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Preface
The intended readership. The nature of the subject. Criticism of criticism. Use
of tenses. Citations and apologies. Acknowledgments.
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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.
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PART I. PHYSICAL
PRINCIPLES
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
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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
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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
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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
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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
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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
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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
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PART II. COMPONENTS AND SYSTEMS
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
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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
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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
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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
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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
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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
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PART III IMPLEMENTATION STRATEGIES
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
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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
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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
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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
Afterword
Symbols, Units, and Constants
Glossary
References
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