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The development of simple mathematical model for representing complicated real-life chemical reaction systems has been a fundamental issue in computational biology and bioinformatics. In particular, the accurate description of chemical events with multi-step chemical reactions has been regarded as an essential problem in chemistry and biophysics. To model chemical reaction systems in a manageable way, multi-step chemical reactions were normally simplified into a one-step reaction. In recent years, a number of modelling approaches have been attempted to use simplified model to describe multi-step chemical reactions accurately. In this work, we proposed a two-variable model to describe chemical events with multi-step chemical reactions. We introduced a new concept to represent the location of molecules in the multi-step reactions, and use it as the second indicator of the system dynamics. The accuracy of the proposed new model was evaluated via using a deterministic model. The proposed model has been applied to study the mRNA degradation process. Numerical simulations of the designed simplified models matched the simulations of multi-step chemical reactions very well.