As many have mentioned, the question of why certain notes sound good together can be kind of difficult to answer scientifically, especially because not everyone can agree on what sounds "good" in the first place.
Hopefully I'm not too late, but here's a suggestion for a similar project which is maybe a little bit easier to tackle. Answer the question "why do different instruments sound different?" It might sound silly at first, but think about it... a quick google search will tell you that a middle C is just an oscillation of around 262 Hz. So why does a middle C on a piano sound so different from a middle C on an electric guitar if they're both just a 262 Hz oscillation?
The nice thing about this question is that you can actually give a decent answer: harmonics. When you play a middle C on a piano, you're actually generating more than just a 262 Hz wave. You're also generating waves at 2*262 Hz, 3*262 Hz, 4*262 Hz, etc, which are called harmonics. The behaviour of these harmonics (how loud they are, how quickly they decay, etc) is an important part of what makes one instrument sound different from another.
This question also lends itself to some nice graphs that are easy to look at and understand. If you play a note into a spectrum analyzer, you can see the different frequency spikes which correspond to different harmonics. You can also see very clearly how the spikes look different for different instruments, even though you're playing the same notes. As a simple example, if you play a note on a piano or guitar, you'll see a big spike at the main frequency, but you'll also see a lot of harmonics at higher frequencies. If you whistle, you'll see one large spike at the frequency you're whistling, but almost no harmonics because whistling is a "purer" sound than a guitar or piano. As another example, singers have to learn to control how "rich" their voice sounds, which basically corresponds to controlling how prominent the harmonics are in the notes they sing. I actually built myself a simple spectrum analyzer on my laptop to help me practise this when I took singing lessons. I could see how "rich" my voice was just by looking at the harmonics.
Of course, you can make this topic as complex as you want (you could probably write a PhD thesis on it), but if you stick to just basic stuff (how big are the harmonic spikes in instrument x vs. instrument y?) it should be pretty manageable I think.
Edit: it's for a completely different non-musical application, but just as an example
this graph is the type of thing you would see if you played a note into a spectrum analyzer. You can see a big spike at around 50 Hz, which would correspond to the main note, but you can also see smaller harmonics at 150 Hz, 250 Hz, 350 Hz, etc. (The ones at 100 Hz, 200 Hz, 300 Hz are missing because this particular graph isn't from a musical instrument)