Responsible Nanotechnology

Synthetic Biology Pathway to Molecular Manufacturing?

I must begin by admitting that my thinking has been limited. When I think of biology, I think of complex poorly-understood feedback loops; designs that have been cobbled together by random chance over billions of years; systems that can be played with, but not really engineered.

When I think about human adaptation of biology, I think of slow improvement via genetic engineering or even breeding. And when I think of a cross between biology and nanotechnology, I think either of nanomedicine, or of the old tired arguments about how nothing can improve on biology so the best we can do is try to imitate nature's designs.

Now let's consider molecular manufacturing. A description of molecular manufacturing might go something like this:

You design machines at the molecular scale - machines that, working collectively, can build more of the same by atomically precise mechanically guided chemistry. You build a set of these machines, by hook or by crook, and fasten them together. They build duplicate machines. Exponential growth allows a tiny construction module, duplicated many times, to produce useful amounts of product. Then, you program the system to build a wide range of products.

There is a branch of synthetic biology that is working toward this same goal. The idea is to design an entire genome, to produce a minimal organism, that can duplicate itself, and eventually can be used for human benefit and profit.

This goal will take many years to achieve; the above-linked paper, which looks a lot like a roadmap, includes an impressive list of unknowns and problems to be solved. And the result will still face many of the limitations of biology: fluid drag from water, chemical transport by diffusion, limited material properties. And many of the components may not be completely understood even after it is built, since they will have been adapted from natural organisms.

But the creation of an engineered, constructed system that builds copies of itself from small molecules would, in my book, count as molecular manufacturing. It would not simply be duplicating existing life forms by means of synthesized chemicals (a project that is also underway). In fact, the roadmap discusses the possibility that the system might work better without membranes - and one of the reasons listed is the possibility of "spacial arraying for nanofabrication."

I don't know whether the first nanofactory will be produced by some other pathway before this synthetic biology project comes to completion. But I think this has to be considered a possible pathway to molecular manufacturing. There are now several pathways, each engaging lab researchers. One way or another, molecular manufacturing is coming.

(Thanks to Herman Salgado for asking the question that led to this post.)

Chris Phoenix

DNA Meets Buckytubes

I've talked recently about some of the cool stuff you can do with DNA. Here's one more: DNA can be used to sort single-walled carbon nanotubes.

Carbon nanotubes come in a variety of different styles. Imagine cutting a narrow strip of plaid cloth and wrapping it around a pencil. Depending on the angle of the wrap, the stripes would line up - or not - at various angles. A carbon nanotube can be thought of as a thin strip of graphite-like carbon, in which the atoms are lined up in regular rows, coiled up to form a tube.

Depending on the angle of the carbon rows - the so-called chirality of the tube - it can be a metal, insulator, or semiconductor. This makes it very interesting for computer applications. The trouble is that it's hard to synthesize just one kind of tube, and until now, it's been hard to separate out one kind from a mixture.

As reported in Nature, a group of researchers has searched among a massive number of DNA sequences to find sequences that will fold just right to wrap around tubes of only one particular chirality. This allows the wrapped tubes to be separated from the mixture. The DNA folds up into zig-zag sheets, which then wrap around the tubes that have just the right chirality.

This isn't the first time DNA has been attached to nanotubes, but it's cool that it is attaching to a single kind. And it sounds like the zone of attachment is large enough to form a reasonably strong connection. Although the researchers are mainly interested in electronic applications (at least, judging from the abstract of their paper), it may be that interesting nanomechanical applications will also be enabled by this work.

(Hat tip to Eric Drexler's Metamodern blog.)

Chris Phoenix

Robust Manufacturing Technology

Paul S commented on my last post: "...if regulation is necessary it will have to be applied before any robust [molecular manufacturing] technology is released to the public."

I agree with this - depending on just what is meant by "robust."

What makes a technology robust? Or, what would make a molecular manufacturing technology difficult to un-release to the public?

Consider first that molecular manufacturing development, along with other technologies, will not be standing still. A ten-year-old nanofactory would be more out of date than a ten-year-old computer. So if a branch of technology is left to stagnate for ten years, then it will effectively be un-released. It will still be able to do what it used to, but relative to the powers of modern technology, its products would be relatively unimportant. And if regulation is needed, ten years of progress in military and law enforcement technologies (including data mining) might make it difficult to use ten-year-old technologies without being spotted.

