Gemstone-like molecular element: Difference between revisions

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'''Diamondoid molecular elements''' (DMEs) are '''[//en.wikipedia.org/wiki/Structural_element structural elements] or [//en.wikipedia.org/wiki/Machine_element machine elements] at the lower physical size limit'''. They are produced via [[mechanosynthesis]] and are often are highly symetrical.
[[File:Tetrapod-openconnects display large square.jpg|300px|thumb|right|Here is a rather small structural [[diamondoid]] [[crystolecule]] with some bonds (brighter red) intentionally being left [[Nanoscale surface passivation|open/dangling/unpassivated]]. A [[crystolecule fragment]]. Such [[surface interface]]s can be fused together via [[seamless covalent welding]] in the [[second assembly level]] and perhaps higher assembly levels.]]
Since '''metals are unsuitable''' (they lack directed bonds and tend to [//en.wikipedia.org/wiki/Surface_diffusion diffuse]) [[diamondoid]] materials must be used. Diamondoid molecular elements are central in [[technology level III]] and [[technology level II]].


* DM machine elements (DMMEs) ([http://www.zyvex.com/nanotech/visuals.html examples]) like e.g. bearigs and gears have completely passivated surfaces.
[[File:atomistic acetylene sorting pump model.jpg|frame|A proposed [[acetylene sorting pump]]. This is a larger [[diamondoid machine element]] (DME). Possibly assembled from several pre-produced smaller [[diamondoid crystolecule]]s. The frame is one big monolithic crystolecule (it may be fused together via [[seamless covalent welding]] during assembly). Other parts are smaller independent crystolecules that may be [[piezochemical mechanosynthesis|mechanosynthesized]] fully passivated as a whole and integrated as a whole without any seamless welding.]]
* DM structural elements (DMSEs) ([http://www.thingiverse.com/thing:13786 example]) are minimally sized structural building blocks that are only partially passivated. They expose multiple radicals on some of their surfaces that act as [[atomic precision|AP]] [[surface interfaces|welding interfaces]] to complementary surfaces. The step of connecting [[surface interfaces]] is done in [[assembly levels|assembly level II]] and is irreversible.


'''Name suggestion:''' since DMEs are somewhat of a cross between crystals and molecules why not call them '''"crystolecules"'''
'''Gemstone-like molecular elements''' (GMEs) here also called '''crystolecules''' for short. Also possible '''crystalecules or crystallecules'''. <br>
Gemstone-like molecular elements are the basic building blocks in <br>
[[gemstone based atomically precise manufacturing]] here aka <br>
[[gemstone metamaterial technology]] or [[gem-gum-tec]]. <br>


*    DME ... Diamodoid Molecular Element (stiff - small - minimal)
The small & simple initial idea was: <br>
*    DMME ... D.M. Machine Element
These objects are somewhat of a '''cross between a crystal and a molecule'''. <br>
*    DMSE ... D.M. Structural Element
So let's use the term '''"crystolecule"''' as a portmanteau. <br>
Below is an evolved much more extensive definition. <br>


= Diamondoid molecular machine elements =
= Definition of crystolecules =


Images of some examples can be found here: [http://www.zyvex.com/nanotech/visuals.html].
Abbreviated tl;dr <br>
'''A crystolecule …''' <br>
★ has fully atomically precise to specification crystal like internal structure <br>
★ has fully atomically precise to specification molecule like surface structure <br>
★ is a single monolithic piece, not an assembly of crystolecules <br>
– is usually but not always on the lowermost physical size limit to fulfill its function <br>
– has usually but not always non-bonding surface passivations <br>


== Types ==
== Hard criteria: ==


=== Bearings  ===
★ '''Crystolecules are''' (unless broken) '''fully [[atomically precise]]'''. <br>
All atoms are at a known and fully intentional position that was desired not accepted. <br>
Some errors may be acceptable so long the parts can still fulfill their tasks. <br>
★ Crystolecules, '''like macroscale crystals''', have a '''crystalline internal structure''' (it is allowed to be strained, stressed, and feature fully intentional and atomically precise "defect" like structures. (A more fitting name might be "perfections" maybe?) <br>
★ Crystolecules, '''like nanoscale molecules''', have both a '''finite, and atomically precisely intentionally defined outer shape''' i.e. surfaces, edges, corners. (Surfaces may feature intentional atomically precise surface reconstructions.) <br>
★ Crystolecules are '''structural and monolithic''', [[molecular machine elements]] with moving parts must contain more than one [[crystolecules]] (excluding flexures).


DMME bearings exhibit [[superlubrication|superlubrication]]. In the case of [[diamondoid]] rotative bearings this looks like described here: [http://e-drexler.com/p/04/02/0315bearingSums.html E.Drexler's blog: Symmetric molecular bearings can exhibit low energy barriers that are insensitive to details of the potential energy function].
== Soft criteria: ==


The occurring friction is orders of magnitude lower than the one occurring when liquid lubricants are used in macro ore microscopic (non [[atomic precision|AP]]) bearings [http://e-drexler.com/p/04/03/0322drags.html E.Drexler's blog: Phonon drag in sleeve bearings can be orders of magnitude smaller than viscous drag in liquids].
These are not strictly necessary but corroborate the crystolecule status. <br>
If these requirements are not met it does not mean it is not a crystolecule. <br>
★ Crystolecules '''usually but not always''' feature an atomically precise monolayer (or near monolayer) '''surface passivation''' such that they feature [[mechanical stability]], [[thermal stability]], [[chemical stability]], and other (electrical optical, …) overall only necessarily sufficient for their intended purpose. Encapsulated crystolecules e.g. need not be stable to air. See: [[Fruit interior analogy]]. <br>
★ Crystolecules '''usually but not always''' are created to '''fulfill a specific structural function''' as whole of (or part of) a structural element, or structural part of a machine element of various kind, (mechanical, electrical, plasmonic). Exceptions: crystolecules in recycling storage, somehow broken crystolecules, mechanosynthesis capability demonstrations (like test-prints), failed prototypes, … <br>
★ Crystolecules '''usually but not always''' are in their size '''at the lowermost physical size limit''' to fulfill their function.<br>
★ Crystolecules are '''usually but not always highly symmetrical'''. <br>
----
★ Diamond crystolecules are '''produced via [[force applying mechanosynthesis]]'''. There seems to be no other viable way to make diamond ones. <br>
★ Crystolecules are generally produced via mechanosynthesis/mechanochemistry or <br>for some (not all) gemstones that are [[cook mix and stir]] in solvent crystallizable a method of [[in nano-mold crystallization]] may be an option. <br>Limits on atomic precision of surfaces are still unclear, early methods will yield rather bad crystolecules to the point of questionability of calling them crystolecules. <br>
Some may not even be releasable from the mold.


