The essential conundrum of modern biology, namely the question of how life emerges from myriad molecules whose behavior is governed by physical law alone, is embodied within a single cell—the quantum of life. The rise of scientific supercomputing has allowed for the study of the living cell in unparalleled detail, from the scale of the atom to a whole organism and at all levels in between. In particular, the past three decades have witnessed the evolution of molecular dynamics (MD) simulations as a “computational microscope”, which has provided a unique framework for the study of the phenomena of cell biology in atomic (or near-atomic) detail.  Our work synergistically combines single-molecule biophysics, structural biology and machine learning techniques to probe the molecular origin of biological phenomena. Here I present an overview of our synergistic efforts with experimentalists to determine the molecular details during the life-cycle of HIV-1. Our work reveals complex relationships between capsid permeability, mechano-elasticity and reverse-transcription, and deciphers the role of cellular host-factors during the life-cycle of the virus.