NanoCAD in

A freeware nanotech design system including source code

Taken to CCL archives from `http://world.std.com/~wware/ncad.html`

If you have a Java-capable web browser, the NanoCAD applet should appear below. If you don't, you may find this page rather boring. This is a big applet, so it may take one or two minutes to load into your browser (sorry for the delay). If you see a molecule below, you can try rotating the molecule in various directions by dragging your mouse on the gray background (be sure to hold down the mouse button while you do that). See the text window for other tricks.

Send suggestions, comments or questions to wware@world.std.com.

NanoCAD uses mathematical techniques of molecular modeling to simulate the behavior of molecules on your web browser. The "Emin" buttons perform energy minimization, that is, they try to nudge the molecule toward a more natural shape where its potential energy will be lower. Real molecules jiggle around their minimal-energy shapes due to thermal vibrations.

NanoCAD was largely inspired by the book Unbounding the Future, in which the second chapter describes a virtual-reality simulation of the molecular-scale world. This simulation is used as a design tool by future students of nanotechnology. For the present, the description is science fiction. I would like to think that NanoCAD may contribute some day to making it real.

Up to now, previous versions of NanoCAD have been written in either Scheme or Common Lisp. This has proved inconvenient for a lot of people, so this Java version should make NanoCAD available to folks who had trouble with it in the past. The earlier versions have been distributed under the somewhat restrictive GNU General Public License, but I'm switching to a more commerce-friendly Berkeley-esque license. Don't worry, it's still free software.

Scary Science Stuff

The most complete and complex (and computation-intensive) chemistry simulators find complete solutions to Schrodinger's wave equation, solving for exact shapes of electron clouds and other horribly messy things. At that level, "chemical bonds" are emergent phenomena and are not a-priori built into the simulation. A few terms for chemistry simulators, in decreasing order of sophistocation, are: ab initio (where you start with just Schrodinger's wave equation and a few fundamental constants, and derive everything else from scratch), semi-empirical (modelling systems that depend partially on empirically gathered data), and molecular mechanics (depending entirely on empirical data to make up mass-and-spring mechanical models of molecular behavior).

Nanotechnology (for the moment, at least) most strongly resembles mechanical engineering. I'm hoping to come up with something simple and practical that would not overburden a desktop PC. I have therefore chosen to stick to molecular mechanics, which I think will serve most of the near-term needs of nanotechnology development.

I was never a very good chemistry student in school, so I've had to do a little reading. For thinking about this stuff, it's useful to know a bit about how atomic bonds work. I can recommend Linus Pauling's book, "The Nature of the Chemical Bond".

The mathematical model of molecular mechanics used by NanoCAD, called MM2, was developed by Norman Allinger of the University of Georgia. MM2 is described in Eric Drexler's book "Nanosystems", starting on page 44. MM2 essentially treats a group of atoms as a collection of masses, non-linear springs, torsion bars, and so on. The NIH has a very pretty summary of the ideas behind modelling molecular mechanics. Based on the MM2 info in Nanosystems, I've computed some typical spring constants that you might expect to see in some typical molecules.

A couple of people have written to say that they had trouble running the NanoCAD applet under MS Windows, getting a message like this: The dynamic link library sc10awt.dll is not in my paths. This is not a problem with NanoCAD, this is a problem with how your web browser is set up. If you run into this, try to find a technical support phone number for whoever made your browser (Netscape, or if you're using Internet Explorer, Microsoft) and ask them for help in configuring your browser to run Java applets correctly.

How about something more like Virtual Reality?

Since NanoCAD was inspired in part by the virtual reality program described in Unbounding the Future, it's reasonable to ask whether we can expect to see a VR version of NanoCAD any time soon. And indeed, there is hope.

Around 1983, I visited Atari's research lab in Cambridge Massachusetts, and got the opportunity to try a force-feedback joystick. A normal joystick feeds X and Y coordinates to the computer, which say how far up or down the stick is, and how far left or right it is. The force-feedback joystick also had motors which allowed the computer to push against your hand. When it was programmed correctly, it gave an incredibly realistic sensation of pushing against a spring, or navigating a maze with solid walls. The sense of realism was indescribable.

There is now a force feedback joystick available in the $90-$100 range, and I've put together a little web page about it. One of these days, I mean to actually buy one, and see if it can be programmed to give the physical feeling of tugging on atoms and molecules. Then you'd be able to see how a molecule deforms as you shake it or stretch it.

Archives and precompiled executables

Click on these files with your right mouse button to download them.

Source file archives, these contain all the source files and compiled class files:
- ncadjava.tgz for Unix
- ncadjava.zip for DOS
nanocad.exe is a Windows executable

Source files

wrapper.java, a class that turns the NanoCAD applet into a Java application
nanocad.java, the NanoCAD applet
atom.java, definition of an atom. The following elements are subclasses of the atom class:
bond.java, definition of a chemical bond
dlentry.java, an entry in a drawing list. The following are subclasses of the dlentry class:
group.java, a group of atoms and bonds, with various useful group-wise operators. The following predefined structures are subclasses of the group class:
view.java, defines a point of view, with conversions between physical locations and screen coordinates
term.java, defines MM2-style energy terms, used to compute approximations of interatomic forces. The following are subclasses of the term class:
- lterm.java, a bond-length term
- aterm.java, a bond-angle term
- tterm.java, a torsion-angle term
- lrterm.java, a long-range term (electrostatic and van-der-Waals forces). As of this writing, these are not implemented yet.

