Genesis is a free physics simulator for Windows, Linux, and macOS (Apple Silicon). It simulates matter at three scales: atomic, nuclear, and subatomic. Unlike scripted animations, every event in Genesis is calculated in real time by a physics engine. The user sets the initial conditions, and the engine applies physical laws to determine the outcome. At the atomic scale, users can build an atom by adding or removing protons, neutrons, and electrons. The atom reacts according to physical rules. An excited electron can drop down and emit a photon. An unstable nucleus decays at a time determined by its half-life. A tunable laser can be used to observe absorption, transmission, or electron ejection. The 3D electron cloud is displayed layer by layer. At the nuclear scale, users can collide two nuclei. The engine calculates the approach, the Coulomb repulsion, and quantum tunneling to determine if the result is fusion, rebound, or fission. A detailed breakdown of products, energy released, and probabilities is provided. At the subatomic scale, users can send electrons onto nucleons, assemble hadrons from quarks, and explore the interior of the proton at different resolutions to observe the parton sea. The user selects an element, two nuclei, an energy level, or a wavelength to set the starting conditions. A Python engine advances time and applies the relevant physical laws. When a model is approximated, the application indicates this. The scene, measurements, and journal display each event and the calculation that explains it. Java 21 and the Python engine are included in every package. The engine runs entirely locally, requiring no account or server connection. The databases are loaded on the first launch, which can take several tens of seconds. Genesis is free for personal and professional use, but the license prohibits resale or redistribution. It is designed and developed independently.