Contents-- -- List of figures -- Acknowledgments -- List of French abbreviations -- Introduction -- Chapter 1 Geometric and botanic simulation -- 1 The probabilistic simulation of branching biological shapes: Cohen (1966) -- 2 The epistemic functions of modular programming, simulation and visualization -- 3 The first geometric and realistic simulation of trees (Honda-Fisher, 1971-1977) -- 4 The limitations of morphometry and of thermodynamics of trees -- 5 The first geometric simulation of an actual tree: Terminalia -- 6 A recap of geometric simulation -- Chapter 2: The logical model and algorithmic simulation of algae -- 1 A botanist won over by logical positivism: the "theory of lifecycles" by A. Lindenmayer (1963-1965) -- 2 Unusable set of axioms and used set of axioms -- 3 From logical theory to automata theory (1966-1967) -- 4 The "developmental model" and the rules of rewriting (1968) -- 5 The dispute with Brian Carey Goodwin regarding "natural" formalisms -- 6 Recap: the computer as automata model and deductive machine -- Chapter 3: The limitations of biometric models and the transition to simulation in agronomy -- 1 The institutional and technical context of the IFCC (1966-1971) -- 2 Transferring a little bit of econometrics to biometrics: a problem of optimization (1974) -- 3 The first application of plant simulation in agronomics (1974-1975) -- 4 Fragmented modelling and geometric simulation: de Reffye (1975-1981) -- 5 Simulation, imitation and the sub-symbolic use of formalisms -- Chapter 4: A random and universal architectural simulation -- 1 Making headway in botany: the notion of "architectural model" (1966-1978) -- 2 The search for botanical realism (1978-1979) -- 3 Criticisms of theoretical models -- 4 Criticisms of biometric models -- 5 A mixed reception (1979-1981) -- Chapter 5: Convergence between integrative simulation and computer graphics -- 1 The relaunch of research into architectural simulation (1985-1991) -- 2 Jaegers thesis: the prefixed model and synthesis of botanical images (1987) -- 3 Blaises thesis: the simulation of buds parallelism (1991) -- 4 How can an integrative simulation be validated? -- Chapter 6: Convergence between universal simulation and forestry (1990-1998) -- 1 An epistemological dispute between modellers: INRA and CIRAD -- 2 Conceptual and institutional convergence: the CIRAD/INRA partner laboratory (1995) -- 3 The empirical value of simulation -- 4 Supra-simulations -- Chapter 7: The remathematization of simulations (from 1998 onwards) -- 1 The first mixed structure-function model: "water efficiency" (1997-1999) -- 2 The parallel evolution of algorithmic simulation: 1984-1994 -- 3 Simulating the individual plant in order to observe crop functioning (1997-2000) -- 4 The association between AMAP and INRIA: sub-structures and factorization (1998-2006) -- 5 Recap: pluriformalized simulation and convergence between disciplines -- Chapter 8: Twenty-one functions of models and three types of simulations Classifications and applications -- 1 General function, main functions and specific functions of models -- 2 General characterization and classification of computer simulations -- 3 System simulation, model simulation, system-simulation model and model-simulation model -- 4 Applications to different plant models and plant simulations -- Conclusion -- --Glossary -- Selected Bibliography -- Index of names -- Index of subjects