Spatiotemporal Modeling and Simulation in Biology

• Published in: Bioinformatics pp. 381 - 432
• Main Author: Sbalzarini, Ivo F.
• Format: Book Chapter
• Language: English
• Published: WORLD SCIENTIFIC 01.04.2009
• Subjects: SECTION IV MODELING OF BIOLOGICAL SYSTEMS
• ISBN: 9789812838773; 9812838775; 9789814468695; 9789812838780; 9812838783; 981446869X
• DOI: 10.1142/9789812838780_0014

The following sections are included: Introduction Properties of Biological Systems Dimensionality and Degrees of Freedom Regulation Geometric Complexity Nonlinearity Coupling Across Scales Temporal Plasticity Nonequilibrium Spatiotemporal Modeling Techniques Phenomenological vs. Physical Models Discrete vs. Continuous Models Stochastic vs. Deterministic Models Spatiotemporal Simulation Methods Methods for Discrete Stochastic Models Methods for Discrete Deterministic Models Methods for Continuous Stochastic Models Methods for Continuous Deterministic Models Representing Complex Geometries in the Computer Introduction to Continuum Particle Methods Function Approximation by Particles Operator Approximation Pure particle methods Hybrid particle-mesh (PM) methods Efficient Algorithms for Particle Methods Fast Algorithms for Short-Range Interactions Fast Algorithms for Long-Range Interactions Particle Methods for the Simulation of Diffusion Processes The Method of Random Walk (RW) Particle Strength Exchange (PSE) PSE for isotropic diffusion Boundary conditions in PSE Comparison of PSE and RW Reaction-Diffusion Processes Previous Approaches and Applications in Biology Reaction-Diffusion in Particle Methods An example with moving reaction front Conclusions References