Saturday, December 31, 2005

Nanomachines in nature

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.

Saturday, December 17, 2005

How molecular modeling works

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.

Monday, December 05, 2005


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.

Wednesday, November 23, 2005

Investing in nanotechnology today

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 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 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.

Monday, November 21, 2005

Steps along the way

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.

Saturday, November 12, 2005

Nanotechnology's long-term prospects

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

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

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

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.


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.

Monday, March 14, 2005

The Broadcast Flag, and GNU Radio

I listened to a talk (broadband, dialup) that Cory Doctorow gave at a conference on the ten-year-old web, about the evils of the broadcast flag.

A receiver is broadcast flag compliant if it recognizes a bit in a broadcasted video or audio signal, and if that bit is set to true, the receiver will not permit full-resolution or full-bandwidth signals to be available to the owner of the receiver. Because that would allow the owner to record that signal and share it with other people. A compliant reciver must also be tamper-resistant, so that the owner can't modify it to make it ignore the bit. The broadcast flag is primarily aimed at high-definition TV signals, but if it goes into effect, it will set precedents that could affect all signals and all receiving devices, and ultimately, all electronic and computing equipment.

There is a law that will go into effect on July 1st 2005, which will criminalize the building or selling of non-compliant receivers in the United States. No doubt there will be subsequent attempts to criminalize non-compliant receivers everywhere else.

It might not look like much, but this is a big issue. Should it be a crime for you to own a computer that does what you want it to do? Should it be a crime to receive a radio signal and be able to look at it?

The really screwed-up thing here is that these guys are getting ready to trade away many of your taken-for-granted liberties regarding privacy, information and computation, really basic First Amendment stuff, and the benefit to their business WILL BE SMALL, and probably temporary. Meanwhile your freedoms will be FUNDAMENTALLY DIMINISHED FOREVER.

I'm thinking about making some affordable hardware for the GNU Radio project (which has a wiki). This is a project where you build radios, and most of the radio is built in software. A single piece of hardware can act like a lot of different regular radios. The hardware I have in mind would cover the band from DC to about 15 megahertz, picking up AM, shortwave, and two ham radio bands. Add up- and downconverters, and you can get those soon-to-be-illegal flagged broadcasts. If I build these things and sell them by July 1st, they won't become criminal. If my time and energy and funds permit, I'd like to build as many as possible and get them to as many people as I can.