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1: what is ment by physical damage when you can see it is physically damaged as opposed to electronically, so in your case one would assume you would be able to see burn marks.
2: how does the physical damage of this kind happen...no clue
3: If the IC burnt then there must have been some fault in the circuitry of the board as it could not prevent the IC from burning. ...possibly....
4: Can my motherboard be replaced since it is under warranty, it will all depend if intel will consider it as customer induced damge or not. the only thing you can do is give intel support a call and see.
5: How to derermine if the IC is actually burnt, have a look on the actual motherboard and see if you can see any sort of damage, i would definately suggest you do thi.