Physical Simulation and Visualization of Cells

Multicellular organisms evolve from one single cell, through repeated cell division. As a result of differentiation at cell division and the environmental influence on the cells, cells will specialize themselves to perform different tasks in the organism. An adult organism contains many different kinds of cell types. Methods that simulate the biological control of the cells and cell division are being developed. This master thesis will look at how this can be visualized in 3D and if this new representation of the cells gives new possibilities to add more parameters to the simulation.


1 Introduction
1.1 Goal
1.2 Outline
2 Cells
2.1 Function and structure of cells
2.2 Cell types
2.3 The cell cycle and cell division
2.3.1 Lineage tree
2.4 Genes and gene expression
2.5 Cell communication
2.6 Caenorhabditis elegans
3 Soft body simulation
3.1 Modeling soft bodies
3.2 Particle systems
3.2.1 Mass-spring systems
3.2.2 Shape matching
3.2.3 A pressure model for soft bodies
3.3 Implicit modeling
3.4 Finite elements method
3.5 Differential equations
3.6 Collision handling
3.6.1 Feature based methods
3.6.2 Hierarchical methods
3.6.3 Spatial hashing
3.6.4 Implicit methods
3.6.5 Collision response
4 Method
4.1 Overview of the simulation
4.1.1 Interfaces
4.2 Soft body simulation
4.2.1 Mass-spring system
4.2.2 Pressure force
4.2.3 Updating the equations
4.2.4 Scaling objects
4.3 Collision handling
4.3.1 Collision detection
4.3.2 Collision response
4.4 Cell simulation
4.4.1 Modeling genes and DNA
4.4.2 Cell division
4.4.3 Cell connections
5 Results
5.1 CellSim 3D
5.1.1 Physical simulator
5.1.2 Biological simulator
5.1.3 Visualization
5.2 Simulations
5.2.1 Simple tree with unique nodes
5.2.2 Simple tree with two equal subtrees
5.2.3 Simulating the tree of C. elegans
6 Conclusions and future work
6.1 Discussion
6.2 Future work
6.2.1 Improvements of the physcical simulator
6.2.2 Cell connections
6.2.3 Cell placement
6.2.4 Use physical data in the model of cell control
6.2.5 Cell communication

Author: Nilsson, Johannes

Source: Linköping University

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