Molecular Machinery,

  Manufacturing,and Computation

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See also: Nanosystems Indian edition (Wiley India, 2010)

Note: Eric Drexler’s 1991 MIT dissertation, “Molecular Machinery and Manufacturing with Applications to Computation” [pdf, 30 MB], is now available online. The dissertation was written as a draft of Nanosystems, and contains most of the content of the book in nearly final form.

Update, Dec. 2012:The following table of contents and sample chapters are now available in a Ukrainian translation.


Chapter 1. Introduction and Overview


Chapter 2. Classical Magnitudes and Scaling Laws

Chapter 3. Potential Energy Surfaces

Chapter 4. Molecular Dynamics

Chapter 5. Positional Uncertainty

Chapter 6. Transitions, Errors, and Damage

Chapter 7. Energy Dissipation

Chapter 8. Mechanosynthesis


Chapter 9. Nanoscale Structural Components

Chapter 10. Mobile Interfaces and Moving Parts

Chapter 11. Intermediate Subsystems

Chapter 12. Nanomechanical Computational Systems

Chapter 13. Molecular Sorting, Processing, and Assembly

Chapter 14. Molecular Manufacturing Systems


Chapter 15. Macromolecular Engineering

Chapter 16. Paths to Molecular Manufacturing

Appendix A. Methodological Issues in Theoretical Applied Science

Appendix B. Related Research


Symbols, Units, and Constants



Detailed Table of Contents:


The intended readership. The nature of the subject. Criticism of criticism. Use of tenses. Citations and apologies. Acknowledgments.

Chapter 1. Introduction and Overview

1.1. Why molecular manufacturing?

1.2. What is molecular manufacturing?

Example: a nanomechanical bearing. A chemical perspective on molecular manufacturing. Exposition vs. implementation sequence.

1.3. Comparisons

Conventional fabrication and mechanical engineering. Microfabrication and microtechnology. Solution-phase chemistry. Biochemistry and molecular biology.

1.4. The approach in this volume

Disciplinary range, level, and presentation. Levels of abstraction and approximation. Scope and assumptions. Objectives and nonobjectives.

1.5. Overview of following chapters

Overview of Part I. Overview of Part II. Overview of Part III. Overview of Appendices. Open problems.


Chapter 2. Classical Magnitudes and Scaling Laws

2.1. Overview

2.2. Approximation and classical continuum models

2.3. Scaling of classical mechanical systems

Basic assumptions. Magnitudes and scaling. Major corrections.

2.4. Scaling of classical electromagnetic systems

Basic assumptions. Major corrections. Magnitudes and scaling: steady-state systems. Magnitudes and scaling: time-varying systems.

2.5. Scaling of classical thermal systems

Basic assumptions. Major corrections. Magnitudes and scaling.

2.6. Beyond classical continuum models

2.7. Conclusions

Chapter 3. Potential Energy Surfaces

3.1. Overview

3.2. Quantum theory and approximations

Overview of quantum mechanics. The Born–Oppenheimer PES. Molecular orbital methods.

3.3. Molecular mechanics

The molecular mechanics approach. The MM2 model. Energy, force, and stiffness under large loads.

3.4. Potentials for chemical reactions

Relationship to other methods. Bond cleavage and radical coupling. Abstraction reactions.

3.5. Continuum representations of surfaces

Continuum models of van der Waals attraction. Transverse-continuum models of surfaces. Molecular models and bounded continuum models.

3.6. Conclusions

3.7. Further reading

Chapter 4. Molecular Dynamics

4.1. Overview

4.2. Nonstatistical mechanics

Vibrational motions. Reactions and transition rates. Generalized trajectories.

4.3. Statistical mechanics

Detailed dynamics vs. statistical mechanics. Basic results in equilibrium statistical mechanics. The configuration-space picture. Equilibrium vs. nonequilibrium processes. Entropy and information. Uncertainty in nanomechanical systems. Mean-force potentials.

4.4. PES revisited: accuracy requirements

Physical accuracy. Chemical accuracy. Accurate energies and nanomechanical design.

4.5. Conclusions

4.6. Further reading

Chapter 5. Positional Uncertainty

5.1. Overview

5.2. Positional uncertainty in engineering

5.3. Thermally excited harmonic oscillators

Classical treatment. Quantum mechanical treatment.

5.4. Elastic extension of thermally excited rods

Classical continuum treatment. Quantum mechanical treatments.

