High Performance Air Quality Simulation in the European CrossGrid Project

This paper focuses on one of the applications involved into the CrossGrid project, the STEM-II air pollution model used to simulate the environment of As Pontes Power Plant in A Coruna (Spain). The CrossGrid project offers us a Grid environment oriented towards computation- and data-intensive applications that need interaction with an external user. The air pollution model needs the interaction of an expert in order to make decisions about modifications in the industrial process to fulfil the European standard on emissions and air quality. The benefits of using different CrossGrid components for running the application on a Grid infrastructure are shown in this paper, and some preliminary results on the CrossGrid testbed are displayed

A PHYSICS-BASED APPROACH TO MODELING WILDLAND FIRE SPREAD THROUGH POROUS FUEL BEDS

Wildfires are becoming increasingly erratic nowadays at least in part because of climate change. CFD (computational fluid dynamics)-based models with the potential of simulating extreme behaviors are gaining increasing attention as a means to predict such behavior in order to aid firefighting efforts. This dissertation describes a wildfire model based on the current understanding of wildfire physics. The model includes physics of turbulence, inhomogeneous porous fuel beds, heat release, ignition, and firebrands. A discrete dynamical system for flow in porous media is derived and incorporated into the subgrid-scale model for synthetic-velocity large-eddy simulation (LES), and a general porosity-permeability model is derived and implemented to investigate transport properties of flow through porous fuel beds. Note that these two developed models can also be applied to other situations for flow through porous media. Simulations of both grassland and forest fire spread are performed via an implicit LES code parallelized with OpenMP; the parallel performance of the algorithms are presented and discussed. The current model and numerical scheme produce reasonably correct wildfire results compared with previous wildfire experiments and simulations, but using coarser grids, and presenting complicated subgrid-scale behaviors. It is concluded that this physics-based wildfire model can be a good learning tool to examine some of the more complex wildfire behaviors, and may be predictive in the near future

Biomass gasification for syngas and biochar co-production: Energy application and economic evaluation

Syngas and biochar are two main products from biomass gasification. To facilitate the optimization of the energy efficiency and economic viability of gasification systems, a comprehensive fixed-bed gasification model has been developed to predict the product rate and quality of both biochar and syngas. A coupled transient representative particle and fix-bed model was developed to describe the entire fixed-bed in the flow direction of primary air. A three-region approach has been incorporated into the model, which divided the reactor into three regions in terms of different fluid velocity profiles, i.e. natural convection region, mixed convection region, and forced convection region, respectively. The model could provide accurate predictions against experimental data with a deviation generally smaller than 10%. The model is applicable for efficient analysis of fixed-bed biomass gasification under variable operating conditions, such as equivalence ratio, moisture content of feedstock, and air inlet location. The optimal equivalence ratio was found to be 0.25 for maximizing the economic benefits of the gasification process

Organ-on-a-Disc: A Scalable Platform Technology for the Generation and Cultivation of Microphysiological Tissues

