This paper describes the development and implementation of a Dynamic Architecture Flow Optimization (DAFO) for Mission, Power and Energy System (MPES) design in surface ship concept and requirements exploration. The DAFO interfaces with a warfighting model, ship operational model, and mission capability models to determine optimum MPES alignment and provide capabilities over multiple time steps as required for operational effectiveness in ship operational situations (OPSITs). These Ship Behavior and Interaction Models (SBIMs) are part of a system design framework that includes architectures for ship operations, physical arrangements and the logical relationship of MPES vital energy and data components (VCs). The mission capability models provide a critical interface between logical and operational architectures, quantifying warfighting capabilities through system measures of performance at specific capability nodes. The operational architecture queries the capability models for necessary operational capabilities and implements them in the warfighting environment. The capability models also provide essential mission and vital component priorities used to guide the alignment of system vital components by the DAFO.