The current needs of new process and materials design require development of a new generation of integrated software tools. These tools should include multi-scale models, staring from atomistic-scale models based on quantum chemistry and molecular dynamics to mesoscale models based on Monte Carlo methods and finally reactor scale continuum models. The integration of different scale models in one software tool is needed to transfer data from low-level model to upper level and back to achieve self-consistent description. At each level of simulation the results are stored in databases with universal data interface to provide data mining capabilities for the models at the upper levels. Moreover databases of experimental kinetic and thermodynamic data can be coupled with calculated data to complete information for reactor models. Usually the reliability of the calculated results should be checked with special tools for data analysis to investigate the dependence of the results on the uncertainties in the model parameters and input data. The current status in achieving these requirements for the simulating software in the materials science is discussed together with recent progress in atomistic scale modeling. In this work attention is paid to the integration of quantum chemical calculations with reactor scale modeling, recovering of kinetic data, generation and verification of kinetic mechanisms and to the modeling of atomistic processes at the time scale of the reactor. Several specific studies will be presented as examples of the applications of the new software tools.