Understanding the battery degradation requires identifying the “irreversible” chemical and structural changes – from atomic to meso-scale – that appear during battery cycling. To design nanostructures mitigating these degradation mechanisms, will further rely on our ability to quantify and predict these irreversible changes. This talk will focus on recent modeling methodology developed to compliment in situ observations in order to elucidate the underlying factors contributing to mechanistic failures. For example, most experimental techniques are not sufficiently sensitive to reveal the amorphous Si and SiO characteristics change upon cycling. Reactive molecular dynamics, along with a new lithiation and delithation algorithm, simultaneously tracks and correlates the lithiation-delithiation rate, compositional change, mechanical property evolution, stress distributions, and fracture. Thus the model can quantify the irreversible volume change of Si and SiO nanostructures, the amount of trapped Li, the generation and distribution of inner pores and coating delamination, and the atomistic structural difference in the amorphous structures, upon cycling. These findings lead to design criteria for mechanically stable coated Si nanostructures and battery operating guidelines to mitigate capacity loss due to trapped Li and coating delamination.