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Intro; Preface; Contents; Contributors; About the Editor; 1 Physical Models of Plant Morphogenesis; 1.1 Describing Morphogenesis; 1.1.1 Quantifying Cell Growth; 1.1.2 Quantifying Organ Growth; 1.2 Forces in Plants; 1.2.1 Forces in Tissues and Cells; 1.2.2 Forces and Growth; 1.3 Modeling Morphogenesis; 1.3.1 Different Types of Models; 1.3.2 Implementation of Growth; 1.4 Case Studies: The Use of Models to Understand Plant Morphogenesis; 1.4.1 Morphogenesis of an Isolated Plant Cell; 1.4.2 Growth Motion of an Elongated Organ; 1.4.3 Shaping a Sheet-Like Organ
1.4.4 Feedback Through Mechanical Signals1.4.5 Variability and Morphogenesis; 1.5 Conclusion; References; 2 Fluid Transport in Plants; 2.1 An Overview of Plant Hydraulics; 2.2 Physical Principles and Basic Equations; 2.2.1 Conservation of Mass; 2.2.2 The Navier-Stokes Equation; 2.2.3 Boundary Conditions; 2.2.4 The Reynolds Number; 2.3 Plant Hydraulics: Flow in Tubes; 2.3.1 Flow in a Straight Tube; 2.3.1.1 Circular Tube Flow; 2.3.1.2 Non-Circular Tube Flow; 2.3.1.3 Tube Collapse and Cavitation; 2.3.2 Flow in a Tube with Varying Diameter; 2.4 Solute Transport; 2.4.1 The Transport Equation
2.4.2 Transport by Diffusion2.4.3 Transport by Convection; 2.4.4 Shear-Enhanced Diffusion; 2.5 Conclusions; References; 3 Modelling Ion Channels; 3.1 Introduction; 3.2 Modelling Single Ion Channel Dynamics; 3.2.1 Diffusion of Ionic Species; 3.2.2 Channel Dynamics; 3.2.3 Markov Processes; 3.3 Modelling the Dynamics of an Ensemble of Ion Channels; 3.3.1 Gillespie Algorithm; 3.3.2 Transition Probabilities; 3.3.3 Many Gates; 3.3.4 Master Equation; 3.3.5 Averaging; 3.4 Modelling Cellular Membrane Excitability; 3.4.1 Nernst Potential; 3.4.2 Membrane Currents; 3.4.3 Action Potentials
3.5 ConclusionsReferences; 4 Modelling the Plant Microtubule Cytoskeleton; 4.1 Microtubules: Dynamic Controllers of Plant Cell Growth and Development; 4.2 Dynamic Self-organization: Exciting Biology and Challenging Physics/Mathematics; 4.3 MT Behaviour at Different Levels of Description; 4.3.1 At the MT Level: Dynamic Instability; 4.3.2 At the Cell Level: Interactions; 4.3.3 At the Tissue Level: Coarse Graining; 4.4 The Consensus Model of MT Dynamics; 4.5 Simulations: Time Steps Versus Event Driven; 4.6 Understanding Order; 4.7 Understanding Orientation; 4.8 The Role of Severing; 4.9 Outlook
1.4.4 Feedback Through Mechanical Signals1.4.5 Variability and Morphogenesis; 1.5 Conclusion; References; 2 Fluid Transport in Plants; 2.1 An Overview of Plant Hydraulics; 2.2 Physical Principles and Basic Equations; 2.2.1 Conservation of Mass; 2.2.2 The Navier-Stokes Equation; 2.2.3 Boundary Conditions; 2.2.4 The Reynolds Number; 2.3 Plant Hydraulics: Flow in Tubes; 2.3.1 Flow in a Straight Tube; 2.3.1.1 Circular Tube Flow; 2.3.1.2 Non-Circular Tube Flow; 2.3.1.3 Tube Collapse and Cavitation; 2.3.2 Flow in a Tube with Varying Diameter; 2.4 Solute Transport; 2.4.1 The Transport Equation
2.4.2 Transport by Diffusion2.4.3 Transport by Convection; 2.4.4 Shear-Enhanced Diffusion; 2.5 Conclusions; References; 3 Modelling Ion Channels; 3.1 Introduction; 3.2 Modelling Single Ion Channel Dynamics; 3.2.1 Diffusion of Ionic Species; 3.2.2 Channel Dynamics; 3.2.3 Markov Processes; 3.3 Modelling the Dynamics of an Ensemble of Ion Channels; 3.3.1 Gillespie Algorithm; 3.3.2 Transition Probabilities; 3.3.3 Many Gates; 3.3.4 Master Equation; 3.3.5 Averaging; 3.4 Modelling Cellular Membrane Excitability; 3.4.1 Nernst Potential; 3.4.2 Membrane Currents; 3.4.3 Action Potentials
3.5 ConclusionsReferences; 4 Modelling the Plant Microtubule Cytoskeleton; 4.1 Microtubules: Dynamic Controllers of Plant Cell Growth and Development; 4.2 Dynamic Self-organization: Exciting Biology and Challenging Physics/Mathematics; 4.3 MT Behaviour at Different Levels of Description; 4.3.1 At the MT Level: Dynamic Instability; 4.3.2 At the Cell Level: Interactions; 4.3.3 At the Tissue Level: Coarse Graining; 4.4 The Consensus Model of MT Dynamics; 4.5 Simulations: Time Steps Versus Event Driven; 4.6 Understanding Order; 4.7 Understanding Orientation; 4.8 The Role of Severing; 4.9 Outlook