A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes

In this paper we show and discuss the use of a versatile interaction potential approach coupled with an immersed boundary method to simulate a variety of flows involving deformable bodies. In particular, we focus on two kinds of problems, namely (i) deformation of liquid-liquid interfaces and (ii) flow in the left ventricle of the heart with either a mechanical or a natural valve. Both examples have in common the two-way interaction of the flow with a deformable interface or a membrane. The interaction potential approach (de Tullio & Pascazio, Jou. Comp. Phys., 2016; Tanaka, Wada and Nakamura, Computational Biomechanics, 2016) with minor modifications can be used to capture the deformation dynamics in both classes of problems. We show that the approach can be used to replicate the deformation dynamics of liquid-liquid interfaces through the use of ad-hoc elastic constants. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as deforming drop in a shear flow or a cross flow. We show that the same potential approach can also be used to study the flow in the left ventricle of the heart. The flow imposed into the ventricle interacts dynamically with the mitral valve (mechanical or natural) and the ventricle which are simulated using the same model. Results from these simulations are compared with ad- hoc in-house experimental measurements. Finally, a parallelisation scheme is presented, as parallelisation is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies on hundreds of distributed memory computing processors

Modeling Cardiovascular Hemodynamics Using the Lattice Boltzmann Method on Massively Parallel Supercomputers

Accurate and reliable modeling of cardiovascular hemodynamics has the potential to improve understanding of the localization and progression of heart diseases, which are currently the most common cause of death in Western countries. However, building a detailed, realistic model of human blood flow is a formidable mathematical and computational challenge. The simulation must combine the motion of the fluid, the intricate geometry of the blood vessels, continual changes in flow and pressure driven by the heartbeat, and the behavior of suspended bodies such as red blood cells. Such simulations can provide insight into factors like endothelial shear stress that act as triggers for the complex biomechanical events that can lead to atherosclerotic pathologies. Currently, it is not possible to measure endothelial shear stress in vivo, making these simulations a crucial component to understanding and potentially predicting the progression of cardiovascular disease. In this thesis, an approach for efficiently modeling the fluid movement coupled to the cell dynamics in real-patient geometries while accounting for the additional force from the expansion and contraction of the heart will be presented and examined. First, a novel method to couple a mesoscopic lattice Boltzmann fluid model to the microscopic molecular dynamics model of cell movement is elucidated. A treatment of red blood cells as extended structures, a method to handle highly irregular geometries through topology driven graph partitioning, and an efficient molecular dynamics load balancing scheme are introduced. These result in a large-scale simulation of the cardiovascular system, with a realistic description of the complex human arterial geometry, from centimeters down to the spatial resolution of red-blood cells. The computational methods developed to enable scaling of the application to 294,912 processors are discussed, thus empowering the simulation of a full heartbeat. Second, further extensions to enable the modeling of fluids in vessels with smaller diameters and a method for introducing the deformational forces exerted on the arterial flows from the movement of the heart by borrowing concepts from cosmodynamics are presented. These additional forces have a great impact on the endothelial shear stress. Third, the fluid model is extended to not only recover Navier-Stokes hydrodynamics, but also a wider range of Knudsen numbers, which is especially important in micro- and nano-scale flows. The tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of such higher-order models and enable efficient modeling of extreme regimes of computational fluid dynamics are discussed. Fourth, the extension of these models to other research questions like clogging in microfluidic devices and determining the severity of co-arctation of the aorta is presented. Through this work, a validation of these methods by taking real patient data and the measured pressure value before the narrowing of the aorta and predicting the pressure drop across the co-arctation is shown. Comparison with the measured pressure drop in vivo highlights the accuracy and potential impact of such patient specific simulations. Finally, a method to enable the simulation of longer trajectories in time by discretizing both spatially and temporally is presented. In this method, a serial coarse iterator is used to initialize data at discrete time steps for a fine model that runs in parallel. This coarse solver is based on a larger time step and typically a coarser discretization in space. Iterative refinement enables the compute-intensive fine iterator to be modeled with temporal parallelization. The algorithm consists of a series of prediction-corrector iterations completing when the results have converged within a certain tolerance. Combined, these developments allow large fluid models to be simulated for longer time durations than previously possible.Engineering and Applied Science

USSR Space Life Sciences Digest, issue 30

This is the thirtieth issue of NASA's Space Life Sciences Digest. It contains abstracts of 47 journal papers or book chapters published in Russian and of three Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 20 areas of space biology and medicine. These areas include: adaptation, biospheric research, cardiovascular and respiratory systems, endocrinology, equipment and instrumentation, gastrointestinal system, group dynamics, habitability and environmental effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, psychology, radiobiology, and space biology and medicine

Aerospace medicine and biology: A continuing bibliography with indexes, supplement 164

This bibliography lists 275 reports, articles, and other documents introduced into the NASA scientific and technical information system in January 1977

