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How to direct it fundamentally revolves around using different method for travel. Classical methods such as working on different direct propulsion methods, all of which rely on Newton's third law, "III. For every action there is an equal and opposite reaction.". This can be used in many ways, but it has a lot of limitations, Physics is such a pain.

Anyways, truthful, the ability to interpret data over concentrated energy would be a way to achieve some real progress. Converting matter into data on one end, sent towards a specific target, and interpreted and recreated on the receiving end. Think of it like the transporter in Star Trek, just a little more realistic.

Dark matter would come in play as a source of energy, in which any form of propulsion needs. If dark matter has the ability to provide substantial amounts of energy, then the conversion will still be plausible.

I'll detail this more in a separate topic...  

The amount of energy being inputted to break down molecules by seperating their subatomic particles would surely be massive in proportions. Clearly, if you plan to use such large resources, the amount of toxic or useless substance being produced would be substancial. Imagine the work your employing at the local power plant and think of the sheer volume of pollution being caused.

Frankly, it has to start from the ground up, basing plans on strategies on newer, safer technology. Removing reliance on petrolium would be a good start.