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Foresight Update 16

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A publication of the Foresight Institute


Foresight Update 16 - Table of Contents | Page1 | Page2 | Page3 | Page4 | Page5

 

Crystal Clear: a Molecular CAD Tool

by Geoff Leach and Ralph Merkle

Background

Geoff Leach has been on sabbatical from the Royal Melbourne Institute of Technology in Australia, visiting Ralph Merkle at Xerox PARC for several months. During that time, he has been writing the first molecular CAD tool designed specifically for work in molecular manufacturing which has a GUI (Graphical User Interface). We have wanted such a tool for some time, for it will automate the tedious task of specifying complex diamondoid structures, and make it possible to rapidly move a design concept to a detailed computational model. Having recently returned to Australia, Geoff continues his work at RMIT.

Introduction

The controlled bonding of individual atoms was first discussed over three decades ago (ref. 2). Today, the major research objectives in molecular nanotechnology are the design, modeling, and fabrication of molecular machines and molecular devices (ref. 3). Although the ultimate objective is economical fabrication, the limitations of present capabilities preclude the manufacture of any but the most rudimentary molecular devices. The design and modeling of molecular machines is, however, quite feasible with present technology. Such modeling allows relatively inexpensive exploration of the truly wide range of molecular machines possible. Obvious dead ends can be identified and eliminated and more promising designs retained for further investigation. While it can be debated exactly how long it will take to develop a broadly based molecular manufacturing capability, it is clear that the right computational support will substantially reduce the development time. With appropriate molecular CAD software, molecular modeling software (including available computational chemistry packages, e.g., molecular mechanics, semi-empirical, and ab initio programs), and related tools, we can plan the development of molecular manufacturing systems on a computer just as Boeing might "build" and "fly" a new plane on a computer before actually manufacturing it.

Diamondoid Material

Diamond is stronger, stiffer, and has better thermal conductivity than other known materials; it also has a wide band gap, excellent transparency, a high breakdown field, and is in general a materials scientist's dream material. Diamondoid materials (ref. 3) resemble diamond in a broad sense: they have strong covalent bonds joining carbon atoms, hydrogen, and various other first and second row elements, such as boron, nitrogen, oxygen, fluorine, sulfur, and the like. Diamond has a strength to weight ratio over 50 times that of steel: an Eiffel tower built out of diamondoid material could reach beyond the atmosphere. At the other end of the scale, nanometer size mechanical components such as bearings, gears, levers, and so forth built from diamondoid material will be extremely stiff, a property of crucial importance in molecular scale robotic arms that must maintain high positional accuracy in the face of thermal noise. Methods of synthesizing diamondoid structures have been discussed elsewhere(ref. 2, 6, 8). In the long run, many manufactured products will be made from diamondoid materials.

Crystal Clear

Crystal Clear (CC) is a molecular CAD tool for the design of diamondoid structures in full atomic detail. Core capabilities are already in place, and future extensions are planned.

Crystals are regular structures. Crystal Clear has powerful crystal lattice operators which leverage this fact. Natural and intuitive operations can be performed over all atoms which are part of a user-selected subset of a diamond lattice. The user can define a basis of a selection lattice by pointing and clicking (selecting) two, three, or four atoms (to define a one, two, or three dimensional selection lattice). That basis may include, for example, every third atom in one direction, every fourth atom in a second direction, and every atom in a third direction. Then using a handle box the user can stretch the basis into a selection lattice of the desired width, height, and length. Repeated applications of a selection lattice can be made by selecting "ground" atoms which become the origin for each application. One use of this capability is to select atoms for deletion, another is to select two groups of atoms in order to bond corresponding atoms to each other.

Designing a structure using Crystal Clear is a two-phase process. In the first phase a block of crystal of a desired height, width, depth, and orientation is chosen. In addition to changing viewing parameters (scale, rotate, translate), the user may also scale, translate, and rotate the crystal lattice relative to the handle box, and stretch the handle box to include more (or less) crystal. The structure is then instantiated. This generates individual data structures for each atom and bond in the structure, and so permits finer editing. In the second phase, the user may delete individual atoms, or groups of atoms using selection lattices, and change the bonding structure. Structures may also be warped.

