Will's Nanotechnology Blog

Dr. Drexler's blog

2009-02-11T07:50:00.000-08:00

Dr. Eric Drexler founded the field of advanced nanotechnology with a 1981 paper in the Proceedings of the National Academy of Sciences, and his book Engines of Creation published in 1986. These two publications laid the intellectual foundation for a complete revision of human manufacturing technology. Like any major shift in technology, there are risks to be aware of, but the promise of advanced nanotechnology is vast: clean cheap manufacturing processes for just about anything you can imagine, products that seem nearly magical by today's standards, medical instruments and treatments far more advanced than today's medicine.

Dr. Drexler has continued to work in the field for over twenty years, promoting research into developmental pathways and awareness of the potential risks. His thoughts on nanotechnology (and technology in general) are unique. With the publication of his Metamodern blog, these are now publicly available. His postings cover a broad range of topics, ranging from the books he's been reading lately to common and misleading errors in molecular animations to his most recent observations and insights on developmental pathways to advanced technologies.

Graphene memory device at Rice University

2008-12-29T14:26:00.000-08:00

James Tour and colleagues at Rice University have demonstrated a switch (described in Nature Materials) composed of a layer of graphite about ten atoms thick. An array of such switches can be built in three dimensions, offering very high densities of storage volume, far exceeding what we now see in hard disks and flash memory USB widgets. The switch has been tested over 20,000 switching cycles with no apparent degradation. The abstract of the Nature Materials article reads:

Transistors are the basis for electronic switching and memory devices as they exhibit extreme reliabilities with on/off ratios of 10⁴–10⁵, and billions of these three-terminal devices can be fabricated on single planar substrates. On the other hand, two-terminal devices coupled with a nonlinear current–voltage response can be considered as alternatives provided they have large and reliable on/off ratios and that they can be fabricated on a large scale using conventional or easily accessible methods. Here, we report that two-terminal devices consisting of discontinuous 5–10 nm thin films of graphitic sheets grown by chemical vapour deposition on either nanowires or atop planar silicon oxide exhibit enormous and sharp room-temperature bistable current–voltage behaviour possessing stable, rewritable, non-volatile and non-destructive read memories with on/off ratios of up to 10⁷ and switching times of up to 1 μs (tested limit). A nanoelectromechanical mechanism is proposed for the unusually pronounced switching behaviour in the devices.

It will be several years before memories based on these switches are available for laptops and desktops, but it's a cool thing. To my knowledge, the mechanism is not yet known, so there may be some interesting new science involved as well.

Encouraging news about mechanosynthesis

2008-12-23T15:29:00.001-08:00

Yesterday there was a very encouraging posting (by guest blogger Tihamer Toth-Fejel) on the Responsible Nanotechnology blog, regarding recent goings-on with mechanosynthesis. What the heck is mechanosynthesis? It is the idea that we will build molecules by putting atoms specifically where we want, rather than leaving them adrift in a sea of Brownian motion and random diffusion. Maybe not atoms per se, maybe instead small molecules or bits of molecules (a CH₃ group here, an OH group there) with the result that we will build the molecules we really want, with little or no waste. The precise details about how we will do this are up for a certain amount of debate. We used to talk about assemblers, now we talk about nanofactories, but the idea of intentional design and manufacture of specific molecules remains.

The two items of real interest in the CRN blog posting are these.

First, Philip Moriarty, a scientist in the UK, has secured a healthy chunk of funding to do experimental work to validate the theoretical work done by Ralph Merkle and Rob Freitas in designing tooltips and processes for carbon-hydrogen mechanosynthesis, with the goal of being able to fabricate bits of diamondoid that have been specified at an atomic level. If all goes well, writes Toth-Fejel:

Four years from now, the Zyvex-led DARPA Tip-Based Nanofabrication project expects to be able to put down about ten million atoms per hour in atomically perfect nanostructures, though only in silicon (additional elements will undoubtedly follow; probably taking six months each).

Second is that people are now starting to use small machines to build other small machines, and to do so at interesting throughputs. An article at Small Times reports:

Dip-pen nanolithography (DPN) uses atomic force microscope (AFM) tips as pens and dips them into inks containing anything from DNA to semiconductors. The new array from Chad Mirkin’s group at Northwestern University in Evanston, Ill., has 55,000 pens - far more than the previous largest array, which had 250 pens.

So there are two take-home messages here. First, researchers are getting ready to work with the large numbers of atoms needed to build anything of reasonable size in a reasonable amount of time. Second, this stuff is actually happening rather than remaining a point of academic discussion.

Toth-Fejel writes:

What happens when we use probe-based nanofabrication to build more probes? ...What happens when productive nanosystems get built, and are used to build better productive nanosystems? The exponential increase in atomically precise manufacturing capability will make Moore’s law look like it’s standing still.

Interesting stuff.

Adventures in protein engineering

2008-12-05T15:36:00.000-08:00

Proteins are a good material to consider for an early form of rationally designed nanotechnology. They are cheap and easy to manufacture, thoroughly studied, and they can do a lot of different things. Proteins are responsible for the construction of all the structures in your body, the trees outside your window, and most of your breakfast.

Why don't we already have a busy protein-based manufacturing base? Because the necessary technologies have arisen only in the last couple of decades, and because older technologies already have a solid hold on the various markets that might otherwise be interested in protein-based manufacturing. Finally, most researchers working with proteins aren't thinking about creating a new manufacturing base. But people in the nanotech community are thinking about it.

One of the classical scientific problems involving proteins is the "protein folding problem". Every protein is a sequence of amino acids. There are 20 different amino acids, which are strung together by a ribosome to create the protein. As the amino acids are strung together, the protein starts folding up into a compact structure. The "problem" with folding is that for any possible sequence of amino acids, it's not always possible to predict how it will fold up, or even whether it will always fold up the same way each time.

But maybe you don't need a solution for all possible sequences. Maybe you can limit yourself to just the sequences that are easy to predict. People have been studying proteins for a long time and it's easy to put together a much shorter list of proteins whose foldings are known. Discard any proteins that sometimes fold differently, to arrive at a subset of proteins whose foldings are well known and reliable.

The next issue is extensibility. Having identified a set of proteins whose foldings are easily predictable, would it be possible to use that knowledge to predict the foldings of larger novel amino acid sequences? A trivial analogy would be that if I know how to pronounce "ham" and I know how to pronounce "burger", then I should should know how to pronounce "hamburger". A better analogy would be Lego bricks or an Erector set, where a small alphabet of basic units can be used to construct a vast diversity of larger structures.

If we can build a large diversity of big proteins and predict their foldings correctly, we're on to something. Then we can design things with parts that move in predictable ways. Some proteins (like the keratin in your fingernails or a horse's hooves) have a good deal of rigidity, and we can think about designing with gears, cams, transmissions, and other such stuff.

More developments in cancer treatment

2008-05-06T19:43:00.000-07:00

Here are some more new cancer therapies under development. Many of these involve some flavor of nanoparticle (a fancy word for a molecule), and a few involve nanomachines (a molecule that does something more interesting than just sitting there).

