PIERS VIA A DETAILED NUMERICAL MODEL

In the search for robust constitutive models suitable for reproducing the performance of bridge piers during a seismic event, this paper details the simulation of the cyclic responses of four rectangular hollow section R/C bridge piers. These four R/C bridge piers were built at scale 1/2.5 and tested experimentally. Both tall and short piers are considered, covering situations where bending or shear are of relevance. Furthermore, the four piers were reinforced according to rather different design strategies: (I) the first is a 30-year-old bridge designed without allowance to the seismic action, and (ii) the second is a bridge fulfilling the EC8 provisions. The detailed constitutive model that provides the numerical predictions includes two submodels: one with two scalar damage variables, reproducing the tensile and compressive degradations of concrete, and the other is based on the Giuffre-Menegotto-Pinto formulation, simulating the cyclic behaviour of the re-inforcement. The Damage Mechanics submodel is implemented at the Gauss points of the finite elements that discretize the concrete, whereas the steel submodel is implemented on the 2-noded truss elements adopted for the rebars. A comparison between the numerical and the experimental results is discussed in detail in this paper.

Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA

BackgroundComparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads, Alosa alosa and A. fallax are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation.ResultsDespite introgressive hybridization, A. alosa and A. fallax are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both A. fallax and A. alosa, most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional Alosa clades occur there. The present day geographic distribution of genetic diversity within European Alosa sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species. Overall mtDNA diversity is considerably lower for A. alosa compared to A. fallax, suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For A. fallax, migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum.ConclusionThe similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities, A. alosa and A. fallax have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For A. fallax, it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.

Recent human evolution has shaped geographical differences in susceptibility to disease

BackgroundSearching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies.ResultsWe report three main findings. First, contrary to previous results, genes associated to complex diseases present lower degrees of genetic differentiation among human populations than average genome-wide levels. Second, also contrary to previous results, the differences in replicability of disease associated-loci between Europeans and East Asians are highly correlated with genetic differentiation between these populations. Finally, highly replicated genes present increased levels of high-frequency derived alleles in European and Asian populations when compared to African populations.ConclusionsOur findings highlight the heterogeneous nature of the genetic etiology of complex disease, confirm the importance of the recent evolutionary history of our species in current patterns of disease susceptibility and could cast doubts on the status as false positives of some associations that have failed to replicate across populations.

SEISMIC BEHAVIOUR OF A R/C WALL: NUMERICAL SIMULATION AND EXPERIMENTAL VALIDATION

This paper describes the numerical simulation of the seismic behaviour of a mock-up of a six-floor building, constituted by two parallel R/C walls and experimentally tested on a shaking table. Within the scope of an international benchmark the mock-up was submitted to three earthquakes with intensities up to 0.71 g, which induced nonlinear behaviour in the concrete and reinforcement. For the numerical simulations concrete is discretised with 2D finite elements, and its behaviour reproduced via a constitutive model with two scalar damage variables. Steel rebars are discretised with 2-noded truss elements, and their constitutive behaviour under cyclic conditions reproduced by the Menegottb-Pinto model. Specific attention is devoted to Rayleigh damping, focusing on two different strategies: (i) disregarding the damping contribution, or (ii) adopting a damping matrix that takes into account the stiffness changes during the nonlinear analyses. Main results and strategies for simulating the benchmark axe presented, with emphasis on the comparison between the numerical and the experimental results, which show good agreement when the damping contribution is neglected.

Nonlinear analysis of RC beams using a hybrid shear-flexural fibre beam model

Purpose – A nonlinear finite element (FE) beam-column model for the analysis of reinforced concrete (RC) frames with due account of shear is presented in this paper. The model is an expansion of the traditional flexural fibre beam formulations to cases where multiaxial behaviour exists, being an alternative to plane and solid FE models for the nonlinear analysis of entire frame structures. The paper aims to discuss these issues. Design/methodology/approach – Shear is taken into account at different levels of the numerical model: at the material level RC is simulated through a smeared cracked approach with rotating cracks; at the fibre level, an iterative procedure guarantees equilibrium between concrete and transversal reinforcement, allowing to compute the biaxial stress-strain state of each fibre; at the section level, a uniform shear stress pattern is assumed in order to estimate the internal shear stress-strain distribution; and at the element level, the Timoshenko beam theory takes into account an av...