Modelování advekčně-difúzních procesů v jaterní tkáni
| Thesis title in Czech: | Modelování advekčně-difúzních procesů v jaterní tkáni |
|---|---|
| Thesis title in English: | Modelling of advection-diffusion processes in liver tissue |
| Key words: | advekčně-difúzní procesy|bilanční vztahy|redukované modely|mikrocirkulace|numerické simulace|metoda konečných objemů |
| English key words: | advection-diffusion processes|conservation laws|reduced models|microcirculation|numerical simulations|finite volume method |
| Academic year of topic announcement: | 2022/2023 |
| Thesis type: | diploma thesis |
| Thesis language: | angličtina |
| Department: | Mathematical Institute of Charles University (32-MUUK) |
| Supervisor: | prof. Dr. Ing. Eduard Rohan, DSc. |
| Author: | hidden - assigned and confirmed by the Study Dept. |
| Date of registration: | 20.04.2023 |
| Date of assignment: | 20.04.2023 |
| Confirmed by Study dept. on: | 25.04.2023 |
| Date and time of defence: | 07.06.2023 08:30 |
| Date of electronic submission: | 04.05.2023 |
| Date of submission of printed version: | 09.05.2023 |
| Date of proceeded defence: | 07.06.2023 |
| Opponents: | doc. RNDr. Ondřej Souček, Ph.D. |
| Guidelines |
| A model describing the bile transport in the bile canalicular network should be proposed, analysed and implemented numerically such that it can provide simulation tool for subsequent case studies and parameter sensitivity, or parameter identification. The following steps should be performed:
1. Coupled physical phenomena included in the model should be identified. An a priori selection of the most relevant phenomena should be considered for modelling (a physical model reduction). 2. Representative geometries relevant to the capillary (sinusoidal) and canalicular resolution (char. scale 10-50 μm) should be proposed and the principal compartments distinguished (hepatic cells, blood vessels, bile canalicular network, the Disse space). 3. Systems of PDEs should be defined in particular compartments in and coupling and transmission conditions on interfaces should be established. 4. A model reduction to 1D problems should be proposed to diminish computational power required for numerical simulations. 5. Using numerical simulations compared with measured data the most important coupled phenomena relevant to the bile salt transport should be identified, incorporating possible sources and sinks for the bile salts. 6. Both reduced and full models should be implemented numerically (using available software computational platforms (OpenFEM, OpenFOAM, SfePy, Matlab, Comsol,....) Relevance of the reduced models, or decoupled computations should be verified. |
| References |
| Noemie Boissier, Dirk Drasdo, Irene E Vignon‐Clementel, Simulation of a detoxifying organ function: Focus on hemodynamics modeling and convection‐reaction numerical simulation in microcirculatory networks. International Journal for Numerical Methods in Biomedical Engineering Vol. 37 (2) e3422 (2021).
Chloe Audebert. Mathematical liver modeling : hemodynamics and function in hep- atectomy. General Mathematics [math.GM]. Université Pierre et Marie Curie - Paris VI, 2017. English. NNT : 2017PA066077. tel-01512620v3 E. Rohan, V. Lukeš, and A. Jonášová, Modeling of the contrast-enhanced perfusion test in liver based on the multi-compartment flow in porous media. J Math Biol., 77:421-454, 2018. Nachiket Vartak, Georgia Guenther, Florian Joly, Amruta Damle‐Vartak, Gudrun Wibbelt, Jörns Fickel, Simone Jörs, Brigitte Begher‐Tibbe, Adrian Friebel, Kasimir Wansing, Ahmed Ghallab, Marie Rosselin, Noemie Boissier, Irene Vignon‐Clementel, Christian Hedberg, Fabian Geisler, Heribert Hofer, Peter Jansen, Stefan Hoehme, Dirk Drasdo, Jan G Hengstler, Intravital dynamic and correlative imaging of mouse livers reveals diffusion‐dominated canalicular and flow‐augmented ductular bile flux, Hepatology 73 (4), 1531-1550 (2021) |
| Preliminary scope of work |
| Zadání diplomové práce je motivováno otevřenými problémy v modelování advekčně-difúzních jevů v jaterní tkáni s potenciálním dopadem na multidisciplinární výzkum fyziologie jater. Kromě mikrocirkulace krve, která se v posledních letech stala předmětem intenzivního výzkumu, nejsou stále zcela pochopeny hnací mechanismy transportu žluči. Ten poměrně významně ovlivňuje mnoho důležitých metabolických procesů a jeho odchylka od normálního fyziologického stavu vyvolává progresi různých tkáňových patologií a závažných onemocnění. Stávající experimentální práce i předběžné výpočetní studie tvoří solidní základ pro další výzkum, jehož část lze v rámci navrhované práce realizovat. Hlavním cílem modelování je lepší pochopení eliminace žlučových solí z jater v důsledku transportu ve tkáni na lobulární úrovni. Zejména role souběžně probíhajících dějů – advekce, difúzně osmotických toků a peristaltiky hepatocytů – by měly být posouzeny pomocí fyzikálně i matematicky relevantních výpočtových modelů. Modelování a simulace by měly být založeny na naměřených datech získaných z experimentů. |
| Preliminary scope of work in English |
| The Thesis specification is motivated by open issues in modelling the advection-diffusion phenomena in liver tissue with potential impact on the multidisciplinary research of the liver physiology. Besides the blood microcirculation which became the subject of intensive research in past years, driving mechanisms of the biliary flow are still not completely understood. The bile flow influences quite significantly many important metabolic processes and its discrepancy from a normal physiological state provoke progression of various tissue pathologies and serious diseases. Existing experimental works as well as preliminary computational studies make a sound basis for further research a part of which can be carried out within the proposed Thesis. As the major objective of the modelling is a better understanding the bile salt elimination from the liver due transport in the tissue at the lobular level. In particular, the roles of competing mechanisms – advection, diffusion osmotic flows and hepatocyte peristalsis – should be assessed using physically and mathematically relevant and computational models. The modelling and simulations should be based on the measured data obtained from experiments. |