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The functional-structural tree growth model LIGNUM was developed as a general research tool that can be applied to several tree species. The growth simulation of short-rotation eastern cottonwood (Populus deltoides Bartr. ex Marsh.) inherits the basic LIGNUM modeling concepts including modular tree structure, L-system-based description of structural development, and carbon budget. New developments of LIGNUM model in this study were the incorporation of a biochemically-derived photosynthesis submodel; nested time steps for simulating physiological processes, structural development, and annual biomass production; incorporation of field-measured weather data for modeling the response of physiological processes to environmental variation; and application of a Monte-Carlo voxel space submodel for simulating the stochasticity of tree growth and improving computational efficiency. A specific parameter system was applied for modeling P. deltoides growth in the central Missouri, USA, environment. This adaptation of LIGNUM was applied on modeling growth of P. deltoides in a short-rotation agroforestry practice. The simulated height and biomass growth were close to field observations. Visualization of simulation results closely resembled the trees growing in an open site. The simulated response of tree growth to variations in photon flux input was reasonable. The LIGNUM model may be used as a complement to field studies on P. deltoides in short-rotation forestry and agroforestry.