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.


References 1500-1599

1500. Steven C. Zimmerman, Fanwen Zeng, “Dendrimers in supramolecular chemistry: From molecular recognition to self-assembly,” Chem. Rev. 97(1997):1681-1712. See also: Steven C. Zimmerman, Fanwen Zeng, David E.C. Reichert, Sergei V. Kolotuchin, “Self-assembling dendrimers,” Science 271(23 February 1996):1095-1098; Thomas W. Bell, “Molecular trees: A new branch of chemistry,” Science 271(23 February 1996):1077-1078.

1501. George R. Newkome, Claus D. Weis, Charles N. Moorefield, Ingrid Weis, “Detection and functionalization of dendrimers possessing free carboxylic acid moieties,” Macromolecules 30(1997):2300-2304.

1502. Jean Haensler, Francis C. Szoka Jr., “Polyamidoamine cascade polymers mediate efficient transfection of cells in culture,” Bioconjugate Chemistry 4(September 1993):372-379.

1503. Julia Uppenbrink, “Completing the cycle,” Science 284(18 June 1999):1942.

1504. K. Kim, “Mechanically interlocked molecules incorporating cucurbituril and their supramolecular assemblies,” Chem. Soc. Rev. 31(March 2002):96-107.

1505. Y. Li, S.T. Lin, W.A. Goddard 3rd, “Efficiency of various lattices from hard ball to soft ball: theoretical study of thermodynamic properties of dendrimer liquid crystal from atomistic simulation,” J. Am. Chem. Soc. 126(18 February 2004):1872-1885.

1506. D.A. Tomalia, H.M. Brothers 2nd, L.T. Piehler, H.D. Durst, D.R. Swanson, “Partial shell-filled core-shell tecto(dendrimers): a strategy to surface differentiated nano-clefts and cusps,” Proc. Natl. Acad. Sci. (USA) 99(16 April 2002):5081-5087;

1507. V. Percec, T.K. Bera, M. Glodde, Q. Fu, V.S. Balagurusamy, P.A. Heiney, “Hierarchical self-assembly, coassembly, and self-organization of novel liquid crystalline lattices and superlattices from a twin-tapered dendritic benzamide and its four-cylinder-bundle supramolecular polymer,” Chemistry 9(17 February 2003):921-935; G. Ungar, Y. Liu, X. Zeng, V. Percec, W.D. Cho, “Giant supramolecular liquid crystal lattice,” Science 299(21 February 2003):1208-1211.

1508. N.R. Luman, K.A. Smeds, M.W. Grinstaff, “The convergent synthesis of poly(glycerol-succinic acid) dendritic macromolecules,” Chemistry 9(21 November 2003):5618-5626.

1509. T. Uchiyama, K. Ishii, T. Nonomura, N. Kobayashi, S. Isoda, “A phthalocyanine dendrimer capable of forming spherical micelles,” Chemistry 9(5 December 2003):5757-5761.

1510. Fraser Stoddart, “Making molecules to order,” Chem. in Britain 27(August 1991):714-718.

1511. Peter R. Ashton, Richard A. Bissell, Neil Spencer, J. Fraser Stoddart, Malcolm S. Tolley, “Towards controllable molecular shuttles,” Synlett (November 1992):914-926.

1512. R.A. Bissell, E. Cordova, A.E. Kaifer, J.F. Stoddart, “A chemically and electrochemically switchable molecular shuttle,” Nature 369(1994):133-137.

1513. Marcos Gomez-Lopez, Jon A. Preece, J. Fraser Stoddart, “The art and science of self-assembling molecular machines,” Nanotechnology 7(September 1996):183-192.

1514. V.V. Balzani, A. Credi, F.M. Raymo, J.F. Stoddart, “Artificial molecular machines,” Angew. Chem. Int. Ed. Engl. 39(2 October 2000):3348-3391.

1515. A.R. Pease, J.O. Jeppesen, J.F. Stoddart, Y. Luo, C.P. Collier, J.R. Heath, “Switching devices based on interlocked molecules,” Acc. Chem. Res. 34(June 2001):433-444.

1516. G. Schill, Catenanes, Rotaxanes and Knots, Academic Press, New York, 1971. See also: D.B. Amabilino, J.F. Stoddart, “Interlocked and intertwined structures and superstructures,” Chem. Rev. 95(1995):2725-2828.

