Connecting high sampling rate DAC and ADC to arduino DUE, timer consideration I'm in the echopen association, our goal is to create a low cost, open source echographic probe. In order to do that, we use an arduino due for the first step. For doing acoustic imaging, we use ultrasonic transducer wich works at high frequency, typically 5 MHz. So, for our purpose we need to send and receive analogic signal at high frequencies.
We want to connect a 80 Msps DAC and a 80 Msps ADC to the arduino due so we can generate and mesure analog signal up to 42 MHz. I have found here (http://www.instructables.com/id/Arduino-Timer-Interrupts/#step0) how to use arduino timer interrupts in order to send and receive data at 84 MHz. I haven't connect my converters for the moment, but I have preliminary questions. 
First, is the definition of the timer is the same for the arduino due (i.e. timer1 is a 16 bits timer) ? Morever, my ADC and DAC are 14 bits converters, can I tell to the arduino to sent only 14 bits digital signal ?
Secondly, as we work at high frequencies we will have to send a lot of data from the microcontroller to a computer via the serial port. I have make a test and at 250000 bauds it takes nearly 0.5 second to transfer 4300*8 bits datas. It is to slow for our purpose, how can I do it faster ?
If I'm interpreting the datasheet correctly, you might be able to use the Static Memory Controller (SMC) capability of the Cortex M3 Sam3X to attach some 128K x 8 SRAM devices to your Due.  If your ADC and DAC support tri-state outputs then they could be attached the same way as memories (but ignoring address lines as irrelevant), allowing memory-to-memory DMA transfers.  Ie one could either input and store batches of ADC results at 42 MSPS, or could output batches of data to DAC at 42 MSPS, or could do simultaneous I/O at 21 MSPS.  I haven't read the DMA section closely enough to verify that this will work with the M3.

See Figure 25-2 in Section 25.6.2 of the datasheet regarding memory controllers, and Section 26, “Peripheral DMA Controller (PDC)”, regarding DMA.  Also see the eevblog.com page, “Looking for Cortex M3 or M4 with DMA to GPIO capability”.