Computational Framework to Evaluate the Hydrodynamics of Cell Scaffold Geometries

Methods for qualitative simulation allow predictions on the dynamics of a system to be made in the absence of quantitative information, by inferring the range of possible qualitative behaviors compatible with the structure of the system. This article reviews QSIM and other qualitative simulation methods. It discusses two problems that have seriously compromised the application of these methods to realistic problems in science and engineering: the occurrence of spurious behavior predictions and the combinatorial explosion of the number of behavior predictions. In response to these problems, related approaches for the qualitative analysis of dynamic systems have emerged: qualitative phase-space analysis and semi-quantitative simulation. The article argues for a synthesis of these approaches in order to obtain a computational framework for the qualitative analysis of dynamic systems. This should provide a solid basis for further upscaling and for the development of model-based reasoning applications of a wider scope.

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Computational framework for monolithic coupling for thin fluid flow in contact interfaces

Computer Methods in Applied Mechanics and Engineering ◽

10.1016/j.cma.2021.113738 ◽

2021 ◽

Vol 379 ◽

pp. 113738

Author(s):

Andrei G. Shvarts ◽

Julien Vignollet ◽

Vladislav A. Yastrebov

Keyword(s):

Fluid Flow ◽

Computational Framework ◽

Thin Fluid

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A computational framework for modeling cell–matrix interactions in soft biological tissues

Biomechanics and Modeling in Mechanobiology ◽

10.1007/s10237-021-01480-2 ◽

2021 ◽

Author(s):

Jonas F. Eichinger ◽

Maximilian J. Grill ◽

Iman Davoodi Kermani ◽

Roland C. Aydin ◽

Wolfgang A. Wall ◽

...

Keyword(s):

Soft Tissues ◽

Three Dimensional ◽

Biological Tissues ◽

Computational Framework ◽

Cell Matrix ◽

Physiological Processes ◽

Matrix Interactions ◽

Mechanical Homeostasis ◽

Cell Matrix Interactions ◽

Short Time

AbstractLiving soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set point. This phenomenon is often referred to as mechanical homeostasis. In contradiction to the prominent role of mechanical homeostasis in various (patho)physiological processes, its underlying micromechanical mechanisms acting on the level of individual cells and fibers remain poorly understood, especially how these mechanisms on the microscale lead to what we macroscopically call mechanical homeostasis. Here, we present a novel computational framework based on the finite element method that is constructed bottom up, that is, it models key mechanobiological mechanisms such as actin cytoskeleton contraction and molecular clutch behavior of individual cells interacting with a reconstructed three-dimensional extracellular fiber matrix. The framework reproduces many experimental observations regarding mechanical homeostasis on short time scales (hours), in which the deposition and degradation of extracellular matrix can largely be neglected. This model can serve as a systematic tool for future in silico studies of the origin of the numerous still unexplained experimental observations about mechanical homeostasis.

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A computational framework for connection matrix theory

Journal of Applied and Computational Topology ◽

10.1007/s41468-021-00073-3 ◽

2021 ◽

Author(s):

Shaun Harker ◽

Konstantin Mischaikow ◽

Kelly Spendlove

Keyword(s):

Matrix Theory ◽

Connection Matrix ◽

Computational Framework

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Furin and the adaptive mutation of SARS-COV2: a computational framework

Modeling Earth Systems and Environment ◽

10.1007/s40808-021-01260-y ◽

2021 ◽

Cited By ~ 1

Author(s):

Ayesha Sohail ◽

Sümeyye Tunc ◽

Alessandro Nutini ◽

Robia Arif

Keyword(s):

Adaptive Mutation ◽

Computational Framework

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PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

npj Computational Materials ◽

10.1038/s41524-021-00506-8 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Mohammadreza Yaghoobi ◽

Krzysztof S. Stopka ◽

Aaditya Lakshmanan ◽

Veera Sundararaghavan ◽

John E. Allison ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Large Scale ◽

Metals And Alloys ◽

Analysis Tool ◽

Computational Framework ◽

Crystal Plasticity Finite Element ◽

Polycrystalline Metals ◽

Simulation Based ◽

Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

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