http://www.technologyreview.com/Nanotech/18999/ -- The new nanoengineered system, designed by physician and researcher James Baker and his colleagues at the University of Michigan, contains gold nanoparticles with branching polymers called dendrimers that sprout off the nanoparticle's surface. The particles could be used to launch a multiprong attack against tumors. The dendrimer arms can carry a number of different molecules, including molecules that target cancer cells, fluorescent imaging agents, and drugs that slow down or kill the cells. Once enough of the nanoparticles have gathered inside cancer cells, researchers could kill the tumors by using lasers or infrared light to heat up the gold nestled inside the dendrimers.
http://www.technologyreview.com/NanoTech/wtr_16690,319,p1.html -- A single treatment of drug-bearing nanoparticles effectively destroys prostate cancer tumors in mice ...the researchers mix together a prostate cancer drug (docetaxel) and polymers that are already FDA-approved... The polymer formed spheres with the drugs trapped within. The researchers then chemically attach pieces of RNA, called aptamers, to the surface of the spheres. The RNA folds into shapes that fit into complementary structures on the surface of prostate-cancer cells... [In placebo groups] almost all the mice died during the experiment. In contrast, all of the mice injected with the targeted nanoparticles survived, and in most cases (five out of seven) the tumors disappeared.
http://www.rsc.org/publishing/journals/CC/article.asp?doi=b800528a -- We present experimental data that demonstrate the potential of synthetic crown ether modified peptide nanostructures to act as selective and efficient chemotherapeutic agents that operate by attacking and destroying cell membranes.
http://www.eurekalert.org/pub_releases/2008-03/uoc--urd033108.php -- Researchers from the Nano Machine Center at the California NanoSystems Institute at UCLA have developed a novel type of nanomachine that can capture and store anticancer drugs inside tiny pores and release them into cancer cells in response to light... the device is the first light-powered nanomachine that operates inside a living cell... [reported on] March 31 in the online edition of the nanoscience journal Small.
http://mednews.wustl.edu/news/page/normal/11449.html -- The nanoparticles are extremely tiny beads of an inert, oily compound that can be coated with a wide variety of active substances. In an article published online in The FASEB Journal, the researchers describe a significant reduction of tumor growth in rabbits that were treated with nanoparticles coated with a fungal toxin called fumagillin. Human clinical trials have shown that fumagillin can be an effective cancer treatment in combination with other anticancer drugs... the nanoparticles' surfaces held molecules designed to stick to proteins found primarily on the cells of growing blood vessels. So the nanoparticles latched on to sites of blood vessel proliferation and released their fumagillin load into blood vessel cells. Fumagillin blocks multiplication of blood vessel cells, so it inhibited tumors from expanding their blood supply and slowed their growth.
http://nano.cancer.gov/news_center/2008/feb/nanotech_news_2008-02-15c.asp -- ...Regulators and drug developers are concerned that these delivery systems may prove difficult to manufacture on a consistent basis... A new study from James Baker, Jr., M.D., PI, Cancer Nanotechnology Platform Partnership at the University of Michigan, and colleagues provides data showing that such concerns can be overcome... the investigators present the results of studies designed to show that they could achieve consistent and specific targeting and cell-killing activity across multiple manufacturing batches of a dendrimer-based therapeutic agent.
http://www.physorg.com/news82653370.html -- A team of investigators has designed a nanoscale, polymeric drug delivery vehicle that when loaded with a widely used anticancer agent cures colon cancer in mice with a single dose... To create their drug delivery vehicle, the investigators used a highly branched polymer, known as a dendrimer, that naturally forms nanoparticles with myriad sites for drug loading. In this particular case, the researchers created what they call a bow-tie polyester dendrimer, whose molecular structure somewhat resembles a bow-tie with two discrete halves... On one half of the dendrimer, the researchers attached a second polymer, poly(ethylene glycol) (PEG), in order to make the dendrimer water soluble... Next, the investigators attached the anticancer drug doxorubicin to the other half of the dendrimer using a chemical linkage designed to break when exposed to acidic conditions. Not coincidentally, the inside of tumor cells is acidic, while the bloodstream has a neutral pH. Results presented in this paper show that the resulting drug-dendrimer formulation releases virtually all of its drug within 48 hours in acidic conditions but less than 10 percent of its payload at neutral pH.
http://www.azonano.com/news.asp?newsID=4087 -- A new type of cancer detector... the simple and inexpensive system, which can be built from off-the-shelf components, can rapidly detect the presence of cancer biomarkers – telltale proteins in body fluids that can signal the presence of malignant tumors – at very low levels... “With this technology, a future scenario might be that you go to the doctor every year for an annual checkup; he draws about 10 cc’s of your blood and runs it through our machine,” said Soman. “The machine is equipped to detect the biomarkers for all the common types of cancer. Half an hour later it produces a list of the biomarkers that it has found. And then either a software program or the physician examines this list to determine whether you have any cancers that need treating.”
http://nanotechwire.com/news.asp?nid=4703 -- There is a growing recognition among cancer researchers that the most accurate methods for detecting early-stage cancer will require the development of sensitive assays that can identify simultaneously multiple biomarkers associated with malignant cells. Now, using sets of nanoparticles designed to aggregate in response to finding more cancer biomarkers, a team of researchers funded by the Alliance for Nanotechnology in Cancer has developed a multiplexed analytical system that could detect cancer using standard magnetic resonance imaging (MRI).
http://www.forbes.com/claytonchristensen/2008/02/22/cancer-nanotechnology-therapies-lead-clayton-in_jw_0222claytonchristensen_inl.html -- A survey of several different developments, but not much deep discussion of any of them. More of a businessman's-eye view of things, not too surprising for Forbes.

TAT variant with magnetic particles

2008-04-27T06:22:00.000-07:00

My last posting about targeted alpha therapy discussed the expense of preparing a sample of radioactive actinium, aside from which, targeted alpha therapy should be a very effective and specific and hopefully affordable cancer therapy. Quentin Pankhurst of the London Centre for Nanotechnology has been working with particles of iron oxide, which has very low toxicity and can be attached to antibodies just like the actinium atoms in cages. Iron oxide can be magnetized so each particle can be a permanent magnet. A magnetized particle can then be detected from outside the body using a weak EM field generated by a hand-held device, or it can be heated with a strong EM field, to the point of destroying the cancer cell .

By combining the iron oxide particle with an antibody for the HER2 protein found in breast cancer cells, Pankhurst should be able to achieve the same specificity and effectiveness that Sloan-Kettering has gotten with radioactive actinium, at vastly lesser cost. In order to commercialize this and related applications, Pankhurst has founded Endomagnetics, a start-up based in Houston, Texas.

Why should iron oxide be so much less expensive than radioactive actinium? "Iron oxide" is the chemical name for rusty metal, which is easy to make and store, and readily available in auto scrap yards everywhere. Actinium-225, the isotope used for TAT, has a half-life of ten days, so you can't make a big batch and store some for later use. According to this website at the Oak Ridge National Laboratory: "The actinium-225 is formed from radioactive decay of radium-225, the decay product of thorium-229, which is obtained from decay of uranium-233. The National depository of uranium-233 is at ORNL, and we have developed effective methods for obtaining thorium-229 (half-life 7340 years) as our feed material to routinely obtain actinium-225."

Targeted alpha therapy

2008-04-21T12:10:00.000-07:00

This is something I read about in 2001, and it still seems to be one of the most promising ideas in cancer therapy. The treatment involves two molecular objects bound together. One is an antibody that gets taken into a cancer cell. The other is a radioactive actinium-255 atom which has a ten-day half-life, and then decays through a few different products, releasing four alpha particles, which rip through the cancer cell and kill it. Luckily alpha particles have only enough energy to destroy one cell, and then they run out of steam and become inert helium nuclei.

At Sloan-Kettering where this work was done, they applied for a patent. A clinical trial was conducted in 2002 with favorable results. There have also been some clinical trials in Australia, I believe.

As far as I am aware, this is a fantastic treatment, due to its being extremely specific, and is applicable to a wide range of cancers, but it's not used much. I would imagine the actinium-255 must be prepared through some process that would probably be very expensive. It would be great if some more affordable alternative could be found. It seems to me that were advanced nanotech available today, some suitable replacement for the radioactive actinium nucleus might be possible.

Nifty stuff over at Machine Phase blog

2008-04-21T09:29:00.001-07:00

A couple of interesting things from Tom Moore's Machine Phase blog. One is a comparison between a carbon buckyball and a geometrically similar structure made from DNA using (what appears to be) Paul Rothemund's DNA origami technique. Note the teeny dot in the middle, that's the carbon buckytube.

The other is very interesting because it combines nanotech with my interest in 3d printers in an unexpected way. Specifically it's about using a 3d printer to print parts for an atomic-force microscope, using selective laser sintering. These microscopes typically cost hundreds of thousands of dollars. Hopefully this approach will make them much more affordable for universities, and perhaps high schools and even individual hobbyists.

The white plastic pieces were the things printed with the 3d printer. I always thought of SLS as something done with metal, but I guess it works with plastic too.

