Responsible Nanotechnology

Exceptionally Stiff Organic Nanostructures

Lots of things work better as they get smaller: power density increases, operating speed increases, and number of features per volume increases dramatically.

One of the few things that doesn't get better is stiffness - in fact, stiffness gets worse. A material that's stiff enough to build human-sized things out of may be too floppy for the nanoscale.

There's been lots of exciting developments over the last decade in organic nanostructures... but one question that's been on my mind is how to make them stiff enough to build conventional mechanical devices out of. (Floppy natural protein machines are cool, but inherently limited in some ways, and stiff devices can benefit from centuries of accumulated invention.)

Now comes an announcement of a new record in stiffness (a Young's modulus of 275 GPa) for aromatic dipeptide nanospheres. Basically, that means they're built out of protein. In fact, they're built out of just two amino acids. And the simple structure means they can be built in shapes other than spheres as well.

This may be a significant enabler toward building engineered nanomachines using protein-handling nanomachinery.

Here's an article that explains the dipeptide nanospheres.

Hat tip to Next Big Future.

Chris Phoenix

They Keep Getting Smaller... And More Powerful

I remember back in the late 1980's, seeing a billboard advertising IBM's studly computer power. In huge words, the billboard proclaimed: "17 MIPS Zone!"

Nvidia is announcing that by the end of next year, they'll have a chip with (Brian Wang calculates) about 1.5 Teraflops. That's 100,000 times as fast.

Even for someone who grew up knowing Moore's Law and laughing at how the old science fiction writers put room-sized computers in space ships, every once in a while my mind gets blown by just how fast computers are getting.

The other thing that impressed me is that this chip will be made with a 28 nm process. The smallest patterned feature on this chip will be smaller than most viruses. And I'm guessing it'll have somewhere around a billion of those features.

(If I remember right, back in the late 80's, the smallest feature on a chip was over 1,000 nm.)

Back in 1998 when I first heard about nanotechnology, there was basically no way to build things that size. Now, industry is doing it.

I don't have a nice conclusion for this post. I just was impressed enough to want to write and say, Wow. 

Chris Phoenix

A Crisp View of Molecules

Molecules are more than fuzzy blobs, but that's all scientists have been able to see... until now.

For a couple of decades, scientists have used tiny needles to poke at single atoms and molecules, displaying the results as fuzzy blob-like structures. This is impressive enough - after all, atoms are a fraction of a nanometer wide. (Your fingernails grow about a nanometer per second.)

But now, a simple new technique has allowed them to see a very crisp view of the electrons that make up the molecule. Click here for the Physical Review Focus story that explains it, and shows how much of a difference the technique makes.

(I don't post pictures because I don't want to worry about copyright. The above link is really worth clicking on.)

Science can get amazingly precise.

Extremely simple techniques can make a huge difference.

Chris Phoenix

Nanorobot Assembly Line Built!

A platform ("walker") moves along a track, past several parts-handling devices, each of which can add a piece to the product - or not, depending on the programming of the system.

This is a robotic, mechanical, digital, programmable system, built out of molecules of DNA. The entire thing is far too small to see with an ordinary microscope.

Here's a pointer to the abstract describing Ned Seeman's lab's work. And here's a pointer to an article explaining how the assembly line works.

This is a major breakthrough. It's not the first programmable assembly device based on DNA - Seeman did that a few years ago, with a machine that was built of DNA, programmed by DNA, and could build one of four different DNA strands. But this one is a lot more complex and modular and flexible, and feels a lot more robotic.

Anyone who's claimed nanoscale robotic construction can't work will have to eat their words! The only question now is how fast the robots and products will improve.

Looking forward: If they had a way to (1) recharge the parts-holders in the middle of construction, and if they (2) had a way to connect the parts directly to each other rather than to the platform (without the parts joining to each other prematurely while loading the parts-handlers), and if they (3) could step the growing product past the walker so that the addition zone was always in the right position, then they could, in theory, make products of arbitrary size and sequence.

My recent DNA-binding research proposal describes one hypothetical way to address the first two of these requirements. There are other ways to achieve them as well. The third requirement doesn't seem very difficult compared to what they've already accomplished.

Big hat tip to Michael who brought this to my attention the day it was published!

Chris

Chris Phoenix

DNA binding research proposal

As I see it, the point of a robot is to do lots of simple things in programmable sequence. A self-replicating robot built of DNA is no exception.

"Sequential" and "self-assembly" don't usually go together, because self-assembly happens by itself (hence the name) which means that everything tends to happen at once. Also, self-assembly usually needs to be reversible, so that components can try various positions until they get it right; but that means that the things you've already done tend to come apart while you're doing more things.

Thus, to make things self-assemble in a lengthy sequence of operations requires re-thinking some assumptions. The assumption I've chosen to re-think is that self-assembly needs to be reversible.

A common problem with irreversible self-assembly is that things tend to stick together where you don't want, and then they can't come apart again to find the correct position. But what if the things were very unlikely to stick while bumping around in solution - but very likely to stick if held in close proximity?

