A new and powerful numerical codebase has been generated, which serves as the basis for coarse-grained atomistic simulations in 3D (and which has been released publicly). Temporal upscaling has been achieved by separating the atomic mean motion (and their mean composition) from statistical variations, and to track those over time. Spatial upscaling has been achieved by coarse-graining, i.e. by simulating the physics of large assemblies of grains by tracking only a few representative atoms and using smart interpolation techniques for the remaining ones. Rather than relying on a static finite-element mesh, the new formulation operates in the current, deformed configuration (using a so-called updated-Lagrangian description). This allows us to more accurately refine the model where higher accuracy and resolution is needed, and it also lays the foundation for fully automatic adaptivity – allowing the code to autonomously maintain a high level of accuracy by introducing higher resolution where it is required within the simulation domain, while modeling other regions at low resolution to gain efficiency. In addition, the new simulation tool has been equipped with finite temperature and thermal effects, following the so-called hotQC approach of “thermalizing” atoms in a statistical-mechanics fashion. Rather than modeling temperature as lattice vibrations of high frequency (which usually dictate the small time steps of atomistic simulations), we separate their slow mean motion (which is of interest for the mechanical behavior of the material) from their statistical fluctuations (now represented by statistical measures rather than being fully resolved). The consequence is an efficient simulation technique, which enables us to simulate atomic ensembles at finite temperature at, in principle, arbitrary time scales. This new methodology has been applied to study the mechanics of crystalline solids with a focus on defects, providing new, accurate, and efficient avenues for determining, e.g. finite-temperature surface or grain boundary properties or defect interactions, which are essential for understanding and improving the mechanical performance of metals. Our simulations also revealed new data on the energetics of defects in metals over a range of temperatures. The new theory and code for mass transport further admit simulating atomic-level diffusion at previously inaccessible time scales, resulting in new insight into mechanisms such as the segregation of solute atoms to defects and interfaces across a wide range of temperature. Results have been widely disseminated through scientific publications in peer-reviewed journals, the public release of the codebase for its usage by the interested community, numerous conference presentations and invited seminars. The project further enabled the training of three talented doctoral students and two outstanding postdoctoral scholars.