@misc {43190,
	title = {The effects of cerebrospinal fluid and hyperelastic model on aneurysm wall vibration using high-fidelity fluid-structure interaction simulations},
	howpublished = {Summer Biomechanics, Bioengineering, and Biotransport Conference},
	year = {2023},
	author = {Yamamoto, Kei and Bruneau, David and Steinman, David and Valen-Sendstad, Kristian}
}
@book {43191,
	title = {In silico Investigation of Sex-Specific Osteoarthritis in Human Articular Chondrocytes},
	volume = {13},
	year = {2023},
	pages = {31 - 44},
	publisher = {Springer Nature Switzerland},
	organization = {Springer Nature Switzerland},
	address = {Cham},
	isbn = {978-3-031-25373-7},
	issn = {2512-1677},
	doi = {10.1007/978-3-031-25374-4_3},
	url = {https://link.springer.com/chapter/10.1007/978-3-031-25374-4_3},
	author = {Ngo, Khoa and Nathaniel T {Herrera} and Folkmanaite, Milda and Yamamoto, Kei and Mary M {Maleckar}},
	editor = {Kimberly J. {McCabe}}
}
@mastersthesis {42632,
	title = {Numerical Investigation of Turbulent Flow in Helically Coiled Pipes},
	journal = {The University of Oslo},
	year = {2022},
	abstract = {Fluid flow in helically coiled pipes is not fully understood. Although many efforts have been devoted to investigating the complex characteristics of the flow in helically coiled pipes, much is unknown for especially high Reynolds numbers, i.e., turbulence. In this thesis, turbulent flow in helically coiled pipes is numerically investigated. First, direct numerical simulation of turbulent flow in a straight pipe is carried out for numerical validation. Then, we examine turbulent flow in helically coiled pipes using the fully turbulent flow from a straight pipe. An increase in the turbulent kinetic energy is observed at the first curve of helically coiled pipes. However, stabilization of the turbulent flow is observed towards the outlet, which is observed numerically for the first time. Due to the curved path and the centrifugal force, two counter-rotating vortices referred to as Dean vortices are observed. These vortices rapidly intensify the dissipation by creating smaller eddies in the flow and hence contribute to stabilizing the flow. We found that the higher curvature and lower torsion are associated with faster stabilization by modifying the geometry. Lastly, numerical simulations of blood flow in the internal carotid artery (ICA), which shares geometrical characteristics with helically coiled pipes, are conducted with patient-specific geometries. Recent studies proposed the correlation between flow instability and the initiation of cerebral aneurysms in the ICA. Therefore, we aim to contribute to understanding the formation of flow instability in the ICA by applying the gained knowledge from helically coiled pipes. In some of the patients, {\textquoteright}turbulent-like{\textquoteright} flow is found. A patient with stable flow has a higher curvature and lower torsion in the carotid siphon, which agrees with the results of helically coiled pipes. Dean vortices are observed for the first time and may be associated with flow instability in the ICA.},
	url = {http://urn.nb.no/URN:NBN:no-98120},
	author = {Yamamoto, Kei}
}
@inbook {42524,
	title = {Ordinary Differential Equation-based Modeling of Cells in Human Cartilage},
	booktitle = {Computational Physiology - Simula Summer School 2021 - Student Reports},
	volume = {12},
	year = {2022},
	pages = {25 - 39},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {Chondrocytes produce the extracellular cartilage matrix required for smooth joint mobility. As cartilage is not vascularised, and chondrocytes are not innervated by the nervous system, chondrocytes are therefore generally considered non-excitable. However, chondrocytes do express a range of ion channels, ion pumps, and receptors involved in cell homeostasis and cartilage maintenance. Dysfunction in these ion channels and pumps has been linked to degenerative disorders such as arthritis. Because the electrophysiological properties of chondrocytes are difficult to measure experimentally, mathematical modelling can instead be used to investigate the regulation of ionic currents. Such models can provide insight into the finely tuned parameters underlying fluctuations in membrane potential and cell behaviour in healthy and pathological conditions. Here, we introduce an open-source, intuitive, and extendable mathematical model of chondrocyte electrophysiology, implementing key proteins involved in regulating the membrane potential. Because of the inherent biological variability of cells and their physiological ranges of ionic concentrations, we describe a population of models that provides a robust computational representation of the biological data. This permits parameter variability in a manner mimicking biological variation, and we present a selection of parameter sets that suitably represent experimental data. Our mathematical model can be used to efficiently investigate the ionic currents underlying chondrocyte behaviour.},
