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In this book, the author provides a deep study into multiscale and multiphysics modeling of nuclear facilities, underscoring the critical role of uncertainty quantification and sensitivity analysis to ensure the confidence in the numerical results and to identify the system characteristics. Through an in-depth study of the liquid metal cooling system from the TALL-3D loop to the SMDFR core, the research highlights the natural circulation instability, strong coupling effects, perturbation tolerance, and system stability. The culmination of the research is the formulation of an optimized uncertainty-based control scheme, demonstrating its versatility beyond the nuclear domain to other energy sectors. This groundbreaking work not only advances the comprehension and utilization of coupling schemes and uncertainty methodologies in nuclear system modeling but also adeptly bridges the theoretical constructs with tangible application, positioning itself as an indispensable resource for design, safety analysis, and advanced numerical modeling in the broader energy sector.