Molecular Machinery

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Dry (Non-biological, NEMS)

Dry. Stiff. Diamond-based. Ultra-high vacuum. Machine-phase chemistry.

Manufacturing

Bottom Level: Tip Chemistry

DC10c Carbon-transfer Tooltip

Pyramidal Hydrogen Abstraction Tooltip

Allis Single-Atom Deposition Tip

Minimal Toolset for Positional Diamond Mechanosynthesis

Main article: Minimal Toolset for Positional Diamond Mechanosynthesis

Freitas Tip

Top Level: Manipulators

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There's little technical information about this; only a few images and a simulation showing that the top bearing can, in fact, be used as a bearing. For now we can assume it's more of an art project than an actual, technical manipulator. The elbow, however, has an interesting geometry.

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MolmacExtended | Name = Fine-Motion Controller | Image = FineMotion.png | Author = Eric Drexler | Date = 2003 | ComponentNumber = 20 | AtomNumber = 2,596 | Width = 37 nm | Height = 43 nm | Depth = 37 nm | Other = File: Download .pdb | FileName = FineMotion | Extension = mmp


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  • Nanotube nanomanipulator

Computation

Computers

Graphene Logic

Helical Logic

Rod Logic

Data Storage

NASA's Diamond Data Storage

This could probably be implemented in Silicon using an scanning tunneling microscope to pop off Hydrogen atoms from an H-terminated Silicon surface (Patterned Atomic Layer Epitaxy), then filling the chamber with something like Fluorine radicals, or some other molecule that will deposit a Fluorine or Chlorine atom on the depassivated spots. Hydrogen is 0, the other element is 1. Then it could be read it with an atomic force microscope, as demonstrated by Oscar Custance and company in "Chemical identification of individual surface atoms by atomic force microscopy" Nature, March 2007.

A particularly important problem, one that would limit the mass-deployment of such technology, is that H-terminated Silicon isn't stable when exposed to air, since the surface Hydrogen atoms are motile at room temperature.

Motors

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Nanotube Electrostatic Motor

[Simulated] Nanotube Electrostatic Motor

Force Transmission

WARNING: Most of the designs that follow are highly speculative and have only been validated by molecular dynamics simulations and scaling law analysis. You decide whether this is satisfactory. It's important to keep an open mind, but, single-atom-wide gear teeth? Seriously?

The following content is mirrored from the NanoEngineer-1 Wiki.

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The design of complex nanosystems with numerous moving parts is made complicated by the fundamental limits of chemical bonding and the possible interfaces between moving parts that can be achieved with certain nanostructures. It is possible that this spatial quantization of atomically precise building materials may also be used to drive the self-assembly of some nanosystems, greatly simplifying the assembly process. The nesting of appropriately sized carbon nanotubes, such as shown here, can serve as a strong driving force for molecular bearing self-assembly.

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This molecular differential gear was designed by K. Eric Drexler and Ralph Merkle sometime around 1995 while working together at Xerox PARC. In the animated sequence above, you can clearly see the casing and six components of the internal assembly as each is hidden in the cutaway view.

This animation loop shows the results of a molecular dynamics simulation done with NanoDynamics-1. The frames of the animation loop were rendered using POV-Ray, generated automatically using NanoEngineer-1. The gearbox casing was hidden to expose the internal gearing mechanism. Notice that the front and back shafts rotate in opposite directions.

Dr. Drexler provides the following brief description of the differential gear:

In this view the two cylindrical shafts and their facing bevel (conical) gears are shown, along with two of the four casing-mounted pinion gears that mesh with both shaft-gears. Acceptably smooth motion (despite the atomic granularity of the building blocks) is made possible by geometry and symmetries. For example, the shaft-gears have 14-fold symmetry, while the casing has 4-fold symmetry; if one pinion gear is exactly opposite a shaft-gear tooth, its 90-degree partners will be opposite shaft-gear grooves. Thus, energy fluctuations at the tooth-meshing frequency will cancel, leaving only higher-frequency, lower-amplitude fluctuations as barriers to rotation. The shafts rotate in the casing on standard sliding-interface bearings, using the same principle to achieve smooth motion. The lowest quality bearings are those between the pinion gears and the casing, which lack the regularity required for high smoothness.
The structure is designed to be built chiefly of hydrogen (white), carbon (gray), silicon (black), nitrogen (blue), phosphorus (purple), oxygen (red), and sulphur (yellow). The larger size of second-row atoms helps in constructing tapered gears and reduces the number of atoms needed to construct the outer cylinder of the casing. Such structures are far beyond the state of the art of chemical synthesis today, but their design and modeling is becoming straightforward.

