Pore-scale simulation of micro and nanoparticle transport in porous media

The transport and deposition of colloidal particles in saturated porous media are processes of considerable importance in many fields of science and engineering, including the propagation of contaminants and of microorganisms in aquifer systems and the use of micro- and nano-particles as reagents for groundwater remediation interventions. Colloid transport is a peculiar multi-scale problem: pore-scale phenomena and inter granular dynamics have an important impact on the larger-scale transport. In this thesis a microscale approach was used to gain a better understanding of the mechanisms underlying colloidal processes, such as deposition and aggregation. The research activity was carried out by performing numerical simulations through the FEM software, COMSOL Multiphysics®. The first part of the study focuses on the development of a new correlation equation to predict single collector efficiency, a key concept in filtration theory, which allows predicting particle deposition on a single spherical collector. By performing Eulerian and Lagrangian simulations in a simple geometry and by using an innovative approach to interpret the results, a new correlation equation to predict single collector efficiency has been formulated. A hierarchical approach to interpret the results was exploited. The proposed correlation equation presents innovative features, such as the validity for a wide range of parameters (also at very small Peclet numbers), the prediction of efficiency values always lower than unity, the total flux normalization and the analysis of the mutual interactions between the main transport mechanisms (advection, gravity and diffusion) and the steric effect. The final formula was also extended to include porosity and a reduced model was proposed. The second part of the study focuses on more realistic systems, characterized by a column of spherical collectors in series. The numerical simulations performed show the limits of the existing models to interpret the experimental data. Therefore, a more rigorous procedure to evaluate the filtration processes in presence of a series of collectors was developed

Chemical communication between synthetic and natural cells: a possible experimental design

The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the synthesis of one or more functional proteins. Thanks to the in situ synthesized proteins, synthetic cells become able to perform several biomolecular functions, which can be exploited for a large variety of applications. This paves the way to several advanced uses of synthetic cells in basic science and biotechnology, thanks to their versatility, modularity, biocompatibility, and programmability. In the previous WIVACE (2012) we presented the state-of-the-art of semi-synthetic minimal cell (SSMC) technology and introduced, for the first time, the idea of chemical communication between synthetic cells and natural cells. The development of a proper synthetic communication protocol should be seen as a tool for the nascent field of bio/chemical-based Information and Communication Technologies (bio-chem-ICTs) and ultimately aimed at building soft-wet-micro-robots. In this contribution (WIVACE, 2013) we present a blueprint for realizing this project, and show some preliminary experimental results. We firstly discuss how our research goal (based on the natural capabilities of biological systems to manipulate chemical signals) finds a proper place in the current scientific and technological contexts. Then, we shortly comment on the experimental approaches from the viewpoints of (i) synthetic cell construction, and (ii) bioengineering of microorganisms, providing up-to-date results from our laboratory. Finally, we shortly discuss how autopoiesis can be used as a theoretical framework for defining synthetic minimal life, minimal cognition, and as bridge between synthetic biology and artificial intelligence.Comment: In Proceedings Wivace 2013, arXiv:1309.712

The true story of Yeti, the "abominable" heterochromatic gene of drosophila melanogaster

The Drosophila Yeti gene (CG40218) was originally identified by recessive lethal mutation and subsequently mapped to the deep pericentromeric heterochromatin of chromosome 2. Functional studies have shown that Yeti encodes a 241 amino acid protein called YETI belonging to the evolutionarily conserved family of Bucentaur (BCNT) proteins and exhibiting a widespread distribution in animals and plants. Later studies have demonstrated that YETI protein: (i) is able to bind both subunits of the microtubule-based motor kinesin-I; (ii) is required for proper chromosome organization in both mitosis and meiosis divisions; and more recently (iii) is a new subunit of dTip60 chromatin remodeling complex. To date, other functions of YETI counterparts in chicken (CENtromere Protein 29, CENP-29), mouse (Cranio Protein 27, CP27), zebrafish and human (CranioFacial Development Protein 1, CFDP1) have been reported in literature, but the fully understanding of the multifaceted molecular function of this protein family remains still unclear. In this review we comprehensively highlight recent work and provide a more extensive hypothesis suggesting a broader range of YETI protein functions in different cellular processes

On the failure of upscaling the single-collector efficiency to the transport of colloids in an array of collectors