A back-of-the-envelope calculation shows that using DNA strands to hold things near each other should be able to increase their effective concentration by a factor of a million or so. (The basic idea is not mine - I learned it from Eric Drexler - but the calculation is mine.)

This is the core of my simple self-replicating robot idea. If things are a million-fold more likely to stick when you hold them where you want them, then you should be able to build structures out of hundreds of the things before something sticks where you don't want it. And my robot design only requires a few dozen building blocks.

The first thing to do is to demonstrate this million-fold speedup in sticking (binding). That's the focus of the current proposal.

My plan is to design some DNA strands to bind very strongly but react very slowly, then demonstrate that they will bind a lot more quickly when held in close proximity. I would do this with pairs of DNA strands, each with a "test" section that binds slowly but strongly to the "test" section on the other strand, and a "holder" section that binds quickly but reversibly to the corresponding "holder" section.

I'd put one FRET pair on the tips of the "holder" sections, and another pair on the "test" sections. This would allow me to tell when the various parts of the strands hooked up.

I'd mix the strands together at a temperature too high for the "holders" to bind, and show that neither FRET pair was close, even after waiting a long time.

Then I'd lower the temperature to where the "holders" would bind, holding the "test" pairs somewhat close to each other. I'd wait a short time, until the "test" pairs also bound.

Then I'd heat the mixture back up, letting the "holder" sections disconnect, and show that the "test" pairs were still together.

Instead of temperature change, I could also use strand replacement to free the "holder" strands to bind to each other, and then another replacement to separate them again. That way, all the "test" activity would happen at the same temperature.

So, if all this works, I would be able to demonstrate irreversible self-assembly on command. Once that was established, I'd be ready to make irreversibly assembling building blocks, and eventually build a DNA-programmed DNA robot to hold them together, one at a time, in the correct sequence to make whatever I wanted.

Chris

Chris Phoenix

Self-Replicating Nano-Robots Now Possible

I believe it is now possible to develop a device with controllable moving parts that can build a copy of its structure from significantly simpler components under external computer control.

Lovers of science fiction or disaster scenarios will be disappointed: the device would have only a few dozen parts, would rely heavily on self-assembly, would have no on-board computer, and would require massive quantities of expensive manufactured molecules to be pumped past it just to make it operate at all.

Basically, all it would do is to sort building blocks out of a mixture, stick them together one at a time in linear sequence, and let the resulting chain fold into the desired structure. But it could, in theory, make any desired structure, perhaps with with low enough error rates and high enough speed to assemble hundreds or even thousands of components. And my design only needs dozens.

Based on what I learned at the recent FNANO conference (which had lots and lots of information about DNA structures, and world-class experts on them), I think all the necessary techniques and knowledge are in place.  Several of those experts told me that my idea is interesting; no one told me it was impossible.

The practical utility of this design is near zero. But it would blow away an important conceptual barrier, and demonstrate several useful new techniques and approaches (including one that Eric Drexler proposed years ago).

Chris Phoenix

Scientific Advances Require Blind Luck

So here I am at this conference on self-assembly, and I'm talking with people about Rothemund's DNA staple technique. The technique is elegant, simple, and powerful. Mix a long DNA strand with a bunch of short strands. The short strands bond to different regions of the long strand, and pucker it up into a shape.

Person after person has told me that they never would have expected this to work! I was really surprised at that, so I've started having conversations about it.

One of the most common reasons has to do with entropy. Perhaps it's not a coincidence that entropy is one of the most common objections to molecular manufacturing. There's a whole lot of very solid theory about entropy, which says that unstable molecules will fall apart. But what's often missed--by the people applying this theory!--is that it assumes a steady state, also known as infinite time! In other words, entropy says diamonds aren't literally forever... but in the real world, we can ignore that. Nanomachines built of diamond could laugh at entropy for far longer than we actually care about.

So, back to entropy vs. DNA self-assembly. I was talking with a physicist over lunch today, trying to figure out why he expected DNA shapes to fall apart on entropic grounds. It turned out that he was right - the shapes will eventually fall apart - but he hadn't thought about the time it would take.

Another entropy-related reason that's often cited is that DNA staple shapes require combining hundreds of molecules into a single structure, and the entropy of a single structure is a lot lower than the entropy of hundreds of fragments. While this is true, the fact remains that DNA does prefer to join in double strands. I haven't found anyone who can explain why increasing the number of strands would significantly reduce the willingness of each strand to join the structure - but I've found lots of people who seem to believe this would be the case.

I can understand how assumptions from one domain (say, the physics of small molecule chemistry at equilibrium) can make it difficult to invent a new concept in another domain (say, DNA binding). It's a bit harder for me to understand how that assumption wouldn't be questioned when confronted with a really good idea.

In fairness, it's true that many seemingly good ideas don't work for reasons that couldn't easily be foreseen. So rejecting a seemingly good idea isn't always a destructive thing to do - it can save a lot of effort that would be wasted trying to develop the idea only to discover that some minor practicality prevented it from actually working.

