Re: molecular interactions
- To: mathgroup at smc.vnet.net
- Subject: [mg22936] Re: molecular interactions
- From: "Kai G. Gauer" <gauer at sk.sympatico.ca>
- Date: Thu, 6 Apr 2000 02:04:52 -0400 (EDT)
- References: <8ce920$sr@smc.vnet.net>
- Sender: owner-wri-mathgroup at wolfram.com
rafie at fk.um.edu.my wrote: > Hai, > > I'm looking for the software that can model and simulate the molecular > interactions. Do you have any idea? I don't know of any freeware mathematica notebooks where you have some nice palettes that will "easily" attach, say a CH3 free radical to any one particular side of a C6 carbon ring (with whatever else attached to the other edges). This will probably need quite a bit of symmetry group theory built in to the notebook as well, which I can't find all that much ease for use with Mathematica (at least, there's very few built-in internals that will call up what, say, a group table of U(prime) without first writing with the modulus function to go with it... I'm surprised there was'nt even a built in way of defining/computing/looking up orders of certain elements) ....anyways, once you've gotten all the short premature codings down to build to morphisms of other symmetry groups, you'll find that you'd probably want a pallette full of common radicals, complete with the pointing of their covalent, hydrogen and ionic bondings. This will require assigning a 3D basis to set the scope of what sort of possible 3D codomain that you would want your free radical most preferentially siting at an one moment (BTW, but my chemistry failing me, would something like a C2H4Cl2 molecule (with exactly one chlorine atom touching exactly one carbon atom) be able spin about the main axis of the C-C through time (like a propellor on an aeroplane)? If it did, these sorts of subprocedures would also probably be wished to be built in). You could also discuss how you might wish to call your function palette easily enough so that you know where each bond should sit (and maybe, what the probability of it remaining there stable for a long period of time ... with respect to where the radical would 'prefer' to sit, because of relative bonding energies needed). Then would come the pretty pictures and sizing everything down to the relative atomic sizes, distances from one another (colours too, maybe ;^) and trying to render a fast 3D picture/ animation that would be: easy enough to zoom in on and look at the perspective from multiple angles possibly from the view of the interior of a DNA strand out, with cutaways to see better, and probably, some better way to render rotating an image when you would have no premature idea of what perspective the molecule's shape should be when seen from that angle. Of course, the BIG idea here is speed in generating the image and computing the ideal shape. I know a little bit of other styles of planar tilings (if you're trying to produce an image of graphite), a bit about non-periodic tilings (penrose tiles, etc), but ask me about trying to build algebra structures that may be describing those non-periodic 3D shapes we see so mush of in Scientific American, I'm only beginning to see the relationships to group theory, nevermind my trying to write programming to emulate this morphism from algebra to symmetry groups! You could also check out an article pertaining to geology crystalline structures which I've found in the Mathematica Journal a few years ago: its by Jorg Enderlein of LANL. ---- could you reply to me if you find better notebooks (for Mathematica, of course)?