1517. C.P. Collier, E.W. Wong, M. Belohradsky, F.M. Raymo, J.F. Stoddart, P.J. Kuekes, R.S. Williams, J.R. Heath, “Electronically configurable molecular-based logic gates,” Science 285(16 July 1999):391-394, 313-314 (discussion).

1518. Gerhard Wenz, Bruno Keller, “Threading cyclodextrin rings on polymer chains,” Angew. Chem. Int. Ed. Engl. 31(1992):197-199. See also: Ivan Amato, “The molecular bead game,” Science 260(16 April 1993):293-294.

1519. H.W. Gibson, H. Marand, “Polyrotaxanes: molecular composites derived by physical linkage of cyclic and linear species,” Advanced Materials 5(1993):11 et seq.

1520. A.S. Lane, D.A. Leigh, A. Murphy, “Peptide-based molecular shuttles,” J. Am. Chem. Soc. 119(1997):11092-11093.

1521. D.A. Leigh, A. Murphy, J.P. Smart, A.M.Z. Slawin, “Glycylglycine rotaxanes – the hydrogen bond-directed assembly of synthetic peptide rotaxanes,” Angew. Chem. Int. Ed. Engl. 36(1997):728-732.

1522. F.M. Raymo, J.F. Stoddart, “Polyrotaxanes and pseudopolyrotaxanes,” Trends Polym. Sci. 4(1996):208-211.

1523. F.M. Raymo, J.F. Stoddart, “Slippage – a simple and efficient way to self-assemble [n]rotaxanes,” Pure Appl. Chem. 69(1997):1987-1997.

1524. Roberto Ballardini, Vincenzo Balzani, Alberto Credi, Maria Teresa Gandolfi, Steven J. Langford, Stephan Menzer, Luca Prodi, J. Fraser Stoddart, Margherita Venturi, David J. Williams, “Simple molecular machines. Cyclical chemically-driven unthreading and re-threading of a [2]pseudorotaxane,” Angew. Chem. Int. Ed. Engl. 35(1996):978-981.

1525. P.R. Ashton, et al., “Molecular Meccano. 24. Multiple stranded and multiply encircled pseudorotaxanes,” J. Am. Chem. Soc. 119(1997):12514-12524.

1526. Guang Li, Linda B. McGown, “Molecular nanotube aggregates of beta- and gamma-cyclodextrins linked by diphenylhexatrienes,” Science 264(8 April 1994):249-251.

1527. A. Harada, “Cyclodextrin-based molecular machines,” Acc. Chem. Res. 34(June 2001):456-464.

1528. D.B. Amabilino, P.R. Ashton, A.S. Reder, N. Spencer, J.F. Stoddart, “The two-step self-assembly of [4]- and [5]-catenanes,” Angew. Chem. Int. Ed. Engl. 33(1994):433-437. See also: “Another Gain in Self-Assembly,” Science 265(29 July 1994):608.

1529. D.B. Amabilino, P.R. Ashton, S.E. Boyd, J.Y. Lee, S. Menzer, J.F. Stoddart, D.J. Williams, “The five-stage self-assembly of a branched heptacatenane,” Angew. Chem. 109(1997):2160-2162; Angew. Chem. Int. Ed. Engl. 36(1997):2070-2072.

1530. Makoto Fujita, Norifumi Fujita, Katsuyuki Ogura, Kentaro Yamaguchi, “Spontaneous assembly of ten components into two interlocked identical coordination cages,” Nature 400(1 July 1999):52-55.

1531. D.B. Amabilino, et al., “Molecular Meccano. 30. Oligocatenanes made to order,” J. Am. Chem. Soc. 120(1998):4295-4307.

1532. P.R. Ashton, et al., “Supramolecular daisy chains,” Angew. Chem 110(1998):1344-1347; Angew. Chem. Int. Ed. 37(1998):1294-1297.

1533. P.R. Ashton, et al., “Self-assembling supramolecular daisy chains,” Angew. Chem. 110(1998):2016-2019; Angew. Chem. Int. Ed. 37(1998):1913-1916.

