This is the MATLAB source code for a stochastic agent-based model of CD8+ T cell responses following vaccination. The model simulates T cell activation, proliferation, contraction, and differentiation into effector and memory populations. Cell division is regulated by intracellular c-Myc dynamics, and the model includes asymmetric inheritance of c-Myc between daughter cells. A lineage tracking module is also added to follow the descendants and division histories of individual simulated T cell families.

Sustainable aviation fuel (SAF) plays a central role in decarbonizing the aviation sector. Brazil is positioned to become a leader in SAF production and consumption from sugarcane-based ethanol. However, integrating SAF into the Brazilian sugarcane industry is challenging due to high production costs, an undeveloped SAF supply chain, and ethanol competition between ground and aviation transportation. The present study uses mixed-integer linear optimization to design SAF supply chains in Brazil under various blend requirements and design scenarios. Three sugarcane mills in São Paulo are identified for strategic SAF investments, with a recommended premium of 2.6 R$ L⁻¹ (0.5 US$ L⁻¹). Furthermore, SAF production increases net CO₂ emissions by up to 2.7 Mt year⁻¹ (relative to a 0% baseline) due to ethanol displacement. Sensitivity analysis reveals SAF conversion and emission targets for net-zero system emissions. These results provide several key insights to guide SAF supply chain growth,... [more]