Simulation seems like a step that requires knowing the initial state of a system. I wish there were more efforts focused on finding ways to scan the constituents of a cell all the way close to the atomic level. As far as I know the closest thing we have are Atomic Force Microscope and Scanning Electron Microscopy both several-decade-old technologies. They're also pretty invasive and require access to the surface area of the object to be scanned.

Knowing the position and charge density of atoms in a cell is required to simulate it.