Kinematic Self-Replicating Machines

© 2004 Robert A. Freitas Jr. and Ralph C. Merkle. All Rights Reserved.

Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines, Landes Bioscience, Georgetown, TX, 2004.


4.11.2 Merkle Replicating Brick Assembler (1995-1997)

During 1995-1997, Merkle [212]) adopted Drexler’s minimal assembler proposal (Section 4.11.1) using the extruding brick architecture (Figure 4.38), and began to flesh it out. Merkle’s device, which he called a “replicating brick” assembler, would be a sealed container with diamondoid walls floating in a liquid medium (Figure 4.41). It was noted that water or a suitable hydrocarbon such as hexane or other liquids would suffice, as long as they could dissolve all required feedstock molecules, as yet unspecified. The inside of the box would be compressed neon gas of unspecified pressure, which would allow acoustic power and control signals to be transmitted from the external liquid environment into the gaseous internal environment, and thence to pressure-driven threshold actuators each ~125 nm3 in volume. A giant sliding end cap “piston” provides pressure equilibration between interior and exterior. A vacuum interior was explicitly rejected because of the requirement for “an internal medium that is able to carry acoustic (pressure) signals.” Merkle agreed with Drexler that helium was an attractive alternative that should also work, but as the design might use sliding seals which should block diffusion of the inert gas, it is convenient to select the slightly larger-atom inert gas neon. “While sliding seals that block the passage of helium should be feasible, they must be tighter and present a greater design challenge.” Also following Drexler, the broadcast architecture was explicitly adopted.

Merkle restricted his assembler “to the class of ‘diamondoid’ structures defined in Nanosystems [208] as including structures made from hydrogen; first row elements such as boron, carbon, nitrogen, oxygen and fluorine; and perhaps some second row elements such as silicon, phosphorous, sulfur and chlorine. Metals and other elements will generally (though not always) be excluded from consideration.” However, Merkle had already recognized that the design might be further simplified, and anticipated his later cased hydrocarbon design, when he added: “We will frequently confine ourselves to hydrogen and carbon, as hydrocarbon structures are relatively easy to analyze and can often provide remarkable materials properties (e.g., diamond, graphite, and related structures). Potential energy functions which provide a good description of the behavior of hydrocarbons are available.” Feedstock molecules would be transported from the exterior of the assembler to the interior using multiple stages of variable affinity binding sites. Once inside, molecular tools with highly reactive tips [2315] – including radicals, carbenes, and other highly reactive species of the general type found today in the CVD synthesis of diamond – would allow the synthesis of diamondoid structures. In 1997, Merkle [216] published a theoretical proposal for a partially complete mechanosynthetic tool set for building hydrocarbons.

Inside the assembler, an unusual double-tripod [215] Stewart platform – a relatively compact, six degrees of freedom positional device combining high stiffness with a wide range of motion – is used for the internal transport of molecular tools and other components via a simple “pick and place” procedure. This design simplification is possible because within the shell of the assembler, the location of every structural atom is known to within the positional uncertainty created by thermal noise – which is small in this case because the internal structural components have relatively high stiffness. Hence “the position of every structural atom in the system can be known to within a fraction of an atomic diameter with high reliability at room temperature and without the need for explicit positional sensing. This approach might be likened to a blind man assembling a product at a workbench where every tool and every component had a known position – the blind man would be able to perform the assembly operations despite the absence of positional sensing capabilities because the location of every nut and bolt was known.”

