We don’t fully understand the mechanism yet. The larger issue is what abstractly computation is relative to the physical world and physical processes. Molecules of water arrange in such a way that they are wet or frozen. A computer simulating water can be neither wet nor frozen. So to with molecules being conscious.
For all the other things in the simulation the water is wet. And any question about how things inside would interact with the simulated water you would be able to answer identically to things in our world. Notice that your physical brain isn't conscious-ey, when it simulates your consciousness either.
Ultimately, I think it comes down to these questions, which I don't think are easy for either of us to answer: If we meet a silicon creature that seems to be conscious: 1. how can you change your mind and decide it is conscious? 2. how can I change my mind and decide it's not? I don't have a good answer for either one