Computational Fluid-Particle Dynamics Modeling for Unconventional Inhaled Aerosols in Human Respiratory Systems

The awareness is growing of health hazards and pharmaceutical benefits of micro-/nano-aerosol particles which are mostly nonspherical and hygroscopic, and categorized as “unconventional” vs. solid spheres. Accurate and realistic numerical models will significantly contribute to answering public health questions. In this chapter, fundamentals and future trends of computational fluid-particle dynamics (CFPD) models for lung aerosol dynamics are discussed, emphasizing the underlying physics to simulate unconventional inhaled aerosols such as fibers, droplets, and vapors. Standard simulation procedures are presented, including reconstruction of the human respiratory system, CFPD model formulation, finite-volume mesh generation, etc. Case studies for fiber and droplet transport and deposition in lung are also provided. Furthermore, challenges and future directions are discussed to develop next-generation models. The ultimate goal is to establish a roadmap to link different numerical models, and to build the framework of a new multiscale numerical model, which will extend exposure and lung deposition predictions to health endpoints, e.g., tissue and delivered doses, by calculating absorption and translocation into alveolar regions and systemic regions using discrete element method (DEM), lattice Boltzmann method (LBM), and/or physiologically based pharmacokinetic (PBPK) models. It will enable simulations of extremely complex airflow-vapor-particle-structure dynamics in the entire human respiratory system at detailed levels

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized

Particle depositions in multi stage liquid impinger as simplified lung model using computational fluid dynamic

Inhaled medication is typically used to treat obstructive pulmonary disease and systemic diseases. The effectiveness of pulmonary drug delivery depends on the amount of drug deposited beyond the oropharyngeal region, the place where the deposition and the uniform distribution occurred. In this study, the performance of multistage liquid impinger (MSLI) simplified model which imitates the physiological lung in delivering the drug was analyzed. In order to achieve this main aim, the airflow patterns and particle depositions efficiency were evaluated in MSLI simplified model using computational fluid dynamic of COMSOL® software. The particle deposition efficiency is studied by varying flowrates (30.0 L/min, 60.0 L/min and 100.0 L/min) and particle sizes (0.1, 1.0, 3.0, 5.0, 10.0 pm) of salbutamol sulphate (density 20.0 kg/m3). The highest particle deposition occurred at flowrate 100.0 L/min and particle size of 1.0 pm as the deposition yield was 15.55% compared to flowrate 60 L/min and 30 L/min which were 10.50% and 3.09% respectively. Previous studies claimed that higher inhalation flowrate generated dispersion forces for sufficient inhalation flowrate thus enhanced higher deposition efficiency. The paired-samples T-test shows there were significant different (t= -15.400, df= 4, p <0.05) in the performance of particle depositions in MSLI simplified model with different flow rates (60.0 L/min and 100.0 L/min). Thus, the efficient fine particle deposition was significantly contributed by higher flowrate. This study also revealed that particle size ranges from 1.0 to 3.0 pm was the most suitable for inhalation treatment. Smaller particle size less than 1.0 pm was not suitable as it tended to exhale before it deposit of while larger particle (more than 5.0 pm) was not suitable for inhaled drug. In conclusion, vigorous air flow pattern promotes higher particle deposition. For efficient fine particle depositions, it is important to consider not only the particle size distribution, but also the flowrate as vital aerosol transportation agent. Statistical analysis, two-way ANOVA indicated that there was a statistically significant interaction between the effect of flowrate and particle size on particle deposition efficiency, F (8, 30)=5.857, p=0.00

