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Improving tradeoffs between noise, fuel consumption, and emissions in future internal combustion engines will require the development of increasingly flexible fuel injection systems, which can deliver more complex injection profiles. Piezoelectric injectors have the ability to deliver multiple, tightly spaced injections in each cycle, but are highly dynamic systems requiring careful voltage input modulation to achieve sophisticated flow profiles. Closed-loop control could prove to be a key enabler for this technology, but will require online estimation of the injected fuel flow rate to be realized. This paper summarizes the development of a physics-based fuel flow estimator. Available measurements of piezo stack voltage and rail-to-injector line pressure are used for dynamic state estimation. Estimator results are compared against both open-loop simulation and experimental data for a variety of profiles at different rail pressures, and show improvement, particularly, for more complex multipulse profiles. Internal states of the estimator are used to evaluate pulse-to-pulse interaction phenomena that make control of multipulse profiles difficult to achieve. A hypothesis for pulse-to-pulse interaction is illustrated by dividing the needle lift versus fuel flow resistance relationship into regimes, and correlating the pulse-to-pulse behavior to the regime switching that occurs for tightly spaced pulses.