Nanotube radio antenna work at U.C. Berkeley

2008-03-13T07:36:00.000-07:00

Alex Zettl at the University of California at Berkeley has invented an interesting radio antenna made from a single conductive carbon nanotube (less than a micron long and ten nanometers wide) positioned between two conductive plates. He has used the antenna to receive songs transmitted by radio, and has posted the results for your listening pleasure. There is a gap between one plate and a free end of the nanotube, across which electrons tunnel. When a voltage is placed across the two plates, the nanotube's free end becomes electrically charged oppositely from the nearby plate, and the electrostatic attraction keeps the nanotube under mechanical tension.

The nanotube's electrically charged free end moves in response to an ambient radio frequency electric field. This changes the gap size, and therefore the measured tunneling current across the gap, just as with a scanning tunneling microscope. The resonant frequency of the antenna is simply the mechanical resonant frequency of the nanotube under tension. The tension can be changed by changing the voltage across the two conducting plates, and in this way the radio can be tuned. The bandwidth of the antenna is determined by the nanotube's stiffness, and (I think) would depend primarily on the length of the nanotube. The space between the two plates should be a vacuum so the nanotube can move freely, and so that Brownian motion does not detune the radio.

The value of a radio antenna this size is that one can communicate with and control nanorobots, for instance in the human body. One could use these nanorobots for diagnostics, reading out blood chemistry or information about various kinds of cell damage, and could send them instructions to intervene.

There are lots of interesting things happening in the area of nanofabrication, such as Andrew Turberfield's tetrahedra discussed in the previous posting. Presently such things are "controlled" by adding solutions of different DNA sequences to the liquid the structure is sitting in, and the new sequence interacts mechanically with the structure to alter it, by binding selectively with some part of the structure already in place. But each step takes tens of minutes as molecules diffuse through water and position themselves to bind correctly. A signal received by a radio antenna might make things happen much quicker.

Too-brief overview of DNA nanotechnology

2008-02-22T09:28:00.000-08:00

A lot of interesting work has been done with DNA nanotechnology, much of it starting with Nadrian Seeman's work on DNA polyhedra in the mid-90s (1, 2).

Around 2000, Andrew Turberfield (Oxford University's Department of Physics) used DNA to make tweezers, with arms 7 nanometers long.

"Of course it's all very speculative," said Dr Turberfield, "but you can imagine, for instance, little factories on chips doing chemistry or simple assembly. You can think of production lines made up of little motors with different reactants being passed from one place to the next."

Things got really interesting in March 2006 with Paul Rothemund's DNA origami technique. Here is the publication. I was working at Nanorex at that time, and we were all quite excited about it.

In 2005 Turberfield and colleagues described a family of DNA tetrahedra consisting of triangles of DNA helices covalently joined at the vertices to form a mechanically rigid 3D structure. This image of a reduced model of one structure, which is less than 10 nanometers on a side, was created using NanoEngineer-1 Alpha 9. The bowing of the DNA helices is pronounced in this rendering and is the result of electrostatic potential terms included in the customized molecular-mechanics-like force field developed by Dr. K. Eric Drexler specifically for DNA structures. Regarding Turberfield's work, New Scientist wrote:

Now Andrew Turberfield [et al] have shown how carefully crafted DNA structures can be made to self assemble and change shape when sent specific DNA signals. The researchers built tetrahedrons ... using four short DNA "struts" that join at each end. The process exploits the way DNA is held together by complementary bases that form the rungs of a ladder-like structure ... the researchers made cages with two extendible struts that could be independently controlled using different DNA sequences. In theory, it should be possible to create cages in which every strut can be controlled independently, Tuberfield says.

These cages are a combination of support material and linear motor, and with the many other DNA tricks being done, they should allow people to build large, complicated, reasonably rigid 3D structures that have controllable moving parts. So this is a very promising development.

A very recent announcement of work by Chad Mirkin and colleagues. They have found a way to use DNA to glue together arbitrary arrangements of teeny gold spheres. People have known for some time now how to make DNA stick to gold spheres, and by careful selection of DNA sequences, Mirkin et al can position groups of spheres in almost any 3D configuration they want.

In light of these developments, Nanorex has narrowed its focus from "general" nanotechnology (anything one might build from common small molecules) to structural DNA nanotechnology. This is likely to be where much progress will occur in the next five years or so. I hope Nanorex will still be around after that, and will be in a good position to shift gears as we move beyond DNA to more general chemistry.

Videos and links, RepRap and Fab@Home

2008-01-27T22:51:00.000-08:00

Since I've been writing a lot about fabbers lately, I've decided to start a fabber blog and start migrating my fabber postings over to it, starting with this one. Fabbers are only peripherally related to advanced nanotechnology (the economics look similar) and I'd like the fabber blog to go into a level of detail that's not appropriate here.

As far as economic similarities, a fabber looks a lot like a crude nanofactory, and raises many of the same societal concerns but in a smaller, safer way. One of the popular speculations about mature nanotechnology goes like this: (1) sufficiently advanced nanofactories will be able to make almost any desired product from materials found in nature, so (2) the price of physical goods drops to nearly zero, and then (3) money ceases to exist and we all live in a post-scarcity society free of poverty, disease, and war.

It's an appealing simple notion, probably too simple. Even when the necessities of life are available essentially for free, humans always envy other humans and there will still be a premium to pay for things beyond the survival level. Economic demand will exist as long as we're still human, and money will too. Besides, physical goods aren't the only things we spend money on. I can imagine a robot bus driver at some future time, but a robot doctor seems a long way off, and it's hard to imagine the board of directors that will appoint the first robot CEO.

Brilliant RepRap video (thanks to Emeka Okafor)

2008-01-05T16:45:00.001-08:00

I've moved this posting over to my new Fabber blog.

3D printer in a knick-knack store

2007-12-21T05:55:00.001-08:00

I've moved this posting over to my new Fabber blog.

Other great nanotech (and related) blogs

2007-12-20T07:12:00.000-08:00

I guess if I say "other great" nanotech blogs, the implication is that my blog is itself great, but many of these listed are much better than mine. The people doing them put in more work and more thought. Not all of these are relevant to long-term nanotech, but anyway here's the list.

Tom Moore's Machine Phase blog -- Tom is now working for Nanorex, and doing a lot of pretty, brilliant nanomachine design work.
Damian Allis's Somewhereville blog -- Damian is Nanorex's consulting quantum chemist, and a fascinating guy in general. He doesn't play a scientist on TV, he's an actual real scientist.
Gina "Nanogirl" Miller's blog needs no introduction for those who've been around nanotech discussions for a while
Blog of the Center for Responsible Nanotechnology
Howard Lovy's NanoBot blog
Foresight Institute's Nanodot blog
Rocky Rawstern's blog
A list of nanotech blogs
An explanatory website (not a blog per se) by one of the authors of "Nanotechnology for Dummies"
A blog about nanocrystals, though I'm not sure what differentiates a nanocrystal from any other crystal
The Singularity Institute is primarily about artificial intelligence rather than nanotechnology but there is a lot of common ground.
The IEEE has an automation blog about present-day industrial robots.
Another present-day robot blog, this one with more of a hobbyist spin.
Emeka Okafor's Timbuktu Chronicles blog is not about nanotechnology or robotics, it's about technologies that help and empower people in developing regions of the world. When not blogging, Okafor sometimes plays basketball, unless it's another guy with the same name.

The Roadmap Report is published!

2007-12-11T18:44:00.001-08:00

The report is now available in PDF format. If you are a Digg subscriber, PLEASE vote up the digg story about it so it reaches the front page. Publicizing the report is a step toward a rational and benign development policy for advanced nanotechnology. I have the privilege of knowing a few of the people who've been involved with the Roadmap project, and they are the kind of people you hope will be involved: very bright, and very ethical.

I haven't gotten far in reading the report yet myself. It's rather thick, in two sections of about 200 pages each. Don't be put off by that, as the language is quite accessible, even in the more technical second half.

