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This paper addresses Hardware-In-the-Loop modeling and simulation for Diesel aftertreatment controls system development. Lean NOx Trap (LNT) based aftertreatment system is an efficient way to reduce NOx emission from diesel engines. From control system perspective, the main challenge in aftertreatment system is to predict temperature at various locations and estimate the stored NOx in LNT. Accurate estimation of temperatures and NOx stored in the LNT will result in an efficient system control with less fuel penalty while still maintaining the emission requirements. The optimization of the controls will prolong the lifespan of the system by avoiding overheating the catalysts, and slow the progressive process of component aging. Under real world conditions, it is quite difficult and costly to test the performance of a such complex controller by using only vehicle tests and engine cells.