Developing numerical methods for fully-coupled nonlinear fluid-structure interaction problems

This thesis is dedicated to developing numerical methods to solve fluid-structure interaction (FSI) problems. FSI features in a vast range of physical systems and has a wide application in engineering. The work of this thesis is focused on the partitioned methods, mostly due to their features of modularity, robustness and reliability. In a partitioned approach, separate solvers are used for the fluid and structural sub-problem domains and a coupling method is devised to account for their mutual interaction. Moreover, the thesis is focused on FSI problems with strong added-mass effect, which are more challenging to solve numerically. For such FSI problems, normally an implicit partitioned method is used which enforces the coupling conditions on the interface through coupling iterations between the fluid and structural solvers. However, these methods are computationally expensive. In this work we follow a semi-implicit approach to develop stable, efficient and accurate numerical methods for FSI problems. In these methods, the fluid pressure term is segregated and strongly coupled to the structure via coupling iterations. However, the remaining fluid terms and the geometrical nonlinearities are treated explicitly. Strong coupling of the fluid pressure term provides for the stability of the method in FSI problems with strong added-mass effect, while loose coupling of the remaining terms reduces the computational cost of the simulations. The work of this thesis could be divided into three major parts. In the first part, we have developed a simple, efficient and robust semi-implicit coupling method for FSI problems with strong added-mass effect. The proposed method is simple and modular. An extensive set of numerical tests were carried out and the results were compared both to literature data (numerical and experimental), as well as domestic results obtained by using a fully-implicit coupling method. Results showed that the proposed method considerably reduces the computational cost of the simulations without degrading the stability or accuracy of the solution. Moreover, the robustness of the method is demonstrated through numerical tests. Furthermore, we have tried to further analyze the semi-implicit methods in order to gain a better understanding of several unaddressed issues concerning different aspects of these methods. The second major part of this thesis is focused on the temporal accuracy of the semi-implicit coupling methods for FSI problems. The semi-implicit methods in the literature appear to be only first-order in time. Most semi-implicit methods rely on using a projection method for the fluid equations, while extending the temporal accuracy of the projection methods is not straightforward. Moreover, mesh-conforming FSI solution methods require solving the ALE form of the Navier-Stokes equations on a moving mesh, which does not necessarily preserve the order of accuracy of the method on a fixed grid. Furthermore, if the FSI coupling technique is not properly designed, the second-order accuracy for the coupled problem is not guaranteed, even though each sub-problem possessed such accuracy. In this work, we have proposed a second-order time accurate semi-implicit method for FSI problems and demonstrated its second-order accuracy through rigorous numerical tests. The last major part of this thesis is concerned with computational efficiency and parallel scalability of the developed methods for numerical solution of complex FSI problems on massively-parallel supercomputers. We have presented a scalable parallel framework for partitioned solution of FSI problems through multi-code coupling. Two instances of our in-house software is used to solve the fluid and structural sub-problems. The communication between the single-physics solvers are carried out using an external coupling library. Parallel efficiency and scalability of the coupled framework is demonstrated in solving practical FSI test cases.Esta tesis está dedicada al desarrollo de métodos numéricos para resolver problemas de interacción de fluido-estructura (FSI). Esta fenomenología aparece en una amplia gama de sistemas físicos y aplicaciones en ingeniería. El trabajo se centra en los métodos de partición, principalmente debido a sus características de modularidad, robustez y fiabilidad. En estos métodos se utilizan solvers distintos para los dominios de fluido y estructura, siendo esencial la técnica de acoplamiento para tener en cuenta su interacción mutua. Además, la tesis se centra en los problemas del FSI con un fuerte efecto de "masa agregada", que son más complejos de resolver numéricamente. Normalmente se usa un método de partición implícito que impone las condiciones de acoplamiento en la interfaz a través de iteraciones entre los solucionadores de fluido y de estructura. Sin embargo, estos métodos son computacionalmente costosos. En esta tesis seguimos un enfoque semi-implícito que permite métodos numéricos estables, eficientes y precisos, en donde el término de presión del fluido está segregado y fuertemente acoplado a la estructura a través de iteraciones de acoplamiento. Sin embargo, los términos fluidos restantes y las no linealidades geométricas se tratan explícitamente. El fuerte acoplamiento del término de presión del fluido proporciona la estabilidad del método en problemas de FSI con un fuerte efecto de masa agregada, mientras que el acoplamiento de los términos restantes reduce el coste computacional. La tesis se divide en tres partes principales. En la primera se desarrolla un método de acoplamiento semi-implícito eficiente y robusto para problemas con un fuerte efecto de masa agregada. El método propuesto es simple y modular. Se llevó a cabo un extenso conjunto de pruebas numéricas. Los resultados se compararon con datos de la literatura (numéricos y experimentales), así como con resultados propios obtenidos mediante el uso métodos de acoplamiento totalmente implícitos. Las pruebas realizadas mostraron que el método propuesto reduce considerablemente el coste computacional de las simulaciones sin degradar su estabilidad y precisión. Además, se ha analizado más a fondo los métodos semi-implícitos con el fin de obtener una mejor comprensión de varias cuestiones no abordadas en relación con algunos aspectos de estos métodos. La segunda parte de esta tesis se centra en la precisión temporal de los métodos de acoplamiento semi-implícitos para problemas de FSI. La mayoría de los métodos semi-implícitos propuestos se basan en el uso de técnicas de proyección para las ecuaciones del fluido, con aproximaciones de primer orden temporal, no siendo sencilla su extensión a alto orden. Además, los métodos de malla-conforme requieren la resolución ALE de las ecuaciones de Navier-Stokes en mallas en movimiento, lo que no necesariamente conserva el orden de precisión del método en una cuadrícula fija. Si la técnica de acoplamiento FSI no está diseñada adecuadamente, no se puede garantizar la precisión de segundo orden para el problema acoplado, aunque cada sub-problema posea tal precisión. En este trabajo se propone un método semi-implícito de segundo orden temporal para este tipo de problemas, y se demuestra dicha precisión a través de rigurosas pruebas numéricas. La última parte de esta tesis se refiere a la eficiencia computacional y la escalabilidad paralela de los métodos desarrollados para la solución numérica de problemas complejos de FSI en supercomputadoras masivamente paralelas. Se presenta un marco paralelo escalable para la solución particionada a través del acoplamiento de múltiples códigos. Se utilizan dos instancias de nuestro software interno para resolver los sub-problemas de fluidos y estructurales. La comunicación entre los solucionadores de física simple se realiza mediante una biblioteca de acoplamiento externa...Postprint (published version