Design of a Tube

We illustrate the idea and current capabilities of CC -- particularly the power of selection lattices -- with the step-by-step design of a tubular structure [step 15]. The basic approach is to take a long thin block of diamond, bond the seam (left and right end), and wrap it around into a tube. Doing so in the most straightforward manner leads to a structure which has unacceptable bond strain, at least for the tube diameters and thicknesses we are interested in. Systematic dislocations are introduced into the block (the particular dislocation used is the Lomer dislocation) to reduce strain in the tube to an acceptable level. They do so by creating gaps in the structure which close up when compressed. The introduction of the dislocations into the crystal lattice makes heavy use of the selection lattice capability.

The sequence of steps discussed below takes about eight minutes. Each step refers to the corresponding picture.

Steps 1 through 3: Sketch out a block of crystal and instantiate.

The start-up state of CC presents the user with one unit cell of diamond, which contains eight atoms, surrounded by a handle box (step 1). A convenient orientation for the design of a tube is obtained by rotating the crystal lattice about the vertical axis by 45 degrees, bringing the (110) surface into view (step 2). The block of crystal is extended in height, depth and length (step 3), which become the thickness of the wall, the length, and the circumference of the tube respectively.

Steps 4-6: Define a selection lattice.

First a one-dimensional basis is defined and stretched (step 4). The selection lattice is made two-dimensional by selecting a third atom for the basis (step 5). Notice that the third atom selected for the basis skips over some atoms. The two dimensional selection lattice is then stretched to run the full length of the block (step 6).

Steps 7-11: Introduce dislocations.

The atoms selected in steps 5 through 7 are deleted (step 7). This is the first stage of introducing dislocations into the structure. Using the same selection lattice more atoms are deleted (step 8). Now, bonds across the gaps created by the deletion of atoms are added. This requires two applications of the selection lattice (step 9) and then a bond-across operation in which corresponding atoms in each application of the selection lattice are bonded to each other (step 10). Another set of bonds added in the same way completes the dislocations (step 11).

Steps 12 and 13: Bond seam.

In order to create a "perfect" seam in the tube, some atoms must be removed from one end so that the crystal lattice is continuous when warped. A one-dimensional selection lattice is defined and repeated applications made to select excess atoms for deletion (step 12). Then, using the same selection lattice, bond-across operations are used to bond the seam (step 13).

Step 14: Warping

The block is warped into a tube. As currently implemented a selection lattice is used to define warp parameters. Notice that the tube is not quite symmetric, for instance some of the pentagons are skewed.

The use of Crystal Clear to design a tube is now finished. The next step is to use a molecular mechanics package to analyze the structure we have designed.

Molecular Mechanics

Molecular mechanics is a method of analyzing the energy of a molecular structure to compute positions and trajectories of atoms (or more strictly, their nuclei) (ref. 4, 5, 7). As discussed by Merkle (ref.1) molecular mechanics can be used to analyze the structures designed by molecular CAD packages such as Crystal Clear. Commercial packages are in routine use (ref. 5, 7).



Step 15 shows the results of energy minimization in Polygraf (ref. 5). The structure does not change much; the most noticeable effect of the minimization is to improve symmetry. After minimization, bond strain can be examined. Bond strain for some bonds around the Lomer dislocation can reach 13%. Carbon-carbon single bonds do not reach their inflection point until they have been stretched by about 22%, and the Lomer dislocation is known to be stable.

Conclusion

Molecular CAD is essential if we are to design complex diamondoid structures. Crystal Clear is a first attempt at an interactive molecular CAD system. At present its capabilities are rudimentary and its user interface crude, but both are sufficient to design structures of genuine interest in molecular machine design.

Acknowledgements

The authors would like to thank Eric Drexler and Markus Krummenacker for their many helpful conversations and observations in the course of this work.

References

1. "Computational Nanotechnology," by Ralph C. Merkle, Nanotechnology 2 (1992) 134-141.

2. "There's Plenty of Room at the Bottom," a talk by Richard Feynman (awarded the Nobel Prize in Physics in 1965) at an annual meeting of the American Physical Society given on December 29, 1959. Reprinted in Miniaturization, edited by H. D. Gilbert (Reinhold, New York, 1961) pp. 282-296.

3. Nanosystems: Molecular Machinery, Manufacturing, and Computation, by K. Eric Drexler, Wiley Interscience 1992.

4. Molecular Mechanics, by Ulrich Burkert and Norman L. Allinger, ACS Monograph 177, American Chemical Society, 1982.

5. DREIDING: A Generic Force Field For Molecular Simulations, by Stephen L. Mayo, Barry D. Olafson, and William A. Goddard III, Journal of Physical Chemistry, 1990, 94, pp. 8897-8909.

