A macroscopic model for immiscible two-phase flow in porous media

This work provides the derivation of a closed macroscopic model for immiscible two-phase, incompressible, Newtonian and isothermal creeping steady flow in a rigid and homogeneous porous medium without considering three-phase contact. The mass and momentum upscaled equations are obtained from the pore-scale Stokes equations, adopting a two-domain approach where the two fluid phases are separated by an interface. The average mass equations result from using the classical volume averaging method. A Green's formula and the adjoint Green's function velocity pair problems are used to obtain the pore-scale velocity solutions that are averaged to obtain the upscaled momentum balance equations. The macroscopic model is based on the assumptions of scale separation and the existence of a periodic representative elementary volume allowing a local description as usually postulated for upscaling. The macroscopic momentum equation in each phase includes the generalized Darcy-like dominant and viscous coupling terms and, importantly, an additional compensation term that accounts for surface tension effects to momentum transfer that is, otherwise, incompletely captured by the Darcy terms. This interfacial term, as well as the dominant and viscous coupling permeability tensors, can be predicted from the solutions of two associated closure problems that coincide with those reported in the literature. The relevance of the compensation term and the upscaled model validity are assessed by comparisons with direct numerical simulations in a model two-dimensional periodic structure. Upscaled model predictions are found to be in excellent agreement with direct numerical simulations

Macroscopic Model for Passive Mass Dispersion in Porous Media Including Knudsen and Diffusive Slip Effects

In this work, a macroscopic model for incompressible and Newtonian gas flow coupled to Fickian and advective transport of a passive solute in rigid and homogeneous porous media is derived. At the pore-scale, both momentum and mass transport phenomena are coupled, not only by the convective mechanism in the mass transport equation, but also in the solid-fluid interfacial boundary condition. This boundary condition is a generalization of the Kramers-Kistemaker slip condition that includes the Knudsen effects. The resulting upscaled model, applicable in the bulk of the porous medium, corresponds to: 1) A Darcy-type model that involves an apparent permeability tensor, complemented by a dispersive term and 2) A macroscopic convection-dispersion equation for the solute, in which both the macroscopic velocity and the total dispersion tensor are influenced by the slip effects taking place at the pore-scale. The use of the model is restricted by the starting assumptions imposed in the governing equations at the pore scale and by the (spatial and temporal) constraints involved in the upscaling process. The different regimes of application of the model, in terms of the Péclet number values, are discussed as well as its extents and limitations. This new model generalizes previous attempts that only include either Knudsen or diffusive slip effects in porous media

3D-PP: A tool for discovering conserved three-dimensional protein patterns

Discovering conserved three-dimensional (3D) patterns among protein structures may provide valuable insights into protein classification, functional annotations or the rational design of multi-target drugs. Thus, several computational tools have been developed to discover and compare protein 3D-patterns. However, most of them only consider previously known 3D-patterns such as orthosteric binding sites or structural motifs. This fact makes necessary the development of new methods for the identification of all possible 3D-patterns that exist in protein structures (allosteric sites, enzyme-cofactor interaction motifs, among others). In this work, we present 3D-PP, a new free access web server for the discovery and recognition all similar 3D amino acid patterns among a set of proteins structures (independent of their sequence similarity). This new tool does not require any previous structural knowledge about ligands, and all data are organized in a high-performance graph database. The input can be a text file with the PDB access codes or a zip file of PDB coordinates regardless of the origin of the structural data: X-ray crystallographic experiments or in silico homology modeling. The results are presented as lists of sequence patterns that can be further analyzed within the web page. We tested the accuracy and suitability of 3D-PP using two sets of proteins coming from the Protein Data Bank: (a) Zinc finger containing and (b) Serotonin target proteins. We also evaluated its usefulness for the discovering of new 3D-patterns, using a set of protein structures coming from in silico homology modeling methodologies, all of which are overexpressed in different types of cancer. Results indicate that 3D-PP is a reliable, flexible and friendly-user tool to identify conserved structural motifs, which could be relevant to improve the knowledge about protein function or classification. The web server can be freely utilized at https://appsbio.utalca.cl/3d-pp/.Peer ReviewedPostprint (published version

The Women’s Civic Party and its ties of international cooperation through Acción Femenina(Chile, 1922-1923)

El objetivo de este trabajo es analizar los lazos de cooperación internacional del Partido Cívico Femenino (Chile 1922-23) para fortalecer su discurso sufragista en Chile a través de la revisión de su revista Acción Femenina (1922-1923). Planteamos que considerando el movimiento internacional de mujeres que abogó tanto por el sufragio femenino y una política feminista en las primeras décadas del siglo XX, el PCF chileno estableció relaciones internacionales con diversas organizaciones del mundo desarrollando una política internacional. Esta decisión orgánica les permitió consolidar su discurso y objetivo político y plantearse como una organización tanto feminista como sufragista a la vez.Montero, Claudia. Universidad de Chile. Universidad de Valparaíso; ChileRamos Valdés, Aylim. Universidad de Valparaíso; ChileRobles Parada, Andrea. Universidad de Valparaíso. Universidad de Chile; Chil