1534. F. Diederich, M. Gomez-Lopez, J.-F. Nierengarten, J.A. Preece, F.M. Raymo, J.F. Stoddart, “The self-assembly of the first fullerene-containing [2]catenane,” Angew. Chem. 109(1997):1611-1614; Angew. Chem. Int. Ed. Engl. 36(1997):1448-1451.

1535. L.Z. Yan, P.E. Dawson, “Design and synthesis of a protein catenane,” Angew. Chem. Int. Ed. Engl. 40(1 October 2001):3625-3627.

1536. P.R. Ashton, A.N. Collins, M.C.T. Fyfe, S. Menzer, J.F. Stoddart, D.J. Williams, “Supramolecular weaving,” Angew. Chem. 109(1997):760-763; Angew. Chem. Int. Ed. Engl. 36(1997):735-739.

1537. A.G. Johnston, D.A. Leigh, R.J. Pritchard, M.D. Deegan, “Facile synthesis and solid state structure of a benzylic amide [2]catenane,” Angew. Chem. Int. Ed. Engl. 34(1995):1209-1212.

1538. Judith Konnert, Doyle Britton, “The crystal structure of AgC(CN)3,” Inorg. Chem. 5(1966):1193-1196.

1539. David J. Duchamp, Richard E. Marsh, “The crystal structure of trimesic acid (benzene-1,3,5-tricarboxylic acid),” Acta Crystallogr. Sect. B 25(1969):5-19.

1540. Robert W. Gable, Bernard F. Hoskins, Richard Robson, “A new type of interpenetration involving enmeshed independent square grid sheets. The structure of diaquabis-(4,4’-bipyridine)zinc hexafluorosilicate,” Chem. Commun. (1990):1677-1678.

1541. Humberto O. Stumpf, Lahcene Ouahab, Yu Pei, Daniel Grandjean, Olivier Kahn, “A molecular-based magnet with a fully interlocked three-dimensional structure,” Science 261(23 July 1993):447-449. See also: Peter Day, “The chemistry of magnets,” Science 261(23 July 1993):431-432.

1542. Jose Antonio Real, Enrique Andres, M. Carmen Munoz, Miguel Julve, Thierry Granier, Azzedine Bousseksou, Francois Varret, “Spin crossover in a catenane supramolecular system,” Science 268(14 April 1995):265-267.

1543. Robert L. Duda, “Protein chain mail: Catenated protein in viral capsids,” Cell 94(10 July 1998):55-60. See also: J. Travis, “Protein chain mail offers armor for viruses,” Science News 154(18 July 1998):38.

1544. Saul Griffith, “Tools for designing programmatic self-assembling systems,” Final Project Paper, Biologically Motivated Programming Technology for Robust Systems, MIT Course 6.978, December 2002;

1545. “Chapter Four. Building Structures at the Nanoscale. 4.2 Self-Assembly,” in Exploring the Nanoworld with LEGO® Bricks, University of Wisconsin, Madison Materials Research Science and Engineering Center (MRSEC) for Nanostructured Materials and Interfaces, Education and Outreach, 23 April 2003;

1546. K. Saitou, “Conformational switching in self-assembling mechanical systems,” IEEE Transactions on Robotics and Automation 15(June 1999):510-520;

1547. Kazuhiro Saitou, Mark J. Jakiela, “Automated optimal design of mechanical conformational switches,” Artificial Life 2(Summer 1995):129-156;

1548. Kazuhiro Saitou, Mark J. Jakiela, “Subassembly generation via mechanical conformational switches,” Artificial Life 2(Summer 1995):377-416;

1549. K. Saitou, M. Jakiela, “On classes of self-assembling automata,” Complex Systems 10(1996):391-416;

1550. K. Saitou, “Self-assembling automata: A model for conformational self-assembly,” Proc. 1998 Pacific Symposium on Biocomputing, Maui, Hawaii, World Scientific, 1998, pp. 609-620;

1551. K. Saitou, “Conformational switching as assembly instructions in self-assembling mechanical systems,” Unifying Themes in Complex Systems: Proc. First Intl. Conf. on Complex Systems, Nashua, New Hampshire, Perseus Books, 1998, pp. 411-431; also available on-line via InterJournal of Complex Systems at:

1552. K. Hosokawa, I. Shimoyama, H. Miura, “Dynamics of self-assembling systems: analogy with chemical kinetics,” Artificial Life 1(1994):413-427; also in Artificial Life IV: Proc. 4th Intl. Workshop on the Synthesis and Simulation of Living Systems, Cambridge, MA, 6-8 July 1995, pp. 172-180.