- K. Eric Drexler

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The high tensile strengths and stiffness of carbon nanotubes have made them important as building materials in many current nanoscience applications. Their range of use is expected to extend to molecular manufacturing applications in nanoscale scaffolding and molecular electronics. Their cylindrical shape and highly delocalized electronic structure make them interesting possible choices for the design of molecular bearing assemblies. In the design at above, the cut-away section is a single covalent structure, around which a low-friction diamondoid bearing is kept from finding a highly stable minimum energy position.

This is interesting because the nanotube is more stable than the diamond bearing, and while under normal conditions the bearing would likely collapse and graphitize due to strain, the nanotube creates positive pressure from the inside, preventing this from happening. Clever, very clever.

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This is the MarkIII(k), a planetary gear created by K. Eric Drexler. A planetary gear couples an input shaft via a sun gear to an output shaft through a set of planet gears (attached to the output shaft by a planet carrier). The planet gears roll between the sun gear and a ring gear on the inner surface of a casing.

The animation above was produced from a NanoDynamics-1 molecular dynamics simulation, which produces a special "movie file" containing the atom positions at each iteration of the simulation run. Selected frames from the movie are then rendered with QuteMolX and finally combined into an animation file. A section of the casing atoms have been hidden to expose the internal gearing assembly.

Planetary gears are attractive targets for molecular modeling because (with careful choice of planet numbers and sun- and ring-gear symmetries) the overall symmetry of the system virtually guarantees low energy barriers along the desired motion coordinate. They also pack considerable complexity into a small structure.

Planetary gears are common mechanical systems used for speed reduction (= torque multiplication). Macroscale versions are found in automobile transmissions, electric screwdrivers, and Mars landers.

The MarkIII(k) gear updates an early 1990s design by Drexler and Merkle, modified to reduce interactions between the sun gear and the bases of the planet gears. The original version was designed with very small moving parts in order to fit the computational constraints of the time. The planet gears are near the lower limits of diameter for functional gear components, and because of this, the "gear teeth" in this system are better thought of as smooth, low-amplitude corrugations in the gear surfaces.

The single covalent (sigma) bonds linking each of the nine planet gears to the carrier gear are easily seen in this POV-Ray image.

Fullerene Gears

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The design and operation of carbon nanotube based gears was originally studied using computational methods at NASA in the late 1990s. Benzyne molecules (as teeth) are attached to carbon nanotubes (shafts) to form gears that can operate at GHz frequencies. The animations above (and below) show how the gears would function.

The NASA research team states:

"Our theoretical investigations of the structure and operating conditions of such machines show that the gear is very robust and can operate under adverse conditions such as slipping, conditions in which an ordinary macro-scale gear would fall apart. Computer simulations also show that nanogears, or other machines, in the future could be powered through lasers or externally controlled electric fields."

"Though when we first designed this and showed its operation through computer simulations, we were not sure if anyone can actually attach molecules to the side of a nanotube or how difficult a job it would be. But recently, research groups have succeeded in attaching atoms and molecules to nanotubes. This is promising. We believe then a gear of this type can actually be made in the lab."

NanoEngineer-1 makes it easy to recreate molecular models of the NASA gears and simulate them using NanoDynamics-1. ND1 produces a special "movie file" containing the atom positions at each iteration of the simulation run. Selected frames from the movie are then rendered with QuteMolX and finally combined into an animation file.

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These gears are called the NASA Globus Gear since a nice rendering of this gear was found on Al Globus' web page.

A gallery of the original NASA carbon nanotube gears is located here.

For further reading:

J. Han, A. Globus, R. Jaffe and Glenn Deardorff, "Molecular Dynamics Simulation of Carbon Nanotube Based Gears", Nanotechnology, Vol. 8, pp. 95-102 (1997).

D. Srivastava,"A Phenomenological Model of the Rotation Dynamics of Carbon Nanotube Gears with Laser Electric Fields", Nanotechnology, Vol. 8, pp. 186-192 (1997).

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This small bearing was designed by Eric Drexler. It was originally written about in his book Nanosystems: Molecular Machinery, Manufacturing and Computation (page 296).

The animation above was created from an NanoDynamics-1 molecular dynamics simulation of the small bearing. The small bearing is an excellent model for the beginner to construct and simulate. It includes two components (ring and shaft) and only 206 atoms, which means that a simulation with complete rather quickly. It is a great way to get some experience using rotary motors in NanoEngineer-1 that create torque to drive components of molecular models.