DMME bearings can be built such that the force between bearing and axle is anti-compressive further lowering dynamic drag but also lowering stiffness possibly down to zero. [http://e-drexler.com/p/04/03/0322nonrepulsive.html E.Drexler's blog: Bearings can be stable despite attractive interactions between their surfaces]
== Reactive crystolecules – subsumed edge case ==


If badly chosen the combined symmetry of bearing and axle can create a bistable tristable or an other low symmetry configuration. This should usually be avoided. Some symmetry considerations can be found here: [http://www.zyvex.com/nanotech/bearingProof.html Zyvex; Ralph C. Merkle: A Proof About Molecular Bearings] and iirc on the Nanoengineer-1 developer wiki which went missing. :(
Absence of surface passivation would make the more exotic crystolecules unstable in air or water. <br>
Future larger scale [[crystolecule]] based systems will be able to provide excellent vacuum ([[PPV]]) though. <br>
Even if passivatable some faces may intentionally be left unpassivated for [[seamless covalent welding]]. <br>


A tutorial on bearing design can be found here: [http://www.somewhereville.com/?p=82 A Low-Friction Molecular Bearing Assembly Tutorial, v1]
= Grey zone of definition =


=== Friction elements ===
== Glassolecules ==


Interlocking teeth with low stiffness can snap back and thermalize energy.
Same as crystolecules just that <br>
[http://e-drexler.com/p/04/02/0315pairSnap.html E.Drexler's blog: Softly supported sliding atoms can undergo abrupt transitions in energy]
the internal structure is not crystalline but [[pseudoamorphous]] <br>
This can serve as a break (analog to an electrical resistor in an electrical circuit)
i.e. it looks random but it is actually very intentional. <br>
e.g. the result of an optimization process. <br>
See page: [[kaehler bracket]]s and … <br>
These may require more advanced [[mechanosynthesis]] capabilities. <br>


=== Gears ===
Related page: [[Amorphous structures]]


Single rows of protruding atoms can be used as gear teeth.
== Nanotubolecules & Graphenolecules ==
Considerations about stiffness as in [[superlubrication]] for DMME bearings are relevant [''more details needed''].
A simple pair of inter-meshing straight bevel-gears have higher bumpiness than well designed DMME bearings.
This can be reduced by making the gears helical. '''Example designs are needed'''.
Using more than one row for a gear tooth will lead to more "bumpiness" but also potentially higher transmittable torque. Further '''investigation needed'''


=== Fasteners  ===
'''Nanotubes & (nano)graphenes''' (as 2D sheet or 1D nanoribboins)''': <br>
Details can be found on the [[locking mechanisms]] page. <br>
These existing established concepts do not strongly require atomically precise terminations at their edges <br>
Enclosed radicals could be used to make very compact reversible connectors (name suggestion: ''covaconns'' - for covalent connectors)
thus they '''can't be counted as-is to crystolecules''' <br>
despite fitting other requirements like being crystalline <br>
with a bit of a stretch to 2D or 1D crystallinity. <br>
And a bit of weakening on the stiffness requirement. <br>


* expanding ridge joint
Thus here we'll introduce the novel terms <br>
'''nanotubolecules & graphenolecules''' (matching to the term "crystolecule") that <br>
'''add the strong requirement of true full atomic precision, particularly the edges'''. <br>


=== Pumps ===
Nanotubolecules & graphenolecules''' <br>
may stretch the concept of crystolecules a bit to 2D & 1D crystals <br>
and to inclusion of lower stiffness structures (due to their typical high aspect ratios). <br>


There is a model of a single atom neon pump which to some degree acts as a filter too.
More formally but a horribly unwieldy mouthful: <br>
Positive displacement pumps like piston pumps scroll pumps or progressing cavity pumps have not yet been designed.
'''atomically precise terminated nano(graphene/tubes)'''.


=== Others  ===
Future more advanced mechanosynthesis may eventually <br>
[[in place mechanosynthesize]] fused structures that contain both … <br>
– 3D structures made from sp3 carbon and <br>
– 2D structures made from sp2 carbon (including rolled up to 1D) <br>
Unless the sp2 part is dominant the resulting structures are best called just crystolecules. <br>
All the same holds for sp2 boron nitride structures. Generally sp2 structures.


[Todo: telescoptc rods; joints; hinges .... ball joints -> issues lack of ball curvature?]
As for sp2 and sp3 structures, they may occur even in intermixed ways too. <br>
– Either in a 3D checkerboard crystal. Related page: [[Pseudo phase diagram]] <br>
– Or glass like (this is an orthogonal classification, see adjacent section on [[glassolecules]]). <br>


== Sets ==
'''Synthesizability:''' <br>
Unlike crystolecules graphenolecules can (as of 2025) be synthesized <br>
via [[cook mix and stir thermodynamic synthesis]].  <br>
Via [[step wise synthesis]] followed by [[on surface synthesis]] ([[cyclodehydrogenation]]) to be precise. <br>
The crucial thing here is the presence of [[termination control]]  <br>
and some means to pick out the truly atomically precise products. <br>
See page: [[graphene nanoribbons]].


=== Minimal set of compatible DMMEs  ===
= Delineation – what crystolecules must not be confused with =


In electric circuits there is one topological and three kinds of basic passive elements.<br>
== Delineation from nanocrystals ==
Adding an active switching element one can create a great class of circuits. <br>
'''0) fork node; 1) capacitors; 2) inductors; 3) resistors'''


Those passive elements have a direct correspondences in rotative or reciprocating mechanics namely: <br>
* There is very little control over the precise shape of nanocrystals. <br>Nanocrystals are created by natural physical chemistry processes. <br> Their shape is the result of thermodynamic equilibria during their history of formation. <br>I.e. they are grown via  [[mix cook and stir thermodynamic synthesis]]. <br>Some crystals faces form faster some slower. The slower growing faces remain.
'''0) planetary or differential gearbox [*]; 1) springs; 2) inertial masses; 3) friction elements''' <br>
* Nanocrystals seem to always be convex (except in case of twinning).
[*] and analogons for reciprocating mechanics
* Nanocrystals are not atomically precise as there is no precise [[termination control]].
* Larger nanocrystals tend to incur unintentional defects especially low energy ones like stacking order.


But there are limits to the electric-mechanic analogy. Some mechanic elements often differ significantly from their electric counterparts in their qualitative behavior.
== Delineation from [[nanoparticle]]s ==
Two examples of elements  quite different in behaviour are:
* transistors & locking pins
* transformers & gearboxes


With creating a set of standard sizes of those elements and a modular building block system to put them together
Nanoparticles are literally any stuff falling in the nanoscale size class <1000nm. <br>
creating rather complex systems can be done in a much shorter time. <br>
'''Nanoparticles are a much more broad concept than crystolecules.''' <br>
Like in electronics one can first create a schematics and subsequently the board.
'''To do:''' Create a minimal set of minimal sized DMMEs for rotative nanomechanics.
Modular housing structures standard bearings and standard axle redirectioning are also needed.