Modelação multiescala de qualidade do ar urbana para cidades mais saudáveis

Ambient air pollution is nowadays a serious public health problem worldwide, especially in urban areas due to high population density and intense anthropogenic activity. Among the main urban air pollution sources, the road traffic sector is one of the major concerns and the largest contributor to nitrogen dioxide (NO2) concentrations, though regional background chemical conditions must also be considered. In this context, the use of modelling tools is crucial to understand atmospheric and social dynamics in multiple scales, as well as to support in defining the best air quality improvement strategies. The main objective of this thesis is to develop and apply a multiscale modelling system able to simulate air quality and health impacts in cities. For this purpose, the modair4health multiscale air quality and health risk modelling system was developed and operationalized. It includes the online model WRF-Chem, which provides air quality and meteorological fields from regional to urban scales, and the Computational Fluid Dynamics (CFD) model VADIS, which uses the urban WRF-Chem outputs to calculate flows and dispersion of traffic emissions-related air pollutants in urban built-up areas. A health module, based on linear and non-linear World Health Organization approaches, was also integrated in modair4health to assess the health impacts resulting from air quality changes, and the overall health damage costs are calculated based on economic studies. The application and assessment of the modair4health system allowed to identify the most appropriate configurations and input data, which were used to apply the system over the case study testing air quality improvement scenarios. One of the busiest road traffic areas of the city of Coimbra (Fernão de Magalhães Avenue) in Portugal was selected as case study. The application considered a 4 domains setup: three nested domains (25, 5 and 1 km2 resolutions) for the WRF-Chem, and the 4th domain (4 m2 resolution) over the target local study area and NO2 for the VADIS. WRF-Chem was applied along the year 2015 and VADIS was simulating two particular periods: one week in winter and another one in summer. Short-term health impacts were estimated and the non-linear approach led to lower health outcomes that seem better adjusted to the local reality. Finally, to assess the modair4health capabilities for decision-making support, two traffic management scenarios were tested over the case study: replacement of 50% of the vehicle fleet below EURO 4 by electric vehicles (ELEC), and introduction of a Low Emission Zone (LEZ). Air quality and health positive impacts were higher for the ELEC scenario. This study represents a scientific advance in multiscale air quality and health modelling. The modair4health system can be easily adapted and applied to other simulation domains, providing urban air pollution levels and subsequent health impacts for different case studies and supporting the assessment of air pollution control policies.A poluição atmosférica é atualmente um sério problema mundial de saúde pública, especialmente em áreas urbanas, devido à elevada densidade populacional e intensa atividade antropogénica. O setor dos transportes rodoviários é uma das principais preocupações e o que mais contribui para concentrações de dióxido de azoto (NO2) na atmosfera, embora as condições químicas de fundo regional devam também ser consideradas. Neste contexto, a utilização de ferramentas de modelação é crucial para compreender a dinâmica atmosférica e humana a diferentes escalas, e apoiar na definição das melhores estratégias para melhoria da qualidade do ar (EMQA). Esta tese tem como objetivo principal o desenvolvimento e aplicação de um sistema de modelação multiescala que permita simular qualidade do ar e impactos na saúde em cidades. Para isso, foi desenvolvido e operacionalizado o sistema modair4health - multiscale air quality and health risk modelling. Este sistema inclui o modelo online WRF-Chem, que fornece campos meteorológicos e de qualidade do ar da escala regional à urbana, e o modelo CFD VADIS, que utiliza os resultados do WRF-Chem para calcular o impacto das emissões do tráfego rodoviário no escoamento e dispersão de poluentes em áreas urbanas. Para avaliar os impactos na saúde humana, foi também integrado um módulo baseado nas abordagens linear e não-linear da Organização Mundial de Saúde (OMS), e os custos são calculados com base em estudos económicos. A aplicação e avaliação do sistema modair4health permitiram identificar as configurações e dados de entrada mais apropriados, que foram posteriormente utilizados para testar EMQA sobre o caso de estudo, que corresponde a uma das áreas de maior tráfego rodoviário da cidade de Coimbra (Avenida Fernão de Magalhães). O WRF-Chem foi configurado com 3 domínios aninhados (resoluções de 25, 5 e 1 km2), simulados para o ano 2015; enquanto que para o VADIS, foi definido um quarto domínio (resolução de 4 m2) sobre o caso de estudo para simular concentrações de NO2 em dois períodos específicos: uma semana no inverno e outra no verão. Para quantificar os impactos na saúde, as duas abordagens da OMS foram aplicadas ao caso de estudo para avaliar efeitos a curto-prazo. A abordagem não-linear apresentou resultados de saúde mais baixos que aparentemente estão melhor ajustados à realidade local. Por fim, foram avaliadas as potencialidades do sistema no apoio à tomada de decisão, testando dois cenários de gestão do tráfego rodoviário: substituição de 50% da frota de veículos abaixo de EURO 4 por veículos elétricos (ELEC), e introdução de uma Zona de Emissões Reduzidas (LEZ). O cenário ELEC potencia melhorias mais significativas na qualidade do ar e saúde. Este estudo representa um avanço científico na modelação multiescala da qualidade do ar e saúde. O sistema modair4health pode ser facilmente adaptado e aplicado a outros casos de estudo para avaliar a qualidade do ar urbana e impactos na saúde, bem como para testar medidas de controlo da poluição atmosférica.Programa Doutoral em Ciências e Engenharia do Ambient

Computational Fluid and Particle Dynamics Simulations for Respiratory System: Runtime Optimization on an Arm Cluster

Computational fluid and particle dynamics simulations (CFPD) are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes involves high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on both Intel- and Arm-based HPC clusters showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2X, keeping the computational resources constant.This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697).Peer ReviewedPostprint (author's final draft

Improving the energy efficiency of buildings based on fluid dynamics models: a critical review