5.5. Elastic bending of thermally excited rods

Classical treatment. Semicontinuum quantum mechanical treatment. Engineering approximations. Shear and bending in the quantum limit.

5.6. Piston displacement in a gas-filled cylinder

Weighting in terms of potential energy and available states. Weighting in terms of a mean-force potential. Weighting in terms of the Helmholtz free energy. Comparison and quantum effects.

5.7. Longitudinal variance from transverse deformation

General approach. Coupling and variance. Rods with tension and transverse constraints. Rods with freely sliding ends and no transverse constraint.

5.8. Elasticity, entropy, and vibrational modes

Neglect of vibrational modes in classical elastic springs. Conservative scaling of variance with temperature.

5.9. Conclusions

Chapter 6. Transitions, Errors, and Damage

6.1. Overview

6.2. Transitions between potential wells

Transition state theories. Classical transition state theories. Quantum transition state theories. Tunneling.

6.3. Placement errors

Time-dependent PES models. Error models. Switched-coupling error models.

6.4. Thermomechanical damage

Overview. Machine- vs. solution-phase stability. Thermal bond cleavage. Thermomechanical bond cleavage. Other chemical damage mechanisms. The stability of surfaces. Thermal ionization and charge separation.

6.5. Photochemical damage

Energetic photons. Overview of photochemical processes. Design for photochemical stability. Photochemical shielding.

6.6. Radiation damage

Radiation and radiation dosage. Classical radiation target theory. Effects of track structure. Radiation shielding.

6.7. Component and system lifetimes

Component lifetimes. System lifetimes.

6.8. Conclusions

Chapter 7. Energy Dissipation

7.1. Overview

7.2. Radiation from forced oscillations

Overview. Acoustic waves and the equal-speed approximation. Oscillating force at a point. Oscillating torque at a point. Oscillating pressure in a volume. Moving disturbances.

7.3. Phonons and phonon scattering

Phonon momentum and pressure. The Debye model of the phonon energy density. Phonon scattering drag. Scattering from harmonic oscillators. Scattering from alignment bands in bearings. Shear-reflection drag. Interfacial phonon-phonon scattering.

7.4. Thermoelastic damping and phonon viscosity

Thermoelastic damping. Phonon viscosity. Application to moving parts and alignment bands.

7.5. Compression of potential wells

Square well compression. Harmonic well compression. Multidimensional systems.

7.6. Transitions among time-dependent wells

Overview. Energy dissipation in merging wells. Free expansion and symmetrical well merging. Asymmetrical well merging. Optimal well merging under uncertainty.

7.7. Conclusions

Chapter 8. Mechanosynthesis

8.1. Overview

Mechanochemistry: terms and concepts. Scope and approach.

8.2. Perspectives on solution-phase organic synthesis

The scale and scope of chemistry. The prominence of qualitative results in organic synthesis. A survey of synthetic achievements.

8.3. Solution-phase synthesis and mechanosynthesis

Analytical approach. Basic constraints imposed by mechanosynthesis. Basic capabilities provided by mechanosynthesis. Preview: molecular manufacturing and reliability constraints. Summary of the comparison.

8.4. Reactive species

Overview. Ionic species. Unsaturated hydrocarbons. Carbon radicals. Carbenes. Organometallic reagents.

8.5. Forcible mechanochemical processes

Overview. General considerations. Tensile bond cleavage. Abstraction. Alkene and alkyne radical additions. Pi-bond torsion. Radical displacements. Carbene additions and insertions. Alkene and alkyne cycloadditions. Transition-metal reactions.

8.6. Mechanosynthesis of diamondoid structures

Why examine the synthesis of diamond? Why examine multiple synthesis strategies? Diamond surfaces. Stepwise synthesis processes. Strand deposition processes. Cluster-based strategies. Toward less diamondlike diamondoids. Mechanosynthesis of nondiamondoid structures.

8.7. Conclusions


Chapter 9. Nanoscale Structural Components

9.1. Overview

9.2. Components in context

9.3. Materials and models for nanoscale components

Classes of materials. Materials vs. molecular structures. The bounded continuum approach.

9.4. Surface effects on component properties

Materials and stiffness. Assigning sizes. Computational experiments on rod modulus.

9.5. Shape control in irregular structures

Control of shape and detail of specification. Estimates of the number of diamondoid structures. Exclusion of structures by geometrical constraints. Exclusion of structures by molecular binding requirements. Kaehler brackets.