On the other hand, this analysis assumes that the governmental version of molecular manufacturing would continue developing rapidly. This is not necessarily a safe assumption. Without lots of minds working on it with the stimulus of economic competition, a technology could easily stagnate. So ten-year-old civilian tech vs. ten years of governmental progress might be a pretty even match. Just look at the U. S. space program.

The second question is whether a particular incarnation of technology is usable and useful. For commercial applications, this means it has to be reliable, predictable, and not too innovative. As a home appliance, it has to be thoroughly simple to use, safe and perceived as safe, and make finished products. For hobbyists, it has to be fairly inexpensive to work on. It's far from obvious that an embryonic molecular manufacturing technology would be adopted by any of these groups in a way that led to its rapid further development.

So if early molecular manufacturing was released to the public, it's not at all certain that this would lead to Pandora's box being opened a decade in the future. This is good news, because in a sense, early molecular manufacturing has already been released.

Chris Phoenix

Graphene Ribbons Now Available

Precise graphene ribbons can be made by chemically unzipping carbon nanotubes.

This adds one more large molecule to the nanoscale construction toolbox. The ribbons may be useful in electronics, since a film of them should be even more conductive than a film of buckytubes. So they will likely be researched.

The article didn't say so, but I also speculate that these ribbons may be useful as reinforcements in composite materials (like a better kind of carbon fiber), since they seem to be water-soluble (which helps with processing) and might be easier to attach other molecules to than nanotubes are. The researchers estimate that they could be available in ton amounts in a couple of years, if there's demand for them.

In any case, I'm sure they'll be experimented on in many ways. They may turn out to be useful in mechanical nanosystems, though they'd probably be pretty floppy in comparison with buckytubes.

The unzipping process was discovered by Dmitry Kosynkin, a post-doctoral research associate at Rice University, who was studying oxidation of nanotubes. Yes, a lot of nanotechnology is accessible through chemistry.

(Hat tip to Mike Treder.)

Chris Phoenix

Solid-State Quantum Computer

It's not nanotech, except in the sense that anything small and interesting enough counts as nanotech. But it's a significant milestone toward a game-changing technology.

An electronic quantum processor with two qubits, each made of about a billion aluminum atoms, has been created at Yale university. They can get the qubits to maintain their state for about a microsecond. And they have a "quantum bus" that can pass information between the bits.

I don't understand all the cool things you can do with a quantum computer, but apparently it can be useful for simulating quantum chemistry. I suspect we'll have covalent-solid molecular manufacturing before this quantum computer technology develops to the point where it can help, but I've been surprised before by how fast technologies can advance.

Chris Phoenix

Today's Tech: Affordable Carbon Capture

Molecular manufacturing will give us the ability to do planet-scale engineering. We may need it.

Polar ice is melting faster than expected, and permafrost is releasing methane. Science tells us that large-scale reduction in atmospheric carbon dioxide may be necessary to avoid major, destructive, near-irreversible climate shifts.

According to a recent CNN news story on carbon capture technology, it may be possible to remove carbon dioxide economically with today's technology. A machine that costs as much as a car could remove the carbon emitted by 20 cars. The power required to remove and liquefy CO2 is 1/5 the power generated by burning coal to produce it.

Of course, removing CO2 is only part of the puzzle. There remains the question of what to do with it. There are several possible answers to that, and it remains to be seen which one is best.

I'm enough of a pessimist to think that this technology will not be adopted until it's too late for it to make much difference. Thus, instead of (for example) a 5% tax on cars to offset their carbon emissions, we'll need a massive crash program. Today's technology will just be a reminder that we don't use technology wisely.

When molecular manufacturing was proposed in the 1980's, there were many applications that could not be achieved by any other technology. As time goes on, some of those applications are being addressed by advances in other fields of technology... at least potentially. Understanding the uses, misuses, and non-uses of today's technologies gives us some clues about how molecular manufacturing may be used and abused.

Chris Phoenix

Planar Assembly Scale

Jim Moore asked how small it would be useful to go with planar assembly.

A bit of background: When Eric Drexler proposed, back in 1992, that molecular manufacturing should be done in tabletop factories rather than vats with floating robots, his proposal had nanoscale sub-components being made and then put together in larger and larger assemblies by converging assembly lines. This design made a lot of sense, and variations of it were studied over the next decade.