As in Drexler’s minimal assembler, Merkle’s replicating brick employs some tens of pressure-actuated ratchets positioned as drivers directly on the struts of the manipulator device. But instead of Drexler’s 20 different threshold pressure bands, Merkle usefully introduces for the first time a two-band signaling model: “Instead of addressing each individual ratchet by assigning it its own pressure range, we use pairs of ratchets and use only two pressure ranges. The first pressure range activates the first of the pair of ratchets, which we will call stepping ratchets, and causes a circular band to be stepped forward. At one or more points on the circular band are notches that indicate that the second of the pair of ratchets is to be made active. Each pair of ratchets has a unique set of notches in its associated circular stepping band. The second ratchets we will call working ratchets: they control the actual activities of the assembler. All working ratchets are either active or inactive, depending on the presence or absence of a notch in the stepping band. Signals sent in the second pressure range cause the active working ratchets to step but have no effect on the inactive working ratchets. By this method an indefinite number of working ratchets can be made active or inactive, and in fact can be made active and inactive in sets. The price we pay for this mechanism is the need to send stepper signals to activate the stepper ratchets and so select which working ratchets are to be active. While this will somewhat slow the signaling process, it has the distinct advantage over [Drexler’s minimal assembler] that the addition of new working ratchets will not require an extension in the pressure range of the system. Thus, new working ratchets can be readily added late in the design or implementation cycle with minimal bother. In addition, the total pressure range that the system must accommodate is made much smaller, simplifying both the pressure control mechanisms and the design of the pressure actuated ratchets (the amount of overpressure that a ratchet is required to tolerate is greatly reduced, for example). Other devices required for assembler operation besides the struts of the double tripod will also be operated by threshold pressure actuated ratchets.” One hidden complexity in this approach is the multitude of circular “stepping bands” at each control site which effectively act as a distributed multiplexor (Section 4.10.2) and could add significant bulk to the machine, and whose design is largely uncompleted.

While a selective transport mechanism for helium might only require simple pores large enough in diameter to permit the passage of helium but sufficiently small to exclude other contaminants, a selective transport mechanism for neon will be more complex because a pore large enough to allow neon to pass might also permit the entry of linear molecules composed of first row elements such as N2, O2, and CO2. One mechanism for dealing with this problem would be to block both ends of a pore that is too short to hold any molecule longer than neon when the pore’s ends are blocked, and then alternately open either end of the pore, making certain that both ends of the pore are never open at the same time as this would permit entry of linear molecules. Drexler [2317] has also proposed a molecular pump that molecular dynamics tests [223] suggest should be able to pump neon, but hydrogen and helium would likely be able to penetrate such a mechanism and hence should be excluded from the external liquid environment. Proposed designs for selective transport mechanisms “must be compared with the expected profile of contaminants in the surrounding liquid to insure that the rate of entry of contaminants is sufficiently small. While the concentration of helium should be kept small, some trace amounts of helium should be harmless. A few other small contaminants (such as N2) might also be of concern. While it seems unlikely that they would enter as readily as Ne, H2 or He, their entry rate might still be unacceptably high. If this proves to be the case, then their concentration in the external liquid environment must also be kept low. For the present proposal this is acceptable as a major objective is to simplify the design of the assembler even if that increases the cost of creating and maintaining the environment in which it operates. More generally, the complexity of the self-replicating component can often be reduced by imposing tighter constraints on the environment in which it functions.”

Merkle notes that self-replicating systems that employ a barrier to prevent external contaminants from entering the internal regions may also require a method of increasing the volume of the internal region, and that the replicating brick approach will allow this: “A brick with dimensions X > Y > Z extrudes a new brick along the Z axis oriented such that the Y dimension of the newly extruded brick is aligned with the X dimension of the original brick, and the Z dimension of the newly extruded brick is aligned with the Y dimension of the original brick. The X dimension of the newly extruded brick is aligned with the Z dimension of the original brick, but because this is the direction of extrusion the fact that X > Z does not create a problem.”

Because it was unclear how to extrude a daughter without poisoning the interior environment of the parent, Merkle proposed extruding a “hollow shell” of more than twice the parental length, permitting “the construction inside it of two assemblers of dimensions X, Y and Z. When the two new assemblers have been manufactured inside the hollow shell, the shell is pushed out of the original assembler. This breaks the seal of the original assembler (the parent ‘dies’ in the process of releasing the two offspring) and opens up one end of the hollow shell, thus permitting the two newly manufactured assemblers to exit the shell. While this process is clearly wasteful (retaining the parent assembler in a functional state would be desirable), it simplifies the design of the extrusion process as the hollow shell is called upon to perform only a single task, rather than also acting as the wall of the new assemblers. Changes in the design of the hollow shell and its extrusion process have little impact on the design of the assembler.” However, as with Merkle’s later cased hydrocarbon design and even with Drexler’s earlier minimal assembler design, a significant amount of waste material is generated and (in Merkle’s designs) all replicative generations prior to the last are thrown away as garbage, an unfortunate result.


Last updated on 1 August 2005