Biophysical modelling as a tool for advancing plant science and engineering

Plant growth, development, and physiology are governed by complex processes operating across scales spanning from molecular, cellular, tissue, and whole organism. Experimental studies have uncovered key mechanisms underlying hormone signalling, gene regulation, metabolism, and environmental responses. However, integrating this information into a unified framework to understand the mechanistic origin, evolution, and robustness of plant form and function remains challenging. Mathematical and computational modelling provides powerful tools to address this challenge, where simulation and predictions offer strategic guidance for efficient experimental search of missing information underlying plant processes. In this review, we discuss a broad spectrum of modelling approaches, including reaction–kinetic and Boolean network models for molecular and genetic regulation; mechanical and geometry-based models for tissue growth and morphogenesis; metabolic and constraint-based models for resource allocation; and hydraulic and electrophysiological models for physiological transport processes. We also propose that by combining different modelling strategies, researchers can develop predictive tools for biotechnological applications, including enhancement of stress tolerance, efficient use of nutrients, regenerative tissue engineering, and biomass productivity.