Shauna's Crazy Idea Project Page

PHYS 210 PROJECTS --> here

Some Ideas to Test

1. I was thinking of modelling Site-Directed Mutagenesis. Something that will take a designated amino acid property, cleaving it, and substituting it with another AA with one of the same characteristics, hydrophobic, hydrophilic etc. Compare original with mutant structurally and how would produce different polypeptide types. Or maybe a particular mutation like cancer or something. Um, how do you cleave a property? This sounds pretty interesting, but it is hard to follow what you're saying -- partly due to my own ignorance of the topic, of course, but also because your description is too vague. As far as I can tell you are proposing to model the effect of AA replacements on the behaviour of polypeptides (proteins?), which I believe is at the cutting edge of biophysics research. Ask Steve Plotkin. If that's the case, you are probably biting off more than you can chew. An impressive project would be to just stick a few AA together and model the "folding" of the resultant molecule, treated as some sticks connected at pivot joints. This would make a handy pedagogical aid to explaining orientational entropy etc. But I may have just misunderstood what you have in mind. -- Jess 22:03, 3 October 2008 (PDT)
2. I think I will focus on this one then. I will draw up something more clear by tomorrow night and share it with you online pdf or acrobat to your phas account. Maybe get some more clarity on the depth of the proposal. Thanks for your feedback! My goal was a little more in depth than that, I see I didn't state it very well. But perhaps I'll take on something a little more basic, for now! I guess I could figure something out with translation.
3. Another one was that having a differential equation/problem of projectile motion, but with the mass also changing, like kicking of electrons etc....or maybe radioactive decay. I have the equation in some notes so I will get together. Not sure how that would happen as the coefficient would need its own DE? Or an electron shot through an electric field, and depending on the strength of the field, the force it hits a place which triggers a to jump energy (which one one depends on force of e^- impact). The jump to a higher level emitting light energy. Again, I get lost in the last couple of sentences. You could certainly draw the trajectory of a nucleus undergoing a randomized series of radioactive decays, or a simplification in the form of a artillery shell that fires off bullets in random directions at random times. It could be interesting, but I'm not sure what your goal is. -- Jess 22:03, 3 October 2008 (PDT) My "goal for this one is to just put together the Differential Equation for it basically that incorporates all the variables.... My DE prof was doing an example but the mass was fixed, and when I asked of decreasing mass at a dependent rate on velocity and trajectory... he didn't know so I wanted to solve it :-)
4. And just in case those aren't possible, or I have too many ideas in my reality, I may post some more for "constructive criticism" or encouragement! I would like to include some linear transformations into it to expand, decrease or shear the structure depending on particular parameters. Maybe around ions and crossing membrane channels, and electric potential. I think the ion channel one is interesting but I am not sure if I could pull it off how I wanted to. So the opening and closing of the channel is dependent on correct electrical impulses, electrochemical gradients etc. So I was thinking of modelling the chain reaction from potential difference to opening and passing of ions through the channel. I did have another idea but there is no information on it yet so I don't know if it's being worked on. There is an electrical engineer who wrote a paper with a bit of the same idea but that's all I've found. I hate to keep harping on this, but ... Huh? How do linear transformations expand, decrease or shear "the structure"? Of what? I'm lost. -- Jess 22:03, 3 October 2008 (PDT) Different standard matrices... Take 2 points (for example), multiply by a standard matrix for shifting just the top corner on the resulting mapping. There's different standard matrices that transform images around axis or any fixed point etc. etc. I'll scrap this one.
5. So maybe having an image of a process, and observing the effect of different standard matrices derived from changes in a particular parameter. I don't have the solid particulars for this one so I'll leave it.
6. I just had another one last night on geothermal energy, seeing how far to drill to create enough heat and pressure to produce steam to drive an engine to create electricity? And then seeing what depth is the most efficient, the energy put out to drill and harvest the energy and the optimal amount of electricity produced. I don't know, but my impression is that all the answers would depend very strongly on where you drill. In the Canadian Shield it would have to be pretty deep, but in Hilo, HI you can probably get by with a few hundred meters. Another problem is that as soon as you start taking heat out you set up thermal gradients that change the answer. Maybe. Ask a geologist. -- Jess 21:32, 4 October 2008 (PDT)

Thanks!

- Jason and Jess, the idea I had about phase shifting, is there a way I could use the wave equation and just do one piece of data or dif reactions to electrical impulses to the molecule and model the changes as it is brought back to its "normal" state...not the crazy grand but 4 year project idea I first had?   :-)

You'll have to remind me about your phase shifting idea. Maybe I'm just especially stupid tonight. -- Jess 22:03, 3 October 2008 (PDT)

The phase shift one I am leaving for now...so nevermind.

Hey Shauna, thanks for your input on my project page. I was just curious as to whether or not you too are in biophysics? Your first idea here sounds kind of biophysics-ee. Good luck with your assignments and project! - Jonny