The Roadmap conference is coming up

2007-09-11T04:18:00.000-07:00

A couple years ago, Foresight, Battelle, the Society of Manufacturing Engineers and a few other organizations put together a project called the Technology Roadmap for Productive Nanosystems. The idea was to figure out the steps that would lead us to a world of safe and mature nanotechnology. I know some of the people involved in this effort. They've had meetings to which I've not been invited, which is appropriate because they have important work to do, and they don't want the distraction of answering questions from the idly curious.

Their work has percolated along for about two years (that I've been aware of, probably more time before that) and finally there will be a conference where they will tell the world what they've been up to. As luck would have it, I have a schedule conflict and will be unable to attend, but there will be a CDROM of the presentations and I hope to ask around and see if I can get a copy.

I have high hopes for the work these people have done. This is a well-organized effort by a lot of very smart people with a wide range of relevant expertise.

The Center for Responsible Nanotechnology website discusses the societal risk of multiple competing nanotechnology development efforts:

The existence of multiple programs to develop molecular manufacturing greatly increases some of the risks listed above. Each program provides a separate opportunity for the technology to be stolen or otherwise released from restriction. Each nation with an independent program is potentially a separate player in a nanotech arms race. The reduced opportunity for control may make restrictions harder to enforce, but this may lead to greater efforts to impose harsher restrictions. Reduced control also makes it less likely that a non-disruptive economic solution can develop.

A unified effort like the Technology Roadmap initiative represents a safeguard against these very realistic concerns.

Aubrey de Grey's tech talk at Google

2007-06-28T09:21:00.000-07:00

This is one of those brilliant things like Cory Doctorow's writing that gives you REAL HOPE that the future will be a good and happy place, and that you might have a chance of making it to that point. Aubrey de Grey has been studying gerontology (the science of ageing) at Cambridge University and he proposes that with some science and engineering smarts, we can make huge progress toward extended lifetimes in the time left to even old farts like me (not quite 50 yet).

As I think about the benefits that I personally would like to get from nanotechnology, I think life extension is a big thing. Of course we'll have ever more powerful computers and capable robots and flying cars and all those nifty toys, and they'll all be very inexpensive, but I really want a lot more time to enjoy everything. And as my parents get older, I'd love to be able to offer that to them as well, though even by de Grey's very optimistic estimates, they're too old to benefit much.

More fabrication techniques

2006-12-29T11:57:00.000-08:00

In the late 1990s, Tom Knight at MIT worked on something he called microbial engineering, the intentional redesign of simple (prokaryotic) bacteria, which has resulted in MIT's Biological Parts Project. The idea is to identify re-usable components that can be included in rationally designed microorganisms to perform various functions.

This idea is not without precedent: in 1978, Genentech re-engineered E. coli bacteria to produce inexpensive human insulin, vital to the survival of diabetes patients. Previously insulin had been extracted from ground-up organs of farm animals at considerably greater expense. The 1978 work did not have access to a catalog of biological parts or many of the techniques and other knowledge infrastructure that will grow up around the MIT work.

In an earlier posting I described some very interesting work being done by Christian Schafmeister, who is assembling monomer chains to create structures with specific, controllable, and reasonably rigid shapes. He is developing a collection of 15 or 20 monomers, and perhaps that number will grow over time, which can be strung together using synthetic chemistry techniques. Schafmeister has an article in this month's Scientific American.

DNA origami exploits the very selective self-stickiness of DNA. It is likely that DNA (which can be created in any desired sequence) will become a very flexible framework on which to position molecules. Proteins can also be engineered, provided we can predict how they will fold, and this should be a solvable problem if we restrict ourselves to a subset of well-understood proteins. Many proteins like to cling to DNA at very specific locations. A combined approach using a DNA scaffolding, with attached proteins to provide local functionality, could yield very interesting results.

Molecular dynamics simulation of small bearing design

2006-12-07T05:04:00.000-08:00

This video was created using the simulation facilities of NanoEngineer-1 (see http://www.nanoengineer-1.com), together with open-source animation tools like Pov-RAY, ImageMagick, and mpeg2encode. This is a simulation of the molecular bearing design on page 298 of "Nanosystems" by Eric Drexler. When viewed at 0.15 picoseconds per second of animation, thermal motion of atoms (particularly hydrogens) is visible. At 0.6 picoseconds per second, thermally excited mechanical resonances of the entire structure are seen. At 6 picoseconds per second, the rotation of the shaft (one rotation every 200 psecs) becomes apparent.

Update: On more careful analysis we discovered that the temperature is incorrectly represented in this video. The atoms should shake more violently to represent an ambient temperature of 300 Kelvin (ordinary room temperature). The vibrations you see in the video correspond to about 70 Kelving (very chilly). In spite of the more violent thermal vibrations, the structure remains chemically stable and mechanically workable at room temperature.

Nature article on molecular motors

2006-10-27T06:51:00.000-07:00

A Nature article on molecular motors found in biology. I'm not sure of the date, I found this on the Advanced Nanotechnology Blog maintained by Brian Wang.

Automated design

2006-08-03T09:34:00.000-07:00

Design is a search problem. A product or machine has some kind of specification or instructions, and you want to find the best possible specification to suit some purpose. The space of all possible specifications is usually too large to be searched exhaustively. The usual response to this is to exercise human cleverness - what the inventor in the garage does. An alternative is to search the design space using computer algorithms.Why would you do that? Isn't it fun to invent stuff? It is, but the stuff we invent these days is getting so complicated that sometimes human cleverness might not suffice to solve a design challenge. Nanotech stuff will be orders of magnitude more complicated than anything we can make today. So it's good to take a look at this approach.

Automated design is the application of global optimization to design problems using techniques like simulated annealing, genetic algorithms, and ant colony optimization to generate candidate problem solutions, and computer simulations to evaluate the fitness of the candidates. Genetic algorithms are the most widely known of these techniques. Here is a discussion of GAs by John Holland, one of the early pioneers in the field.

There has been a lot of research and development applying GAs to
engines and other machinery.Here are two applications of GAs to optimize the design of diesel engines. Somebody else optimized a valvetrain., and somebody else, an exhaust manifold. There is also work on a flywheel made of composite materials, and some work on reducing engine emissions by optimizing the chemical reaction rate of the fuel. In a more nanotech-ish vein, there is some work on the molecular design of novel fibers and polymers.

One of the more interesting efforts in this field is John Koza's invention machine, which applies GAs to a very wide variety of design problems, and which has produced a number of new patents for designs that did not originate in human imaginations.

NASA used genetic algorithms to design microwave antennas for the ST5 mission to measure the Earth's magnetosphere. There is some discussion of this work on Wikipedia.

While genetic algorithms are the most widely known of this class of algorithms, simulated annealing has a decades-long history of success in the placing and routing of FPGAs and custom integrated circuits. Other applications for global optimization include scheduling and resource allocation.

Random links

Spimes

2006-07-24T19:33:00.001-07:00

Bruce Sterling gave an interesting talk at a SIGGRAPH conference in 2004. He described two kinds of human artifacts, blobjects and spimes. Blobjects are simply artifacts that have been designed with modern CAD systems, so their shapes are more curvy and sexy than the same-functioned artifacts of past generations. Examples are the iMac and the new VW beetle.

The spime is a different beast. It is jam-packed full of information technology. It has RFID or Bluetooth to talk to nearby computers (or maybe other spimes). It has GPS so it knows where on Earth it is. It knows how to connect to the Internet. It willingly participates in data mining efforts by Google and other search engines and advertisers. In addition to being designed with a CAD system, it might be manufactured with rapid prototyping techniques such as 3D printers.

Sterling's predictions about the spimes' use of information are cynical. They are programmed by the corporations that built them. They collect consumer demographics information about the people who buy and use them. Their first allegiance is to their manufacturer. They are smart enough that the distinction has teeth - the hand drill I bought at Sears does not change its behavior to act in Sears' best interests rather than mine.

If spimes aren't nanotechnology, why am I writing about them in a nanotech blog? Because they shake loose my thinking about what products could be. I hadn't thought about ANY of this stuff before I read the transcript of Sterling's talk. My cell phone today has way more computing power than the Apollo guidance computer had. When a ballpoint pen has way more computing power than my cell phone has today, of course somebody will program it to do things like this.