9.6. Components of high rotational symmetry

Strained-shell structures. Curved-shell structures. Special-case structures.

9.7. Adhesive interfaces

Van der Waals attraction and interlocking structures. Ionic and hydrogen bonding. Covalent interfacial bonding.

9.8. Conclusions

Chapter 10. Mobile Interfaces and Moving Parts

10.1. Overview

10.2. Spatial Fourier transforms of nonbonded potentials

Barrier heights and sums of sinusoids.

10.3. Sliding of irregular objects over regular surfaces

Motivation: a random-walk model of barrier heights. A Monte Carlo analysis of barrier heights. Implications for constraints on structure. Energy dissipation models. Static friction. Coupled sites.

10.4. Symmetrical sleeve bearings

Models of symmetrical sleeve bearings. Spatial frequencies and symmetry operations. Properties of unloaded bearings. Properties of loaded bearings. Bearing stiffness in the transverse-continuum approximation. Mechanisms of energy dissipation. Sleeve bearings in molecular detail. Less symmetrical sleeve bearings.

10.5. Further applications of sliding-interface bearings

Nuts and screws. Rods in sleeves. Constant force springs.

10.6. Atomic-axle bearings

Bonded bearings. Atomic-point bearings.

10.7. Gears, rollers, belts, and cams

Spur gears. Helical gears. Rack-and-pinion gears and roller bearings. Bevel gears. Worm gears. Belt-and-roller systems. Cams. Planetary gear systems.

10.8. Barriers in extended systems

Sliding of irregular objects over irregular surfaces.

10.9. Dampers, detents, clutches, and ratchets

Dampers. Detents. Clutches. Ratchets and reversibility.

10.10. Perspective: nanomachines and macromachines

Similarities between nanomachines and macromachines. Differences between nanomachines and macromachines.

10.11. Bounded continuum models revisited

10.12. Conclusions

Chapter 11. Intermediate Subsystems

11.1. Overview

11.2. Mechanical measurement devices

Well partitioning and indicator latching. Force discrimination. Shape and position discrimination. Reliability through iterated measurements.

11.3. Stiff, high gear-ratio mechanisms

Harmonic drives. Toroidal worm drives.

11.4. Fluids, seals, and pumps

Fluid micromechanics. Walls and seals. Pumps and vacuum systems.

11.5. Convective cooling systems

Murray's Law and fractal plumbing. Coolant design. Cooling capacity in a macroscopic volume.

11.6. Electromechanical devices Conducting paths

Insulating layers and tunneling contacts. Modulated tunneling junctions. Electrostatic actuators. Electrostatic motors.

11.7. DC motors and generators

Charge carriers and charge density. Electrode charging mechanism. Motor power and power density. Energy dissipation and efficiency. Motor start-up. Speed regulation.

11.8. Conclusions

Chapter 12. Nanomechanical Computational Systems

12.1. Overview

12.2. Digital signal transmission with mechanical rods

Electronic analogies. Signal propagation speed.

12.3. Gates and logic rods

Electronic analogies. Components and general kinematics. A bounded continuum model. Dynamics and energy dissipation in mobile rods. Dynamics and energy dissipation in blocked rods. Fluctuations in stored energy. Thermal excitation and error rates. Summary observations based on the exemplar calculations.

12.4. Registers

Kinematics of an efficient class of register. Device size and packing. Energy dissipation estimates. Fluctuations in stored energy.

12.5. Combinational logic and finite-state machines

Finite-state machine structure and kinematics. Finite-state machine timing and alternatives. Fan-in, fan-out, and geometric issues. Signal propagation with acoustic transmission lines.

12.6. Survey of other devices and subsystems

Gates for non-PLA combinational logic. Carry chains. Random-access memory. Mass storage systems. Interfaces to macroscale systems.

12.7. CPU-scale systems: clocking and power supply

Clocking based on oscillating drive rods. A CPU-scale drive system architecture. Energy flows and clock skew. Power requirements. Power supply and energy buffering.

12.8. Cooling and computational capacity

12.9. Conclusion

Chapter 13. Molecular Sorting, Processing, and Assembly

13.1. Overview

13.2. Sorting and ordering molecules

Modulated receptors for selective transport. Cascades of modulated receptors. Ordered input streams.

13.3. Transformation and assembly with molecular mills

Reactive encounters using belt and roller systems. Interfacing mechanisms. Reagent preparation. Reagent application. Size and mass estimates. Error rates and fail-stop systems. Estimates of energy dissipation. Mechanochemical power generation.

