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.