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Here is a project I almost finished, a quantum computing simulator: https://github.com/aromanro/QCSim
I've got a lot of physics-related projects on GitHub, most of them use matrices, even if sometimes it's not obvious. For example, this one: https://github.com/aromanro/SolarSystem uses matrices for changing from one coordinate system to another, rotations and so on.
NOTE:
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Hence, a higher number means a more popular project.