Creepy crawlies 2

2006-04-27T17:15:00.000-07:00

The gray goo scenario is not an immediate threat. Evolution of nanomachines can be prevented, and gray goo replicators can simply not be designed, as long as everybody agrees to those rules. If that were that, we could prevent the gray goo scenario forever. But not everybody will agree. Some, having loudly agreed in public, will quietly break the rules in private. But real live gray goo won't become possible very soon.

There are lots of "interesting" lesser threats.

At the time of the Pontiac rebellion in 1763, Sir Jeffrey Amherst, the Commander-in-Chief of the British forces in North America, wrote to Colonel Henry Bouquet: 'Could it not be contrived to send smallpox among these disaffected tribes of Indians? We must use every stratagem in our power to reduce them.' The colonel replied: 'I will try to inoculate the [Native American tribe] with some blankets that may fall in their hands, and take care not to get the disease myself.' Smallpox decimated the Native Americans, who had never been exposed to the disease before and had no immunity.
Silent Weapon: Smallpox and Biological Warfare by Colette Flight writing for bbc.co.uk/history

What we can expect in the near term is biological warfare, evolving along lines similar to biological warfare today, and with similar motives. If we are interested in a future world that is benign, we can try to remove the incentives for biological warfare, so that there is as little of it as possible. This is an area where I myself can offer no particular insight. There have been many many different manifestations of human evil in recent decades and centuries. I would like to think I could entrust politicians and diplomats to go about its prevention, but they are usually the ones who start the next one. This is a thorny problem involving culture clashes, economics, religion, and many other topics beyond the scope of this blog.

Another possibility is to educate ourselves about the possible range of weapons, in the hopes of designing effective defenses. This is a much more technically tractable problem, and it's one of the reasons I work for Nanorex. Our software can help people to explore the space of possible threats and defenses more quickly, and to create an active research literature.

Is an active literature a good idea? Would it not be an enabler for those who wish to do harm? Should it not be suppressed or at least discouraged?

This is like the relinquishment question. If the bad guys have an active research literature and the good guys don't, then the first bad guy attack could reduce the good guys to a state where they could never again hope to meaningfully protect themselves.

Ideally, thoroughly effective defenses would be deployed everywhere, long before the first offensive weapons appear. I hope it goes that way. If we're not so lucky, there may turn out to be such a diversity of possible offensive weapons that "effective defenses" aren't practical.

Lessons from software development

2006-04-26T08:24:00.000-07:00

I've been a software engineer for ten years now. Software engineers build and maintain very complex systems, so complex that no single engineer can grasp the whole thing in all its details all at once. Coming from electrical engineering, I found that a humbling new experience.

Software engineering looks a particular way, because bits are much much cheaper than transistors. Software products are generally much more complex than hardware products. So software engineering has a richer set of tools for managing complexity than hardware engineering has.

Testing is hugely important. Engineers test products, and the more testing they do earlier, the fewer bugs they need to fix later. If you've got a system that's incomprehensibly complex, you can still understand how to test it.

Modularity is an example of information hiding. Designs are made up of individually comprehensible pieces or modules. Each piece has complexity inside and simplicity outside. The simple outside part, the interface, determines how that piece works with its neighbors.

nanoENGINEER-1, alpha 7 release

2006-04-25T10:38:00.000-07:00

The Nanorex team is proud to announce the release of nanoENGINEER-1 Alpha 7, the seventh major release of nanoENGINEER-1. This is the first major release since Alpha 6 was announced on August 17, 2005. Alpha 7 has many improvements and new features.

Undo/Redo

Alpha 7 now includes a new Undo/Redo system making it easy to undo accidental changes to models.

Simulator/Minimizer Improvements

The nanoENGINEER-1 simulator and minimizer have undergone major revisions since Alpha 6. A7 introduces our new and improved molecular force field. We have expanded the list of parameters from our initial testing set to include more atoms and bond types from among the main group elements. It is our intent to have all possible bond types for the first three rows of the main group of the periodic table (B-F, Al-Cl, Ga-Br, and H with all chemically possible combinations of single, double, and triple bonding) accounted for with the completion of the simulator work, except for bond torsion terms, which are planned for Alpha 8. Once this initial set is complete, we will welcome requests for other bond types.

To ensure the accuracy of the minimizer and, consequently, our new molecular force field model, we are developing tests which compare the minimizer output to quantum mechanical results performed at the same high level of theory (B3LYP/6-31+G(d,p)) as the force field itself. These tests have been run on a variety of small structures to cover as many of the force field parameters as possible.

Improved Modeling Interface

Making nanoENGINEER-1 easy to learn and use is one of our highest priorities. With Alpha 7, building models has never been easier and more intuitive. Chemists using commercial molecular modeling programs such as Chem3D, Spartan or Accelrys will find nanoENGINEER-1 a breeze and enjoy its ability to manipulate large chemical species just as easily as small molecules. Mechanical engineers experienced with traditional CAD programs like SolidWorks or Pro/ENGINEER will feel right at home creating and viewing models even though their knowledge of chemistry may be limited.

Wiki-based Help

A new Wiki web site for nanoENGINEER-1 hosts a set of on-line Help pages that can be accessed by pressing the F1 Key while the cursor is hovering over objects in the nanoENGINEER-1 user interface. Users are able (and encouraged) to create a Wiki user account and add or edit the Help pages themselves. We anticipate that over time the Wiki will become an invaluable resource for users of nanoENGINEER-1.

Improved Graphics

Graphics quality and POV-Ray support has been improved significantly. We’ve included animation when switching between views, specular highlighting and improvements to the general graphics and lighting control system that give nanoENGINEER-1 a professional luster it lacked in previous versions.

Nano-Hive Support

nanoENGINEER-1 can serve as a general purpose molecular modeling front-end to Nano-Hive, a nanospace simulator written by Brian Helfrich. Working together, nanoENGINEER-1 allows users to interactively define, calculate and visualize 2D electrostatic potential (ESP) images of molecular models. To see an example of this new capability, check out the ESP Image jig in the nanoENGINEER-1 Gallery.

Mac OS X

Alpha 7 does not yet work on Intel-based Mac systems. We are working on this and hope to support Intel-based Mac systems in the coming weeks. We also just discovered a problem plotting nanoENGINEER-1 simulation trace files using GNUplot on Mac OS X. We will be fixing this problem in the next day or two and posting a new MacOS install package in the Download Area.

Creepy crawlies

2006-04-15T07:23:00.000-07:00

When Eric Drexler published Engines of Creation, he included a section on run-away nanotech replicators. The notion is that if there are replicators running around that can use almost anything as feedstock, they buzz through the biosphere converting everything to copies of themselves, leaving behind an ocean of replicators. This is called the "gray goo scenario".

This idea has been popularized by Bill Joy and Michael Crichton and, along with the toxicity of present-day nanoparticles, is considered by many to be one of the grave risks we face in pursuing nanotechnology. Bill Joy's article in Wired recommends that we (the U.S.? the developed nations? Bill and the mouse in his pocket?) simply refrain from developing the technology.

There's a problem: we might refrain, but others won't. The research is difficult but not impossible. Those who pursue the research would be the people who didn't agree to refrain from development, and this dangerous new technology would end up in the hands of those we'd be most fearful of having it.

Drexler and the Foresight Institute, seeking to educate the public and help reason win out over panic, have struggled with these worries for years now. He has argued that building a free-ranging eat-anything replicator is a very difficult engineering problem, comparable to building a car that can forage in the woods for fuel when it runs out of gasoline. Nobody designs a foraging car by accident. A gray-goo replicator may not be possible at all, and if it is possible, it will be the design work of many years.

A dangerous replicator might evolve from nanomachines that started out safe. Many troublesome viruses probably started out as mutations of innocent snippets of DNA. Human-designed nanomachines should not be permitted to evolve. There has been keen interest in nanofactories in recent years, where the instructions are clearly separate from the assembly machinery (what Ralph Merkle calls a broadcast architecture, and computer folks call a SIMD architecture). The instructions are only put to use when the human user decides to push the button to make stuff happen. Autonomous self-replication can not occur, and therefore evolution cannot occur.

