The Physical Basis
of High-Throughput
Atomically Precise Manufacturing

As outlined below, atomically precise manufacturing (APM) can be understood through physics, engineering design principles, proof-of-concept examples, computational modeling, and parallels with familiar technologies. Several chapters in Radical Abundance discuss these topics in depth.

Parallels between APM and familiar technologies

In brief, APM is a prospective production technology based on guiding the motion of reactive molecules to build progressively larger components and systems. Bottom-up atomic precision can enable production with unprecedented scope (in terms of product materials, components, systems, and performance), while fundamental mechanical scaling laws can enable unprecedented productivity. Several familiar technologies offer strong parallels:

  • Chemistry and biochemistry, which (like APM) produce nanoscale structures with atomic precision by combining molecular building blocks.
  • Additive manufacturing, which (like APM) is a general-purpose production technology that employs compact machines (desktop scale and larger) to build intricate objects from small bits of material, directed by digital data.
  • Conventional manufacturing, which (like APM) uses systems of machinery to move, position, and assemble components, solving essentially identical motion problems by similar means.
  • Digital logic systems, which (in analogy to APM, with differences highlighted) employ macroscopic arrays of high-frequency nanoscale electronic devices to process discrete parts, bits packaged in bytes, to form complex patterns.

To complete the digital logic analogy: APM systems employ macroscopic arrays of high-frequency nanoscale mechanical devices to process discrete parts, atoms packaged in molecules, to form intricate patterns.

Thus, APM can be described a prospective technology based on compact, general-purpose manufacturing systems that use macroscopic arrays of nanoscale devices to move, position, and assemble molecular (and larger) components, bonding them with atomic precision to build macroscale products from the bottom up. Roughly speaking, APM can be described as manufacturing based on a programmable “factory on a chip” technology.

APM rests on familiar principles

Current knowledge regarding potential systems for high-throughput APM rests on textbook science and engineering principles. This is a deliberate engineering choice: The methodology used at the current level of analysis — exploratory engineeringdeliberately excludes speculations regarding unknown or poorly understood physical phenomena. Exercises in design and analysis have shown that a composition of unproblematic components can suffice to implement surprising system-level capabilities.

Must new and surprising system-level results stem from new developments at a fundamental, physical level? A moment’s thought shows that this cannot be a fixed rule, because most innovation in engineering — whether surprising or not — involves no new scientific principles.

This is why the fundamental physical principles and operations that enable APM are quite familiar. Here’s an outline:

The physical basis of APM-based fabrication
Atomically precise nanoscale devices can bind both chemically reactive molecules and large molecular structures.
Nanoscale devices can position reactive molecules with atomic precision relative to large structures.
Positioning reactive molecules with atomic precision can direct structure-building chemical reactions to specific sites on large structures.
Programmable devices, or a series of specialized devices, can direct sequences of site-specific, structure-building chemical reactions.
Sequences of site-specific, structure-building chemical reactions can build complex, atomically precise nanostructures, including atomically precise nanoscale devices.

Note that each of these operations — though in a context very different from an APM-style factory — is demonstrated by ribosomes, devices that build peptide nanostructures by positioning a series of activated molecular building blocks (aminoacyl-tRNA molecules) in sequences programmed by mRNA.

See also: From Self-Assembly to Mechanosynthesis

Predictive computational modeling of stiff structures

For suitably selected non-biological chemical and mechanical systems, each of these fundamental operations can be analyzed quantitatively.

In doing so, it’s convenient to explore systems built of components that consist of strong, stiff, covalent structures because these are easier to model than biomolecular systems. There are two key features of stiff covalent structures that facilitate modeling: First, these structures are insensitive to small errors in the potential-energy functions that underlie simulations of molecular dynamics; and second, severe conformational restrictions (a consequence of ubiquitous polycyclic structures) avoid the familiar challenge of evaluating the delicately balanced free energies that determine (for example) how proteins fold and interact with ligands in aqueous environments. Computational chemists will immediately see that these characteristics can greatly increase the predictive power and reduce the computational cost of simulations.

Similar remarks apply to the molecular physics of chemical transformations, where restricting translational and rotational degrees of freedom (and choosing favorable, well-understood reactions) can greatly increase the predictive power of density functional theory, and can facilitate the use of fully ab initio methods to model reactive structures and transition states.

As before, these features follow from design choices made in order to avoid poorly understood phenomena. Choices made to facilitate implementation of precursor technologies by means of accessible techniques lead to different structures and different challenges: Not rigid covalent structures, but flexible folding polymers and larger structures built using Brownian self-assembly.

Stiff covalent structures, although attractive and easy to model, will be among the most challenging synthetic targets; From Self-Assembly to Mechanosynthesis discusses a spectrum of prospective materials and techniques.

Thus, the current state of physical and computational technologies forces a choice between studying devices that are designed as targets for laboratory development and studying devices that are designed as targets for reliable computational modeling. In other words, relaxing the constraint of present-day synthetic accessibility enables the freedom to choose designs that enable confident present-day analysis.

