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Cycles is a process-based model of the soil–plant–atmosphere continuum that functions as both a knowledge repository and analytical tool. This chapter outlines its structure, highlights its use in in-silico trait exploration and modeling of biogenic carbon and water cycles, and presents three case studies. The model integrates energy, water, carbon, and nitrogen cycles, coupling plant photosynthesis, partially based on stomatal optimization theory, with soil heterotrophic respiration based partially on carbon saturation theory. These features reflect theoretical and empirical rigor adapted for practical applications. The input/output system is streamlined and high-performance computing compatible. Applications include: (1) exploring maize root phenotypes under variable hydric regimes; (2) comparing greenhouse gas emissions in till and no-till systems across more than 871,000 fields in Iowa; and (3) evaluating maize–sorghum polycultures for stabilizing silage yield in the U.S. Together, these examples illustrate how Cycles advances agroecosystem modeling for both scientific discovery and landscape management.
- 1 Introduction
- 2 Coupling energy fluxes with the cycles of water, carbon, and nitrogen
- 3 Input and output file structure
- 4 The crop growth module
- 5 Transpiration
- 6 Crop parameters and genetic coefficients
- 7 The soil carbon balance and carbon saturation
- 8 Model testing
- 9 Applications
- 10 Conclusion and future trends
- 11 Where to look for further information
- 12 References