'''To investigate:''' how can reciprocating mechanics be implemented considereng the [[passivation bending issue]]
The main concern with nanoparticles is of them being free floating and a health hazard. <br>
With dedicated efforts crystolecules could eventually be made into one form of free nanoparticles. <br>
But such efforts are not needed for getting towards [[advanced productive nanosystem]]s. <br>


= Diamondoid molecular structural elements =
== Delineation from foldamer crystals ==


[[File:Wiki-tetrapod-openconnects-black-135.png|frame| An example of a diamondoid molecular structural element (DMSE). The bright red spots are open bonds.]]
Crystolecules must not be confused with nanoscale crystals out of folded up polypeptide molecules aka proteins. <br>
Crystals of proteins may seem weird when first encountered. <br>
Micro- to macroscale protein crystals are made today to find the locations of their constituent atoms using X-ray diffraction. <br>


==sets==
The closest foldamer analog to a crystolecule <br>
in the sense of precisely defined surface and surface passivation) <br>
might be a [[fully termination controlled monolithic foldamer assembly]] {{wikitodo|This may need a name.}}<br>
See pages: [[foldamer]], [[termination control]], [[hierarchical selfassembly]]


* standardized building block systems
= Related but different concepts – intentionally factored apart on this wiki =
* housing structures
* standard corner pieces connecting the various crystallographic planes
* in edge passivation with hydrogen can be problematic
* issue of non androgynous [[surface interfaces|sinterfaces]]
* brackets for sub bond length positioning [[http://www.foresight.org/Updates/Update10/Update10.3.html]]
* standard pipe and channel segments - the [[passivation bending issue]] is of relevance


= Molecular transport elements =
== Crystolecular units ==


Elements that create one dimensional structures for the logistic transport of different media are a bit of a
'''See main page: [[Crystolecular unit]]'''
cross between machine elements and structural elements.


== data transmission ==
These are bigger assemblies of basic structural crystolecules. <br>
Assembled from crystolecules either via [[seamless covalent welding]] or [[Van der Waals force sticking]] and/or [[shape closing interlocking]]


For transmission of data in Nanosystems [//en.wikipedia.org/wiki/Polyyne polyyine] rods where proposed.
Let's use a different name for crystolecules or assemblies of crystolecules that are typically:
They constitute the thinnest physically possible rod manufacturable and consist out of sp hybridized carbon which must be [[mechanosynthesis|mechanosynthesizable]] for their construction which goes beyond minimal necessary capabilities.
* a bit bigger
Handling of sp carbon is involved in already analyzed [[tooltip chemistry]] though and thus likely to be available.
* also functional in nature not just structural
Polyyne rods obviously are rather susceptible to radiation damage thus it might be wise to use chains of benzene rings which are more stable.
* not monolithic
With the first few additional ring widths the event of non self healing catastrophic damage becomes drastically more unlikely per unit of time. ['''Todo''': calculate estimations]
* do feature irreversibly enclosed moving parts
Still two of those ribbons like to fuse under UV irradiation (see: [//en.wikipedia.org/wiki/Anthracene anthracene])
* may involve pick and place post assembly (from constituent crystolecules) at the next higher assembly level
Going to cyclohexan chains and bigger diamondoid rods makes the surface a lot more bumpy and the housings a lot more bulky.


== energy transmission ==
Generally crystolecules and [[crystolecular unit]]s will be made from [[gemstone like compound]]s. <br>
One subclass already investigated a bit in molecular detail are the [[crystolecular unit]]s made from [[diamondoid like compound]].
Specifically some ones made from [[diamond]] and [[moissanite]] were investigated.
See: '''[[Examples of diamondoid molecular machine elements]].'''


For power transmission strained shell near cylindrical diamondoid axles are a good possibility reciprocative movement may be better for high power densities.
== Diamondoid/Gemstone-based Molecular (Structural and Machine) Elements – term introductions and definitions ==


== heat transport ==
Note that this classification is orthogonal to the distinction between <br>
single monolithic crystolecule ~and~ crystolecular unit. <br>
{{Wikitodo|Make a graphic with a 2x2 matrix showing example cases. tetrpod, flexstage/flexgripper/flexhinge, ReChain, bearing/pumps}} <br>


For thermal drain water works well because of its very high heat capacity. To drastically reduce friction one should pass it around enclosed in diamond pellets to get it in either one needs to use very high pressure (sealing might be difficult; thermal conductance may suffer) or the insides are made hydrophobic by adding -OH insted of -H surface terminations. In the latter case mechanosynthetic oxygen placement capabilities are needed which go beyond minimal necessary capabilities. Pipes are easily creatable but work better at the macroscale.
Diamondoid or gemstone-based molecular elements (DMEs/GMEs) may come as both. <br>
It may be possible to use the phase trasition ice water to keep the the factory at constant tempertaure but note that superclean water (that occurs as waste see below) does not necessarily freeze when supercooled and the melting point might be significantly altered in small possibly hydrophobic encapsulation.
* Structural elements may lean to the smaller monolithic crystolecule side <br>(exception e.g. [[ReChain frame systems]] as have slidingly movable elements and decent complexity)
* Machine elements will be crystolecular units (except for monolithic flexures).


== raw material supply ==
Let's use:
* Diamondoid molecular structural elements (DM'''S'''Es) for structural ones of all sizes including beside small ones also bigger ones
* Diamondoid molecular machine elements (DM'''M'''Es) for functional ones that are typically bigger in size
* Diamondoid molecular elements (DMEs) for structures of all sized including both of the former
* ("Diamondoid" can be replaced by "Gemoid" to include more general gemstone like compounds like e.g. [[sapphire]])
* Or G for D if it's a gemstone that is not diamondoid.


For supply of solvated raw material the same method as for the cooling solvent can be used.
Examples:
* On this wiki: [[Examples of diamondoid molecular machine elements]]
* (DM'''M'''Es) ([http://www.zyvex.com/nanotech/visuals.html examples]) like e.g. bearings and gears have completely passivated surfaces.
* (DM'''S'''Es) ([http://www.thingiverse.com/thing:13786 example]) these are typically only partially passivated. They can expose multiple radicals on some of their surfaces that act as [[positional atomic precision|AP]] [[surface interfaces|welding interfaces]] to complementary surfaces. The assembly step of connecting [[surface interfaces]] is here called "[[seamless covalent welding]]" and is done in the next higher assembly level ([[assembly levels|assembly level II]]?). [[Seamless covalent welding]] it usually is irreversible but sparsely linking versions may be reversible.


