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If you were to put your laptop in a thin, cheap backpack, and then lay it down too hard on the pavement, there is a chance that your laptop would crack and perhaps stop working. The idea behind a backpack with a special padded compartment for a laptop, is to hopefully prevent this type of thing from happening by providing protective cushioning on either side of your electronic devices. They may be more expensive than regular thin backpacks, but when you consider how much you spent on your laptop, it may well be worth it.
Padded laptop backpack:
Padded laptop backpacks pictured:
Left: SwissGear ScanSmart Laptop Backpack – Black
Right: Wenger Backpack by SwissGear with Padded Sleeve for Laptops (SA1537 Grey)