Organ-on-Chip (OoC) systems culture human tissues in a controllable environment under microfluidic perfusion and enable a precise recapitulation of human physiology. Although recent studies demonstrate the potential of OoCs as alternative to traditional cell assays and animal models in drug development as well as personalized medicine, unmet challenges in device fabrication, parallelization and operation hinder their widespread application. In order to overcome these obstacles, this thesis focuses on the development of the Organ-on-a-Disc technology for the scalable generation and cultivation of microphysiological tissues. Organ-Discs are fabricated using precise, rapid and scalable microfabrication techniques. They enable the pump- and tubing-free perfusion as well as the parallelized generation and culture of tailorable and functional microtissues using rotation-based operations. The Organ-Disc setup is suitable for versatile tissue readouts, treatments and even whole blood perfusion with minimal handling and equipment requirements. Overall, the Organ-Disc creates a scalable and userfriendly platform technology for microphysiological tissue models and paves the way for their transition towards high-throughput systems.:Abbreviations Symbols 1 Introduction 2 Background 2.1 Fluid Dynamics 2.1.1 Flow Equations 2.1.2 Hydraulic Resistance 2.1.3 Wall Shear Stress 2.1.4 Centrifugal Microfluidics 2.2 Microfluidic Chip Fabrication 2.2.1 Chip Materials 2.2.2 Microstructuring 2.2.3 Bonding 3 State of the Art 3.1 Cell Culture Systems 3.2 3D Tissue Generation in Microfluidic Systems 3.3 Organ-on-Chip 3.4 Scale-up of Organ-on-Chip Systems 3.4.1 Scalable Fabrication Technologies 3.4.2 Parallelization Approaches 3.4.3 Integrated Fluid Actuation 3.5 Centrifugal Microfluidics 4 Objectives 5 Materials and Methods 5.1 Organ-Disc Fabrication 5.1.1 Materials 5.1.2 2D Structuring 5.1.3 Hot Embossing Stamp Fabrication TPE Hot Embossing 5.1.4 Bonding Solvent Vapor Bonding Thermal Fusion Bonding TPE Bonding 5.1.5 Characterization Methods Structure Sizes Bonding Strength Optical Properties 5.2 Organ-Disc Spinner 5.2.1 Centrifugal Loading Setup 5.2.2 Centrifugal Perfusion Setup 5.2.3 Peristaltic Pumping Setup 5.3 Organ-Disc Perfusion 5.3.1 Centrifugal Perfusion 5.3.2 Peristaltic Perfusion 5.4 Preparatory Cell Culture 5.5 Organ-Disc Cell Loading 5.5.1 Centrifugal Cell Loading 5.5.2 Endothelial-lining 5.6 Organ-Disc Cell Culture 5.6.1 Staining and Imaging Live Cell Labeling Live/Dead Staining CD106 Staining CD41 Staining Fixation, Permeabilization and Blocking Actin/Nuclei Staining CD31/Nuclei Staining 5.6.2 Media Analysis 5.6.3 Endothelial Cell Activation 5.6.4 Whole Blood Perfusion 5.7 Data Presentation and Statistics 6 Concept and Design 6.1 Organ-Disc Technology 6.2 Organ-Disc Design 6.3 Centrifugal Cell Loading 6.4 Endothelial Cell Lining 6.5 Centrifugal Perfusion 6.6 Peristaltic Perfusion 7 Building Blocks 7.1 Microfabrication Technology 7.1.1 Structuring 2D Structuring Hot Embossing 7.1.2 Bonding Solvent Vapor Bonding Thermal Fusion Bonding TPE Bonding 7.2 Organ-Disc Spinner 8 Perfusion 8.1 Centrifugal Pumping 8.2 Peristaltic Pumping 9 Tissue Generation and Culture 9.1 3D Tissue Generation 9.2 Stratified Tissue Construction 9.3 Generation of Endothelial-lined Channels 9.4 Perfusion of Endothelial-lined Channels 9.4.1 Media Monitoring Evaporation Cell Metabolism 9.4.2 Inflammatory Cell Stimulation 9.4.3 Whole Blood Perfusion 10 Discussion 10.1 Organ-Disc Technology 10.2 Scalable, Precise and Robust Organ-Disc Fabrication 10.2.1 Fabrication of Thermoplastic Organ-Discs 10.2.2 Fabrication of TPE Modules 10.2.3 Integration of TPE Modules to Organ-Discs 10.3 Tunable, Pump- and Tubing-free Perfusion 10.4 On-Disc Tissue Culture 10.4.1 3D Tissues 10.4.2 Blood Vessel-like Structures 10.4.3 Tissue Characterization and Treatment 10.5 On-Disc Blood Perfusion 11 Summary and Conclusion 12 References 13 AppendixIn Organ-on-Chip (OoC)-Systemen werden menschliche Gewebe mittels