In this work, we present a multiscale simulation platform as a viable tool to engineer novel electron devices. The tool connects the specific material properties (as atomic defects, interfaces, material morphology) to the electrical behavior of the device, representing a virtual space for the design of novel electrons device purposely exploiting atom-electron interactions. This simulation platform is based on the modeling the microscopic interactions and chemical reactions (e.g. bond breaking) between electrons and atomic species (ions, vacancies, dangling bonds). In this work, we show how this tool can be used to design resistive memory devices based on binary oxides. The fundamental importance of the complex interplay between charge carriers and atomic species is highlighted by showing how these interactions determine many electrical characteristics of the device, including charge transport, structural modifications associated with resistive switching, variability, and noise fluctuations.