The modeling platform µic has been extended to study the hydration of cement based systems. It is shown that the hydration kinetics of alite can be described through the implementation of two mechanisms: a solution controlled dissolution (SCD) mechanism for the first two stages of hydration and nucleation and densifying growth (NDG) of products for the last three stages of hydration. The dissolution rate is varied according to the ratio between the ion activity product and the equilibrium solubility product. The solution concentrations are computed directly from the amount of alite dissolved taking into account the amount of water present and the amount of products formed, with activities and complex ions formation according to standard thermodynamic rules. Saturation index calculations are implemented to compute the time of precipitation of C-S-H and portlandite individually. After the precipitation of portlandite, the rate controlling mechanism is switched to nucleation and densifying growth. C-S-H grown in a diffuse manner in which the packing density increases with hydration. The overall heat-evolution profile is obtained by combination of heat evolved as obtained from the SCD and NDG mechanisms. The approach is used to describe the influence of particle sizes, thermal treatment, mixing conditions and additions of alkali hydroxides, alkali sulfates and gypsum on hydration of alite. Through a study of systems with wide variations in the process parameters, it is shown that the hydration kinetics of alite can be generically described using the combination of SCD and NDG mechanisms and a limited number of fit parameters. The results obtained from simulations were found to be in good agreement with a variety of experimental results. The various simulations parameters are shown to be strongly correlated to the initial states of the systems. A model is presented to describe the hydration of aluminate+gypsum systems. It is shown that the reaction rate profile can be numerically reproduced by using two mechanisms: dissolution of the aluminate phase in the first stage and boundary nucleation and growth of monosulfate phase in the second stage of reaction. It is shown that the effects of particle sizes and composition on hydration of aluminate can be described using just one fit variable, isotropic growth rate of monosulfate phase, which correlates well the space available in the microstructural volume. Using the combination of mechanisms that describe hydration of alite and aluminate, a model is presented to describe the hydration of multi-phase systems. Preliminary simulations of the heat-evolution profiles of alite-aluminate-gypsum and commerical cementitous systems are presented. Good agreement was found between the simulated and measured results. The current study demonstrates the versatility of µic and shows that the use of mechanistic, rather than empirical, rules can be an important tool to achieve better understanding of cement hydration.