== waste removal ==
Naming the base material makes the "crystal" part in "crystolecular" redundant. <br>
So here the choice has been taken to go back to just "molecular" to avoid nesting custom terms. <br>
Well, not fully consistently ATM: [[Diamondoid crystolecular machine element]] <br>


A waste that always occurs at a low rate comes from oxidation of excess hydrogen - atomically clean water.
Section possibly deprecated due to too many (eight) naming possibilities. <br>
Water can be drained via pipes or enclosed in pellets [more investigation of existing literature needed]
(Diamondoid|Gem-based)(Molecular|Crystolecular)(Structural|Machine)Element


Beside that depending on how much self repair capability is included
= Base material =
waste can be constituted out of shunned microcomponents because they are irreparable or likely to be broken or dirt contaminated.
(see: "[[microcomponent tagging]]") or out of dysfunctional DMEs caused by assembly errors. ...


= General properties of DMEs =
== Specific focus (diamond & co) ==


[Todo: slim down this page by split up to other pages]
Of especially high interest are [[diamond]], its hexagonal version called [[lonsdaleite]], and [[diamond like compounds]]. <br>
Many semiconductors fall in this class too. <br>
As of 2025 other compounds still remain largely unexplored for use as crystolecules. <br>


DMEs with carbon, silicon carbide or silicon as core material can be can have internal structure like
A subset of crystolecules (or [[gemstone-like molecular element]]s) are <br>
* diamond / [//en.wikipedia.org/wiki/Lonsdaleite lonsdaleite]
'''diamondoid crystolecules''' ([[diamondoid molecular element]]s).
* or other possibly strained [//en.wikipedia.org/wiki/Sp3_bond#sp3_hybrids sp<sup>3</sup>] configurations.
Due to the lack of defects the [//en.wikipedia.org/wiki/Ultimate_tensile_strength ultimate tensile strength] of larger DMEs lies above diamond of thermodynamic origin.


== Strained shell structures ==
== General focus (gemstones) ==


To form cylindrical or helical structures with high to maximal rotational symmetries for their size (good axles for [[superlubrication]]) one usually constructs wedge shaped segments and put them together until they naturally turn around 360 degree. Bending can be induced from internal structure or surface passivation (since passivation atoms haven't got the exact same bond length like the internal atoms, see: [[passivation bending issue]]).
[[Gemstone-like compounds]] are the most suitable base material for crystolecules. <br>
If 360° are exactly met the structures bending results from internal unstrained structure the whole structure is unstrained - a goal to aim for. If not bending to a strained shell is required.
For a collection of gemstones of particular interest see page: <br>
For thin tubes of high diameter a completely unstrained lattice of the used diamondoid material can be bent around.
'''[[Base materials with high potential]]'''.
A note on bending tools can be found on the "[[mechanosynthesis]]" page.


Spheres are rather rather hard to approximate. [to investigate: feasability of ball joints]
Beside classical gemstones like diamond other semi-precious minerals including <br>
bio-minerals that are synthesizable in solution also fall under gemstone-like compounds. <br>
Along the [[incremental path]] these may be accessible earlier. <br>
See page: [[technology level II]]for semi advanced precursor technologies. <br>


== Forces from compressive and tensile stresses  ==
Some gemstones like periclase MgO and Transition metal nonmetallides (TiC, TiN, TiO) <br>
transition over from mainly covalent to ionic salt like. See next section.


It can be helpful or at least satisfying to get something of an '''intuitive understanding for the consistence or "feel" of DME components'''.
== Exotic focus (salts, metals, …) ==


As the size of a rod of any material shrinks linearly (in all three dimensions) the area of the cross section shrinks quadratically.
Use of [[pure metals and metal alloys]] is limitedly suitable for crystolecules for a number of reasons.
Consequently when keeping tension/compression stress constant the forces fall quadratically and one arrives at very low forces.  
* Mechanical sliding interfaces can't be done with blank metal on metal surfaces due to [[seamless metallic welding]] on contact. Also, surfaces are likely difficult to passivate (for allowing sliding interfaces that way) due to the catalytic nature of metals. A full gemstone layer may suffice (possibly oxidic) but that just goes back to gemstones. Structural applications are less problematic but face issues too.
'''[Sacling law: longitudinal force ~ length^2]'''
* Metallic bonds with free electron gas are not directed like covalent bonds and sort of more "slippery". High performance gemstones are notably stronger especially when sticking with one's choice to [[abundant elements]]. Best of todays steels will pale compared to say [[superelastic]] sapphire based [[gem-gum]]. Also (gemstone typical) full breakage might be a preferable digital yes/no failure mode over (metal typical) plastic deformations.
This can be seen nicely in the low seeming inter-atomic spring constants.
* Metal ad-atoms on metal surfaces tend to [//en.wikipedia.org/wiki/Surface_diffusion diffuse] away from where they have been deposited. Likely ok with sticking to flat surfaces during crystolecule usage and with sticking with [[mechanosynthesis]] at sufficiently deep cryo temperatures in fabrication.
E.g. the equilibrium position spring constant of an bond in diamond (sp3 carbon-carbon-bond) is about 440nN/nm or 0.44daN/cm (1daN~1kg).


In order to get a feel for these forces one can transform atomic spring constants unchanged to the macrocosm.
* Usage of salts like gemstones should face fewer issues than metals structurally in limited scale. Flawless nanoparts will be [[superelastic]] but interlocking to make large scale [[gem-gum]] faces the issue of [[seamless ionic welding]].
This can be done by letting the number of parallel and serial bonds grow equally so that the changement of stiffness through [http://en.wikipedia.org/wiki/Series_and_parallel_springs serial and parallel] connection of bonds compensate.
* Salt like gemstones (just like metals) can't be passivated well for sliding interfaces. Salt like gemstones as base material are thus likely mostly useful for structural framework purposes. Possible exception: Enforced non-bonding spacing may allow to play some tricks with discrete notched motion.
Here for convenience 10,000,000,000 bonds are assumed to be chained serially.
We must apply this scaling to the number of parallel bonds too but here it divides up in each dimension of the cross-section sqrt(10^10) = 100,000.
With the diamond bond (C-C sp3) length of 1.532Amstrong and area per bond of 6.701Amstrong^2 = (2.59Amstrong)^2 one gets a diamond string (with square cross-section) of 1.532m length and 25.9um thickness side to side (half a hair) that retains the atomic spring constant of 440N/m or 0.44daN/cm (1daN~1kg)
If you bind up a half liter bottle of water with that (somewhat dangerous knife like) string it will bend around 1cm.


Putting one end of the sting in a vacuum filled square piston that seals tightly shows how little effect everyday pressures have at the micro and nanocosmos.
= How crystolecules will be made and used =
Taking 1bar = 10^5N/m^2 ambient pressure the string experiences a force of only 67.1µN and elongates 0.152µm an invisible amount.


'''Though''' as seen '''bonds are rather compliable DMEs are still hard diamond since''' [//en.wikipedia.org/wiki/Hardness hardness] is closely related to
== From atoms to crystolecules ==
'''tensile and compressive stress''' which '''is scale invariant'''.
The small force representation of high pressures might be a bit counterintuitive and hard to grasp.