Then, just a few years ago, John Burch and Eric Drexler came out with a new nanofactory architecture: one that made medium-small components, and then stuck them directly onto the surface of a product under construction, building it up block by block. This works because, as long as the machinery handling the block can scale down in proportion to the block (and scale up accordingly in operation speed), the linear deposition rate does not change.

So how small can planar assembly go? Well, the machinery to handle feedstock molecules will probably be quite a bit bigger than the molecules. So planar assembly probably doesn't work all the way down.

But it can go pretty far. The smallest number Jim asked about is 100 nm - the size of a smallish bacterium. Well, you can fit a lot of machinery into a block of that size. In my Primitive Nanofactory paper, I suggested 200 nm blocks - only eight times the volume.

It seems to me that the lower bound on size is set by the interfaces between blocks. If the blocks are intended to be functional - to include nanomachinery - then there will have to be interconnections between each block. If the interconnection systems are 10 nm thick, then almost 50% of a 100-nm block will be used up in connection hardware. A 200 nm block would use only a bit over 25% of its volume for interconnects.

There's not necessarily any upper bound on block size, but I don't see any reason to make them bigger than 200 nm. One nice feature about 200 nm blocks is that there's a fairly low chance per block of background radiation damage. You can pretty much design the machinery in a single block without worrying about fault-tolerance, and do your fault-tolerant design at a higher level. If your block was a micron or bigger, you'd have to assume that something inside it would probably be hit by background radiation in less than a year, so each block design would have to include some fault tolerance.

Jim's question included the suggestion that planar assembly might be used at small scales to make parts that could be assembled into the final product. To a first approximation, I don't think this is necessary, since the final product can be made directly with the small blocks. Rather than building a part and then fitting it into place, just build the part by planar assembly in its final position. That means you'll be building lots of fractional parts in layers at the same time, but I don't see a problem with that. The block-joining mechanisms should work the same in either case.

One more advantage to building the entire product directly out of small blocks: you never have to handle parts that are big enough to be heavy. In other words, you don't have to worry about gravity.

So planar assembly is an extremely flexible approach to building products, and should save a lot of volume and design complexity in nanofactories.

Chris Phoenix

Breakthrough! Particle Assembly Technique

Stick nanoparticles together only when you want to! Researchers at NYU have announced a way to use DNA strands to make nanoparticles sticky only under certain conditions.

If you can make nanoparticles stick on command, you're a big step closer to building a simple nanofactory.

In the study that I did with Tee Toth-Fejel for NIAC a few years ago on Large-Product General-Purpose Design and Manufacturing Using Nanoscale Modules, I proposed that a primitive sort of nanofactory might be built with molecular building blocks that would bind together when pressed together, but otherwise float around in solution. The idea was that the blocks would bind weakly to the tip of a "tattoo needle" which would then press them into a workpiece, where they would stick. Given an appropriate set of building blocks, it should be possible to build arrays of tattoo needles.

DNA strands stick together when their sequences match up properly. Sticking nanoparticles together by coating them with matching DNA strands has been done for a while. But the innovation here is that a strand with the right sequence can fold back and stick to itself.

A particle coated with doubled-over DNA strands will not be very sticky. But heat can unstick the strands from themselves, making them able to stick to each other, linking the attached particles. The article implies that holding a particle in position long enough will allow the strands to randomly uncoil and stick - whereas particles that bumped into each other in solution would almost always drift away before this could happen.

Another interesting point in the article: by making use of reversible attachment and conditional attachment, it seems possible to make intricate building block arrangements that can template copies of themselves. This could allow exponential growth of the patterns, even without externally controlled mechanical guidance.

DNA is extremely versatile, and the strength of the attachment between strands can be fine-tuned. The main thing I don't know here is the time scales involved. If it takes an hour to deposit a molecular building block, then this may not be useful for construction. But if it takes a minute or less, then things get very interesting.

I don't know yet if this innovation will go down in history beside Rothemund staples. But it is certainly complementary to it (no pun intended) since suitable molecular building blocks can be very easily built out of Rothemund-stapled DNA.