Defining the removal efficiency of a filter is a key aspect for colloid transport in porous media. Several efforts were devoted to derive accurate correlations for the single-collector removal efficiency, but its upscaling to the entire porous medium is still a challenging topic. A common approach involves the assumption of deposition being independent of the history of transport, that is, the collector efficiency is uniform along the porous medium. However, this approach was shown inadequate under unfavorable deposition conditions. In this work, the authors demonstrate that it is not adequate even in the simplest case of favorable deposition. Computational Fluid Dynamics (CFD) simulations were run in a vertical array of 50 identical spherical collectors. Particle transport was numerically solved by analyzing a broad range of parameters. The results evidenced that when particle deposition is not controlled by Brownian diffusion, nonexponential concentration profiles are retrieved, in contrast with the assumption of uniform efficiency. If sedimentation and interception dominate, the efficiency of the first sphere is significantly higher compared to the others, and then declines along the array down to an asymptotic value. Finally, a correlation for the upscaled removal efficiency of the entire array was derived

A Normalized and Extended Correlation Equation for Predicting Single-Collector Efficiency in Physicochemical Filtration in Saturated Porous Media

The colloidal transport and deposition are phenomena involved in different engineering problems. In the environmental engineering field the use of micro- and nano-scale zerovalent iron (M-NZVI) is one of the most promising technologies for groundwater remediation. Colloid deposition is normally studied from a micro scale point of view and the results are then implemented in macro scale models that are used to design field-scale applications. The single collector efficiency concept predicts particles deposition onto a single grain of a complex porous medium in terms of probability that an approaching particle would be retained on the solid grain. Different approaches and models are available in literature to predict it, but most of them fail in some particular conditions (e.g. low fluid velocity and/or very small or very big particle dimension) because they predict efficiency values exceeding unity. By analysing particle fluxes and deposition mechanisms and performing a mass balance on the entire domain, the traditional definition of efficiency was reformulated and a novel total flux normalized correlation equation is proposed for predicting single-collector efficiency under a broad range of parameters. The new equation has been formulated starting from a combination of Eulerian and Lagrangian numerical COMSOL Multiphysics® simulations, performed under Smoluchowski-Levich conditions in a geometry which consists of a sphere enveloped by a cylindrical control volume (Figure 1). The normalization of the deposited flux is performed accounting for all of the particles entering into the control volume through all transport mechanisms (not just the upstream convective flux as conventionally done) to provide efficiency values lower than one under any possible combination of transport mechanisms. The particle fluxes onto the collector and through the control volume have been described mathematically as a summation of terms. In order to guarantee the independence of each term, the correlation equation is derived through a rigorous hierarchical parameter estimation process, accounting for single and mutual interacting transport mechanisms. The new correlation equation provides efficiency values lower than one over a wide range of parameters (Figure 2) and it is valid both for point and finite-size particles. Moreover the correlation equation is extended to include porosity dependence and reduced forms are also proposed by elimination of the less relevant terms without losing the main features of the full equation

An extended and total flux normalized correlation equation for predicting single-collector efficiency

In this study a novel total flux normalized correlation equation is proposed for predicting single-collector efficiency under a broad range of parameters. The correlation equation does not exploit the additivity approach introduced by Yao et al. (1971), but includes mixed terms that account for the mutual interaction of concomitant transport mechanisms (i.e., advection, gravity and Brownian motion) and of finite size of the particles (steric effect). The correlation equation is based on a combination of Eulerian and Lagrangian simulations performed, under Smoluchowski–Levich conditions, in a geometry which consists of a sphere enveloped by a cylindrical control volume. The normalization of the deposited flux is performed accounting for all of the particles entering into the control volume through all transport mechanisms (not just the upstream convective flux as conventionally done) to provide efficiency values lower than one over a wide range of parameters. In order to guarantee the independence of each term, the correlation equation is derived through a rigorous hierarchical parameter estimation process, accounting for single and mutual interacting transport mechanisms. The correlation equation, valid both for point and finite-size particles, is extended to include porosity dependency and it is compared with previous models. Reduced forms are proposed by elimination of the less relevant terms

Potential application and beneficial effects of a marine microalgal biomass produced in a high-rate algal pond (HRAP) in diets of European sea bass, Dicentrarchus labrax

