Productive Nanosystems as a Milestone Toward Geoethical Nanotechnology
James B. Lewis, Ph.D.
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Proteins could be useful partners for DNA in engineering MMCNs. Proteins are composed of 20 monomers and have a thinner backbone than do DNA molecules, so that they provide for a wider range of fine-grained molecular shapes and surface properties. Proteins also offer great mechanical stiffness compared to DNA—greater by a factor of 16 (horn) to 160 (silk) [12]. One consequence of the match between protein structures and DNA structures is that proteins can easily be engineered that will recognize specific DNA sequences from the outside of the DNA double helix so that proteins will bind to specific addresses on a DNA structure without needing to unwind the helix. Proteins can bind other molecules in precise orientations, and can thus act as atomically precise connectors to assemble other structures to uniquely addressable locations on DNA frameworks. Proteins and nucleic acids, in the form of ribosomes and DNA polymerases, cooperate to assemble monomers into polymers of specified sequences, suggesting that they could be engineered to make productive nanosystems that assemble other types of polymers from specified sequences of monomers.
Artificial oligomers called bis-peptides are promising alternatives to proteins for some uses. Unlike the single peptide bonds that link amino acids together to form flexible protein chains, bis-peptides connect monomers with two covalent bonds to form rigid ladder-like chains with pre-determined structures. Other types of non-natural polymers that resemble biopolymers are also being studied.
In addition to DNA and proteins, MMCNs could incorporate specialized functional components from other areas of nanotechnology.
The roadmap envisions the first generation of artificial systems performing the same function with artificial monomers as biological APPNs perform with the monomers of proteins and nucleic acids—adding specified monomers to the growing end of a one dimensional polymer, which then folds into a three-dimensional shape determined by weak interactions among monomers. It moves on to consider construction of two-dimensional and three-dimensional polymers that would depend upon networks of covalent bonds to specify their structures, and which would thus have more favorable mechanical properties. One approach would be patterned atomic layer epitaxy (PALE), in which a scanning probe microscope tip uses atomically precise removal of surface hydrogen atoms from a crystal (a process called depassivation) to create a pattern of sites that will react with a gas or liquid to bond atoms to those sites, thus forming an atomically precise, densely bonded structure as a result of growth of the crystal lattice. Another approach would use a probe tip to place multifunctional molecular building blocks at specific reactive sites on a crystal surface.
Theoretical studies have already investigated the possibility of using highly reactive molecular fragments (for example, building diamond lattice using carbon radicals and carbenes). However, such high energy, reactive building blocks are difficult to work with, requiring ultra-high vacuum conditions. The roadmap considers highly reactive building blocks to be appropriate for advanced systems, but proposes early systems use less exotic building blocks to produce dense networks of mixed ionic and covalent bonding. Possible building blocks include silicic acid (a precursor of silica) and other oxide ceramics, semiconductors, metals, or graphite, or using highly branched polymers called dendrimers. Tip-based mechanosynthesis using less reactive building blocks may be compatible with an aqueous environment and therefore able to make use of biopolymer-based atomically precise tools. However, these entire scanning probe approaches to atomically precise manufacturing are in very early stages of development,
Hybrid systems that combine atomically precise and atomically imprecise components may have a role to play in developing early generation APPNs. Noteworthy contributions include two molecular motors mounted on substrates fabricated lithographically. The first is an electromechanical motor in which a metal rotor is suspended among electrodes on a bearing composed of a multiwalled carbon nanotube. The second is a biomolecular motor in which the molecular motor protein F1-ATPase mounted on a nickel substrate spins a nickel propeller, fueled by the chemical energy in ATP. Such motors could furnish mechanical motion to drive components of early productive nanosystems. Further, multiwalled carbon nanotubes have been characterized as molecular bearings and nanosprings, and might be pressed into service to direct mechanical motion in early nanosystems.
Clarifications and elaborations
Included with the roadmap document is a collection of thirty-nine papers resulting from the roadmap Working Group deliberations. These papers extend or elaborate on points made in the main roadmap document. Some focus on specific applications of APM and others consider computational tools and other enabling technologies. Among those that deal with the transition from current APM technologies to APPNs are the following, which clarify or elaborate upon the above points.
J. Randall [13] discusses the main limitation with current technology for spatially controlled (tip-based) assembly and proposes a way forward. The problem is not lack of atomic precision in tip positioning, but rather the lack of atomically precise tips able to capture atoms or molecules in the correct orientation and transfer them reliably to the specified binding site. The solution with current technology is to forgo mechanosynthesis for now and instead use atomically precise deprotection (depassivation) to remove a surface atom and create an active site—a capability that has already been demonstrated, for example by the ability of electron tunneling from an STM tip to remove a hydrogen atom from a silicon crystal surface with atomic precision. A specified atom or molecule to react with that site and with other deprotected sites—and no other sites—can be delivered by diffusion from gas or liquid. This process has been named patterned atomic layer epitaxy (PALE). The end result is silicon or other atoms deposited at those sites from which hydrogen atoms had been removed. More advanced work might use two different passivation/depassivation chemistries that differ in stability.
