Design of crystolecules

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This article is a stub. It needs to be expanded.

This page is about issues with the design of crystolecules / DMEs.
For a definition of what they are see here: "What are crystolecules DMEs?"

Applicability of 3D FDM printing for Crystolecule Design

Main article: applicability of macro 3D printing for nanomachine prototyping

Some strong limitations for plastic FDM 3D-printing also hold for mechanosynthesis of crystolecules. (FDM ... fused deposition modelling i.e. printing with molten plastic from a nozzle) Thus, in the context of these limitations, if something works for FDM 3D-printing then chances are that the tested mechanical concept in question will work for mechanosynthesis of crystolecules too. (Not quite exploratory engineering but conservative design.)

Of course there clearly are limitations in the mechanosynthesis of crystolecules that are not present in FDM 3D-printing. One needs to look out for those in the judgment whether bulk macroscale designs could be ported over to nanoscale crystolecule designs.

physical models for visualization only

Non functional models purely for visualization that have all their surface atoms visible and color coded require more expensive full color powder printing. (Hard brittle and rough material)

demos of principles

The author of this Wiki (about) conducts a meta project that aims to build up a collection of 3D-printable 3D-models (mainly in atom aware bulk limit) that will hopefully turn out to be useful in the development and understanding of advanced nanofactories. See main article: The DAPMAT demo project

Some things to take care of

avoid quartz like solid CO2 or the like

Too much oxygen must not be brought in direct bonding contact with carbon atoms since this may practically represent solid CO2 which will likely behave like an highly potent explosive. The same goes for other combinations that are known to be highly energetic from normal cemistry. Some examples: room temperature solid nitrogen (in sp3 hybridisation), oxygen chains, ...

avoid too high interface pressure in sleeve bearings

If the fit gets too tight the atom "teeth" may spontaneously jump back with thermal speeds instead of lowly bend back with machine speeds the induced snap back overshoot vibrations will be fully dissipated and not, as desired, almost fully recuperated. Instead as a bearing the device will work as friction unit.

check for too strained spots in auto-generated passivation layers

Concave edges passivated with hydrogen sometimes causes the hydrogen atoms to massively overlap. Sometimes two hydrogens can be replaced by a oxygen bridge but this introduces tension that may detrimentally deform the crystolecule. Alternating with oxygen with its bigger cousin sulfur or nitrogen with phosphor might help in some cases.

Since passivation atoms add thickness it can be tricky to create parts complementary in shape.
(wiki-TODO: collect some tricks here how this can be made easier)

avoid situations where poisonous molecules may be released on thermal or chemical attack

(wiki-TODO: elaborate on this)

Designing mechanical metamaterials in such a way that in case of overload they do only break at predeterimined internal surfacts allow one to keep internal machinery as isolated as possible. Thus one can very effectively protect internal materials from chemical attack.

Regarding molecular dynamics

avoid elements left of the carbon group (at least for now)

Electron deficiency bonds are misrepresented nanoengineer-1's current force field models. A nitrogen atom adjacent to a boron atom embedded in a diamond crystal shouldn't strongly repel each other but instead behave almost like carbon atoms since the boron has the space for the nitrogens excess electron. Since aluminium is to an electron deficient element it is likely to misbehave the same way as boron does in the nanoengineer-1 model. A safe way to go is to not use them yet in crystolecule designs.

Equilibration method

Nanoenginer-1 (TODO: version?) seems to use a rather naive force field equilibration method of just iteratively equilibrating all the atoms one after another and applying the changes all at once (not sure if this is the case - (TODO: check code)) that does not scale well. A self adapting (TODO: add implementation ideas) 6D space Fourier space deformation method might be implementable to speed up equilibration massively. (TODO: IIRC there where news of a new faster equilibration method - find it and link it here)

The three levels of stability - chemical, thermal, mechanical

Stability against chemical attacks is hardest to achieve followed by stability against thermal loads (high temperatures). Stability against mechanical loads is easiest to achieve.

A good design software should keep track of high energy bonds. Bonds can carry high energies either due to chemical instability (weak bonds that could form strong ones if rearranged) or due to very high strain. Some local spots / nests of high energy bonds may be ok but the products as a whole should not become explosive or a fire hazard.

Silicon (or metals) as fire quenching agent:
Materials that contain a lot of energy when located in an oxygen atmosphere (like on earth) are not necessarily a fire hazard. Physical processes can stop a runaway chain reaction (a blazing major fire). In nature on earth there's the quenching agent is water (which unfortunately can evaporate and lead to very dangerous situations) In advanced gem-gum products of large scale (e.g. cities on Earth or balloons on Venus) one could use silicon as quenching agent. By replacing half of the carbon atoms in diamond (or lonsdaleite or other sp3 carbon compounds) one gets various forms of moissanite (SiC) which is ridiculously hard to burn. Very quickly a protection layer of glassy slack forms which very effectively prevents further oxygen from reaching more of the moissanite.

Due to the possibility of sealing most of the nano-machinery in into a highly inert internal environment (practically perfect vacuum) the strongest restriction (chemical stability) can for the most part be lifted. (For everything not facing weather exposed surfaces). Water soluble compounds and even compounds that moderately react with water can be considered for usage.

For thermal stability one needs to mind "consistent design for external limiting factors". Weak or extremely strained bonds may limit heat resistance.

Avoidance of toxicity

A good design software should constantly look at which elements are put near each other and in which bond topologies. When advanced gem-gum products are attempted to be burned (which one may want to avoid in most cases - see: diamondoid waste incineration) then certain configurations are likely to undergo thermally induced reconstructions (and oxidations / nitrations) that lead to products compounds that can be slightly to highly toxic. There's a huge amount of knowledge about simple compounds and their toxicity and environmental impact. Even on the "surface" of the web (wikipedia) alone. This needs to be unified for a standard software interface.

Two abundant elements that are especially prone to create problematic compounds are phosphorus and chlorine. Also sometimes problematic: fluorine, boron, ...


Intended working environment: vacuum / aggressive medium

At any time the accessible crystolecule structures are given by the available capabilities of Mechanosynthesis.

External links


  • NanoEngineer-1
    Here some active development continues to happen:
    (Umbrella brand: MDS Molecular Dynamics Studio)
    The new focus though seems to go more in the direction of science than engineering.

Situations to avoid or at least to be aware of: