References of "Farina, Sofia 50034179"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailA cut finite element method for spatially resolved energy metabolism models in complex neuro-cell morphologies with minimal remeshing
Farina, Sofia UL; Claus, Susanne; Hale, Jack UL et al

in Advanced Modeling and Simulation in Engineering Sciences (2021), 8

A thorough understanding of brain metabolism is essential to tackle neurodegenerative diseases. Astrocytes are glial cells which play an important metabolic role by supplying neurons with energy. In ... [more ▼]

A thorough understanding of brain metabolism is essential to tackle neurodegenerative diseases. Astrocytes are glial cells which play an important metabolic role by supplying neurons with energy. In addition, astrocytes provide scaffolding and homeostatic functions to neighboring neurons and contribute to the blood–brain barrier. Recent investigations indicate that the complex morphology of astrocytes impacts upon their function and in particular the efficiency with which these cells metabolize nutrients and provide neurons with energy, but a systematic understanding is still elusive. Modelling and simulation represent an effective framework to address this challenge and to deepen our understanding of brain energy metabolism. This requires solving a set of metabolic partial differential equations on complex domains and remains a challenge. In this paper, we propose, test and verify a simple numerical method to solve a simplified model of metabolic pathways in astrocytes. The method can deal with arbitrarily complex cell morphologies and enables the rapid and simple modification of the model equations by users also without a deep knowledge in the numerical methods involved. The results obtained with the new method (CutFEM) are as accurate as the finite element method (FEM) whilst CutFEM disentangles the cell morphology from its discretisation, enabling us to deal with arbitrarily complex morphologies in two and three dimensions. [less ▲]

Detailed reference viewed: 101 (7 UL)
Full Text
Peer Reviewed
See detailA CutFEM Method for a spatial resolved energy metabolism model in complex cellular geometries
Farina, Sofia UL

Scientific Conference (2021, January)

Computational techniques have been widely used to tackle problems in the biological sciences. A com- promise between high quality simulations and simple but accurate models can help to understand un ... [more ▼]

Computational techniques have been widely used to tackle problems in the biological sciences. A com- promise between high quality simulations and simple but accurate models can help to understand un- known aspects of this field. In this work, we will show how the Cut Finite Element Method (CutFEM) [1] can be a powerful tool to solve a reaction diffusion PDE system that models the energy metabolism of a cell. The main difficulty to approach this problem is dealing with the morphology of the cell that can have sharp edges and evolves over time. While classical FEM requires the mesh conform to the domain boundary, CutFEM allows a non-conforming discretisation of the domain, and thus is especially suited for modeling complex and evolving cellular geometries. First, we introduce our simplified model for metabolic pathways taking place in a region small enough to consider the material property as homogeneous. The results obtained with FEM (FENICS Project [2][3]) and CutFEM suggest that the two methods are equivalent. This allows us to use CutFEM to increase the complexity of the domain, from a spherical shaped cell to an irregular astrocyte. We conclude that CutFEM is a robust method for tackling biological problems with complex geometries, opening the possibility to extend the complexity of our mathematical model including more features and to consider real cellular shapes that evolve in time in future work. [less ▲]

Detailed reference viewed: 93 (7 UL)
Full Text
See detailProject Advanced Discretisaztion Methods
Farina, Sofia UL

Presentation (2019, February 01)

Detailed reference viewed: 124 (27 UL)