Another way to prevent evolution is to ensure that every mutation is fatal. Suppose the replicator's only copy of its blueprint is encrypted, and replication requires decrypting the blueprint each time. If you change one bit or one character in an encrypted document and try to decrypt it, the whole thing becomes meaningless garbage. Any change to the encrypted blueprint will turn the decryption into garbage, and the machine won't be able to build anything.

Finally, there are different ways to pull the plug. One is to stop supplying the energy required for replication. Another is to require tha replication depend upon some exotic "vitamin" available only in a controlled environment.

Scanning probe microscopy

2006-04-10T09:04:00.000-07:00

SPM is a collection of microscopy techniques (of which the first was the scanning tunneling microscope or STM) that permit the imaging of individual atoms. The resolution of the microscopes is not limited by diffraction, but only by the size of the probe-sample interaction volume, which can be as small as a few picometres. The interaction can be used to modify the sample to create small structures.

The STM is an ingenious gadget, invented in 1981 at IBM Zurich. An atomically sharp probe is positioned above a sample; the gap is typically on the order of a nanometer. The probe and the sample are both electrically conductive. A voltage is applied between the probe and the sample. Electrons tunnel across the gap.

It turns out that the tunneling current is very strongly dependent upon the gap distance. So you build a servomechanism that moves the probe up and down in the Z direction, to keep the gap distance constant by keeping the tunneling current constant. Next, you scan the probe in the X and Y directions, tracking out a raster pattern like the one on your television screen. By looking at the Z position information from the servomechanism, you end up with a function Z = f(X, Y) and when you plot that function, or use it to color the pixels on a computer screen, you get pretty pictures of atoms.

The STM is so conceptually simple that it's possible to build one as a hobbyist.

A few years after the STM, the AFM or atomic force microscope was invented. With this device, the interaction between the probe (this time on the end of a cantilever) and sample is not an electric current flow. Instead it is a force due to the Van der Waals interaction. The force can be measured using piezoelectric strain gages built into the cantilever, or using a reflected laser beam to measure deflection of the cantilever.

You would have hoped that these microscopes would have been useful in pushing atoms around as well as seeing them. To a limited extent they are, but not so useful that you can start to build molecular machines with them. Darn.

Molecular electronics

2006-04-10T07:05:00.000-07:00

Over the past few years there has been a lot of fascinating work in molecular electronics. Because of the success of digital logic implemented in VLSI over the past several decades, molecular electronics researchers have focused most of their attention on implementing digital circuits using logic gates.

Early work included the identification of a molecular rectifier or diode, a device that allows electrical current to pass one way but not the other. Arranging diodes in a crossbar arrangement is a major step toward the implementation of complex logic circuits. Additional pieces required to make it practical include nanoscale wires, inverters, and amplifiers, and maybe a flip-flop.

Carbon nanotubes can have different chiralities, which give different electrical properties. Some chiralities give conduction so that the nanotube functions as a wire. Other chiralities give semiconductor behavior, introducing the possibility that a nanotube may be useful as a carbon transistor.

There was some very interesting work done by HP and UCLA in January 2002, basically a way to build a rectangular array of north-south and east-west wires, and connect them by fuses that could be selectively blown. That permits a lot of flexibility in wiring up circuits, which you need to do anything interesting. I haven't heard much more about the HP-UCLA work since 2002, though, and I wonder if they've hit some kind of stumbling block. Their work was based on rotaxanes and catenanes.

There is more to say on this topic, and it will merit another posting one of these days.

More molecular machines in nature

2006-04-06T11:41:00.000-07:00

Painless blog posting: plug "molecular machine" into Google Scholar, and cut-and-paste whatever comes out! I'm not quite that lazy, I looked at them to see if they were reasonably complete, and weren't of such narrow interest that only three people in the world would want to read them.

Two molecular machines combined

2006-04-06T08:31:00.000-07:00

The first combination of two molecular machines has been claimed by Kazushi Kinbara at the University of Tokyo, Japan. The first piece is a light-driven actuator which twists a double bond one way in UV light, and the other way in visible light, causing a pliers-like pair of pieces to hinge closed and open. The ends of the pliers connect to a couple of flippers. By pulsing the light correctly, one can presumably get the flippers to kick, and make the thing swim around in a liquid.

Click for larger image

According to the article, research labs have produced a profusion of interesting molecular machines, but none by itself does anything complex enough to be really useful or extensible. The innovation here is supposed to be the combination of multiple machines. I'm not sure that flapping flippers is much more useful behavior than any of the individual machines would perform. It would be interesting Kinbara had found some kind of general approach by which different submachines could be built into large assemblies, but there is no evidence for that in the articles I could find. Kinbara evidently sees the value of that as a goal, and guesses that large assemblies are about five years out.

More steps along the way

2006-03-26T16:46:00.000-08:00

If one thinks about this stuff much, one must inevitably ask, what is the pathway to get from here to there? Ordinarily when attacking a big complicated task, one partitions it into many small subtasks. Then you can draw a big diagram with little boxes connected by lines, the boxes representing subtasks and the lines representing dependencies between subtasks, what the project management weenies call a PERT chart. So where is the PERT chart for developing advanced molecular manufacturing?

Rob Freitas took a stab at one a couple years ago, aimed specifically at diamondoid systems. At the most recent Foresight conference, Drexler and Damian Allis presented work on a tooltip similar in appearance to those described by Freitas, and also intended for extracting and depositing individual atoms on a work surface. More or less simultaneously the Foresight Institute announced their plan to develop a technology roadmap to get us to "productive nanosystems", which is basically the nanofactory shown in the animation. From there it's a relatively small step to any other form of nanotechnology. The nanofactory is the preferred concept today because there is no conceivable way that it could get loose or mutate or go out of control, and people worry about such things.

The people doing Foresight's technology roadmap stuff are talking to people with money, so that might turn out to be interesting. There is also the work by Schafmeister and Rothemund. So it's a pretty interesting time.

DNA origami

2006-03-20T13:28:00.000-08:00

There is an MSNBC story about "DNA origami", a technique invented by Paul Rothemund at Caltech to form large complicated shapes by controlling folding patterns in long DNA chains.

Each of the two smiley faces are giant DNA complexes, imaged with an atomic force microscope. Each is about 100 nanometers across (1/1000th the width of a human hair), 2 nanometers thick, and comprised of about 14,000 DNA bases. 7000 of these DNA bases belong to a long single strand. The other 7000 of these bases belong to about 250 shorter strands, each about 30 bases long. These short strands fold the long strand into the smiley face shape. - Paul Rothemund

Rothemund's work is published in Nature, and the full text is available as a PDF at his website. Rothemund works in the DNA and Natural Algorithms Group headed by Erik Winfree.

Other peoples' related blogs

2006-03-06T13:52:00.000-08:00

DNA computing progress

2006-03-06T04:11:00.000-08:00

On February 24th, National Geographic reported on progress in DNA computing. This field began in 1994 with Leonard Adelman's work on solving the Hamiltonian path problem, and then I didn't hear much about it after that.

Ehud Shapiro and his colleagues at the Weizmann Institute in Israel have developed a DNA computer that can perform 3.3x10¹⁴ operations per second. A cubic centimeter of "computer soup" contains about 1.5x10¹⁶ individual computers, with a memory capacity of about 6x10²⁰ bytes (ten billion 60-gigabyte hard drives). The two primary advances are that the system is generally programmable, and that the computation is powered by DNA rather than ATP.

"Autonomous bio-molecular computers may be able to work as 'doctors in a cell,' operating inside living cells and sensing anomalies in the host," said Shapiro. "Consulting their programmed medical knowledge, the computers could respond to anomalies by synthesizing and releasing drugs."

This approach appears applicable only to embarrassingly parallel problems involving no inter-processor communication. It should be able to tackle some problems in global optimization, though probably not very complicated ones like de-novo protein design, one of the possible pathways toward advanced nanotechnology. For the time being, it's not yet clear that this is a very useful technique.