The built environment is the global sector with the greatest energy use and greenhouse gas emissions. As a result, building energy savings can make a major contribution to tackling the current energy and climate change crises. Fluid dynamics models have long supported the understanding and optimization of building energy systems and have been responsible for many important technological breakthroughs. As Covid-19 is continuing to spread around the world, fluid dynamics models are proving to be more essential than ever for exploring airborne transmission of the coronavirus indoors in order to develop energy-efficient and healthy ventilation actions against Covid-19 risks. The purpose of this paper is to review the most important and influential fluid dynamics models that have contributed to improving building energy efficiency. A detailed, yet understandable description of each model’s background, physical setup, and equations is provided. The main ingredients, theoretical interpretations, assumptions, application ranges, and robustness of the models are discussed. Models are reviewed with comprehensive, although not exhaustive, publications in the literature. The review concludes by outlining open questions and future perspectives of simulation models in building energy research

Parallel Lagrangian particle transport : application to respiratory system airways

This thesis is focused on particle transport in the context of high computing performance (HPC) in its widest range, from the numerical modeling to the physics involved, including its parallelization and post-process. The main goal is to obtain a general framework that enables understanding all the requirements and characteristics of particle transport using the Lagrangian frame of reference. Although the idea is to provide a suitable model for any engineering application that involves particle transport simulation, this thesis uses the respiratory system framework. This means that all the simulations are focused on this topic, including the benchmarks for testing, verifying and optimizing the results. Other applications, such as combustion, ocean residuals, or automotive, have also been simulated by other researchers using the same numerical model proposed here. However, they have not been included here in the interest of allowing the project to advance in a specific direction, and facilitate the structure and comprehension of this work. Human airways and respiratory system simulations are of special interest for medical purposes. Indeed, human airways can be significantly different in every individual. This complicates the study of drug delivery efficiency, deposition of polluted particles, etc., using classic in-vivo or in-vitro techniques. In other words, flow and deposition results may vary depending on the geometry of the patient and simulations allow customized studies using specific geometries. With the help of the new computational techniques, in the near future it may be possible to optimize nasal drugs delivery, surgery or other medical studies for each individual patient though a more personalized medicine. In summary, this thesis prioritizes numerical modeling, wide usability, performance, parallelization, and the study of the physics that affects particle transport. In addition, the simulation of the respiratory system should carry out interesting biological and medical results. However, the interpretation of these results will be only done from a pure numerical point of view.Aquesta tesi se centra en el transport de partícules dins el context de la computació d'alt rendiment (HPC), en el seu ventall més ampli; des del model numèric fins a la física involucrada, incloent-hi la part de paral·lelització del codi i de post-procés. L'objectiu principal és obtenir un esquema general que permeti entendre tant els requeriments com les característiques del transport de partícules fent servir el marc de referència Lagrangià. Encara que la idea sigui definir un model capaç¸ de simular qualsevol aplicació en el camp de l'enginyeria que involucri el transport de partícules, aquesta tesi utilitza el sistema respiratori com a temàtica de referència. Això significa que totes les simulacions estan emmarcades en aquest camp d'estudi, incloent-hi els tests de referència, verificacions i optimitzacions de resultats. L'estudi d'altres aplicacions, com ara la combustió, els residus oceànics, l'automoció o l'aeronàutica també han estat dutes a terme per altres investigadors utilitzant el mateix model numèric proposat aquí. Tot i així, aquests resultats no han estat inclosos en aquesta tesi per simplificar-la i avançar en una sola direcció; facilitant així l'estructura i millor comprensió d'aquest treball. Pel que fa al sistema respiratori humà i les seves simulacions, tenen especial interès per a propòsits mèdics. Particularment, la geometria dels conductes respiratoris pot variar de manera considerable en cada persona. Això complica l'estudi en aspectes com el subministrament de medicaments o la deposició de partícules contaminants, per exemple, utilitzant les tècniques clàssiques de laboratori (in-vivo o in-vitro). En altres paraules, tant el flux com la deposició poden canviar en funció de la geometria del pacient i aquí és on les simulacions permeten estudis adaptats a geometries concretes. Gràcies a les noves tècniques de computació, en un futur proper és probable que puguem optimitzar el subministrament de medicaments per via nasal, la cirurgia o altres estudis mèdics per a cada pacient mitjançant una medicina més personalitzada. En resum, aquesta tesi prioritza el model numèric, l'amplitud d'usos, el rendiment, la paral·lelització i l'estudi de la física que afecta directament a les partícules. A més, el fet de basar les nostres simulacions en el sistema respiratori dota aquesta tesi d'un interès biològic i mèdic pel que fa als resultats