mikrofluidischer Versorgung in einer kontrollierten Umgebung kultiviert und so die Physiologie des Menschen nachgebildet. Obwohl aktuelle Studien zeigen, dass dieser Ansatz Alternativen zu herkömmlichen Zellbasierten Tests und Tiermodellen in der Arzneimittelentwicklung und der personalisierten Medizin bietet, stehen einer breiteren Anwendung Hürden im Bereich der Herstellung, Parallelisierung und Handhabung im Weg. Deshalb ist das Ziel dieser Arbeit die Entwicklung der Organ-on-a-Disc-Technologie, die eine skalierbare Erzeugung und Kultur von mikrophysiologischen Geweben ermöglicht. Für die Herstellung von der Organ-Disc kommen präzise, schnelle und skalierbare Mikrofabrikationsmethoden zum Einsatz. Die Organ-Disc schafft die Basis für die parallelisierte Erzeugung und Kultur von maßgeschneiderten und funktionellen Mikrogeweben, sowie deren Versorgung durch rotationsbasierte Prozesse und ohne zur Hilfenahme von Pumpen oder Schläuchen. Die Organ-Disc eignet sich für unterschiedliche Charakterisierungsmethoden sowie der Gewebestimulation und sogar der Vollblutperfusion mit minimalem Aufwand und Equipment. Insgesamt stellt die Organ-Disc eine skalierbare und benutzerfreundliche Plattformtechnologie für mikrophysiologische Modelle dar und bereitet den Weg für Hochdurchsatzanwendungen.:Abbreviations Symbols 1 Introduction 2 Background 2.1 Fluid Dynamics 2.1.1 Flow Equations 2.1.2 Hydraulic Resistance 2.1.3 Wall Shear Stress 2.1.4 Centrifugal Microfluidics 2.2 Microfluidic Chip Fabrication 2.2.1 Chip Materials 2.2.2 Microstructuring 2.2.3 Bonding 3 State of the Art 3.1 Cell Culture Systems 3.2 3D Tissue Generation in Microfluidic Systems 3.3 Organ-on-Chip 3.4 Scale-up of Organ-on-Chip Systems 3.4.1 Scalable Fabrication Technologies 3.4.2 Parallelization Approaches 3.4.3 Integrated Fluid Actuation 3.5 Centrifugal Microfluidics 4 Objectives 5 Materials and Methods 5.1 Organ-Disc Fabrication 5.1.1 Materials 5.1.2 2D Structuring 5.1.3 Hot Embossing Stamp Fabrication TPE Hot Embossing 5.1.4 Bonding Solvent Vapor Bonding Thermal Fusion Bonding TPE Bonding 5.1.5 Characterization Methods Structure Sizes Bonding Strength Optical Properties 5.2 Organ-Disc Spinner 5.2.1 Centrifugal Loading Setup 5.2.2 Centrifugal Perfusion Setup 5.2.3 Peristaltic Pumping Setup 5.3 Organ-Disc Perfusion 5.3.1 Centrifugal Perfusion 5.3.2 Peristaltic Perfusion 5.4 Preparatory Cell Culture 5.5 Organ-Disc Cell Loading 5.5.1 Centrifugal Cell Loading 5.5.2 Endothelial-lining 5.6 Organ-Disc Cell Culture 5.6.1 Staining and Imaging Live Cell Labeling Live/Dead Staining CD106 Staining CD41 Staining Fixation, Permeabilization and Blocking Actin/Nuclei Staining CD31/Nuclei Staining 5.6.2 Media Analysis 5.6.3 Endothelial Cell Activation 5.6.4 Whole Blood Perfusion 5.7 Data Presentation and Statistics 6 Concept and Design 6.1 Organ-Disc Technology 6.2 Organ-Disc Design 6.3 Centrifugal Cell Loading 6.4 Endothelial Cell Lining 6.5 Centrifugal Perfusion 6.6 Peristaltic Perfusion 7 Building Blocks 7.1 Microfabrication Technology 7.1.1 Structuring 2D Structuring Hot Embossing 7.1.2 Bonding Solvent Vapor Bonding Thermal Fusion Bonding TPE Bonding 7.2 Organ-Disc Spinner 8 Perfusion 8.1 Centrifugal Pumping 8.2 Peristaltic Pumping 9 Tissue Generation and Culture 9.1 3D Tissue Generation 9.2 Stratified Tissue Construction 9.3 Generation of Endothelial-lined Channels 9.4 Perfusion of Endothelial-lined Channels 9.4.1 Media Monitoring Evaporation Cell Metabolism 9.4.2 Inflammatory Cell Stimulation 9.4.3 Whole Blood Perfusion 10 Discussion 10.1 Organ-Disc Technology 10.2 Scalable, Precise and Robust Organ-Disc Fabrication 10.2.1 Fabrication of Thermoplastic Organ-Discs 10.2.2 Fabrication of TPE Modules 10.2.3 Integration of TPE Modules to Organ-Discs 10.3 Tunable, Pump- and Tubing-free Perfusion 10.4 On-Disc Tissue Culture 10.4.1 3D Tissues 10.4.2 Blood Vessel-like Structures 10.4.3 Tissue Characterization and Treatment 10.5 On-Disc Blood Perfusion 11 Summary and Conclusion 12 References 13 Appendi