High-throughput APM

Exploratory engineering methods have been applied to characterize devices with a range of functions sufficient to implement a broad class of mechanical systems, a class that includes conservatively designed APM systems.

Rather then designing devices and systems for optimal performance or near-term implementation, they can be designed to facilitate high-confidence modeling and analysis by means of standard physics-based methods. Within this constraint, conservative engineering choices can establish conservative lower bounds on system performance. Fortunately, devices based on stiff covalent structures can have favorable mechanical properties — high strength and stiffness, for example, and low sliding friction.

System-level analysis

At a molecular level, the fabrication of small building blocks is governed by the molecular physics of chemical reactions, and must be analyzed as such, and not in terms of conventional mechanical operations (or naïve anthropomorphic “fingers”). Organic synthesis and surface science provide a range of model reactions (for example, the reactions employed in chemical vapor deposition); quantum chemistry can used to study a yet wider range of reactions.

Studies of carefully selected structures at a larger scale (several nanometers) show that components and systems can be engineered to emulate a wide range of familiar mechanical devices. Here, several considerations are important. At interfaces between components, it is necessary to choose structures that are chemically stable and have favorable non-bonded surface interactions. For reliable mechanical operation, thermal fluctuations are a key concern. Thermal fluctuations impose requirements for energy barriers large enough to block transitions to unwanted states (typically ≥ 50 kBT), entailing a suitable combination of structural stiffness (providing elastic restraints) and tolerance for positional displacements.

With care in design, the structural stiffness, ks, can typically be ≥ 20 N/m, constraining r.m.s. displacements (kBT/ks)–½ to ≤ 1.4 × 10–11 m at 300 K. A typical tolerance for displacement is ~1.5 × 10–10 m, and with ks = 20 N/m, a ~1.5 × 10–10 m displacement is opposed by an elastic energy barrier > 50 kB at at 300 K.)

To summarize the results of an extended design exercise (presented in Nanosystems: Molecular Machinery, Manufacturing, and Computation, and reviewed in a National Academy of Sciences report), conservative engineering analysis shows that high-throughput APM can be performed by non-biological, factory-style systems that operate on a wide range of molecular building blocks to produce a wide range of non-biological materials, atomically precise nanostructures, and larger assemblies. These products include components and assemblies of the kinds necessary to implement similar factory-style systems.

These conclusions are a consequence of chemical and physical principles, and can be summarized as follows:

The physical basis of high-throughput
APM-based fabrication of large products:
Atomically precise nanostructures can implement components that provide a full range of ordinary mechanical functions: These include motors, bearings, gears, conveyors, and so forth.
This range of component functions is sufficient to implement machinery like that found in high-throughput assembly systems.
At and above the nanometer-scale building-block level, chemical and intermolecular interactions can play roles like those of fasteners, and can bind and align surfaces to form atomically precise interfaces.
Assembly of small atomically precise components can therefore yield larger atomically precise components, and similar assembly operations can be extended to micro- and macroscopic scales.
The mechanical stiffness of suitably designed nanoscale machinery can limit the r.m.s. amplitude of thermal fluctuations to ~10–11 m at 300 K.
Mechanical stiffness together with tolerances for positional offsets during assembly can be great enough to limit error rates induced by thermal fluctuations to (for example) ~10–15 per operation.
Energy dissipation per molecule processed and incorporated into a product structure can be limited to a small multiple of the energy dissipated in conventional chemical processing of materials.
The natural motion speeds of mechanical devices are independent of scale, hence the natural frequencies of mechanical operations are inversely proportional to scale.
On a throughput-per-unit-mass basis, the natural productivity of assembly machinery is proportional to the frequency of operations, hence inversely proportional to scale.
The size and frequency ratios of conventional manufacturing machinery in comparison to machinery based on atomically precise nanoscale components are, respectively, approximately 1 : 10–6 and 1 : 106.
The natural productivity of nanoscale manufacturing machinery on a per unit mass basis can therefore exceed that of conventional machinery by a factor of ~106.
In a full production system, throughput is limited by the speed of assembly of the largest (end-stage) components that result from convergent assembly of smaller components.
The natural productivity of a full APM system, from raw materials to products, is therefore similar to the productivity (measured by mass-based throughput) of final assembly operations in conventional manufacturing.
The broader physical and engineering analysis supporting the above indicates that additional system-level constraints not mentioned above can be satisfied. These include providing means for

  • power supply,
  • waste heat removal,
  • feedstock purification,
  • binding of feedstock molecules,
  • molecular transport and activation,
  • molecular placement,
  • control signals,
  • fault-tolerance adequate to enable reliable system operation in the presence of manufacturing defects, background radiation, and failures of nanoscale components.

Lengthy yet accessible development paths lead from today’s extensive, million-atom scale capabilities for atomically precise fabrication to APM-level technologies of the kind outlined above; incremental development paths are outlined in the post From Self-Assembly to Mechanosynthesis and discussed in more depth in Appendix II of Radical Abundance.


Relevant posts include: