Touching Molecules With Your Bare Hands

FiReaNGeL writes "Researchers at the Scripps Institute just devised an incredibly interactive way to manipulate complex molecules, such as proteins and DNA, with your bare hands. Combining 3D printed hand-held objects with sophisticated computer displays & cameras, this technology allow more natural and intuitive interactions with biological molecules - you can manipulate them with your hands and visualize the results on the computer in real time. Don't miss the incredibly cool movies and images illustrating the 3D printing process and augmented reality interaction with diverse proteins, viral self-assembly simulation and HIV-1 protease folding. A detailed press release is available."

Comments

Opposite

[LiquidCoooled]

I assume you could expand on the principal and have an entire galaxy at your fingertips.

Sure would be cool to have hanging around.

Re:Opposite

[jessecurry]

this is a very cool technology that seems to have applications for anything that is either too large or too small to directly interact with. One of the limitations that many people have when learning is that they cannot visualize the concepts, this sort of evens the playing field for those people that have trouble.

Re:HIV

[wideBlueSkies]

The other night I kissed the cheek molecules of one of my dear friends, and I saw the molecules of her lips form into a smile. :)

Technology is great.... firendship is better.

wbs.

TFA is a lie

[mrRay720]

That's no more "touching molecules" than owning a copy of playboy is having a girlfriend. It's touching a solid immitation of one.

(Ignoring the obvious complaint that most stuff is made of molecules.)

Augmented reality...

[FireballX301]

I skimmed the article, and apparently, what happens is that they have a machine that will manufacture molecules out of plaster and such. That model can then be manipulated, and the manipulations will occur on the computer. A camcorder feed records your hands and the molecule, and will display it, along with the computer's own overlay. Thus, the pictures are all CG, and the weird effect is simply an overlay of a normal molecule model.

IMO, not as impressive as a video I saw, where there was a desk that had virtual (i.e. you could put your hand through them) objects moving around and interacting with some real objects (a plug outlet). Also had a guy turning his mic into a rose. I forget the link.

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[account_deleted]

Comment removed based on user account deletion

Blue Gene

[karvind]

I am not sure if I understand this completely (I read the Press Release).Blue gene does protein folding computations which requires hours of CPU time. How can you understand these molecular interactions in real-time ? Article doesn't give detail about how they implemented the time-consuming computation.

Re:Blue Gene

[t35t0r]

The fold of the proteins in question are already known. That's how they know how to construct them physically using the magnets or 3d printers. It's how the protein will interact with other molecules that makes this approach useful.

Re:Blue Gene

[tfoss]

First, Blue Gene's aren't yet up to the task of true de novo protein folding simulation (and there is debate about when/if we'll be able to actually do that with the knowledge we have now). Molecular interaction calculations on the other hand, aren't nearly so challenging, and many can be done in real-time (there are obviously many caveats to that, but...).

Second and more importantly, that isn't what this does. This setup is mainly to help in teaching about molecular interactions by providing an enhanced tactile environment. Lots of people learn better when they can actually touch models. This is a system that takes these models and adds a layer of virtual reality on top of them. So not only can you play with a model of your favorite protein..feel it, turn it around in your hands, etc etc, but now you can have a computer superimpose various types of information on that model. Show the structure of any residue's sidechain, show the electrostatic potential around any part of the protein, show how a small molecule docks inside a protein, etc etc. All types of information that has been represented by static pictures, then pre-rendered movies, then interactive movies, are now able to be demonstrated in an even more intuitive system.

-Ted
And let me just say how cool it was to click on a Slashdot story that has one of my phd committee members (Art Olson) in it!

Science Fiction

[Qwerpafw]

Once again, we see a real advancement predicted by a science fiction author.

In his work The Diamond Age (which was published, I believe, in 1995), Neal Stephenson predicted that nanotech engineers would manipulate molecules by hand, maneuvering them into position to create microscopic engines, rod-based logic elements, and other devices. John Percival Hackworth, one of the semi-protagonists of the novel (Stephenson has a nasty tendency to complicate his writing with multiple protagonists who follow divergent paths), is such an engineer, an individual who creates 'bespoke' nanotech designs.

