A process model was developed to establish dynamic connections between system design and treatment performance by considering a series of physicochemical and biological processes in an encapsulated anaerobic environment (SI section S1). Decision variables and technological assumptions were input to the process model for simulations of the mass and energy balances in the system. After converging to steady state, the model was used to translate the mass flow data of the simulated system's effluent and biogas streams into indicators of treatment performance, such as COD removal percentage and CH4 production rate.