	isbn = {978-3-031-05163-0},
	issn = {2512-1677},
	doi = {https://doi.org/10.1007/978-3-031-05164-7_3},
	url = {https://link.springer.com/chapter/10.1007/978-3-031-05164-7_3$\#$chapter-info},
	author = {Yamamoto, Kei and Fischer-Holzhausen, Sophie and Maria Perona {Fjelstad} and Maleckar, Molly},
	editor = {Kimberly J {McCabe}}
}
@misc {42960,
	title = {SimCardioTest Open Source Software {\textendash} Demo on OASIS: Computational fluid dynamics solver \& SOFA: Simulation Open Framework Architecture},
	howpublished = {VPH2022, Porto, Portugal},
	year = {2022},
	publisher = {VPH2022 Porto},
	abstract = {SimCardioTest is a collaborative project between 10 organizations from 6 European countries and United States funded by the European Commission (EU H2020). The aim of the project is to provide new insight into designing predictive tools in cardiac pathologies and to accelerate the uptake of computer simulations for testing medicines and medical devices.The aim of the workshop is\&nbsp; hands on/demonstration of the open source OASIS and SOFA software.},
	url = {https://vph-conference.org/call-for-proposals/},
	author = {Yamamoto, Kei and Valen-Sendstad, Kristian}
}
@misc {42961,
	title = {Turbulent-like flow as a cause of cerebral aneurysm initiation: Can flow instability promote pathophysiological wall remodeling?},
	year = {2022},
	publisher = {Blood-Tissue Interface conference},
	address = {Blood-Tissue Interface conference, Montpellier, France},
	url = {https://bti.sciencesconf.org},
	author = {Yamamoto, Kei and Valen-Sendstad, Kristian}
}
@misc {42959,
	title = {Under-resolved DNS of turbulent flow in straight and helically coiled pipes},
	howpublished = {FEniCS 2022, San Diego, USA},
	year = {2022},
	publisher = {FEniCS2022},
	abstract = {Oasis\&nbsp;is an open-source Navier-Stokes solver built on FEniCS entirely written in Python. There are other open-source Navier-Stokes solvers available, such as openFOAM, but it is written in low-level programming language C++. One of the advantages of using Oasis over openFOAM is the usage of high-level Python code that enables users to flexibly control the implementation of problems. In addition, Oasis utilizes MPI to ensure high-performance and scalability on parallel clusters. Oasis has been previously verified and validated, but verification and validation is a continuous process that can establish the reliability of the solver when applied to new problems.\&nbsp;\&nbsp;Here, we present two turbulent flow problems that can illustrate flexible implementation of Oasis with fast and accurate performance. First, direct numerical simulation (DNS) of turbulent flow in a straight pipe was carried out for numerical validation, and the results were compared against published DNS data-set. Second, we examined turbulent flow in helically coiled pipes using fully developed turbulent flow from straight pipes as an inlet velocity profile.\&nbsp;In the straight pipe, our quantitative results showed convergence towards the DNS reference data, as the mesh was refined. In the helically coiled pipe, reported for the first time for a numerical model, stabilization of the turbulent flow was observed towards the outlet. Due to the curved path and the centrifugal force, two counter-rotating vortices referred to as Dean vortices were formed on the cross-section of the pipe. These vortices rapidly intensified the dissipation by creating smaller eddies in the flow and hence contributing to stabilizing the flow.\&nbsp;},
	url = {https://fenicsproject.org/fenics-2022/},
	author = {Yamamoto, Kei and Valen-Sendstad, Kristian}
}
@article {28130,
	title = {Probing the putative role of KATP channels and biological variability in a mathematical model of chondrocyte electrophysiology},
	journal = {Bioelectricity},
	volume = {3},
	year = {2021},
	pages = {272-281},
	publisher = {Mary Ann Liebert Inc},
	doi = {http://doi.org/10.1089/bioe.2021.0034},
	author = {Fischer-Holzhausen, Sophie and Yamamoto, Kei and Maria Perona {Fjelstad} and Maleckar, Molly}
}