1553. Radhika Nagpal, “Programmable Self-Assembly: Constructing Global Shape Using Biologically-Inspired Local Interactions and Origami Mathematics,” MIT Artificial Intelligence Lab, June 2001; See also: Radhika Nagpal, “Programmable Pattern-Formation and Scale-Independence,” International Conference on Complex Systems (ICCS), June 2002,; Radhika Nagpal, “Programmable Self-Assembly Using Biologically-Inspired Multiagent Control,” Proceedings of the 1st International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS), Bologna, Italy, July 2002,

1554. Tad Hogg, Yong Chen, “Interfacing to Dense Nanowire Circuits with Self-Assembled Connectors,” 11th Foresight Conference on Molecular Nanotechnology, October 2003; See also: Tad Hogg, Yong Chen, Phil Kuekes, “Assembling Nanoscale Circuits with Randomized Connections,” 7 August 2003, submitted for publication.

1555. Andre DeHon, Patrick Lincoln, John E. Savage, “Stochastic assembly
of sublithographic nanoscale interfaces,” preprint, July 2003.

1556. J. Liu, M. Casavant, M. Cox, D.A. Walters, P. Boul, W. Lu, A.J. Rimberg, K. Smith, D.T. Colbert, R.E. Smalley, “Controlled deposition of individual single-walled carbon nanotubes on chemically functionalized templates,” Chem. Phys. Lett. 303(2 April 1999):125-129;’s%20publications/CPL303-125.pdf

1557. Jia Liu, Takhee Lee, B.L. Walsh, R.P. Andres, D.B. Janes, M.R. Melloch, J.M. Woodall, R. Reifenberger, “Guided self-assembly of Au nanocluster arrays electronically coupled to semiconductor device layers,” Appl. Phys.Lett. 77(2000):373;

1558. Xiao M. Yang, Richard D. Peters, Paul F. Nealey, Harun H. Solak, Franco Cerrina, “Guided self-assembly of symmetric diblock copolymer films on chemically nanopatterned substrates,” Macromolecules 33(26 December 2000):9575-9582. See also: Xiao M. Yang, Richard D. Peters, Qiang Wang, Juan de Pablo, Paul Nealey, “Guided self-assembly of the domain structure in thin films of diblock copolymers using substrates patterned with nanolithography,” AIChE 2000 Annual Meeting, Los Angeles, CA, November 2000; (abstract)

1559. Ward A. Lopes, H.M. Jaeger, “Hierarchical self-assembly of metal nanostructures on diblock copolymer scaffolds,” Nature 414(13 December 2001):735-738; (abstract)

1560. H.H. Solak, C. David, J. Gobrecht, S.O. Kim, P.F. Nealey, “Guided self-assembly of copolymer films on templates patterned with x-ray interference lithography,” PSA Scientific Report 2002, Volume VII, Laboratory for Micro- and Nanotechnology, Paul Scherrer Institut, Switzerland;

1561. P. Mesquida, A. Stemmer, “Guiding self-assembly with the tip of an atomic force microscope,” Scanning 24(May-June 2002):117-120.

1562. Chris Dwyer, Russell Taylor, Richard Superfine, Sean Washburn, Dorothy Erie, “Methodology for the DNA-guided self-assembly of novel computing circuitry,” paper presented at the 10th Foresight Conference on Molecular Nanotechnology, October 2002;

1563. Y.F. Gao, Z. Suo, “Guided self-assembly of molecular dipoles on a substrate surface,” J. Appl. Phys. 93(2003):4276;

1564. Jiyun C. Huie, “Guided molecular self-assembly: a review of recent efforts,” Smart Mater. Struct. 12(April 2003):264-271; (abstract)

1565. Tad Hogg, “Robust self-assembly using highly designable structures,” Nanotechnology 10(September 1999):300-307. See also: Tad Hogg, “Robust self-assembly using highly designable structures,” presentation at the Sixth Foresight Nanotechnology Conference, November 1998; see at: or