Journal of Non-Newtonian Fluid Mechanics

A macroscopic model for unsteady incompressible isothermal non-Newtonian flow in homogeneous porous media, taking into account inertial and slip effects at solid–fluid interfaces, is derived in this work. The development is carried out considering a general Newton’s law of viscosity for the fluid phase. Using the classical volume averaging method, the seepage velocity is shown to be solenoidal. The macroscopic momentum equation is derived in the Laplace domain, employing a simplified version of the volume averaging method, which calls upon Green’s formulas and adjoint problems for Green’s function pairs for the velocity and pressure. In the Laplace domain, the macroscopic momentum equation takes the form of Darcy’s law corrected by a term that accounts for the initial flow condition. Once transformed back into the time domain, this equation provides the macroscopic velocity that depends on two terms. The first one is under the form of a time convolution between the macroscopic pressure gradient and the time derivative of an apparent permeability tensor. The second one is a memory term that accounts for the effect of the initial flow conditions. These two effective quantities are determined from the solution of a single closure problem that naturally results from the derivations. The model is consistent with the unsteady model in the Newtonian case and simplifies to the steady versions of some non-Newtonian macroscopic flow models. The macroscopic model is validated with pore-scale simulations performed in 2D model porous structures, considering a Carreau fluid. The impact of inertia and non-Newtonian effects on the dynamics of the macroscopic coefficients is highlighted

Desigualdad en México bajo el enfoque de una Economía de Mercado Jerárquica (EMJ)

En este artículo, a través del enfoque de Economía de Mercado Jerárquica (EMJ), se hace unanálisis contextual y descriptivo sobre dos de las cinco esferas que conforman está noción de Variedades de Capitalismo (VoC). Buscando determinar cómo esas esferas de relaciones laborales y capacitación y educación se complementan negativamente, intensificando la desigualdad económica que genera ingresos dispares y menores oportunidades de crecimiento intelectual para la población. Obteniendo como hallazgo que, este modelo de capitalismo favorece esquemas de excesiva flexibilidad laboral que se puede constatar con el bajo índice de salario mínimo, la falta de protección al empleo y la baja capacitación que reciben los trabajadores en México.A contextual and descriptive analysis of two of the five spheres that make up the notion of Varieties of Capitalism is made in this article by means of the hierarchical market economy approach. We seek to determine how the spheres of labor relations, and training and education complement each other negatively, intensifying the economic inequality that generates disparate incomes and fewer opportunities for intellectual growth among the population. We find that this model of capitalism favors schemes of excessive labor flexibility, a fact that is validated by the low minimum wage index, the lack of employment protection and the low training that workers in Mexico receive 

A new strategy for multitarget drug discovery/repositioning through the identification of similar 3D amino acid patterns among proteins structures: The case of Tafluprost and its efects on cardiac ion channels

The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. Also, it would be a reasonable first step for the design of novel multitarget compounds. Most of the current computational tools employed for this aim are limited to the comparisons among known binding sites, and do not consider several additional important 3D patterns such as allosteric sites or other conserved motifs. In the present work, we introduce Geomfinder2.0, which is a new and improved version of our previously described algorithm for the deep exploration and discovery of similar and druggable 3D patterns. As compared with the original version, substantial improvements that have been incorporated to our software allow: (i) to compare quaternary structures, (ii) to deal with a list of pairs of structures, (iii) to know how druggable is the zone where similar 3D patterns are detected and (iv) to significantly reduce the execution time. Thus, the new algorithm achieves up to 353x speedup as compared to the previous sequential version, allowing the exploration of a significant number of quaternary structures in a reasonable time. In order to illustrate the potential of the updated Geomfinder version, we show a case of use in which similar 3D patterns were detected in the cardiac ions channels NaV1.5 and TASK-1. These channels are quite different in terms of structure, sequence and function and both have been regarded as important targets for drugs aimed at treating atrial fibrillation. Finally, we describe the in vitro effects of tafluprost (a drug currently used to treat glaucoma, which was identified as a novel putative ligand of NaV1.5 and TASK-1) upon both ion channels’ activity and discuss its possible repositioning as a novel antiarrhythmic drug.This research was funded by the Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) grants numbers 1191133, 1170662 and from Spanish Ministry of Economy and Competitiveness (projects SEV-2015-0493 and TIN2015-65316-P, grant BES-2016-078046), and from Generalitat de Catalunya (contracts 2017-SGR-1414 and 2017-SGR-1328). The financial support by DICYT-USACH grant 5392102RP-ACDicyt is also acknowledged. The web-server is hosted in the cluster obtained with the grant CONICYT-FONDEQUIP-EQM160063.Peer ReviewedPostprint (published version

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia

Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge–microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment

Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

A wide variety of techniques have been developed to homogenize transport equations in multiscale and multiphase systems. This has yielded a rich and diverse field, but has also resulted in the emergence of isolated scientific communities and disconnected bodies of literature. Here, our goal is to bridge the gap between formal multiscale asymptotics and the volume averaging theory. We illustrate the methodologies via a simple example application describing a parabolic transport problem and, in so doing, compare their respective advantages/disadvantages from a practical point of view. This paper is also intended as a pedagogical guide and may be viewed as a tutorial for graduate students as we provide historical context, detail subtle points with great care, and reference many fundamental works

On the well-posed coupling between free fluid and porous viscous flows

International audienceWe present a well-posed model for the Stokes/Brinkman problem with {\em jump embedded boundary conditions (J.E.B.C.)} on an immersed interface. It is issued from a general framework recently proposed for fictitious domain problems. Our model is based on algebraic transmission conditions combining the stress and velocity jumps on the interface $\S$ separating the fluid and porous domains. These conditions are well chosen to get the coercivity of the operator. Then, the general framework allows to prove the global solvability of some models with physically relevant stress or velocity jump boundary conditions for the momentum transport at a fluid-porous interface. The Stokes/Brinkman problem with {\em Ochoa-Tapia \& Whitaker (1995)} interface conditions and the Stokes/Darcy problem with {\em Beavers \& Joseph (1967)} conditions are both proved to be well-posed by an asymptotic analysis. Up to now, only the Stokes/Darcy problem with {\em Saffman (1971)} approximate interface conditions was known to be well-posed