Development of the adjoint of GEOS-Chem

We present the adjoint of the global chemical transport model GEOS-Chem, focusing on the chemical and thermodynamic relationships between sulfate – ammonium – nitrate aerosols and their gas-phase precursors. The adjoint model is constructed from a combination of manually and automatically derived discrete adjoint algorithms and numerical solutions to continuous adjoint equations. Explicit inclusion of the processes that govern secondary formation of inorganic aerosol is shown to afford efficient calculation of model sensitivities such as the dependence of sulfate and nitrate aerosol concentrations on emissions of SOx, NOx, and NH3. The adjoint model is extensively validated by comparing adjoint to finite difference sensitivities, which are shown to agree within acceptable tolerances; most sets of comparisons have a nearly 1:1 correlation and R2>0.9. We explore the robustness of these results, noting how insufficient observations or nonlinearities in the advection routine can degrade the adjoint model performance. The potential for inverse modeling using the adjoint of GEOS-Chem is assessed in a data assimilation framework through a series of tests using simulated observations, demonstrating the feasibility of exploiting gas- and aerosol-phase measurements for optimizing emission inventories of aerosol precursors

Hydrodynamic instabilities in gaseous detonations: comparison of Euler, Navier–Stokes, and large-eddy simulation

A large-eddy simulation is conducted to investigate the transient structure of an unstable detonation wave in two dimensions and the evolution of intrinsic hydrodynamic instabilities. The dependency of the detonation structure on the grid resolution is investigated, and the structures obtained by large-eddy simulation are compared with the predictions from solving the Euler and Navier–Stokes equations directly. The results indicate that to predict irregular detonation structures in agreement with experimental observations the vorticity generation and dissipation in small scale structures should be taken into account. Thus, large-eddy simulation with high grid resolution is required. In a low grid resolution scenario, in which numerical diffusion dominates, the structures obtained by solving the Euler or Navier–Stokes equations and large-eddy simulation are qualitatively similar. When high grid resolution is employed, the detonation structures obtained by solving the Euler or Navier–Stokes equations directly are roughly similar yet equally in disagreement with the experimental results. For high grid resolution, only the large-eddy simulation predicts detonation substructures correctly, a fact that is attributed to the increased dissipation provided by the subgrid scale model. Specific to the investigated configuration, major differences are observed in the occurrence of unreacted gas pockets in the high-resolution Euler and Navier–Stokes computations, which appear to be fully combusted when large-eddy simulation is employed

