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I am planning to use Atxmega128A1U in a battery monitoring system. This chip comes with USB device support. However, it is a 3.3V logic chip with input voltage limit of 3.6V and I want to use the USB port on my laptop to program the chip. How to interface the 5V USB port to 3.3V atmega chip? Shall I use a logic-level converter or is there any other better solution? I want the system to be self-sufficient, so I don't want to use an external programmer, once the Arduino bootloader is burned.

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If you are planning to use USB as the power source, of course you should use 3.3 v regulator like AMS1117 to convert 5 v to 3.3v. If you are asking about the USB communication between computer and atmega, level converter is not required since the usb signal lines D+ and D- is 3.3 v differential signal. That is the USB standard, it is same for every usb device. More about USb http://www.beyondlogic.org/usbnutshell/usb2.shtml

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