Help! What should I model?

[Reverse Transcriptase]

Hey folks,

I want to learn how to use Smoldyn http://www.smoldyn.org/algorithms.html

Which is a simulation system for molecular biology. You can create membranes and objects to try to create simulations. I'm just.... totally out of interesting ideas to do.

And it doesn't have to be molecular biology stuff I model... just anything. But the environment is like being inside a drop of water.

 

[Da Blob]

The Kreb's cycle could be interesting(?)

 

[fullerene]

DNA reproduction during mitosis

 

[Chronomar]

The spindle fibers in mitosis! In plant cells, which have no centriols (I've always wondered about that...animal cells need centriols, yet plant cells do...what's going on?).

Or: how about the functioning of the influenza virus? Or a different kind of virus? Or...a protein in a virus.

How about the DNA-inspired molecular wires that are being developed for use in biological computers? A friend I know who is in graduate school is working on that.

 

[Reverse Transcriptase]

How about the DNA-inspired molecular wires that are being developed for use in biological computers? A friend I know who is in graduate school is working on that.

WTF I want more info on that!

Actually the first step for me is going to be figuring out how to install it and going through the tutorial.... :3

 

[Chronomar]

Oh. Sorry.

http://www.sciencedirect.com/scienc...serid=10&md5=4d5dcc8e1ebbb5cf418830d03461e94b

Also: Try searching things on the Protein Databank website (it's called the PDB...search it in google or something). It will give you a script file of the 3D structure of the protein as well as information about it. The script file could be useful, depending on what kind of modeling program you're using.

 

[Reverse Transcriptase]

Yeah I know about the PDB. It could be useful giving me information about what other proteins it binds to! However, this modeling program treats everything as point-particles.

Thanks for the article

 

[Chronomar]

Let us know what protein, or whatever, you decide to model! (and post pictures of the end result?).

 

[Trebuchet]

How about they way cholesterol controls the permeability of cell membranes?

 

[Polaris]

Bacteria? They are terribly interesting. E-coli?

*wishes for geek-smiley....*

 

[cuterebra]

Lipid rafts!