The central conceit of the novel is that Nanotechnology has entirely replaced conventional manufacturing through the use of a "feed"--a dedicated line of raw materials which couples with computers to create almost any object desired. How long until such things become reality? Only time will tell. Obviously though, we're on our way.

Nice learning tool

[InternationalCow]

But nothing more. I agree with other posters. Now, if you could get some kind of force feedback that would tell you if one molecule can dock to the other in a particular orientation, or whether a, say, DNA molecule will accept a transcription factor and bend in the right direction, or.... - that would make a really useful tool for research. As it is now, this is a nice way of helping students to visualize the spatial properties of complex molecules. Useful, but hardly revolutionary in any sense.

Meanwhile, back in the article

[mcc]

This is a visualization technology, and not actually connected to the idea of moving around literal molecules. That is to say, the technology on display here allows you to move around molecules in a computer model, but those molecules are computer constructs and don't actually exist.

If someday we find a way to manipulate single molecules with such precision that we can mechanically and specifically control their movement freely, then we could of course use a technology such as this one to specify those movements. However such manipulation of molecules is the "hard part" of nanotechnology and not likely to happen any time soon. When nanotechnology becomes feasible it seems most likely that for a very long time we will be stuck with using assembly methods which are much more indirect.

The technology is however it seems immensely useful to people, such as biologists, who wish to understand and visualize how molecules, once constructed by whatever means, will interact with each other in a theoretical model.

Re:Indeed

[DaoudaW]

Seeing these posts makes me wonder what kind of molecules are neccessary to construct a sense of humor.

Amen!
Mostly the OP was simply making fun of the headline. My first thought when I saw it before I RTFA was "I'm doing that right now!" Then I took my hand off the mouse and thought for a moment that I wasn't Touching Molecules With My Bare Hands(tm), but then I remembered the O2, CO2, et al that I was still touching. I just started laughing at the really bad choice of headline made by Zonk, but was really curious what the article was about.

After I RTFA, I tried to think of a better headline. At first I thought it should be, "Manipulating Molecular Models with your bare hands," but that just reminded me of all the painted styrofoam balls I'd stuck onto straws. I got pretty close by adding "computer-generated", but even that seems inadequate. The process described is really quite cool. I guess the bottom-line is "Ignore this headline, RTFA"

Not so

[exp(pi*sqrt(163))]

Computing the forces required high-end equipment at the time, but should be very doable today

I wasn't doable on high end equipment then, it still isn't doable today. I spent 2 years working in computational chemistry and I've never seen such voodoo in my life. Yes - there are formulae for computing forces. But no, they don't bear much relation to reality Any simulation running anywhere near realtime is likely to be a purely classical simulation - balls and springs. This bears no relation to reality. Someone will run a simulation a few hundred times and after much tweaking of spring stiffnesses and so on they'll get results that vaguely approximate something measured in a lab. In the next simulation they'll need different parameters with no way of predicting what that change should be. Basically people in computational chemistry are doing post hoc fitting of models with close to zero predictive power. I've seen it happen over and over again and from time to time other people will also confess this is what they are doing. Occasionally someone will even run a quantum simulation - often a single electron model that is about as representative of a full quantum model as an elephant's dung is about its trunk.

Unfortunately, with the advent of fancy graphics workstations came the belief that these methods worked - after all, people could see pictures, on a computer at that. These new methods make things even worse, people will feel forces generated by a fictional simulation and be even more convinced that what they are experiencing really does reflect reality. If you care to check you'll find very few cases of a drug discovery, say, resulting from a theoretical prediction about receptor binding. And when you do, you'll find plenty of people questioning that interpretation. After all, drug discovery is largely about dumb luck, and every so often the next randomly suggested compound for testing comes from a computational chemistry lab, even if a bunch of fortune tellers using the I Ching to predict drug designs might score just as well.

Sometimes I worry if atmospheric sims used to predict global warming are just as bad - not not having worked in atmospheric science I've no evidence to back it up. The tricky thing is that anyone who works with sims is likely to have a vested interest in maintaining their use.