But I'm starting to think that the stated reason for rejecting the idea is frequently unrelated to the reason that the idea wouldn't actually work. In other words, science has developed a rule of thumb that works: Reject most ideas, accepting only the most compelling and fully demonstrated ones. And a procedure that works: To reject an idea, find and cite some overly-generalized and poorly understood theory. The fact that the procedure is groundless does not mean that science's rate of rejection of new ideas is wrong. The rate of rejecting new ideas may, in fact, be highly functional.

If the rejection of new ideas is basically random, then I'm saying that science advances by blind luck. In fact, that's plausible. Any exploration of a sufficiently unfamiliar and difficult problem domain must advance by blind luck. What makes science (and evolution) work is that they can, after the fact, detect and preserve lucky accidents.

A question we might ask is whether things would be better with a somewhat lower idea rejection rate, and if so, how to shift the rate. The answer is probably somewhere along the lines of increasing funding for researching crazy ideas. I don't know if there would be any point in trying to convince scientists that they're routinely rejecting ideas randomly.

Another question we might ask is what to do when scientific advances are needed to achieve a technological goal. The answer seems to be: Don't expect the scientific establishment, as a whole, to work toward that goal, no matter how workable or clearly articulated or well-calculated. The goal will simply be treated as a new idea, and rejected. Instead, find a way to pay individual scientists to work on it.

By the way, I just heard a talk in which a DNA cascade circuit was developed and tested to compute the square root of a four-bit number. It involved about 130 strands, implementing about 76 logic gates. It would be very easy to find a theoretical reason why this couldn't possibly work... but in fact, it did work.

Chris Phoenix

Regulating Advanced Nanotech

An email correspondent asked an interesting question (thanks, Wendy!) about whether we've missed the moment to regulate molecular manufacturing.

I see two main sources of regulation, plus a distant third:

1) Commercial regulation, dealing with the economic implications of a manufacturing revolution.

2) Military regulation, dealing with the weapons and geopolitical aspects.

3) Maybe criminological regulation, since new products can often be used for new forms of crime.

I think commercial development of molecular manufacturing will likely be too fragmented for effective regulation. There may be some regulations that have substantial negative impact, comparable to the creation of software patents in the mid-1980's. But I suspect most commercial regulation will be trying to solve non-problems (defend obsolete monopolies) after the fact, and won't have too much impact.

A major question on military regulation is whether molecular manufacturing will be developed mainly on the commercial side, incrementally, as computers have been, or whether it will be developed first in a "Nanhattan" project. In the latter case, it might be seen as dangerous (especially if used in war in an especially flashy and gruesome way) and susceptible to blanket regulation. That could hamper commercial use for decades. But if molecular manufacturing develops incrementally, it may be no more regulated than computers or biotech.

Regulation of crimes and other social impacts will probably be about as effective as regulating illegal drugs.

Thoughts?

Chris Phoenix

CRN Inspired Cutting-Edge Nano-science

Back in 2005, I had several long discussions / debates (e.g. this discussion) with two scientists, Richard Jones and Philip Moriarty. They attempted to convince me that molecular manufacturing couldn't work. (Richard Jones is the author of Soft Machines, which argues that biochemical-based systems are far superior to diamond-like systems.) I attempted to convince them that it could. The argument was somewhat frustrating on both sides...

In an online interview, Philip Moriarty has recently acknowledged those discussions as being the inspiration for his current research: attempting to demonstrate or disprove calculations of atomic bond manipulation and structure formation - including 3D structures - on silicon and diamond surfaces.

In other words, he's trying to learn whether or not Drexler-style mechanical chemistry works the way it's been calculated to work. This does not make him a supporter of Drexler, but it does mean he has an open mind. Open-minded scientists are what makes science work, and Moriarty's work is doubly valuable for its rarity.

(Richard Jones, by the way, went on to lead a group that was convened in order to allocate several million dollars of scientific funding; the funds went toward projects that had the potential to substantially advance molecular manufacturing.)

I'm glad to see that CRN made this contribution to scientific progress in the field of molecular manufacturing.

(Hat tip to Brian Wang at NextBigFuture.com.)

Chris Phoenix

Chem Prof Teaches Bad Physics

Why does it matter whether atoms are moved by quantum effects?

A few days ago, I received an email from a student who was interested in molecular manufacturing. He had asked a chemistry professor whether molecular manufacturing could work.

The professor said no: quantum uncertainty would mean that the atoms could be in two places at once, so they couldn't be picked up by machines or used to make gears.

It is a crying shame that in 2010, some university professors are 1) so uninformed about the physics of atoms and 2) so willing to talk beyond their knowledge.

Richard Feynman, who won his Nobel Prize for his work in quantum physics, believed that mechanical-style molecular manufacturing would work just fine.

Single atoms have been imaged using scanning probe microscopes, even at room temperature.

I hesitate to make blunt statements that other people are wrong. It's not good politics, and it's not good debating tactics. But I don't know what else to say in this case. Dozens of experiments, plus Richard Feynman, say that the chemistry professor is simply wrong.

Why does it matter? First, it's shameful to teach students incorrect scientific information. And second, if we don't know what can be done with nanotechnology, we cannot prepare for the problems nanotechnology will create, and we cannot benefit from the potential advantages.

Chris Phoenix