Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation

The simulation of invadopodia replication holds significance in establishing its biological relevance, as it contributes to a deeper comprehension of cancer invasion and metastasis. Additionally, it offers valuable insights into potential strategies for impeding the dissemination of this life-threat...

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Main Author:	Muhammad Akmal, Ramlee
Format:	Thesis
Language:	English English
Published:	2024
Subjects:	QA Mathematics QA76 Computer software
Online Access:	http://ir.unimas.my/id/eprint/45965/1/Master%20Thesis_Muhammad%20Akmal%20Bin%20Ramlee.pdf http://ir.unimas.my/id/eprint/45965/5/dsva_%20Akmal.pdf
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spelling	my-unimas-ir.459652024-09-10T01:26:48Z Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation 2024-09-05 Muhammad Akmal, Ramlee QA Mathematics QA75 Electronic computers. Computer science QA76 Computer software The simulation of invadopodia replication holds significance in establishing its biological relevance, as it contributes to a deeper comprehension of cancer invasion and metastasis. Additionally, it offers valuable insights into potential strategies for impeding the dissemination of this life-threatening disease. In this study, we present a mathematical model that describes the behaviour of an individual cell, with the aim of extending the simulation of invadopodia creation to a three-dimensional (3D) environment, thereby incorporating a higher level of realism and complexity. The formation of invadopodia is approached utilising the Stefan problem framework, wherein the cell membrane is defined by the Stefan free boundary condition, which entails that the boundary membrane is not predetermined. The proposed method for characterising the behaviour of the cell interface and the mobility of the plasma membrane is the level set method. The modelling process incorporated the following parameters: ECM c, MMPs f, ligands c*, and signal σ. Furthermore, we enhanced the fidelity of the simulation results by employing an alternative simulation methodology and domain, along with a distinct dataset. This was achieved by applying the finite element method (FEM) and employing software tools such as FreeFem++ for simulation and Gmsh for mesh generation. The presence of singularities and instabilities was successfully eradicated and our comparison of the findings demonstrates their near resemblance to the actual ones. The attained outcomes have the potential to offer valuable insights for innovative methodologies and can be further applied to enhance the precision of numerical simulations. - 2024-09 Thesis http://ir.unimas.my/id/eprint/45965/ http://ir.unimas.my/id/eprint/45965/1/Master%20Thesis_Muhammad%20Akmal%20Bin%20Ramlee.pdf text en public http://ir.unimas.my/id/eprint/45965/5/dsva_%20Akmal.pdf text en public masters Universiti Malaysia Sarawak Faculty of Computer Science and Information Technology
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English English
topic	QA Mathematics QA Mathematics QA76 Computer software
spellingShingle	QA Mathematics QA Mathematics QA76 Computer software Muhammad Akmal, Ramlee Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
description	The simulation of invadopodia replication holds significance in establishing its biological relevance, as it contributes to a deeper comprehension of cancer invasion and metastasis. Additionally, it offers valuable insights into potential strategies for impeding the dissemination of this life-threatening disease. In this study, we present a mathematical model that describes the behaviour of an individual cell, with the aim of extending the simulation of invadopodia creation to a three-dimensional (3D) environment, thereby incorporating a higher level of realism and complexity. The formation of invadopodia is approached utilising the Stefan problem framework, wherein the cell membrane is defined by the Stefan free boundary condition, which entails that the boundary membrane is not predetermined. The proposed method for characterising the behaviour of the cell interface and the mobility of the plasma membrane is the level set method. The modelling process incorporated the following parameters: ECM c, MMPs f, ligands c*, and signal σ. Furthermore, we enhanced the fidelity of the simulation results by employing an alternative simulation methodology and domain, along with a distinct dataset. This was achieved by applying the finite element method (FEM) and employing software tools such as FreeFem++ for simulation and Gmsh for mesh generation. The presence of singularities and instabilities was successfully eradicated and our comparison of the findings demonstrates their near resemblance to the actual ones. The attained outcomes have the potential to offer valuable insights for innovative methodologies and can be further applied to enhance the precision of numerical simulations.
format	Thesis
qualification_level	Master's degree
author	Muhammad Akmal, Ramlee
author_facet	Muhammad Akmal, Ramlee
author_sort	Muhammad Akmal, Ramlee
title	Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
title_short	Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
title_full	Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
title_fullStr	Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
title_full_unstemmed	Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation
title_sort	three-dimensional simulation of invadopodia formation associated with ligand and signal stimulation
granting_institution	Universiti Malaysia Sarawak
granting_department	Faculty of Computer Science and Information Technology
publishDate	2024
url	http://ir.unimas.my/id/eprint/45965/1/Master%20Thesis_Muhammad%20Akmal%20Bin%20Ramlee.pdf http://ir.unimas.my/id/eprint/45965/5/dsva_%20Akmal.pdf
_version_	1811771583236145152

Three-dimensional Simulation of Invadopodia Formation Associated with Ligand and Signal Stimulation

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