Design tools for nanotechnology

2006-01-30T06:35:00.000-08:00

I've thought a lot about nanotechnology design systems over the past ten years. First I read a beautiful description of a virtual reality system for studying molecular machines up close. It was feasible but not economical; some day that will change. Next I read a little about molecular mechanics, and realized that the principles involved were well within my mathematical and programming abilities.

So I wrote some code (first C, then Lisp, finally Java) that allowed you to put together a little structure with carbon, hydrogen, oxygen, and nitrogen. You could energy-minimize it, and theoretically I could have done equations of motion, but at some point I got busy with other things.

On mailing lists and Usenet, I continued to think more about design systems for nanotech.

In the electronics world there is a language for design and simulation called VHDL, which offers a lot of great facilities for managing the complexity of very large projects. Some day nanotech will have its own version of VHDL. Developing it will require learning which details can be safely ignored to give a really terse description of a useful structure.

When simulating, you don't want to model every single atom in a huge structure. Frequently you want to say that these million atoms just act like a big block, with a little rubberiness or sponginess, but I don't care about their individual vibrations inside the block.

It would be extraordinarily cool if I could put on VR goggles and force-feedback gloves and physically interact with the structures I design.

If we accept the premise that real nanotech hardware may be potentially dangerous, we should develop design and simulation software first, so that we're familiar with the dangerous things before they actually exist.

With nanoENGINEER-1, all these ideas and more are much closer to being implemented, or becoming much easier to implement. This whole collection of ideas will become much more accessible to many more people, and many will have much better ideas than I've had.

Nanomachines in nature

2005-12-31T08:05:00.000-08:00

Kinesin and dynein are proteins that move along a microtubule and can drag along a mechanical load (another molecule). They are among several molecular motors found in nature. Another example is the flagella that push bacteria around in pond water, driven by a motor that looks like it came from a mechanical parts catalog. Click the image below for an enlarged version.

Ribosomes translate RNA sequences into proteins a chemical/mechanical process.

Some people are using these molecular machines to plan nanotechnology roadmaps, and there has been some laboratory progress. We won't have real nanotechnology any time soon, but these are excellent steps in that direction. Biomechanics hints at a lot of interesting things we can do with available cellular mechanisms.

To people thinking about the long term, as I like to do, these efforts are stepping stones. We'll use them to build tools, and use those tools to build other tools, with the eventual goal of a manufacturing infrastructure that permits us to build large rationally-designed products to atomic precision.

How molecular modeling works

2005-12-17T12:41:00.000-08:00

I learned about molecular modeling while working on my NanoCAD applet. Now we use it in nanoENGINEER-1.

Atoms are comprised of a small dense positively-charged nucleus surrounded by a probabilistic cloud of negatively-charged electrons. The shape and behavior of the electron cloud is governed by quantum mechanics. The nucleus is heavy enough that you can think of it in classical terms. The electrons and the nucleus electrically attract each other.

If you want to get really accurate information about molecular mechanics, you get a cluster of computers and run software that solves the quantum mechanical wave equation. Generally this is a hugely compute-intensive undertaking. If you want to see behavior over a series of moments in time, like an animation, you probably can't afford to do real quantum mechanics, so you've got to cheat.

The way to cheat is to regard the nuclei as point masses connected by non-linear springs. These non-linear springs take into account the electrostatic forces with the electrons and other nearby nuclei. This formulation gives energies in terms of geometric properties such as bond lengths, bond angles, and dihedral angles. Additionally there are grosser electrostatics to think about (charged ions, and bonds have electrical dipole moments if the atoms have different electronegativities) and one more force between unbonded atoms called the van der Waals force. The NIH has a great web page about this stuff.

Each of these things gives a component of potential energy in terms of the geometry of the molecule. Taking the negative gradient of that energy in the 3N space of atom coordinates gives you the forces acting on the atoms. Plug those into equations of motion, and integrate, and you're done.

There are still a few things to think about. One is numerical instabilities: any non-zero time step will give approximate answers, and you end up with violations of conservation of energy. Another thing is that you can't model the making and breaking of chemical bonds this way, you can only model stable structures that aren't reacting.

There are some things that can help with numerical stability. One is to notice that the quick motion of the hydrogens, which will consume a lot of your computrons, isn't very interesting. So you can play tricks like making the hydrogens heavier, or locking the hydrogens' positions relative to the atom they bond to (just add their masses to its mass), allowing a longer time step. Another is to use an integration method like Verlet that does better with energy conservation.

I'll probably write more about this topic in the future. It's deep and interesting, and if the Nanorex experience adds some modest qualifications in molecular modeling to my resume, it will have been time very well spent.

Design-ahead

2005-12-05T21:18:00.000-08:00

Design-ahead is the idea that we can design things that cannot be built yet. The products of future nanotechnology will follow the laws of physics, just as horseshoes and jet engines do. Those laws are knowable today, and they allow us to reason about future gadgets that we can't yet make.

Using hammers and tongs and a forge to make metal hot and soft, a blacksmith can make a horseshoe. He can make an axe or a sword or metal parts for a wagon. But he can't make a jet engine. The reason he can't make a jet engine is because the necessary tolerances are much too precise. Building a jet engine takes a more advanced form of manufacturing technology than blacksmithing.

The blacksmith can read about thermodynamics and materials and fluid mechanics and other sciences, and he can start to reason about whether a jet engine could actually work. Given a jet engine design, he can calculate how strong the metal needs to be, the pressure and temperature of gasses flowing through the engine, how much thrust it could deliver, and other such things. He can determine whether a design is theoretically feasible or theoretically disallowed by physical laws, even if he can't build the engine.

Many indicators suggest that within a few decades, we will be building machines of molecular size. These machines will have moving parts: gears, axles, bearings, rods, pistons, all the machine parts we are familiar with today, in addition to much smaller versions of today's electronics. We will be able to fit hundreds of millions of moving parts inside a small fraction of the volume of a human cell. These can be used to build machines that monitor the cell's health and protect it from viruses and some effects of ageing. We will also be able to make much stronger materials than we can make today, because we'll make large pieces with no material flaws in them.

Why bother with design-ahead? For a few reasons. One is that it will help us get to the point of really doing this stuff. Another is that it will help us plan for things that can go wrong, like nanotech weapons getting into the hands of terrorists and rogue states. Another is to encourage people to learn about nanotech so that the economic disruption is mitigated when it arrives. The kids who study physics and chemistry and computers today can be the designers of tomorrow's nanotechnological gadgets.

Investing in nanotechnology today

2005-11-23T17:48:00.000-08:00

I was initially drawn to nanotechnology in the late 1980s because the ideas were so interesting, but now there's money involved too. Let's see what's going on with that.

Nanovip is a database of businesses involved in nanotechnology, organized by industry. There is information about funding, software, MEMS, tools and instruments, and nanotube suppliers.

There is another nanotech business portal at nanotechnology.com. It's nice that their research section is about scientific and technological research, and separate from their financial section. One of the regular columnists there seems to think we're in the midst of a sea change. They've even got a blog.

There's another blog by Steve Forbes and Josh Wolfe that frequently touches on topics of nanotechnology and investing.

Another interesting site is NanotechnologyInvestment.com. There I learned that there are now venture capitalists who specialize in nanotechnology. Merrill Lynch has a nanotech index.

The ventures described are working with the technology available today. From the perspective of the longer-term outlook described in other postings, these efforts will seem as primitive as a blacksmith's work seems today. Their range of uses will be quite limited compared to what else will then be available.

Steps along the way

2005-11-21T16:35:00.000-08:00

Initially, the direction we want is molecules that do stuff under some kind of external control. Lucent's DNA tweezers from five years ago are a good example. The fact that they're tweezers tells you that they are doing something: they don't merely have material properties, they have actual mechanical behaviors. The external control comes in the form of "fuel strands" and "anti-fuel strands" which, when added to the test tube, make the tweezers close and open respectively.

The tweezers were cool but they obviously didn't usher in a brave new world of full-blown nanotechnology. So it's got to be small, but it's also got to be capable. And because we want to tell it what to do, it needs to be controllable from the human scale.