By making the compliance at the nanolevel experiencable
'''Buildability''': Unfortunately crystolecules and their assemblies <br>
the model with the weight on the ''one bond equivalent diamond string'' should make one (maybe obvious) '''practical thing''' clear.
[[crystolecular element|crystolecular (machine) elements]] cannot be produced yet (state 2015..2025). <br>
That '''it is very effective to focus forces'''.
See page: [[Why natural chemistry can not be used to make crystolecules]]


In [[mechanosynthesis]] conical tips can easily focus forces down to a more compliable size level. Not much of a size difference is needed.
[[Mechanosynthesis]] can start to be prototyped today 2025 with [[scanning probe microscopy]] technology. <br>
Nanoscale manipulators in the [[machine phase]] can hold back on their supporting structures they're mounted to.
This does not cover scaling yet. For that see page: [[Bootstrapping]]
It is easy to create DMEs with high internal strains such as strained shell cylindrical structures, press fittings, structures under high tensile stress and more.
'''Great amounts of elastic energy can be stored''' (permanently or temporarily).


Example of safely usable pressures from [[Nanosystems]] section 2.3.2.:
== From smaller crystolecules to larger crystolecules ==
Assuming ~1% strain the required stress is ~1% of diamonds young modulus.
10nN/nm^2 = 10GPa = 1000daN/mm^2 (1daN~1kg)
this is 20% of the tensile strength of macro-scale diamond with natural flaws.
Flawless [[mechanosynthesis|mechanosynthetically]] assembled diamond will be capable of handling more stress.


[Todo: add info about shearing stress]
See page: [[Seamless covalent welding]] <br>
Any form of non-bonded assembly ([[form closure]],[[vdW force]], [[clipping]], …) <br>
is not subsumed here but is subsumed in the next section.


== Surfaces ==
== From crystolecules to their assemblies ==


When viewing the thickness of a surface as the distance from the point of maximally attractive VdW force to the point of equally repulsive VdW force (experienced by some probing tip) the thickness of the surface relative to the thickness of the diamondoid part is enormous.
'''Assembly in [[advanced productive nanosystem]]s.'''
This makes DMEs somewhat soft in compressibility but not all that much as can be guessed by the compressibility of [http://en.wikipedia.org/wiki/HOPG single crystalline graphite] which is a stack of graphene sheets.
In advanced nanofactories crystolecules would be:
* assembled from small [[molecule fragments]] – in the [[Assembly level 1 (gem-gum factory)|first assembly level]] – typically mostly irreversible
* assembled to bigger [[crystolecular unit]]s – in the [[Assembly level 2 (gem-gum factory)|second assembly level]] – typically partially irreversible


[Todo: add further relevant scaling laws & example calculation]
* '''[[Diamondoid molecular machine element]]s''' (DMMEs) are assemblies of some diamondoid crystolecules implementing one specific mechanical function
* '''[[Diamondoid molecular structural element]]s''' (DMSEs) are crystolecules or assemblies of some diamondoid crystolecules implementing a structural function


== VdW sticking ==
= Misleading aspects in [[molecular dynamics simulation|MD simulations]] of crystolecules and their assemblies =


[Todo: add calculation of how much surface is needed to securely overcome the characteristic thermal energy  (100kT?) -- to locking mechanisms?? -- techlevel I related too ...] <br>
See main page: [[Misleading aspects in animations of diamondoid molecular machine elements]]
[Todo: link to force estimation]


== Acceleration tolerance ==
== Beware of the "nanodiamond-is-jelly availability bias" misjudgement ==


[Todo: add calculation of a block on a neck model - for "intuitive" understanding]
[[File:DiamondoidsAreNotJellyLikeFloppy.jpeg|600px|thumb|right|Molecular dynamics simulations are typically run simulating extremely high speeds thus showing jelly like wobbling which would not at all occur when operated at actually proposed (steady state) speeds many orders of magnitude slower.]]
 
No, crystolecules (nanoscale diamond or other gemstones) do not normally behave like jelly. It is just that … <br>
* it is so much easier to simulate them at extremely high speeds and … <br>
* unlike strong non-rubber macroscale materials they don't break or bent at these speeds and … <br>
* unlike macroscale materials they even could dissipate the heat but … <br> with the important caveat of being as lone standing nanomachine coupled to cooling bulk.<br>
 
See page: [[A better intuition for diamondoid nanomachinery than jelly]]
 
== Beware of the stroboscopic illusion ==
 
'''Simulations of [[diamondoid molecular elements|DMEs]] often show a stroboscopic effect'''
this can be misleading and make one believe that the operation frequencies lie near the thermal frequencies,
thereby giving the false impression of enormously high friction.
 
'''Why the strobe effect?''' <br>
To make the machine motion visible in a movie despite them being slow compared to the thermal motions
many molecular dynamics simulation frames are dropped and only a few are taken as movie frames.
Thus in the movie the atoms are at a random point in their wiggle cycle at each movie frame making them jump around erratically at e.g. at gif file frame rate.
 
'''How to fix the strobe effect?''' <br>
Averaging atom positions for the merged simulation frames and increasing apparent size based on their momentary wiggle amplitude would be an easy huge improvement. Blurring and following even thermal torsional motion of H atoms on OH groups more advanced possibilities.
 
'''What else is misleading?''' <br>
Note that even with the stroboscopic effect fixed simulation speeds are still picked extremely high (m/s to km/s).
Way above speeds that were actually proposed for productive nanosystems (mm/s).
So there is jelly like wobble visible that would be the rare exception rather than the norm in nanomachine operation.
Exception: Rare high energy [[snaps]]. Norm [[steady state near reversible operation]].
 
At proposed speeds gemstone like molecular machine elements with sliding interfaces will work exceptionally well. <br>
See related pages: [[Superlubricity]], [[Friction in gem-gum technology]] <br>
There is both experimental evidence and theoretical evidence for that. <br>
(See e.g.: [[Evaluating the Friction of Rotary Joints in Molecular Machines (paper)]] and the friction analysis in [[Nanosystems]])
 
{| class="wikitable floatright" style="margin-left: auto; margin-right: 0px;"
|-
|'''well animated bearing''' <br> The fast thermal vibrations are more realistically blurred out. The remaining localized periodic average deformations (visible here if one looks closely) are highly reversible. (See page about "[[superlubrication]]".)
|'''badly animated bearing''' <br> The present stroboscopic effect can be misleading in that friction is likely to be grossly overestimated. It deceivingly looks like as if the operating speed would be close to the speed of the thermal vibration. If that were the case it indeed would cause massive friction (strong coupling of motions with similar frequency).
|-
| [[File:SmallBearingSmoothAnimation.gif|right|DMME - bearing with blurred out fast vibrations]]
|[[File:SmallBearingStrobeAnimation.gif|right|DMME - bearing with misleading stroboscopic effect]]
|}
…
 
= History of this page =
 
Since the here described physical objects have no official name yet (2016..2025) <br>
something sensible had to be invented to refer to them in this wiki.
 