Things to Do in the Future

Electrostatics forces need to be implemented. When two atoms of differing electronegativies are connected by a covalent bond, the bond has an electric dipole moment; this hasn't been implemented either.
I discovered a problem with how torsion forces were computed. This has been fixed, by using the torsion expression from another program called NAMD.
It should be possible to read PDB or XYZ files, and write VRML files.
Add more elements, and maybe more predefined structures. This is a lot less painful than it was in Scheme, thanks to the OOP approach and a couple of Perl scripts.
It would be nice to be able to select a group of atoms and be able to cut, copy, paste, and move them. Maybe there should be some sort of clipboard for "structure scraps".
The wrapper.java application has some stubs for reading and writing structure files, but they don't do anything yet. It would be really nice to be able to read in PDB files. It would be especially nice to be able to import structures directly from repositories like the Brookhaven Protein Data Bank.

NanoCAD mailing list

There is a mailing list available for anyone interested in discussion of NanoCAD or related topics. To subscribe, send a message to majordomo@world.std.com with the line "subscribe nanocad" in the body (not the subject) of the message. You may then send email to everyone on the list by sending it to nanocad@world.std.com. As of this writing (4 Jan 98) there are about 50 people on the list.

I welcome discussion of possible future features or directions for NanoCAD. I'm not interested in suggestions about what people think I should work on (NanoCAD has been, and remains, a volunteer effort, and my spare time is scarce). I'm much more interested in what others are willing to do with it, which is why I've posted the source code. Before you send me mail about what you think I should do, read the source code yourself and pick up a copy of the Java Development Kit, and if you need to read some Java books, I can recommend the books published by O'Reilly. Either that, or take a swing at translating the current Java version to C++.

Chemistry Tutorials, Modeling Kits, etc...

If I'm typical (and in my experience, I am), the people who develop an interest in nanotechnology tend to be software types who don't know a heck of a lot about chemistry. Alas, chemistry is a central part of nanotechnology. But software types usually have web access, so what we need are on-line chemistry tutorials:

A useful list of on-line tutorials and resources
CHEMystery: An Interactive Guide to Chemistry, an on-line tutorial. I like this one a lot. Very attractively done, and goes into reasonable depth.
The ESG Biology Hypertextbook Home Page, another on-line chemistry tutorial, with a biological emphasis. It tells how to do your own recombinant DNA research.
Theory of Atoms in Molecules, a bit heavy on the math, lots of quantum mechanics. Go here when you're ready to give up your amateur ranking. I'm not quite ready yet.

These folks in New Hampshire make some pretty nice, inexpensive plastic modeling kits for building molecules in something more tangible than graphics on a computer screen. They also have another on-line chemistry tutorial. If I can find some information on other molecular modeling kits, I'll post that here as well. The New Hampshire folks don't like ball-and-stick models, but I find that sometimes they make the geometry of a molecule more obvious.

Some Nanotechnology-Related Links

This page has been mentioned in the Foresight Update! Very cool.

Here is a really fantastic animation of a molecule undergoing thermal vibration, by Horst Vollhardt of the Department of Physical Chemistry, at Darmstadt University of Technology in Germany. It doesn't allow you to modify the structure, but it does a beautiful job with the molecular dynamics.

Lee Moon has ported NanoCAD to the Apple Newton. It looks like he's offering it as a 3D drawing program only, without any molecular modeling. But it's kinda cool to think you could run it on a palmtop. If anybody wants to port it to the USR Palm Pilot, with modeling intact, I'd really like to see that.

Ralph Merkle has written a beautiful, concise introduction to the ideas of nanotechnology.

Web Annotation

The folks at the Foresight Institute have thought long and hard about how to make the web a more flexible place for discussion. They have recently developed a series of tools for critical discussion, hosted at crit.org. Their software allows you to annotate a document without the author's permission (since the annotations themselves reside on the crit.org server, not the author's server). Ka-Ping Yee has done an excellent job on the CritLink tool. If you would like to try annotating this very web page, visit http://crit.org/http://world.std.com/~wware/ncad.html.

There is also the idea of coarse backlinks implemented by sending tricky commands to search engines, like this:

Acknowledgements

Lots of people have contributed to NanoCAD in lots of different ways over the past couple of years. (Some of these people have perhaps never heard of NanoCAD, but they have my gratitude anyway.) They are: Norman Allinger, Alan Ames, Andrew Babian, Darius Bacon, Eric Drexler, Will Dye, Matthew Flatt, Chris Fry, Erick Gallesio, Konrad Hinsen, Aubrey Jaffer, Markus Krummenacker, Brad Lucier, Thomas Marsh, Gayle Pergamit, Chris Peterson, Jay Ponder, Roger Sayle, Julian Smart, Dejan Vucinic, John Warner, and the members of the M.I.T. Nanotechnology Study Group. Thanks, everybody.