Chris Schafmeister at the University of Pittsburgh is considerably further along. His lab has figured out a Lego set of little molecules that snap together rigidly into any shape. Schafmeister can control the assembly sequence and therefore control what shape he gets.

Peixuan Guo at Purdue is doing some similarly interesting stuff with RNA. This work has already resulted in more specific delivery systems for chemotherapeutic drugs used to treat cancer.

Another promising direction is to harness ribosomes, the widgets inside our cells that produce proteins. We can specify any DNA sequence we want, so we can instruct ribosomes to build any of a wide variety of novel human-designed proteins. We are already doing some of that; what we need to do more is to understand proteins better. Some of that is science, but a lot of it is just simulation horsepower.

Nanotechnology's long-term prospects

2005-11-12T07:56:00.000-08:00

In the wake of the National Nanotechnology Initiative, a lot of money has appeared for anything with the prefix "nano-" stuck on it. So now we are being told that a pair of pants is a product of advanced nanotechnology. We are told to expect modest improvements in the performance of items like toothpaste and laundry detergent.

That's not really very interesting or ground-shaking. These are instances where we are building teeny things with existing machines. The exciting nanotechnology is when you build things with teeny machines. So far, we don't have teeny machines. Nature does, and some researchers are investigating that route. Nature's machines have evolved to do very specific jobs and making them do other jobs takes a lot of ingenuity, when it's possible at all.

The currently popular definition for nanotechnology is objects with feature sizes of about a nanometer. But with that definition we don't get medical nanobots....

or space elevators....

or nanocomputers....

...or possible solutions to a host of other social ills.

Working at Nanorex

2005-11-12T07:33:00.000-08:00

A couple of months ago, I was laid off from a job that had stopped being fun. Within a few weeks I started working for Nanorex, which is a big improvement. Nanorex is engaged in writing an open-source computer-aided design package for molecules, called nanoENGINEER-1.

The company founder has made several other significant contributions to the development of nanotechnology, including a lot of support for the nanofactory animation. We are in discussions with just about everybody interested in the direction of nanotech CAD software. I myself have thought about nanotech CAD software in past years.

It's important that nanoENGINEER-1 be open-source, even if we have to delay getting revenue for a while. In a world that's rapidly approaching real nanotech, we don't want a big gap between the haves and the have-nots. There are a lot of important policy discussions that need to take place, and it's good if the largest possible number of people are able to follow and participate in those discussions. Tools like nanoENGINEER-1 can help people to study nanotechnology proposals and understand how the technology will work.

The RepRap Project, and globalization

2005-11-12T07:01:00.000-08:00

The RepRap project (blog here) aims to create a sort of general-purpose numerically-controlled machine tool that can be deployed in the developing world. It should have such general capabilities that it can be used to make another RepRap tool. Many great successes have come from humble beginnings, so although it isn't super-impressive now, it may yet achieve great and interesting things. Even if this particular effort doesn't prove very fruitful, the IDEA is out there, and in the long run that's more important.

The idea is that it should be open-sourced, and that it should be possible (with human involvement) to use one to make another, in addition to making many other useful things. The idea is to decentralize and spread and commoditize the benefits of the Industrial Revolution to ease the plight of poverty everywhere. For this reason, the RepRap guys have decided to GPL everything they do. The RepRap tool becomes cheap because one RepRap can be used to make another. This is a very powerful idea.

The RepRap doesn't accept natural materials (rocks, bark, twigs, dirt) as raw materials. The villager who wants to make a widget for his family must be able to buy or barter for raw materials. Stuff doesn't become free, but it does become much cheaper. The same globalization that hurts workers in the developed world helps the developing-world villager.

Building a complete self-replicative manufacturing unit in another country would be a ridiculously expensive undertaking. Training, machine tools, buildings - millions or billions of dollars involved. Its size would necessitate organizing it as several individual businesses that buy and sell intermediate products to one another, and there'd be business failures.

People gripe about how Walmart is destroying American jobs, but Walmart is simply hastening the approach of an inevitable economic equilibrium, Developing countries (primarily China) are getting paid to build more manufacturing infrastructure for themselves. Japan ate our manufacturing lunch in the 1980s, today China is eating Japan's lunch.

The economic long term equilibrium outlook: The whole world is "developed". American wages drop, wages elsewhere rise, eventually all that settles. Speaking as a comfortable middle-aged American, I can't say I look forward gleefully to my own plight in the coming decades, but hopefully development will help the rest of the world.

The post-scarcity economy

2005-11-12T07:00:00.000-08:00

The phrase post-scarcity economy was coined in the 1950s by economist Louis Kelso, but it could have been envisioned any time after the Industrial Revolution. The idea is that automation drives down the price of all goods to effectively zero, money becomes meaningless, and the entire population goes on perpetual vacation.

I want to distinguish between what venture capitalists call "nanotechnology" today and the real thing. The quickest way to do that is to refer you to Ralph Merkle's website, or the Wikipedia article. When referring to real nanotechnology, I'll use the abbreviation "MNT".

Many have conjectured that MNT will bring about a post-scarcity economy. There is also conjecture that sophisticated robots could do the same without nanotechnology (see Marshall Brain's novella Manna). In the robot case, an important axiom is that the robots can build more robots, thereby driving down the price of robots. The same axiom exists in the nanotech case; nanotech fabricators can make more nanotech fabricators.

The big idea here is self-replication. A robot is self-replicating if it can build a copy of itself from the available raw materials. The idea is that the first robot costs a huge amount in development, and every robot after that is free because it's built by another robot. But available raw materials turns out to be a fly in the ointment. If the raw materials are sand and gravel, then robots are indeed cheap. But if the necessary raw materials are subassemblies from Home Depot and Radio Shack, then robots can't get any cheaper than the stuff you need to buy for the next one to be built. The price of raw materials plays a very important limiting role in this picture of abundant free robots doing all our work for us.

For a robot to build more robots from sand and gravel, it must replicate all the arts of ore mining, metal smelting, and machining, to make just the metal parts. There will also be rubber and plastic parts, and probably silicon electronic parts. The "self-replicative robot" probably now occupies several acres, and is really a self-replicating robot factory, producing both robots and more robot factories. In order to accept cheaper less-organized raw materials, the unit of replication needs to be more complex.

MNT simplifies matters somewhat. Products are built out of carbon and other common elements, "machining" is done at a molecular level, and no smelting is needed. Putting all the pieces together into one desktop nanofactory becomes feasible. The raw materials are atoms (dirt, air, water), time, energy, and software.

Sometimes, what we really want from a post-scarcity economy is self-sufficiency. Complete self-sufficiency means that you can trundle off into the woods, build a log cabin, catch your own food, make your own clothers, and perform your own medical services. A nanofactory will make all that much more practical.

In the meanwhile, a limited form of self-sufficiency is the freedom to choose whether or not to trade with other people or businesses. This is feasible as long as the things I'm buying aren't products made by monopolies.

Nanofactories

2005-11-12T06:58:00.000-08:00

Recently I've been thinking a good deal about Foresight's efforts to animate a nanofactory (see the slideshow) and turn it into a DVD, with presumably wide distribution.

Click here for larger image.

This was originally blogged in December 2004. Since that time, a very pretty final version has been finished, which you can find on Foresight's website or at Google Video.

I like this idea a lot. I think it can impress upon people that nanotech is really a pretty simple idea (although some of the engineering details will be quite complicated). Right now, the possibility of really mature nanotechnology ("make anything that doesn't violate the laws of physics") is probably viewed by most people as centuries in the future, if it's on their radar at all. The real point of the DVD is that this stuff isn't incomprehensible, and it needn't wait 50 or 100 years to happen. That's important, because there are huge benefits to be gained, particularly in terms of human health and longevity, and the sooner they come, the better.

The public relations effort to put real nanotechnology on the map is important. It would be particularly valuable for the medical profession to wrap their brains around this. If a doctor starts to advocate for real nanotech, maybe some of his patients are CEOs or senators. Maybe the doctor mentions that nanotech will usher in an age of treatments that, today, we could only call "miracle cures". Maybe the next bill before Congress advocating nanotech research says, hey, let's throw some money at the real thing, rather than mislabelled silly tricks.