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SOFC stacks respond quickly to changes in load while the balance of plant subsystem (BOPS) responds in times several orders of magnitude higher. This dichotomy diminishes the reliability and performance of SOFC electrodes with increasing load as do current and voltage ripples which result from particular power electronics subsystem (PES) topologies and operation. These ripples and the difference in transient response between the electrical-electrochemical components for the PES and stack subsystem (SS) and those for the chemical-thermal-mechanical components of the BOPS must be approached in a way which makes operation of the entire system not only feasible but ensures that efficiency and power density, fuel utilization, fuel conversion, and system response is optimal at all load conditions. Thus, a need exists for the development of transient component- and system-level models of SOFC-power conditioning systems (i.e. coupled BOPS, SS, and PES) and the development of methodologies for optimizing subsystem responses and for investigating system-interaction issues, which reduce the lifetime and efficiency of a SOFC. A preliminary set of chemical, thermal, electrochemical, electrical, and mechanical models based on the first principles and validated with experimental data were developed and implemented using a number of different platforms. These models were then integrated in such a way as to permit component, subsystem, and system analyses; the development of control strategies; and the synthesis/design and operational optimization of a SOFC based auxiliary power unit (APU) and its components both for steady state and transient operation in transportation and stationary applications. Some pertinent results of these efforts are presented below.