I am thinking about making a simulator type game that will involve having lots of small objects in a 3D space. What is the typical solution for handling these objects? The first thing that comes to mind is a 3D Array, but I can't help but think there is a more efficient solution. Another idea that comes to mind is objects having possession of smaller items. For example a House possesses a Table which possesses a Cup and Bowl.
The final way I can think of handling this is just having an array of "objects" that each have an x, y, z value. While this would make storing them easy I do not understand how you would detect collisions without just looking at every possible object and checking to see if it is in the way.
Are there other ways of holding onto these objects that is more efficient?
Edit: Following up with the comments below, are there typical thread-safe ways of implementing these structures in Java?