Molecular Computing

To approach the cognitive capabilities of the human brain, Al must emulate brain structure at the nanoscale. Computer hardware is indeed evolving to smaller switching components, and advantages of proteins themselves are being considered. The smallward evolution of technological computing elements embraces a number of concepts and material collectively known as "molecular computing."

The potential advantages of molecular computers have been described by D. Waltz (1982) of Thinking Machines Corporation. 1) Current "planar" computer design is limited in overall density and use of three dimensional space. 2) Further miniaturization is limited with silicon and gallium arsenide technologies. Chips and wires cannot be made much smaller without becoming vulnerable to stray cosmic radiation or semiconductor impurities. 3) Biomolecular based devices may offer possibilities for self-repair or self-regeneration. 4) Certain types of analog, patterned computation may be particularly suited to molecular computers.

Forrest L. Carter (1984) of the Naval Research Laboratory has catalyzed the molecular computing movement through his own contributions and by sponsoring a series of meetings on Molecular Electronic Devices (in 1981, 1983, 1986). Strategies described by Carter and others at his meetings have been aimed at implementing nanoscale computing through switching in material arrays of polyacetylenes, Langmuir-Blodgett films, electro-optical molecules, proteins and a number of other materials. Interfacing between nanoscale devices and macroscale technologies is an obstacle with several possible solutions: 1) engineering upward, self assembling components, 2) optical communication, 3) molecular wires, 4) don't interface; build systems that are totally nanoscale (though they'd have to be somehow developed and tested), and 5) a sensitive bridge between macroscale and nanoscale. Technologies which may fulfill this latter possibility include ion beam nanolithography, molecular spectroscopy, quantum well devices, and scanning tunneling microscopy (STM). In STM, piezoceramic positioners control an ultra sharp conductor with a monoatomic tip which can probe and image material surfaces with atomic level resolution. STM related nanotools may soon be capable of ultraminiature fabrication and interfacing: "nanotechnology" (Chapter 10).

The medium of information flow in conventional computers is electronic current flow, but electron transfer may be too energetically expensive and unnecessary at the molecular nanoscale. Many of the projected modes of molecular computing rely on propagation of nonlinear coupling waves called "solitons" similar to what Davydov proposed for linear biomolecules. Carter

(1981) proposed that solitons could propagate through switching circuits made of branched polyacetylene chains. He has also considered molecular computing in periodic arrays using electron tunneling, soliton "valving" and photo-activated conformational changes in lattice materials. He envisions three dimensional molecular scale memory and switching densities of 1015 to 1018 elements per cubic centimeter, near the theoretical limit for charge separation. A number of materials may be suitable for soliton switching and biological propagation of solitons in proteins has been suggested. Several authors have argued for cytoskeletal solitons mediating information processing (Chapter 8).

Wayne State University's Michael Conrad has defined his vision of a molecular computer in which proteins integrate multiple input modes to perform a functional output (Conrad, 1986). In addition to smaller size scale, protein based molecular computing offers different architectures and computing dimensions. Conrad suggests that "non-von Neumann, nonserial and non-silicon" computers will be "context dependent," with input processed as dynamical physical structures, patterns, or analog symbols. Multidimensional conditions determine the conformational state of any one protein: temperature, pH, ionic concentrations, voltage, dipole moment, electroacoustical vibration, phosphorylation or hydrolysis state, conformational state of bound neighbor proteins, etc. Proteins integrate all this information to determine output. Thus each protein is a rudimentary computer and converts a complex analog input to an output state or conformation.

Conrad and Liberman (1982) have defined an "extremal computer" as one which uses physical resources as effectively as possible for computation. They suggest that an extremal computer should be a molecular computer, with individual switches or information representation subunits composed of molecules. The state of each information. subunit should be coupled to an energy event near the quantum limit. Protein conformational states leveraged to dipole oscillations in the nanoscale may be that limit. Conrad and Liberman conclude that, within biological systems, macromolecular computing occurs by conformational changes generating "reaction diffusion patterns" of concentrations of biochemical energy molecules (cyclic AMP).

A 1984 conference (Yates, 1984) considered Chemically Based Computer Designs (Yates, 1984) and attempted to answer 6 relevant questions. 1) Are there fundamental, quantum mechanical limitations on computation? This question deals with energy loss due to friction or other factors in computation. The work of Benioff (1980, 1982), Landauer (1982) and Feynman (1986) lead to the conclusion that, in principle, computation can be achieved by a frictionless, energy conserving system. Thus there appear to be no quantum mechanical limitations on computation. 2) Are there fundamental, thermodynamic limitations on computation? Although there are some computing operations that are irreversible and dissipative, the work of Landauer (1982) and Bennett (1982) show that there are no fundamental thermodynamic limitations on computation per se. 3) Are there fundamental limits to serial processing on digital computers based on binary switches? This question has philosophical implications (does the universe function through continuous or discrete processes?) and so cannot be answered assuredly. The consensus of the conference was that there are probably limits on serial, digital computing. 4) What are the practical physical limitations on computer design? There are several practical limitations to the further miniaturization of digital switching circuits. However those limits probably won't be reached for decades. 5) What are the potential contributions of molecular electronics to digital computer design? The conference considered molecular conformational changes, solitons, charge flow and other approaches. Molecular gates, wires and switches may be worth trying to build, although redundancy and parallelism may be necessary. 6) Do biochemical systems inspire technological imitations for the purpose of computer design? Many biological systems (DNA, antibodies, receptors, enzymes) were reviewed and a major conclusion was that,

None of these materials is as rich in chemoelectric physical phenomena as are (cytoskeletal) microscopic biological objects. Microtubules offer the most possibilities for inspiring chemically based computation! (Yates, 1984)

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