The MD simulation you see above took only 2 minutes to complete on my laptop with the following parameters:

  • frames: 500
  • steps per frame: 10.0 femtoseconds
  • temperature: 300K

The animation loop was rendered using QuteMol. Creating an animation like this one is relatively easy since QuteMol can be launched from within NanoEngineer-1. Each frame of an animation can then be saved from QuteMol.

To learn how to model the small bearing, check out this video tutorial.

The small bearing is also featured in a new video produced by Will Ware and Dr. Eric Drexler. To learn more about the video, read the article "Unmasking the Stroboscopic Illusion - Why the thermal motion shown in standard MD videos is misleading".

SRG-II Speed Reducer Gear

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The SRG-II is another parallel-shaft speed reducer gear created by Mark Sims. It was designed and modeled completely from scratch using NanoEngineer-1 (Alpha 6). The goal of the SRG-II was to create a robust nanoscale gear complete with a casing and extended connector shafts. As you can see, the SRG-II looks every bit like a speed reducer gear. Although the casing is a single component, its atoms have been grouped into sections and hidden in the animated sequence above so that you can better visualize the casing arrangement.

The animation loop show a 9.6 picosecond segment of the first successful simulation of the SRG-II. The following parameters were used:

  • Frames: 940
  • Steps per Frame: 50.0 femtoseconds
  • Temperature: 300K

As can be seen from this speed plot of the rotary motor attached to the pinion gear, the acceleration time was about 23 picoseconds. The duration of the simulation was 47 picoseconds.

Successfully simulating the SRG-II required two attempts. The first simulation of the SRG-IIa uncovered a design flaw in the casing, which was corrected in the SRG-IIb. The problem involved the top and bottom crossbeams that connected the front and back faces of the casing, which compressed the casing too tightly around the gears. Below you can see the difference between the casings of the SRG-IIa (left) and SRG-IIb (right). Notice the two upper and lower crossbeams missing from the SRG-IIb.

I also removed material from the left and right casing walls, creating four crossbeams at the corners. This reduced the number of atoms while maintaining the shape and rigidity of the casing structure. The rightmost image shows the casing, which is made of silicon carbide (SiC), a rigid material well suited for designing enclosures like this. It is displayed in tubes display style so that the two gears can be more easily seen. The gears are displayed in the CPK display style.

SRG-III Gear Train

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The SRG-III is the third parallel-shaft speed reducer gear created by Mark Sims. A hybrid of the SRG-I and SRG-II, it is the first molecular gear train ever designed. With 15,342 atoms, the SRG-III is the second largest nano-mechanical device ever modeled in atomic detail.

The animation loop in the infobox shows a segment of a molecular dynamics simulation that took almost 31 hours to complete on my Dell laptop. I've hidden the atoms in the front-top half of the silicon carbide casing to expose the gear train.

The rotary motor (not shown) is connected to the largest gear and has the following parameters:

  • Torque: 10 nN-nm
  • Initial Speed: 0 GHz
  • Final Speed: 100 GHz

I used the following parameters for this simulation:

  • Frames: 1100
  • Steps per frame: 10.0 femtoseconds
  • Temperature: 300

This animation loop shows the casing displayed in tubes mode.

Strained-shell Sleeve Bearing

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This is the strained-shell sleeve bearing from Nanosystems (page 296) designed by K. Eric Drexler while working at Xerox PARC. The model comprises two molecular components; the inner shaft and the outer sleeve and contains a total of 2,808 atoms.

With practice, an experienced user can create this bearing in 10-15 minutes. NanoEngineer-1 includes an extrusion tool for creating rods and rings from a molecular fragment (called a chunk in NanoEngineer-1).

The contraption with spokes connected to the inner shaft is called a Rotary Motor. This is a type of jig in NanoEngineer-1 that applies torque to the atoms to which it is attached during a molecular dynamics simulation, driving the inner shaft. The rotary motor here had a torque setting of 1.0 nN-nm and a speed of 10 GHz. These values are extreme and were used to produce an interesting simulation as quickly as possible. A serious engineer assessing the operating conditions of this bearing would have used more reasonable numbers.

The black boxes (visible in the top image) are constraints called anchors and are attached symmetrically to atoms around the outer sleeve. Anchors are used to hold individual atoms in place during a molecular dynamics simulation.