The small & simple initial idea was: <br>
These objects are somewhat of a '''cross between a crystal and a molecule'''. <br>
So let's use the term '''"crystolecule"''' as a portmanteau. <br>
 
With time this page amassed a lot of discussion regarding <br>
the choice of terminology and refinement on the definition. <br>
What was later eventually worked out into the extensive definition here. <br>
See the intro of this page. <br>
 
"crystolecule" is nice because it's:
* quite accurate in descriptiveness
* quite conveniently usable in natural language
* quite memorably (catchy) because it seems unusual (clickbait effect)
 
----
 
{{wikitodo|This section is a bit redundant with the definition, maybe to clean up later.}}
 
Specifically let's use the term "crystolecule" for ones that are typically are:
* small – stiff – minimal
* structural
* monolithic (like illustrated)
* do (typically) do not yet feature irreversibly enclosed moving parts – (no [[form closure]] yet – there may be exceptions)
* are assembled purely at the [[first assembly level]] by [[force applying mechanosynthesis]] (direct [[in place assembly]]) – exception being [[seamless covalent welding]]
 
= Related =
 
* '''[[Terminology for parts]]'''
* '''[[Design of crystolecules]]'''
* For components at different size scales see: [[Components]]
* [[Stroboscopic illusion in crystolecule animations]]
* [[Example crystolecules]]
* [[In place assembly]]
* putting molecule-fragments together to crystolecules [[Mechanosynthesis core]]
* putting crystolecules together to microcomponents [[Crystolecule assembly robotics]]
-----
* [[Mechanical circuit element]]s
-----
Terms for bigger assemblies of several [[crystolecules]] but not yet as big (and disassemblable) as [[microcomponents]]
* [[Diamondoid crystolecular machine element]] – diamond like structure – See: [[Diamondoid]]
* [[Crystolecular machine element]] – more general gemstone like structure – See: [[gemstone like compound]]
-----
* assembled from [[molecule fragments]]
* assembled to [[crystolecular element]]s
* assembly is typically irreversible
-----
* [[Amorphous structures]]
* [[Nanoparticle]]s


= External links =
= External links =


At K. Eric Drexlers website:
* [http://e-drexler.com/p/04/02/0315bearingDiag.html A shaft in a sleeve can form a rotary bearing]
* [http://e-drexler.com/p/04/03/0323bearingDesigns.html Sleeve bearings have been designed and modeled in atomic detail] (here shown minus the stroboscopic illusion)
----
* [//en.wikipedia.org/wiki/Structural_element structural elements]
* [//en.wikipedia.org/wiki/Machine_element machine elements]
* [http://www.iberchip.net/iberchip2006/ponencias/86.pdf Design of Nanomachines using NanoEngineer-1]
* [http://www.iberchip.net/iberchip2006/ponencias/86.pdf Design of Nanomachines using NanoEngineer-1]
* "Nanomachines: How the Videos Lie to Scientists" [https://web.archive.org/web/20160322114752/http://metamodern.com/2009/02/10/nanomachines-how-the-videos-lie-to-scientists/ (archive)] [http://metamodern.com/2009/02/10/nanomachines-how-the-videos-lie-to-scientists/ (old dead link)]
* without stroboscopic illusion: [https://www.youtube.com/watch?v=RosHyQUw5jI  Molecular dynamics simulation of small bearing design]
* [http://www.somewhereville.com/?p=82 A Low-Friction Molecular Bearing Assembly Tutorial, v1]
[[Category:Technology level III]]
[[Category:Far term target]]

Latest revision as of 19:12, 29 March 2026

Here is a rather small structural diamondoid crystolecule with some bonds (brighter red) intentionally being left open/dangling/unpassivated. A crystolecule fragment. Such surface interfaces can be fused together via seamless covalent welding in the second assembly level and perhaps higher assembly levels.
A proposed acetylene sorting pump. This is a larger diamondoid machine element (DME). Possibly assembled from several pre-produced smaller diamondoid crystolecules. The frame is one big monolithic crystolecule (it may be fused together via seamless covalent welding during assembly). Other parts are smaller independent crystolecules that may be mechanosynthesized fully passivated as a whole and integrated as a whole without any seamless welding.

Gemstone-like molecular elements (GMEs) here also called crystolecules for short. Also possible crystalecules or crystallecules.
Gemstone-like molecular elements are the basic building blocks in
gemstone based atomically precise manufacturing here aka
gemstone metamaterial technology or gem-gum-tec.

The small & simple initial idea was:
These objects are somewhat of a cross between a crystal and a molecule.
So let's use the term "crystolecule" as a portmanteau.
Below is an evolved much more extensive definition.

Definition of crystolecules

Abbreviated tl;dr
A crystolecule …
★ has fully atomically precise to specification crystal like internal structure
★ has fully atomically precise to specification molecule like surface structure
★ is a single monolithic piece, not an assembly of crystolecules
– is usually but not always on the lowermost physical size limit to fulfill its function
– has usually but not always non-bonding surface passivations

Hard criteria:

★ Crystolecules are (unless broken) fully atomically precise.
All atoms are at a known and fully intentional position that was desired not accepted.
Some errors may be acceptable so long the parts can still fulfill their tasks.
★ Crystolecules, like macroscale crystals, have a crystalline internal structure (it is allowed to be strained, stressed, and feature fully intentional and atomically precise "defect" like structures. (A more fitting name might be "perfections" maybe?)
★ Crystolecules, like nanoscale molecules, have both a finite, and atomically precisely intentionally defined outer shape i.e. surfaces, edges, corners. (Surfaces may feature intentional atomically precise surface reconstructions.)
★ Crystolecules are structural and monolithic, molecular machine elements with moving parts must contain more than one crystolecules (excluding flexures).

Soft criteria:

These are not strictly necessary but corroborate the crystolecule status.
If these requirements are not met it does not mean it is not a crystolecule.
★ Crystolecules usually but not always feature an atomically precise monolayer (or near monolayer) surface passivation such that they feature mechanical stability, thermal stability, chemical stability, and other (electrical optical, …) overall only necessarily sufficient for their intended purpose. Encapsulated crystolecules e.g. need not be stable to air. See: Fruit interior analogy.
★ Crystolecules usually but not always are created to fulfill a specific structural function as whole of (or part of) a structural element, or structural part of a machine element of various kind, (mechanical, electrical, plasmonic). Exceptions: crystolecules in recycling storage, somehow broken crystolecules, mechanosynthesis capability demonstrations (like test-prints), failed prototypes, …
★ Crystolecules usually but not always are in their size at the lowermost physical size limit to fulfill their function.
★ Crystolecules are usually but not always highly symmetrical.