Catalytic flow with a coupled Finite Difference -- Lattice Boltzmann scheme

Many catalyst devices employ flow through porous structures, which leads to a complex macroscopic mass and heat transport. To unravel the detailed dynamics of the reactive gas flow, we present an all-encompassing model, consisting of thermal lattice Boltzmann model by Kang et al., used to solve the heat and mass transport in the gas domain, coupled to a finite differences solver for the heat equation in the solid via thermal reactive boundary conditions for a consistent treatment of the reaction enthalpy. The chemical surface reactions are incorporated in a flexible fashion through flux boundary conditions at the gas-solid interface. We scrutinize the thermal FD-LBM by benchmarking the macroscopic transport in the gas domain as well as conservation of the enthalpy across the solid-gas interface. We exemplify the applicability of our model by simulating the reactive gas flow through a microporous material catalysing the so-called water-gas-shift reaction

Inertial-Based Filtration Method for Removal of Microcarriers from Mesenchymal Stem Cell Suspensions

© 2018, The Author(s). Rapidly evolving cell-based therapies towards clinical trials demand alternative approaches for efficient expansion of adherent cell types such as human mesenchymal stem cells (hMSCs). Using microcarriers (100–300 µm) in a stirred tank bioreactor offers considerably enhanced surface to volume ratio of culture environment. However, downstream purification of the harvested cell product needs to be addressed carefully due to distinctive features and fragility of these cell products. This work demonstrates a novel alternative approach which utilizes inertial focusing to separate microcarriers (MCs) from the final cell suspension. First, we systematically investigated MC focusing dynamics inside scaled-up curved channels with trapezoidal and rectangular cross-sections. A trapezoidal spiral channel with ultra-low-slope (Tan(α) = 0.0375) was found to contribute to strong MC focusing (~300 < Re < ~400) while managing high MC volume fractions up to ~1.68%. Accordingly, the high-throughput trapezoidal spiral channel successfully separated MCs from hMSC suspension with total cell yield~94% (after two passes) at a high volumetric flow rate of ~30 mL/min (Re~326.5)

Tissue engineering and regenerative medicine research - how can it contribute to fight future pandemics?

Understanding the pathogenesis of viral infection is of paramount importance for the development of better therapies. In the particular case of COVID-19, the mechanism of infection is highly complex and involves a critical cascade of events, which can lead to the death of the patient. Intense research is currently being performed to gain mechanistic insights about the virus etiology and to evaluate new therapeutic approaches. The development of point-of-care diagnostic tools, predictive drug screening platforms, and biomimetic models of the disease could play a key role in understanding the cellular and molecular mechanism of viral infection and its response to drugs. In this regard, specific tissue engineering and regenerative medicine approaches, such as microfluidics and organ-on-a-chip technologies, as well as bioprinted in vitro disease models, could be used to develop a technological platform to fight COVID-19, and other virus pandemics yet to come. Herein, we briefly discuss about how such approaches can contribute to address current and future viral pandemics by highlighting recent successful examples.D. Caballero acknowledges the financial support from the Portuguese Foundation for Science and Technology under the program CEEC Individual 2017 (CEECIND/00352/2017) and the project 2MATCH (02/SAICT/2017 - nº 028070) funded by the Programa Operacional Regional do Norte supported by FEDER. M. Carvalho would like to acknowledge IET Harvey Research Prize 2017. The authors also acknowledge the financial support from the EU Framework Programme for Research and Innovation Horizon 2020 on Forefront Research in 3D Disease Cancer Models as in vitro Screening Technologies (FoReCaST- no. 668983), the Portuguese Foundation for Science and Technology (FCT) distinction attributed to J. M. Oliveira (IF/00423/2012, IF/01285/2015) and FCT, Fundo Europeu de Desenvolvimento Regional (FEDER) and Programa Operacional Competitividade e Internacionalização (POCI) for funding the projects B-Liver (PTDC/EMD-EMD/29139/2017), Hierarchitech (M-ERA-NET/0001/2014) and 3BioMeD (JICAM/0001/2017)