General Problems of Biological Modeling -- Trends and Tools for Modeling in Modern Biology -- Scaling and Integration of Kinetic Models of Photosynthesis: Towards Comprehensive E-Photosynthesis -- Modeling of Light Harvesting and Primary Charge Separation -- Modeling Light Harvesting and Primary Charge Separation in Photosystem I and Photosystem II -- Unraveling the Hidden Nature of Antenna Excitations -- Modeling Electron Transport and Chlorophyll Fluorescence -- Models of Chlorophyll a Fluorescence Transients -- Modeling of Chlorophyll a Fluorescence Kinetics in Plant Cells: Derivation of a Descriptive Algorithm -- Modeling of the Primary Processes in a Photosynthetic Membrane -- Clustering of Electron Transfer Components: Kinetic and Thermodynamic Consequences -- Integrated Modeling of Light and Dark Reactions of Photosynthesis -- Biochemical Model of C3 Photosynthesis -- Modeling the Temperature Dependence of C3 Photosynthesis -- A Model of the Generalized Stoichiometry of Electron Transport Limited C3 Photosynthesis: Development and Applications -- Modeling the Kinetics of Activation and Reaction of Rubisco from Gas Exchange -- Leaf C3 Photosynthesis in silico: Integrated Carbon/Nitrogen Metabolism -- Leaf C4 Photosynthesis in silico: The CO2 Concentrating Mechanism -- Flux Control Analysis of the Rate of Photosynthetic CO2 Assimilation -- From Leaves to Canopies to the Globe -- Packing the Photosynthetic Machinery: From Leaf to Canopy -- Can Increase in Rubisco Specificity Increase Carbon Gain by Whole Canopy? A Modeling Analysis -- Role of Photosynthetic Induction for Daily and Annual Carbon Gains of Leaves and Plant Canopies -- Photosynthesis Within Large-Scale Ecosystem Models -- Photosynthesis in Global-Scale Models. Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems is a unique book that aims to show an integrated approach to the understanding of photosynthesis processes. In this volume - using mathematical modeling - processes are described from the biophysics of the interaction of light with pigment systems to the mutual interaction of individual plants and other organisms in canopies and large ecosystems, up to the global ecosystem issues. Chapters are written by 44 international authorities from 15 countries. Mathematics is a powerful tool for quantitative analysis. Properly programmed, contemporary computers are able to mimic complicated processes in living cells, leaves, canopies and ecosystems. These simulations - mathematical models - help us predict the photosynthetic responses of modeled systems under various combinations of environmental conditions, potentially occurring in nature, e.g., the responses of plant canopies to globally increasing temperature and atmospheric CO2 concentration. Tremendous analytical power is needed to understand nature's infinite complexity at every level. This book is not a list of equations and computer programs, but the emphasis is on analytical ideas facilitating the understanding of complex interactions governing the photosynthetic process on every level and between different levels of hierarchy. The book provides the necessary background on photosynthesis and demonstrates the benefits of the computer-aided quantitative analysis of its reactions; it is designed for graduate students and researchers in plant physiology, functional plant biology, plant biochemistry, systems biology, biophysics, bio-energy and bio-fuel.