The animation above was created using NanoDynamics-1. Selected frames of the simulation (movie) were then rendered with QuteMolX and combined into the animated GIF. To setup this NanoDynamics-1. molecular dynamics simulation, I used the following parameters:

  • Frames: 1500
  • Steps per frame: 20.0 femtoseconds
  • Temperature: 300K

NanoEngineer-1 has a full-featured movie player that allows a NanoDynamics-1 simulation (movie) to be played in forward and reverse, paused, played in a loop, etc. While the movie is playing, it is possible to rotate, pan and zoom the model interactively. Other useful features include the ability to select and change the display style of different parts of the model (while the movie is paused) and then continue playing the movie.

The second image was rendered in POV-Ray after exporting the sleeve bearing model as a POV-Ray file. This is one of many features that make NanoEngineer-1 an excellent tool for creating professional looking graphics for use on web sites and publications.

Universal Joint

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This molecular model of a universal joint is based on a 1992 design by K. Eric Drexler and Ralph Merkle while working together at Xerox PARC. The animation loop (above) was created from a NanoEngineer-1 (NanoDynamics-1) MD simulation run. The animation shows the results of the universal joint in which the shafts are bent at 40° relative to each other.

Two rotary motors, shown in the image above, are connected to a set of atoms in each shaft and have the following parameters:

  • Torque: 1 nN-nm
  • Initial Speed: 0 GHz
  • Final Speed: 50 GHz

This image shows the universal joint displayed in lines mode. This provides a clearer look at the two rotary motors and how they are connected to the atoms in the shaft. In these images, the shafts connected to the hinge of the universal joint are bent at 20°.

I used the following parameters to create the molecular dynamics simulation shown in the two animated GIFs above (which took ~24 hours to complete on my Dell laptop):

  • Frames: 2000
  • Steps per frame: 10.0 femtoseconds
  • Temperature: 300

This pair of images show the newer design (left) next to the original design (right) by Drexler and Merkle. The new version contains roughly %55 of the atoms of the original, which makes a big difference when running molecular dynamics simulations on your laptop like I do. This was the primary motivation behind trimming down the original model.

Dr. Merkle provides this background about the original universal joint:

The design was part of an effort to design molecular machines that have no sliding parts. Like the buckling logic, it has only bending and flexing, eliminating any concerns about sliding motion causing some mysterious problems (recall that people were more skeptical of molecular machines back then). It was originally designed on PolyGraf from BioDesign (later to become MSI).

You can check out pictures of two variants at http://www.zyvex.com/nanotech/visuals.html which has both a pure hydrocarbon design, and a design with N and O terminations of the surface (in addition to H termination).

- Dr. Ralph Merkle

A universal joint is a joint in a rigid rod that allows the rod to 'bend' in any direction. It consists of a pair of ordinary hinges located close together, but oriented at 90° relative to each other.

Universal joints are common wherever a driveshaft needs to turn a corner; a driveshaft with a universal joint can freely rotate through the universal joint, and no gears are required to couple the two ends. The most obvious example of this application of a universal joint is in the driveshafts of automobiles, a technology known as the Hotchkiss drive.

Worm Drive

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This model of a worm drive is based on a collaborative design by K. Eric Drexler and Mark Sims while working together at Nanorex. It is actually a sub-assembly of a larger design, the sorting pump. This is the first molecular scale worm drive ever modeled in atomic detail and has been simulated using NanoDynamics-1, a custom MD engine integrated with NanoEngineer-1.

Below are two animation loops showing the results of an MD run of this model. In both animations, the front wall of the casing is hidden to allow viewing of the vertical worm gear in the middle of the assembly. The animation on the right shows all atoms of the casing rendered in tubes display style to allow viewing of the two worms and the worm gear. The two counter-rotating worms are the input gears, which then drive the middle worm gear.

200px 200px 150px

In the rightmost image above, one quarter of the casing has been hidden to show the internal structure of the worm drive assembly.

Structural Support

The following content is mirrored from the NanoEngineer-1 Wiki.

Carbon Nanotube Crimp Junction

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The high tensile strengths of carbon nanotubes make them likely material candidates in future nanoscale manufacturing applications. In the absence of atomically precise manufacturing methods for fabricating continuous scaffoldings of a single nanotube, methods that lock nanotubes into place by strong electrostatic and/or steric approaches may be possible. The diamondoid crimp junction shown at left is a single covalent nanostructure that fixes two nanotubes at right angles.

Carbon Nanotube 6-way Junction

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The junction above is generated by three pairs of carbon nanotubes fixed along (x,y,z) axes. The interfaces at the center of this junction are composed of 6 adamantane molecules covalently bound to each carbon nanotube and functionalized with either nitrogen (N) or boron (B) atoms. These nanotubes are not covalently bound to one another, instead employing dative bonding between nearest-neighbor B-N pairs to hold the six nanotubes in place, a method that offers the possibility of complex structure formation via familiar chemical self-assembly.