6. "Theoretical studies of a hydrogen abstraction tool for nanotechnology," by Charles B. Musgrave, Jason K. Perry, Ralph C. Merkle, and William A. Goddard III, Nanotechnology 2 (1991) 187-195.

7. Reviews in Computational Chemistry, Vol. 2, Kenny B. Lipkowitz and Donald B. Boyd, VCH Publishers, 1991.

8. "Molecular Manufacturing: Adding Positional Control to Chemical Synthesis," by Ralph C. Merkle, Chemical Design Automation News, September 1993 [in press].

Current information on Crystal Clear (now Crystal Sketchpad)


Foresight Update 16 - Table of Contents

 

Not More Dinosaurs!

by K. Eric Drexler

Jurassic Park is based on the rather silly premise that entire dinosaur genomes will one day be reconstructed from DNA found in dinosaur blood cells ingested by blood-sucking insects preserved in amber. This seems unlikely.

Present methods recover DNA from amber by using mechanical grinding and chemical dissolution to put molecules into solution, then apply enzymatic methods to amplify any resulting DNA fragments. Despite the relatively rapid chemical breakdown of wet DNA (which degrades to small fragments in several thousand years at moderate temperatures [Lindahl, Nature 362:709, 1993 --MEDLINE Abstract]), weevil DNA sequences have been recovered from an extinct weevil embedded in 120 to 135 million-year-old amber. The extinction of the dinosaurs occurred only 65 million years ago.

Consider the analysis of amber in an era of advanced molecular machinery. Molecular machine systems can characterize surfaces with atomic resolution, then remove and characterize molecular fragments from those surfaces, generating fresh surfaces. Repeating this process layer by layer will yield an imperfect but highly detailed and information-rich map of the molecular structures in the initial block of amber. Such maps will reveal not only chemically intact DNA fragments of the sort observed by present methods, but chemically modified DNA-derived structures that now elude observation owing to their insolubility or to failures in enzymatic amplification. Sequences could often be traced past breaks in the molecule, provided the broken ends are still held close together in the solid matrix. Even bases chemically modified and split from the backbone by hydrolysis could often be identified and assigned to their place in the sequence, provided they have not moved far. This detailed chemical and geometrical information will permit recovery of extensive genetic information, even from specimens now regarded as lacking recoverable DNA.

Using present techniques, DNA has been recovered from many sources: hair, white cells in dried blood, dried skins in museums, even bear DNA from bear droppings [Höss et al., Nature, 359:199, 1992 --MEDLINE Abstract]. Using future techniques, DNA could surely be recovered from similar materials preserved in amber. By examining damaged structures from many cells from the same organism, complete genetic information could be reconstructed by combining and correcting the information -- random chemical damage is unlikely to obliterate the very same information in each of a thousand copies of a genome.

Dinosaurs presumably left dried bits of themselves blowing across the landscape: scales, scabs, and bits of skin shed either naturally or as a result of scrapes both minor and horrendous. These materials would stick to sap. Thus, it seems that most of the dinosaur DNA in amber will be found not in pretty preserved insects, but in dinosaur dandruff mixed with the embedded dirt that makes so much amber opaque and ugly. Although one could probably reconstruct genomes more or less as described in Jurassic Park, this would be doing the job the hard way.

The world presumably contains much more amberlike material than meets the eye. Amber itself is widely distributed, and small resinous specks of no interest to jewelers are large enough to preserve a huge amount of genetic information. To illustrate, imagine that a square kilometer slab one meter thick consists of deposits containing 0.01% of amberlike material that in turn contains 0.01% of dried biological materials in 100 micron particles (totaling 10 parts per billion in the deposit as a whole). A hundred micron particle has room enough for tens of thousands of dried cells, and the deposit just described would contain 10 billion such particles. The genetic record of life on Earth may be surprisingly rich.

Previous articles [Peterson, Update 4, 1988 ; Brin and Drexler, Update 5, 1989] have proposed a Bioarchive Project aimed at systematically preserving genetic information from endangered species, to aid in the restoration of biodiversity in a future where human encroachment on the biosphere has been reduced. The recovery of DNA from amber suggests that robust and inexpensive procedures can help. Drying almost any kind of tissue sample and embedding it in a stable resinous matrix should suffice to preserve DNA for a long, long time. This can be done by almost anyone, anywhere, with no special facilities.


Foresight Update 16 - Table of Contents | Page1 | Page2 | Page3 | Page4 | Page5


From Foresight Update16, originally published 1 July 1993.


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