A modified Finite Element formulation for the imposition of the slip boundary condition over embedded volumeless geometries

This work describes a novel formulation for the simulation of Navier-Stokes problems including embedded objects. The new proposal is based on the use of a modified finite element space, which replaces the standard one within the elements intersected by the immersed geometry. The modified space is able to exactly reproduce the jumps happening at the embedded boundary while preserving the conformity across the faces intersected by the embedded object. The paper focuses particularly on the imposition of a slip boundary condition on the surface of the embedded geometry, proposing a new technique for the application of such constraint. The new proposal is carefully benchmarked using the results of a body fitted technique and of an alternative embedded approach. Potential applications of interest are also presented

Parameter characterization of HTPEMFC using numerical simulation and genetic algorithms

This paper develops a novel approach to the parameterisation of high temperature exchange membrane fuel cells (HTPEMFC) with limited and non-invasive measurements. The proposed method allows an effective identification of electrochemical parameters for three-dimensional fuel cell models by combining computational simulation tools and genetic algorithms. To avoid each evaluation undertaken by the optimisation method involving a complete computational simulation of the 3D model, a strategy has been designed that, thanks to an iterative process, makes it possible to decouple the fluid dynamic resolution from the electrochemistry one. Two electrochemical models have been incorporated into these tools to describe the behaviour of the catalyst layer, Butler-Volmer and spherical aggregate. For each one, a case study has been carried out to validate the results by comparing them with empirical data in the first model and with data generated by numerical simulation in the second. Results show that, from a set of measured operating conditions, it is possible to identify a unique set of electrochemical parameters that fits the 3D model to the target polarisation curve. The extension of this framework can be used to systematically estimate any model parameter in order to reduce the uncertainty in 3D simulation predictions. © 2021 The Author(s

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozo rrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses

Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Hyper-reduction for Petrov-Galerkin reduced order models

Projection-based Reduced Order Models minimize the discrete residual of a "full order model" (FOM) while constraining the unknowns to a reduced dimension space. For problems with symmetric positive definite (SPD) Jacobians, this is optimally achieved by projecting the full order residual onto the approximation basis (Galerkin Projection). This is sub-optimal for non-SPD Jacobians as it only minimizes the projection of the residual, not the residual itself. An alternative is to directly minimize the 2-norm of the residual, achievable using QR factorization or the method of the normal equations (LSPG). The first approach involves constructing and factorizing a large matrix, while LSPG avoids this but requires constructing a product element by element, necessitating a complementary mesh and adding complexity to the hyper-reduction process. This work proposes an alternative based on Petrov-Galerkin minimization. We choose a left basis for a least-squares minimization on a reduced problem, ensuring the discrete full order residual is minimized. This is applicable to both SPD and non-SPD Jacobians, allowing element-by-element assembly, avoiding the use of a complementary mesh, and simplifying finite element implementation. The technique is suitable for hyper-reduction using the Empirical Cubature Method and is applicable in nonlinear reduction procedures

A new species of Polydiscia (Acari, Prostigmata, Tanaupodidae) with reference to its host: a new species of Deuterosminthurus (Collembola, Symphypleona, Bourletiellidae)

During the sampling campaign to describe the Iberian fauna of Collembola, an undescribed species of the family Bourletiellidae living on Genista hispanica L. was found with parasitic mites. The attached parasitic mites were identified as the larval instar of a new species of Polydiscia, a prostigmatid mite of the family Tanaupodidae Thor, 1935. The genus was previously cited in Austria. The Collembola, Deuterosminthurus bisetosus sp. nov, which was found in distant localities on the Iberian Peninsula, and Polydiscia deuterosminthurus sp. nov., are both here described. Both species were found together on Genista for three consecutive years. The abundant material obtained has allowed us to study both species with SEM (Scanning Electron Microscopy), and show characteristics in greater detail than has been possible with light microscopy

Metodología para la optimización conjunta de la programación del riego y estaciones de bombeos directos

Se describe una nueva metodología para reducción de los costes energéticos de operación del riego en redes de riego con bombeo directo, contemplando la optimización conjunta de la organización de los riegos y la modulación de las presiones de la estación de bombeo a lo largo de diferentes periodos tarifarios. Se describe el funcionamiento del método de optimización investigado, que es una extensión y mejora del algoritmo inicial existente desarrollado en (Faci E., 2014) destacando las diferencias y mejoras. Por último, se muestran los resultados en el caso de la red de la CR Callén (Huesca), y se comparan con los obtenidos en un estudio para la optimización energética utilizando el algoritmo inicial.A new methodology to reduce energy cost in irrigation networks is developed in this paper. Its goal is to optimize simultaneously both pumping station and hydrant operation by setting different discharge pressure on the pumping station and distributing adequately hydrant irrigation during different tariff periods. methodology is an extension an existing one described in Faci E., (2014) which is only capable of optimize hydrant operation. Advantages and differences between them are described and they are compared in the case study of CR Callén network (Huesca) which shows the new methodology is capable to save an additional 10% of the annual electricity costs