Sorting

Neon Pump

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"That is also a rotary motor driven by gas pressure if you operate it in the opposite direction. Push gas through it and you’ll get rotary motion. It’s a really nice motor." - Robert Freitas

This design of a neon pump includes two components. The pump casing, which includes a chamber wall with a hollow tube containing the rotor housing, and the rotor itself. In one mode of operation it could serve as a pump (for neon atoms) and in another it could be used to convert neon pressure to drive the rotor, making it a rotary motor.

This NanoEngineer-1 molecular dynamics simulation of the neon pump took over 8 hours to complete on a Dell laptop (Pentium M, 2.0GHz and 1GB RAM).

The jiggling of atoms seen in this simulation results from the thermal motion of atoms, not from mechanically induced vibration. Thermal vibration is a natural occuring phenomenon that is visible in dynamical simulations at this scale.

Dr. Drexler provides this description of the pump:

The left image shows the chamber wall on the bottom, followed by a tube containing the pump housing; above this is the pump rotor.
The right image is a close-up view of the rotor, showing a grooved cylindrical bearing surface at each end, supporting a screw-threaded cylindrical segment in the middle. In operation, rotation of the shaft moves a helical groove past longitudinal grooves inside the pump housing. Only where facing grooves cross is there room for even a small gas molecule, and these crossing points move from one side to the other as the shaft turns.

- K. Eric Drexler

Sorting Pump

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This molecular sorting pump was a Nanorex collaborative design led by K. Eric Drexler, Josh Hall and Damian Allis starting in late 2006. The idea for this pump was inspired by the sorting pump depicted in the Nanofactory video (at 1:30) which selectively processes acetylene molecules. The goal was to design a sorting mechanism that was more detailed (and plausible) than the sorting rotor depicted in the animation.

The pump is driven by a worm drive that was modeled and then simulated using NanoDynamics.

An animation depicting the operation of this molecular sorting pump can be viewed here at YouTube.

Abstract Sorting Pump

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Compound

Turbopump

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Not much is known about this design. Macroscale vacuum pumps are limited by the vapor pressure of their lubricants. Fullerene, being a superlubricant, has no such problem, and so fullerene-coated diamondoid positive-displacement pumps can be constructed to serve as UHV pumps.

The effectiveness of such pumps depends on the ratio of blade speed to thermal speed of the lightest molecule being pumped. Using diamondoid, the speed will easily exceed the thermal speed of Hydrogen, providing a <math>\geq</math>10 ratio for each blade row[1].

Wet (Biologically-derived)

Wet. Squishy. Flexible. Solution-phase chemistry.

Manufacturing

The Ribosome

Computation

Computers

Data Storage

Motors

Force Transmission

Structural Support

The Cytoskeleton

Microtubule

Tubulin

Microfilament

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Sorting

Templates

Molmac

The Molmac template can be used as a kind of infobox to showcase the main features of molecular machines. It's usage is:

{{Molmac
| Name = Name
| Image = SomePicture.gif
| Author = The author
| Date = Year it was made, discovered, or the closest to that
| ComponentNumber = The number easily differentiable components
| AtomNumber = The number of atoms
| Width = Width (Specify the unit. Generally 'nm' is fine)
| Height = Height (Specify the unit. Generally 'nm' is fine)
| Depth = Depth (Specify the unit. Generally 'nm' is fine)
| FileName = The name of the file that contains the machine's atomic coordinates, without the file extension
| Extension = The file extension
}}

MolmacExtended

In case the default template doesn't have the parameters you want (For example, a way to add a row for the efficiency of a particular machine), you can use the MolmacExtended template like this:

{{MolmacExtended
| Name = Name
| Image = SomePicture.gif
| Author = The author
| Date = Year it was made, discovered, or the closest to that
| ComponentNumber = The number easily differentiable components
| AtomNumber = The number of atoms
| Width = Width (Specify the unit. Generally 'nm' is fine)
| Height = Height (Specify the unit. Generally 'nm' is fine)
| Depth = Depth (Specify the unit. Generally 'nm' is fine)
| Other =
'''Efficiency:''' 95% <br>
'''Time to complete an operation:''' 10ps
| FileName = The name of the file that contains the machine's atomic coordinates, without the file extension
| Extension = The file extension
}}

See also

People

References

  1. 'The statistical theory of turbomolecular pumps, J.G Chu and Z.Y. Hua, The Modern Physics Institute, Fudan University, Shanghai, PRC.