The more robust passivation layer would be patterned with atomic precision, while the process that deposited silicon in the patterned layer would use a less robust passivation process that could be removed in a bulk process that did not affect the more robust passivation. Combining layers of different materials could provide more varied properties and the capability of releasing from the surface complex 3D structures. Atomically precise parts produced by PALE using two materials will “enable the design of near-arbitrary 3D structures,” which might make possible the construction of atomically precise nanoscale positioning devices and, eventually, APPNs.
D.G. Allis [14] provides an overview of mechanosynthesis, the process in which molecules or materials are assembled by using mechanical control of the placement of one or more reactants to direct the formation of chemical bonds. This positional control of reactants offers important benefits. Side reactions can be avoided; mechanical energy can be used to overcome barriers to reaction; highly cross-linked products can be more easily constructed; very high effective concentrations of reactants lead to very fast reactions. These advantages sum to the ability to synthesize extremely complex structures built from small reactive molecules. Mechanosynthesis favors the use of a single reactant in a multi-step process to assemble complex products. The dozen or so landmark studies that are surveyed include both experimental and theoretical achievements. Chemically non-reactive atoms have been arranged on a metallic surface at very low temperatures. Weak covalent bonds have been mechanically broken to create radicals that were then combined to form a molecule. Single silicon atoms have been removed from and then added back to a specific site on a silicon surface. Computational studies have focused on removing hydrogen atoms from surfaces or using very reactive carbon radicals to synthesize diamond—structures more reactive than those so far explored experimentally.
J. Storrs Hall [15] considers what deposition methodology would make possible a 3D printer capable of constructing atomically precise products through a process of molecular epitaxy in which atomically precise building blocks are deposited in layers to built up the product. Crucial design considerations include the interaction between tool tip and building block so that the building block and be precisely positioned on the surface in the proper orientation for binding to the surface or to other building blocks, and then cleanly released. Specific issues include the trade-offs among building block size, interaction strength, and available chemical functionality. In general, the difficulties of working with highly reactive species are avoided by using weaker interactions between stable building blocks.
D.R. Forrest, R. A. Freitas Jr., and N. Jacobstein [16] consider the diamondoid mechanosynthesis (DMS) path to APPNs, in which scanning probes with novel reactive tips are used to fabricate atomically-precise diamondoid components, as an alternative to the path proposed by Drexler in which polymeric structures and solution-phase synthesis are employed as intermediate technologies. They note that existing scanning probe microscopes have the resolution required for DMS, but that repeatability must be improved about twenty-fold. They further note that the use of mechanical force to break and make specific covalent bonds on a crystal surface was demonstrated in 2003 (by the Custance group). Further, extensive computational studies have concluded that DMS could be used to build single crystal diamond, carbon nanotubes, and at least nine reactive tool tips for DMS.
J. Lewis [17] reviews how structural DNA nanotechnology provides the ability to construct molecularly precise structures based upon the well-understood molecular recognition properties of DNA. A wide variety of atomically precise DNA nanostructures of diverse shapes have been created. At the 100-nm scale, arbitrary aperiodic patterns have been constructed in two dimensions. Some DNA nanostructures are capable of mechanical movement, and DNA actuators in an array can be individually addressed and controlled. Frameworks constructed from DNA nanostructures have been used to organize arrays of guest molecules. DNA devices have been constructed that 'walk' along DNA tracks, and that organize components for covalent bond formation.
Footnotes
[12] See “Toward Advanced Nanotechnology: Nanomaterials (2)” posted by Eric Drexler, Jan. 16, 2009, http://metamodern.com/2009/01/16/toward-advanced-nanosystems-materials-2/ [accessed Mar. 1, 2009].
[13] J. Randall “Atomically precise manufacturing processes” (pp. 01-1 to 01-5) and “Patterned ALE Path Phases” (pp. 03-1 to 03-5) in Working Group Proceedings (see [11] above).
[14] D.G. Allis “Mechanosynthesis” pp. 02-1 to 02-6 in Working Group Proceedings (see [11] above).
[15] J. Storrs Hall “Numerically Controlled Molecular Epitaxy (Atomically Precise 3D Printers)” pp. 04-1 to 04-5 in Working Group Proceedings (see [11] above).
[16] D.R. Forrest, R. A. Freitas Jr., and N. Jacobstein “Scanning Probe Diamondoid Mechanosynthesis” pp. 05-1 to 05-4 in Working Group Proceedings (see [11] above).
[17] J. Lewis “Nucleic Acid Engineering” (pp. 07-1 to 07-7) and “DNA as an Aid to Self-Assembly” (pp. 08-1 to 08-9) in Working Group Proceedings (see [11] above).