Notwithstanding dramatic advances in experimental characterization of nanoscale systems, some of the nanoscale processes are simply too fast to register by experimental approaches or involve displacements at scales too fine for direct experimental observation. Microscopic simulations have emerged as a kind of a computational microscope that can characterize processes inaccessible to experimental techniques, revealing not only the sequence of events underlying an experimental measurement but also the forces and energies involved. This lecture will use several systems to illustrate the application of high-end all-atom, coarse-grained, and multi-resolution simulations to obtain information inaccessible to experimental approaches. The topics to be covered will include phase separation in biological condensates, transport through nuclear pores, and packaging of viral genome. The lecture will provide a forward-looking perspective on modeling an entire biological cell at all-atom resolution.