New applications in materials, medicine, and computers are being discovered where the control of events at the molecular and nanoscopic scales is critical to product quality, although the primary manipulation of these events during processing occurs at macroscopic length scales. This motivates the creation of tools for the engineering of multiscale reacting systems that have length scales ranging from the atomistic to the macroscopic. This paper describes a systematic approach that consists of stochastic parameter sensitivity analysis, Bayesian parameter estimation applied to ab initio calculations and experimental data, model-based experimental design, hypothesis mechanism selection, and multistep optimization. (C) 2004 Elsevier Ltd. All rights reserved.