Cell mechanics in flow: algorithms and applications

The computer simulations are pervasively used to improve the knowledge about biophysical phenomena and to quantify effects which are difficult to study experimentally. Generally, the numerical methods and models are desired to be as accurate as possible on the chosen length and time scales, but, at the same time, affordable in terms of computations. Until recently, the cell mechanics and blood flow phenomena on the sub-micron resolution could not be rigorously studied using computer simulations. However, within the last decade, advances in methods and hardware catalyzed the development of models for cells mechanics and blood flow modeling which, previously, were considered to be not feasible. In this context, a model should accurately describe a phenomenon, be computationally affordable, and be flexible to be applied to study different biophysical changes. This thesis focuses on the development of the new methods, models, and high-performance software implementation that expand the class of problems which can be studied numerically using particle-based methods. Microvascular networks have complex geometry, often without any symmetry, and to study them we need to tackle computational domains with several inlets and outlets. However, an absence of appropriate boundary conditions for particle- based methods hampers study of the blood flow in these domains. Another obstacle to model complex blood flow problems is the absence the highperformance software. This problem restricts the applicability of the of particlebased cell flow models to relatively small systems. Although there are several validated red blood cell models, to date, there are no models for suspended eukaryotic cells. The present thesis addresses these issues. We introduce new open boundary conditions for particle-based systems and apply them to study blood flow in a part of a microvascular network. We develop a software demonstrating outstanding performance on the largest supercomputers and used it to study blood flow in microfluidic devices. Finally, we present a new eukaryotic cell model which helps in quantifying the effect of sub-cellular components on the cell mechanics during deformations in microfluidic devices

Book of Abstracts 15th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 3rd Conference on Imaging and Visualization

In this edition, the two events will run together as a single conference, highlighting the strong connection with the Taylor & Francis journals: Computer Methods in Biomechanics and Biomedical Engineering (John Middleton and Christopher Jacobs, Eds.) and Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization (JoãoManuel R.S. Tavares, Ed.). The conference has become a major international meeting on computational biomechanics, imaging andvisualization. In this edition, the main program includes 212 presentations. In addition, sixteen renowned researchers will give plenary keynotes, addressing current challenges in computational biomechanics and biomedical imaging. In Lisbon, for the first time, a session dedicated to award the winner of the Best Paper in CMBBE Journal will take place. We believe that CMBBE2018 will have a strong impact on the development of computational biomechanics and biomedical imaging and visualization, identifying emerging areas of research and promoting the collaboration and networking between participants. This impact is evidenced through the well-known research groups, commercial companies and scientific organizations, who continue to support and sponsor the CMBBE meeting series. In fact, the conference is enriched with five workshops on specific scientific topics and commercial software.info:eu-repo/semantics/draf

Aerospace medicine and biology: A cumulative index to the continuing bibliography of the 1973 issues

A cumulative index to the abstracts contained in Supplements 112 through 123 of Aerospace Medicine and Biology A Continuing Bibliography is presented. It includes three indexes: subject, personal author, and corporate source