Molecular Machinery: различия между версиями

= Dry (Non-biological, NEMS) =

<div align=center>

=== Top Level: Manipulators ===

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.

<gallery>

File:Crank.jpg

File:Tripod.jpg

</gallery>

==== 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 [http://www.nature.com/nature/journal/v446/n7131/edsumm/e070301-01.html "Chemical identification of individual surface atoms by atomic force microscopy"] Nature, March 2007.

== Motors ==

=== Nanotube Electrostatic Motor ===

The following content is mirrored from the [http://nanoengineer-1.net/mediawiki/index.php?title=Main_Page NanoEngineer-1 Wiki].

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.

This molecular [http://en.wikipedia.org/wiki/Differential_%28mechanical_device%29 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 [[Software#NanoDynamics|NanoDynamics-1]]. The frames of the animation loop were rendered using POV-Ray, generated automatically using [[Software#NanoEngineer|NanoEngineer-1]]. The gearbox casing was hidden to expose the internal gearing mechanism. Notice that the front and back shafts rotate in opposite directions.

The animation above was produced from a [[Software#NanoDynamics|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 [[Software#QuteMol|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.

D. Srivastava,"[http://www.iop.org/EJ/abstract/0957-4484/8/4/005 A Phenomenological Model of the Rotation Dynamics of Carbon Nanotube Gears with Laser Electric Fields]", Nanotechnology, Vol. 8, pp. 186-192 (1997).

{{Molmac

===SRG-II Speed Reducer Gear===

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:

* 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 '''''[http://en.wikipedia.org/wiki/Space-filling_model CPK display style]'''''.

* Initial Speed: 0 GHz

* Final Speed: 100 GHz

I used the following parameters for this simulation:

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 [http://nanoengineer-1.net/mediawiki/index.php?title=Feature:Rotary_Motor 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.

This molecular model of a [http://en.wikipedia.org/wiki/Universal_joint 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:

* 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°.

* 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.

===Worm Drive===

This model of a [http://en.wikipedia.org/wiki/Worm_drive 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 [[Molecular Machinery#Sorting Pump | sorting pump]]. This is the first molecular scale worm drive ever modeled in atomic detail and has been simulated using [[Software#NanoDynamics|NanoDynamics-1]], a custom MD engine integrated with [[Software#NanoEngineer|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.

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

===Carbon Nanotube Crimp Junction===

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===

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.

===Neon Pump===

''"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:

===Sorting Pump===

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 [http://www.youtube.com/watch?v=vEYN18d7gHg 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.

===Abstract Sorting Pump===

==== Compound ====

=== Turbopump ===

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.

==== Microfilament ====

== Sorting ==