Cellular potts models: multiscale extensions and biological applications

✍ Scribed by Marco Scianna; Luigi Preziosi

• Publisher: CRC Press / Taylor & Francis
• Tongue: English
• Leaves: 300
• Series: Chapman & Hall/CRC mathematical and computational biology series (Unnumbered)
• Category: Library

✦ Synopsis

"All biological phenomena emerge from an intricate interconnection of multiple processes occurring at different levels of organization: namely, at the molecular, the cellular and the tissue level, see Figure 1. These natural levels can approximately be connected to a microscopic, mesoscopic, and macroscopic scale, respectively. The microscopic scale refers to those processes that occur at the subcellular level, such as DNA synthesis and duplication, gene dynamics, activation of receptors, transduction of chemical signals, diffusion of ions and transport of proteins. The mesoscopic scale, on the other hand, can refer to cell-level phenomena, such as adhesive interactions between cells or between cells and ECM components, cell duplication and death and cell motion. The macroscopic scale finally corresponds to those processes that are typical of multicellular behavior, such as population dynamics, tissue mechanics and organ growth and development. It is evident that research in biology and medicine needs to work in a multiscale fashion. This brings many challenging questions and a complexity that can not be addressed in the classical way, but can take advantage of the increasing collaboration between natural and exact sciences (for more detailed comments the reader is referred to [90, 262]). On the other hand, the recent literature provides evidence of the increasing attention of the mathematical, statistical, computational and physical communities toward biological and biomedical modeling, consequence of the successful results obtained by a multidisciplinary approach to the Life Sciences problems"-- Read more...

✦ Table of Contents

Content: I Basic Cellular Potts Model and Applications Basic CPM The CPM Domain The CPM Algorithm The Hamiltonian Evaluation of Some Kinematic Parameters Some Illustrative Simulations HGF-Induced Cell Scatter Biological Introduction Mathematical Model for ARO Aggregates Scattering of ARO Aggregates Mathematical Model for MLP-29 Aggregates Scattering of MLP-29 Aggregates Mesothelial Invasion of Ovarian Cancer Biological Introduction Mathematical Model Single Cell Transmigration Multicellular Spheroid Invasion II Extended Cellular Potts Model and Applications Extended Cellular Potts Model Advantages and Limitations of the Basic CPM Compartmentalization Approach Nested Approach Motility of Individuals Wound Healing Assay Biological Introduction Mathematical Model Simulations Effect of Calcium-Related Pathways on Single Cell Motility Biological Introduction Mathematical Model Simulation Details and Parameter Estimates Simulations in Standard Conditions Interfering with Calcium Machinery Altering Cell Morphology Varying the Chemical Source Tumor-Derived Vasculogenesis Biological Introduction Mathematical Model Simulations in Standard Conditions Varying Cell Density Testing Anti-Angiogenic Therapies Different Morphologies of Tumor Invasion Fronts Biological Introduction Mathematical Model Simulations in Standard Conditions Varying Cell Adhesive Properties Varying Cell Elasticity Altering Cell-Substrate Interactions Effect of Cell Proliferation Early Stages of Tumor Spheroid Growth Mathematical Model Simulations Cell Migration in Extracellular Matrices Biological Introduction Mathematical Model Isotropic Matrices Anisotropic 2D and 3D Matrices Varying Fiber Density Varying Cell-Fiber Adhesiveness Varying Fiber Elasticity of 3D Matrix Scaffold Effect of Varying Nucleus Compressibility in 3D Effect of Matrix Degradation in 3D Cancer Cell Migration in Matrix Microchannels Biological Introduction Mathematical Model Simulations Migration Velocities Migration Modes Appendices A: Computational Implementation B: Glossary C: Parameter Values D: Color Insert Bibliography Index
Abstract: "All biological phenomena emerge from an intricate interconnection of multiple processes occurring at different levels of organization: namely, at the molecular, the cellular and the tissue level, see Figure 1. These natural levels can approximately be connected to a microscopic, mesoscopic, and macroscopic scale, respectively. The microscopic scale refers to those processes that occur at the subcellular level, such as DNA synthesis and duplication, gene dynamics, activation of receptors, transduction of chemical signals, diffusion of ions and transport of proteins. The mesoscopic scale, on the other hand, can refer to cell-level phenomena, such as adhesive interactions between cells or between cells and ECM components, cell duplication and death and cell motion. The macroscopic scale finally corresponds to those processes that are typical of multicellular behavior, such as population dynamics, tissue mechanics and organ growth and development. It is evident that research in biology and medicine needs to work in a multiscale fashion. This brings many challenging questions and a complexity that can not be addressed in the classical way, but can take advantage of the increasing collaboration between natural and exact sciences (for more detailed comments the reader is referred to [90, 262]). On the other hand, the recent literature provides evidence of the increasing attention of the mathematical, statistical, computational and physical communities toward biological and biomedical modeling, consequence of the successful results obtained by a multidisciplinary approach to the Life Sciences problems"