Microalgae have been used as live food in aquatic species. In recent years, the interest in microalgae has considerably increased, thanks to the evolution of production techniques that have identified them as an ecologically attractive aquafeed ingredient. The present study provides the first data about the effects of dietary inclusion of a microalgae consortium grown in a high-rate algal pond system on zootechnical performance, morphometric indices, and dietary nutrient digestibility as well as morphology and functionality of the digestive system of European sea bass, Dicentrarchus labrax. A dietary treatment including a commercial mono-cultured microalgae (Nannochloropsis sp.) biomass was used for comparison. Six hundred and thirty-six European sea bass juveniles (18 \ub1 0.28 g) were randomly allotted into 12 experimental groups and fed 4 different diets for 10 weeks: a control diet based on fish meal, fish oil, and plant protein sources; a diet including 10% of Nannochloropsis spp. biomass (100 g/kg diet); and two diets including two levels (10% and 20%) of the microalgal consortium (100 and 200 g/kg diet). Even at the highest dietary inclusion level, the microalgal consortium (200 g/kg diet) did not affect feed palatability and fish growth performance. A significant decrease in the apparent digestibility of dry matter, protein, and energy was observed in diets including 10 and 20% of the microalgal consortium, but all fish exhibited a wellpreserved intestinal histomorphology. Moreover, dietary inclusion with the microalgal consortium significantly increased the enzymatic activity ofmaltase, sucrase-isomaltase, and &4-glutamil transpeptidase in the distal intestine of the treated European sea bass. Algal consortium grown using fish farm effluents represents an attempt to enhance the utilization of natural biomasses in aquafeeds when used at 10 % as substitute of vegetable ingredients in diet for European sea bass

Normalization and extension of single-collector efficiency correlation equation

The colloidal transport and deposition are important phenomena involved in many engineering problems. In the environmental engineering field the use of micro- and nano-scale zerovalent iron (M-NZVI) is one of the most promising technologies for groundwater remediation. Colloid deposition is normally studied from a micro scale point of view and the results are then implemented in macro scale models that are used to design field-scale applications. The single collector efficiency concept predicts particles deposition onto a single grain of a complex porous medium in terms of probability that an approaching particle would be retained on the solid grain. In literature, many different approaches and equations exist to predict it, but most of them fail under specific conditions (e.g. very small or very big particle size and very low fluid velocity) because they predict efficiency values exceeding unity. By analysing particle fluxes and deposition mechanisms and performing a mass balance on the entire domain, the traditional definition of efficiency was reformulated and a novel total flux normalized correlation equation is proposed for predicting single-collector efficiency under a broad range of parameters. It has been formulated starting from a combination of Eulerian and Lagrangian numerical simulations, performed under Smoluchowski- Levich conditions, in a geometry which consists of a sphere enveloped by a control volume. In order to guarantee the independence of each term, the correlation equation is derived through a rigorous hierarchical parameter estimation process, accounting for single and mutual interacting transport mechanisms. The correlation equation provides efficiency values lower than one over a wide range of parameters and is valid both for point and finite-size particles. A reduced form is also proposed by elimination of the less relevant terms

EMT/MET at the crossroad of stemness, regeneration and oncogenesis. The Ying-Yang equilibrium recapitulated in cell spheroids

The epithelial-to-mesenchymal transition (EMT) is an essential trans-differentiation process, which plays a critical role in embryonic development, wound healing, tissue regeneration, organ fibrosis, and cancer progression. It is the fundamental mechanism by which epithelial cells lose many of their characteristics while acquiring features typical of mesenchymal cells, such as migratory capacity and invasiveness. Depending on the contest, EMT is complemented and balanced by the reverse process, the mesenchymal-to-epithelial transition (MET). In the saving economy of the living organisms, the same (Ying-Yang) tool is integrated as a physiological strategy in embryonic development, as well as in the course of reparative or disease processes, prominently fibrosis, tumor invasion and metastasis. These mechanisms and their related signaling (e.g., TGF-β and BMPs) have been effectively studied in vitro by tissue-derived cell spheroids models. These three-dimensional (3D) cell culture systems, whose phenotype has been shown to be strongly dependent on TGF-β-regulated EMT/MET processes, present the advantage of recapitulating in vitro the hypoxic in vivo micro-environment of tissue stem cell niches and their formation. These spheroids, therefore, nicely reproduce the finely regulated Ying-Yang equilibrium, which, together with other mechanisms, can be determinant in cell fate decisions in many pathophysiological scenarios, such as differentiation, fibrosis, regeneration, and oncogenesis. In this review, current progress in the knowledge of signaling pathways affecting EMT/MET and stemness regulation will be outlined by comparing data obtained from cellular spheroids systems, as ex vivo niches of stem cells derived from normal and tumoral tissues. The mechanistic correspondence in vivo and the possible pharmacological perspective will be also explored, focusing especially on the TGF-β-related networks, as well as others, such as SNAI1, PTEN, and EGR1. This latter, in particular, for its ability to convey multiple types of stimuli into relevant changes of the cell transcriptional program, can be regarded as a heterogeneous "stress-sensor" for EMT-related inducers (growth factor, hypoxia, mechano-stress), and thus as a therapeutic target