1566. P.W.K. Rothemund, E. Winfree, “The program-size complexity of self-assembled squares,” Proc. 32nd Annual ACM Symp. On Theory of Computing (STOC 2000), ACM, New York, 2000, pp. 459-468;

1567. Jarle Breivik, “Self-organization of template-replicating polymers and the spontaneous rise of genetic information,” Entropy 3(20 November 2001):273-279; See also: Vivo Innovation: Interactive Life Science – Self-Replicating Polymers, 2000;

1568. David H. Gracias, Joe Tien, Tricia L. Breen, Carey Hsu, George M. Whitesides, “Forming electrical networks in three dimensions by self-assembly,” Science 289(18 August 2000):1170-1172;

1569. Insung S. Choi, Ned Bowden, George M. Whitesides, “Macroscopic, hierarchical, two-dimensional self-assembly,” Angew. Chem. Int. Ed. Engl. 38(1999):3078-3081.

1570. N. Bowden, A. Terfort, J. Carbeck, G.M. Whitesides, “Self-assembly of mesoscale objects into ordered two-dimensional arrays,” Science 276(11 April 1997):233-235.

1571. A. Terfort, N. Bowden, G.M. Whitesides, “Three-dimensional self-assembly of millimeter-scale components,” Nature 386(1997):162-164.

1572. Paul W.K. Rothemund, “Using lateral capillary forces to compute by self-assembly,” Proc. Natl. Acad. Sci. (USA) 97(1 February 2000):984-989.

1573. T.D. Clark, M. Boncheva, J.M. German, M. Weck, G.M. Whitesides, “Design of three dimensional, millimeter-scale models for molecular folding,” J. Am. Chem. Soc. 124(2002):18-19.

1574. J. Tien, T.L. Breen, G.M. Whitesides, “Crystallization of millimeter-scale objects with use of capillary forces,” J. Am. Chem. Soc. 120(1998):12670-12671.

1575. Hongkai Wu, N. Bowden, G.M. Whitesides, “Selectivities among capillary bonds in mesoscale self-assembly,” Appl. Phys. Lett. 75(15 November 1999):3222-3224.

1576. N. Bowden, I.S. Choi, B.A. Grzybowski, G.M. Whitesides, “Mesoscale self-assembly of hexagonal plates using lateral capillary forces: synthesis using the ‘capillary bond’,” J. Am. Chem. Soc. 121(1999):5373-5391.

1577. I.S. Choi, M. Weck, B. Xu, N.L. Jeon, G.M. Whitesides, “Mesoscopic, templated self-assembly at the fluid-fluid interface,” Langmuir 16(2000):2997-2999.

1578. S.R.J. Oliver, T.D. Clark, N. Bowden, G.M. Whitesides, “Three-dimensional self-assembly of complex, millimeter-scale structures through capillary bonding,” J. Am. Chem. Soc. 123(2001):8119-8120.

1579. N. Bowden, F. Arias, T. Deng, G.M. Whitesides, “Self-assembly of microscale objects at a liquid/liquid interface through lateral capillary forces,” Langmuir 17(2001):1757-1765.

1580. J. Tien, A. Terfort, G.M. Whitesides, “Microfabrication through electrostatic self-assembly,” Langmuir 13(1997):5349-5355.

1581. R.S. Fearing, “Micro structures and micro actuators for implementing sub-millimeter robots,” in H.S. Tzou, T. Fukuda, eds., Precision Sensors, Actuators and Systems, Kluwer Academic Publishers, Boston MA, 1992, pp. 39-72.

1582. E. Shimada, J.A. Thompson, J. Yan, R.J. Wood, R.S. Fearing, “Prototyping millirobots using dexterous microassembly and folding,” Symposium on Microrobotics, ASME Int. Mechanical Engineering Cong. and Exp., Orlando, FL, 5-10 November 2000, DSC-Vol. 69-2, pp. 933-940;

1583. M. Weck, I.S. Choi, N.L. Jeon, G.M. Whitesides, “Assembly of mesoscopic analogues of nucleic acids,” J. Am. Chem. Soc. 122(2000):3546-3547.