13.4. Assembly operations using molecular manipulators

A bounded-continuum design for a stiff manipulator. Self-aligning tips and compliant manipulators. Error rates and sensitivities. Larger manipulator mechanisms.

13.5. Conclusions

Chapter 14. Molecular Manufacturing Systems

14.1. Overview

14.2. Assembly operations at intermediate scales

Joining building blocks. Reliability issues.

14.3. Architectural issues

Combining parts to make large systems. Delivering products to an external environment. Redundancy, reliability, and system lifetimes.

14.4. An exemplar manufacturing-system architecture

General approach. Products, building blocks, and assembly sequences. Throughput, delays, and internal inventories. Mass and volume. System lifetime. Feedstock materials. Byproducts. Energy output and dissipation. Information requirements. Manufacture of manufacturing systems.

14.5. Comparison to conventional manufacturing

Feedstocks and energy requirements. Byproducts and recycling. Internal component sizes and frequencies. Productivity. Some feasible product characteristics. Manufacturing costs.

14.6. Design and complexity

Part counts and automation in design and computation. Design of components and small systems. Automated generation of synthesis and assembly procedures. Shape description languages and part arrays. Compilers. Relative complexities.

14.7. Conclusions


Chapter 15. Macromolecular Engineering

15.1. Overview

15.2. Macromolecular objects via biotechnology

Motivation. DNA, RNA, and protein. Protein folding: prediction vs. design. Rational design and evolutionary approaches. Material and device properties.

15.3. Macromolecular objects via solution synthesis

Motivation. Basic design principles. Alternatives to standard proteins. Strategies for stabilizing specific folds. Consequences for design. Trade-offs and applications.

15.4. Macromolecular objects via mechanosynthesis

Motivation. Tip-array geometry and forces. Molecular tips and supports in AFM. Attachment of supporting molecules. Imaging with molecular tips. Solution-phase mechanosynthesis. Summary.

15.5. Conclusions

Chapter 16. Paths to Molecular Manufacturing

16.1. Overview

16.2. Backward chaining to identify strategies

Forward vs. backward chaining. Evaluating paths to molecular manufacturing. Overview of the backward chain.

16.3. Smaller, simpler systems (stages 3–4)

Macroscopic via microscopic manufacturing systems. Acoustic power and control. Simpler manipulators. Inert internal environment. Sorting and ordering molecules. Minimal diamondoid-material systems.

16.4. Softer, smaller, solution-phase systems (stages 2–3)

Diamondoid via nondiamondoid systems. Inert environments from solvent-based systems. Solution-synthesized pressure-threshold actuators. Smaller liquid-based mechanisms.

16.5. Development time: some considerations

Determinants of the development time. Stage 1a: Brownian assembly of medium-scale blocks. Stage 1b: Mechanosynthetic assembly of small building blocks. Stage 2: First-generation solution-based systems. Stage 3: Inert environments, diamondoid materials.

16.6. Conclusions

Appendix A. Methodological Issues in Theoretical Applied Science

A.1. The role of theoretical applied science

A.2. Basic issues

Establishing upper vs. lower bounds. Are there objective, physical limits to device performance? Certainties, probabilities, and possibilities.

A.3. Science, engineering, and theoretical applied science

Science and engineering. Engineering vs. theoretical applied science.

A.4. Issues in theoretical applied science

Product manufacturability. Product performance. Direct experimentation. Accurate modeling. Physical specification. Confidence despite reduced detail. Unique answers (and confidence from "uncertainty"). Reliable reasoning.

A.5. A sketch of some epistemological issues

Philosophy of science (i.e., of physics). Philosophy of engineering. Philosophy of theoretical applied science.

A.6. Theoretical applied science as intellectual scaffolding

Scaffolding for molecular manufacturing.

A.7. Conclusions

Appendix B. Related Research

B.1. Overview

B.2. How related fields have been divided

Scientific goals vs. technological goals. Top-down vs. bottom-up approaches. Immediate goals vs. long-term prospects.

B.3. Mechanical engineering and microtechnology

B.4. Chemistry

B.5. Molecular biology

B.6. Protein engineering

B.7. Proximal probe technologies

B.8. Feynman's 1959 talk

B.9. Conclusions


Symbols, Units, and Constants



Copyright © 1998 by John Wiley & Sons, Inc

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