It wouldn't surprise me at all to see a computer-controlled DNA-based molecular manufacturing system within a few years. The material properties would not be all that great, and it might or might not have fast actuation, and it would require expensive feedstock and carefully controlled laboratory conditions, so it would not be revolutionary in an economic or military sense. But it would be an awesome proof of concept, leading people to wonder what other materials and binding systems might be used to build higher-performance nanofactories.

Chris Phoenix

Concise Summary of Molecular Manufacturing

Eric Drexler over on Metamodern has posted a summary of "The Physical Basis of Atomically Precise Manufacturing."

Most of what he says isn't new - it comes straight from his 1992 reference/analysis work Nanosystems. Small things work faster and have higher power density. Detailed and conservative analysis shows that molecular-scale objects can be built by molecular-scale objects. (Biology is an existence proof of this last point - but the kind of machines Drexler analyzed have fundamental performance advantages over biology.)

Drexler makes an interesting point about the difference between design for easy analysis and design for easy construction, and he provides links to earlier posts of his on things like alternative materials for machine-type nanoscale manufacturing systems.

He also discusses the amount of time required for fabrication, pointing out that this is proportional to operation speed, and thus can be expected to be faster (per machine mass) in smaller machines. Perhaps in a future post he'll go into more detail on nanofactory architecture and molecular fabrication vs. component assembly. (My nanofactory paper explores these issues for a particular desing of fabricator, but it's a lengthy read and the convergent-assembly design is now probably outdated - the Burch/Drexler planar assembly design seems better in almost every way.)

Though he didn't include this observation, scaling laws also describe the huge difference between handling molecules with big machines and handling them with small machines. Not only do the small machines work faster in proportion to their size, but their volume changes drastically. People's intuition correctly tells them that a desktop machine could never build a copy out of molecules - it would take billions of billions of years. But what their intuition won't tell them is that, if you shrink the machine by a factor of a million, it should be able to build a duplicate out of molecules in a few minutes.

Even if you're familiar with molecular manufacturing, it's worth reviewing all the cool and useful things that happen at the nanoscale - which means it's worth reading Drexler's article.

Chris Phoenix

Ions Smooth The Way For Protein On DNA

Although I generally prefer machine-like nanosystems to squishy nanosystems, I am capable of appreciating elegance in the squishy realm. The latest Physical Review Focus story, "The Electric Slide," explains how proteins can slide along DNA.

Some proteins perform operations on DNA at specific points - they recognize particular sequences of base pairs. For efficiency, this recognition has to happen in several steps: first, the protein snuggles up to the DNA at a random location; then, it slides back and forth; then, since it's close to the DNA, it can recognize the spot where it's supposed to act; finally, it does its job. So it has to be close to the DNA, but not too close.

This is not as simple as it sounds. Although some atomic surfaces - including stiff machine-like interfaces such as tungsten on graphene - can be almost friction-free, many similarly bumpy surfaces are not. In order to slide smoothly, the protein has to avoid binding too tightly to the DNA. It has to stay physically distant from the DNA - but not too distant: it doesn't just float randomly near the strand, but actually slides along it without touching it, like a mag-lev train.

The researchers simulated a simpler version of protein and DNA. Instead of simulating every atom in the molecules, they abstracted them as a long skinny cylinder for the DNA, and a cylinder with a notch in it for the protein. (They tried several other shapes, but that's the combination that worked.)

Protein and DNA are charged molecules; DNA has a negative charge, meaning that it will attract positive ions from salt water, and protein has a positive charge. So the two molecules will attract each other. But why don't they stick together too tightly to slide?

It turns out to be important that DNA has a stronger charge than protein. When protein and DNA get close, there is still a layer of positive ions between them to balance out the charge. And if they get too close, the ions will be too concentrated relative to the water. So the charge difference keeps a layer of ions between the DNA and protein, and osmotic pressure keeps a cushion of water around the ions, and the water holds the DNA and protein apart.

The researchers did some analysis of real DNA-binding proteins, and found that the proteins have on average 17% of the charge of DNA. Plugging this into their model, they found a separation of half a nanometer - which matches what's been observed, and is a suitable spacing for low-friction sliding.

Since this sliding mechanism relies on the motion of ions and water molecules, I suspect (though I haven't calculated) that it would only be low friction at low speeds. A graphene bearing would require less motion of its atoms, so it should be able to move considerably faster. So I still like machine-type bearings better. But as long as you're working under water anyway, you might as well use ion cushions.

Chris Phoenix