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Real-time control of Reactivity Controlled Compression Ignition (RCCI) during engine load and speed transient operation is challenging, since RCCI combustion phasing depends on nonlinear thermo-kinetic reactions that are controlled by dual-fuel reactivity gradients. This paper discusses the design and implementation of a real-time closed-loop combustion controller to maintain optimum combustion phasing during RCCI transient operations. New algorithms for real-time in-cylinder pressure analysis and combustion phasing calculations are developed and embedded on a Field Programmable Gate Array (FPGA) to compute RCCI combustion and performance metrics on cycle-by-cycle basis. This cycle-by-cycle data is then used as a feedback to the combustion controller, which is implemented on a real-time processor. A computationally efficient algorithm is introduced for detecting Start of Combustion (SOC) for the High Temperature Heat Release (HTHR) or main-stage heat release.