1584. H.R. Crane, “Principles and problems of biological growth,” Scientific Monthly 70(June 1950):376-389.

1585. M. Calvin, Chemical Evolution, Oxford Press, 1969.

1586. Arthur Winfree, “Rotating chemical reactions,” Sci. Am. 230(June 1974):82-95; A.T. Winfree, “The prehistory of the Belousov-Zhabotinsky oscillator,” J. Chem. Educ. 61(1984):661-663.

1587. B.J. Welsh, J. Gomatam, A.E. Burgess, “Three?dimensional chemical waves in the Belousov-Zhabotinskii reaction,” Nature 304(1983):611?614.

1588. John J. Tyson, The Belousov?Zhabotinskii Reaction, Springer-Verlag, New York, 1976; John J. Tyson, “What everyone should know about the Belousov-Zhabotinsky Reaction,” in S.A. Levin, ed., Lecture Notes in Biomathematics, Vol. 100, Springer-Verlag, New York, 1994, pp. 569-587.

1589. “The Belousov?Zhabotinskii Reaction,” see and; see also “Picture Gallery” at

1590. Q. Ouyang, H.L. Swinney, G. Li, “Transition from spirals to defect-mediated turbulence driven by a Doppler instability,” Phys. Rev. Lett. 84(31 January 2000):1047-1050.

1591. R.J. Field, E. Ko’ros, Richard Macy Noyes, “Oscillations in chemical systems. II. Thorough analysis of temporal oscillations in the bromate-cerium-malonic acid system,” J. Am. Chem. Soc. 94(1972):8649-8664; Richard Macy Noyes, R.J. Field, “Oscillations in chemical systems. V. Quantitative explanation of band migration in the Belousov?Zhabotinskii reaction,” J. Am. Chem. Soc. 96(1978):2001-2006; R.M. Noyes, “Some models of chemical oscillators,” J. Chem. Educ. 66(1989):190-191.

1592. P. Gray, S.K. Scott, “Autocatalytic reactions in isothermal, continuous stirred tank reactor: oscillations and instabilities in the system A+2B ? 3B,B ? C,” Chem. Eng. Sci. 39(1984):1087-1097. See also: “Gray Scott Model of Reaction Diffusion,”

1593. John E. Pearson, “Complex patterns in a simple system,” Science 261(9 July 1993):189-192; W.N. Reynolds, J.E. Pearson, S. Ponce-Dawson, “Dynamics of self-replicating pattern in reaction-diffusion systems,” Phys. Rev. Lett. 72(1994):2797-2800; W.N. Reynolds, S. Ponce-Dawson, J.E. Pearson, “Self-replicating spots in reaction-diffusion systems,” Phys. Rev. E 56(1997):185-198.

1594. K.J. Lee, W.D. McCormick, Qi Ouyang, H.L. Swinney, “Pattern formation by interacting chemical fronts,” Science 261(9 July 1993):192-194; K.J. Lee, W.D. McCormick, J.E. Pearson, H.L. Swinney, “Experimental observation of self-replicating spots in a reaction-diffusion system,” Nature 369(1994):215-218; D. Haim, G. Li, Q. Ouyang, W.D. McCormick, H.L. Swinney, A. Hagberg, E. Meron, “Breathing spots in a reaction-diffusion system,” Phys. Rev. Lett. 77(1 July 1996):190-193.

1595. V. Petrov, S.K. Scott, K. Showalter, “Excitability, wave reflection, and wave splitting in a cubic autocatalysis reaction-diffusion system,” Phil. Trans. R. Soc. Lond. A 347(1994):631-642.

1596. K.J. Lee, H.L. Swinney, “Lamellar structures and self-replicating spots in a reaction-diffusion system,” Phys. Rev. E. 51(March 1995):1899-1915.

1597. K.E. Rasmussen, W. Mazin, E. Mosekilde, G. Dewel, P. Borckmans, “Wave-splitting in the bistable Gray-Scott model,” Int. J. Bifurcation and Chaos 6(1996):1077-1092.

1598. Y. Nishiura, D. Ueyama, “A skeleton structure of self-replicating dynamics,” Physica D 130(1999):73-104.

1599. H. Takagi, K. Kaneko, “Differentiation and replication of spots in a reaction-diffusion system with many chemicals,” Europhys. Lett. 56(April 2001):145-151;


Last updated on 1 August 2005