★ Diamond crystolecules are produced via force applying mechanosynthesis. There seems to be no other viable way to make diamond ones.
★ Crystolecules are generally produced via mechanosynthesis/mechanochemistry or
for some (not all) gemstones that are cook mix and stir in solvent crystallizable a method of in nano-mold crystallization may be an option.
Limits on atomic precision of surfaces are still unclear, early methods will yield rather bad crystolecules to the point of questionability of calling them crystolecules.
Some may not even be releasable from the mold.

Reactive crystolecules – subsumed edge case

Absence of surface passivation would make the more exotic crystolecules unstable in air or water.
Future larger scale crystolecule based systems will be able to provide excellent vacuum (PPV) though.
Even if passivatable some faces may intentionally be left unpassivated for seamless covalent welding.

Grey zone of definition

Glassolecules

Same as crystolecules just that
the internal structure is not crystalline but pseudoamorphous
i.e. it looks random but it is actually very intentional.
e.g. the result of an optimization process.
See page: kaehler brackets and …
These may require more advanced mechanosynthesis capabilities.

Related page: Amorphous structures

Nanotubolecules & Graphenolecules

Nanotubes & (nano)graphenes (as 2D sheet or 1D nanoribboins):
These existing established concepts do not strongly require atomically precise terminations at their edges
thus they can't be counted as-is to crystolecules
despite fitting other requirements like being crystalline
with a bit of a stretch to 2D or 1D crystallinity.
And a bit of weakening on the stiffness requirement.

Thus here we'll introduce the novel terms
nanotubolecules & graphenolecules (matching to the term "crystolecule") that
add the strong requirement of true full atomic precision, particularly the edges.

Nanotubolecules & graphenolecules
may stretch the concept of crystolecules a bit to 2D & 1D crystals
and to inclusion of lower stiffness structures (due to their typical high aspect ratios).

More formally but a horribly unwieldy mouthful:
atomically precise terminated nano(graphene/tubes).

Future more advanced mechanosynthesis may eventually
in place mechanosynthesize fused structures that contain both …
– 3D structures made from sp3 carbon and
– 2D structures made from sp2 carbon (including rolled up to 1D)
Unless the sp2 part is dominant the resulting structures are best called just crystolecules.
All the same holds for sp2 boron nitride structures. Generally sp2 structures.

As for sp2 and sp3 structures, they may occur even in intermixed ways too.
– Either in a 3D checkerboard crystal. Related page: Pseudo phase diagram
– Or glass like (this is an orthogonal classification, see adjacent section on glassolecules).

Synthesizability:
Unlike crystolecules graphenolecules can (as of 2025) be synthesized
via cook mix and stir thermodynamic synthesis.
Via step wise synthesis followed by on surface synthesis (cyclodehydrogenation) to be precise.
The crucial thing here is the presence of termination control
and some means to pick out the truly atomically precise products.
See page: graphene nanoribbons.

Delineation – what crystolecules must not be confused with

Delineation from nanocrystals

  • There is very little control over the precise shape of nanocrystals.
    Nanocrystals are created by natural physical chemistry processes.
    Their shape is the result of thermodynamic equilibria during their history of formation.
    I.e. they are grown via mix cook and stir thermodynamic synthesis.
    Some crystals faces form faster some slower. The slower growing faces remain.
  • Nanocrystals seem to always be convex (except in case of twinning).
  • Nanocrystals are not atomically precise as there is no precise termination control.
  • Larger nanocrystals tend to incur unintentional defects especially low energy ones like stacking order.

Delineation from nanoparticles

Nanoparticles are literally any stuff falling in the nanoscale size class <1000nm.
Nanoparticles are a much more broad concept than crystolecules.

The main concern with nanoparticles is of them being free floating and a health hazard.
With dedicated efforts crystolecules could eventually be made into one form of free nanoparticles.
But such efforts are not needed for getting towards advanced productive nanosystems.

Delineation from foldamer crystals

Crystolecules must not be confused with nanoscale crystals out of folded up polypeptide molecules aka proteins.
Crystals of proteins may seem weird when first encountered.
Micro- to macroscale protein crystals are made today to find the locations of their constituent atoms using X-ray diffraction.

The closest foldamer analog to a crystolecule
in the sense of precisely defined surface and surface passivation)
might be a fully termination controlled monolithic foldamer assembly (wiki-TODO: This may need a name.)
See pages: foldamer, termination control, hierarchical selfassembly

Related but different concepts – intentionally factored apart on this wiki

Crystolecular units

See main page: Crystolecular unit

These are bigger assemblies of basic structural crystolecules.
Assembled from crystolecules either via seamless covalent welding or Van der Waals force sticking and/or shape closing interlocking

Let's use a different name for crystolecules or assemblies of crystolecules that are typically:

  • a bit bigger
  • also functional in nature not just structural
  • not monolithic
  • do feature irreversibly enclosed moving parts
  • may involve pick and place post assembly (from constituent crystolecules) at the next higher assembly level

Generally crystolecules and crystolecular units will be made from gemstone like compounds.
One subclass already investigated a bit in molecular detail are the crystolecular units made from diamondoid like compound. Specifically some ones made from diamond and moissanite were investigated. See: Examples of diamondoid molecular machine elements.

Diamondoid/Gemstone-based Molecular (Structural and Machine) Elements – term introductions and definitions

Note that this classification is orthogonal to the distinction between
single monolithic crystolecule ~and~ crystolecular unit.
(wiki-TODO: Make a graphic with a 2x2 matrix showing example cases. tetrpod, flexstage/flexgripper/flexhinge, ReChain, bearing/pumps)

Diamondoid or gemstone-based molecular elements (DMEs/GMEs) may come as both.

  • Structural elements may lean to the smaller monolithic crystolecule side
    (exception e.g. ReChain frame systems as have slidingly movable elements and decent complexity)
  • Machine elements will be crystolecular units (except for monolithic flexures).

Let's use:

  • Diamondoid molecular structural elements (DMSEs) for structural ones of all sizes including beside small ones also bigger ones
  • Diamondoid molecular machine elements (DMMEs) for functional ones that are typically bigger in size
  • Diamondoid molecular elements (DMEs) for structures of all sized including both of the former
  • ("Diamondoid" can be replaced by "Gemoid" to include more general gemstone like compounds like e.g. sapphire)
  • Or G for D if it's a gemstone that is not diamondoid.

Examples:

Naming the base material makes the "crystal" part in "crystolecular" redundant.
So here the choice has been taken to go back to just "molecular" to avoid nesting custom terms.
Well, not fully consistently ATM: Diamondoid crystolecular machine element

Section possibly deprecated due to too many (eight) naming possibilities.
(Diamondoid|Gem-based)(Molecular|Crystolecular)(Structural|Machine)Element

Base material

Specific focus (diamond & co)

Of especially high interest are diamond, its hexagonal version called lonsdaleite, and diamond like compounds.
Many semiconductors fall in this class too.
As of 2025 other compounds still remain largely unexplored for use as crystolecules.

A subset of crystolecules (or gemstone-like molecular elements) are
diamondoid crystolecules (diamondoid molecular elements).

General focus (gemstones)

Gemstone-like compounds are the most suitable base material for crystolecules.
For a collection of gemstones of particular interest see page:
Base materials with high potential.

Beside classical gemstones like diamond other semi-precious minerals including
bio-minerals that are synthesizable in solution also fall under gemstone-like compounds.
Along the incremental path these may be accessible earlier.
See page: technology level IIfor semi advanced precursor technologies.

Some gemstones like periclase MgO and Transition metal nonmetallides (TiC, TiN, TiO)
transition over from mainly covalent to ionic salt like. See next section.

Exotic focus (salts, metals, …)

Use of pure metals and metal alloys is limitedly suitable for crystolecules for a number of reasons.

  • Mechanical sliding interfaces can't be done with blank metal on metal surfaces due to seamless metallic welding on contact. Also, surfaces are likely difficult to passivate (for allowing sliding interfaces that way) due to the catalytic nature of metals. A full gemstone layer may suffice (possibly oxidic) but that just goes back to gemstones. Structural applications are less problematic but face issues too.
  • Metallic bonds with free electron gas are not directed like covalent bonds and sort of more "slippery". High performance gemstones are notably stronger especially when sticking with one's choice to abundant elements. Best of todays steels will pale compared to say superelastic sapphire based gem-gum. Also (gemstone typical) full breakage might be a preferable digital yes/no failure mode over (metal typical) plastic deformations.
  • Metal ad-atoms on metal surfaces tend to diffuse away from where they have been deposited. Likely ok with sticking to flat surfaces during crystolecule usage and with sticking with mechanosynthesis at sufficiently deep cryo temperatures in fabrication.
  • Usage of salts like gemstones should face fewer issues than metals structurally in limited scale. Flawless nanoparts will be superelastic but interlocking to make large scale gem-gum faces the issue of seamless ionic welding.
  • Salt like gemstones (just like metals) can't be passivated well for sliding interfaces. Salt like gemstones as base material are thus likely mostly useful for structural framework purposes. Possible exception: Enforced non-bonding spacing may allow to play some tricks with discrete notched motion.

How crystolecules will be made and used

From atoms to crystolecules

Buildability: Unfortunately crystolecules and their assemblies
crystolecular (machine) elements cannot be produced yet (state 2015..2025).
See page: Why natural chemistry can not be used to make crystolecules

Mechanosynthesis can start to be prototyped today 2025 with scanning probe microscopy technology.
This does not cover scaling yet. For that see page: Bootstrapping

From smaller crystolecules to larger crystolecules

See page: Seamless covalent welding
Any form of non-bonded assembly (form closure,vdW force, clipping, …)
is not subsumed here but is subsumed in the next section.

From crystolecules to their assemblies

Assembly in advanced productive nanosystems. In advanced nanofactories crystolecules would be:

Misleading aspects in MD simulations of crystolecules and their assemblies

See main page: Misleading aspects in animations of diamondoid molecular machine elements

Beware of the "nanodiamond-is-jelly availability bias" misjudgement

Molecular dynamics simulations are typically run simulating extremely high speeds thus showing jelly like wobbling which would not at all occur when operated at actually proposed (steady state) speeds many orders of magnitude slower.

No, crystolecules (nanoscale diamond or other gemstones) do not normally behave like jelly. It is just that …

  • it is so much easier to simulate them at extremely high speeds and …
  • unlike strong non-rubber macroscale materials they don't break or bent at these speeds and …
  • unlike macroscale materials they even could dissipate the heat but …
    with the important caveat of being as lone standing nanomachine coupled to cooling bulk.

See page: A better intuition for diamondoid nanomachinery than jelly

Beware of the stroboscopic illusion

Simulations of DMEs often show a stroboscopic effect this can be misleading and make one believe that the operation frequencies lie near the thermal frequencies, thereby giving the false impression of enormously high friction.

Why the strobe effect?
To make the machine motion visible in a movie despite them being slow compared to the thermal motions many molecular dynamics simulation frames are dropped and only a few are taken as movie frames. Thus in the movie the atoms are at a random point in their wiggle cycle at each movie frame making them jump around erratically at e.g. at gif file frame rate.

How to fix the strobe effect?
Averaging atom positions for the merged simulation frames and increasing apparent size based on their momentary wiggle amplitude would be an easy huge improvement. Blurring and following even thermal torsional motion of H atoms on OH groups more advanced possibilities.

What else is misleading?
Note that even with the stroboscopic effect fixed simulation speeds are still picked extremely high (m/s to km/s). Way above speeds that were actually proposed for productive nanosystems (mm/s). So there is jelly like wobble visible that would be the rare exception rather than the norm in nanomachine operation. Exception: Rare high energy snaps. Norm steady state near reversible operation.

At proposed speeds gemstone like molecular machine elements with sliding interfaces will work exceptionally well.
See related pages: Superlubricity, Friction in gem-gum technology
There is both experimental evidence and theoretical evidence for that.
(See e.g.: Evaluating the Friction of Rotary Joints in Molecular Machines (paper) and the friction analysis in Nanosystems)

well animated bearing
The fast thermal vibrations are more realistically blurred out. The remaining localized periodic average deformations (visible here if one looks closely) are highly reversible. (See page about "superlubrication".) 		badly animated bearing
The present stroboscopic effect can be misleading in that friction is likely to be grossly overestimated. It deceivingly looks like as if the operating speed would be close to the speed of the thermal vibration. If that were the case it indeed would cause massive friction (strong coupling of motions with similar frequency).
DMME - bearing with blurred out fast vibrations
DMME - bearing with blurred out fast vibrations
DMME - bearing with misleading stroboscopic effect
DMME - bearing with misleading stroboscopic effect

…

History of this page

Since the here described physical objects have no official name yet (2016..2025)
something sensible had to be invented to refer to them in this wiki.

The small & simple initial idea was:
These objects are somewhat of a cross between a crystal and a molecule.
So let's use the term "crystolecule" as a portmanteau.

With time this page amassed a lot of discussion regarding
the choice of terminology and refinement on the definition.
What was later eventually worked out into the extensive definition here.
See the intro of this page.

"crystolecule" is nice because it's:

  • quite accurate in descriptiveness
  • quite conveniently usable in natural language
  • quite memorably (catchy) because it seems unusual (clickbait effect)

(wiki-TODO: This section is a bit redundant with the definition, maybe to clean up later.)

Specifically let's use the term "crystolecule" for ones that are typically are:

Related

Terms for bigger assemblies of several crystolecules but not yet as big (and disassemblable) as microcomponents

External links

At K. Eric Drexlers website:

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