Nanoscale process systems engineering: Toward molecular factories, synthetic cells, and adaptive devices

AIChE Journal

Volumn 51, Issue 7, 2005, Pages 1858-1869

  Stephanopoulos, Nicholas ^a   Solls, Earl O P ^a   Stephanopoulos, George ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 24944571423     PISSN: 00011541     EISSN: None     Source Type: Journal    
DOI: 10.1002/aic.10618     Document Type: Conference Paper

References (91)

1. Roco MC. Nanoscale science and engineering: unifying and transforming tools. AIChE J. 2004;5:890-897.
2. Heath JR, Phelps ME, Hood L. Nanosystems biology. Molecular Imaging and Biology. 2003;5:312.
3. Chow AW. Lab-on-a-Chip: opportunities for chemical engineering. AIChE J. 2002;48:1590-1595.
4. Jensen KF. Microreaction engineering: Is small better?. Chem. Eng. Sci., 2001; 56,:293-303
5. Mitsos A, Palou-Rivera I, Barton PI. Alternatives for micropower generation processes. Ind & Eng Chemistry Res. 2004;43(1):74-84.
6. Hosseini MW. Molecular Tectonics: from simple tectons to complex molecular networks. Acc. Chem. Res. 2005;38:313-323.
7. Michl J, Magnera TF. "Two-dimensional supramolecular chemistry with molecular Tinkertoys. Proc. of the Natl Acad of Sci. 2002;99:4788.
8. Stupp SI. (Guest Editor). Functional nanostructures. Chemical Reviews. 2005; 105:1377-1562.
9. Reed CA. (Guest Editor). Molecular architectures. Accounts of Chem Res. 2005;38:215-378.
10. Shimizu T, Masuda M, Minamikawa H. Supramolecular nanotube architectures based on amphiphilic molecules. Chem Reviews. 2005;105:1401-1444.
11. Lehn J-M. Toward complex matter: supramolecular chemistry and self-organization. Proc Natl Acad Sci. 2002; 99(8):4763-4768.
12. Wolfram S. A New Kind of Science, Champaign, IL: Wolfram Media, Inc.; 2002.
13. Ottino JM. Complex systems. AIChE J. 2003;49:292-299.
14. Winfree E. DNA computing by self-assembly. The Bridge. National Academy of Engineering. 2003:33(4):31-38.
15. Rothemund PWK, Papadakis N, Winfree E. Algorithmic self-assembly of DNA siepinski triangles. PLoS Biology. 2004;2:2041.
16. Ottino JM. Engineering complex systems. Nature. 2004; 427:399.
17. Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. Molecular Cell Biology. New York, NY: W.H. Freeman and Company; 2004. Images in Figure 1 reprinted with permission. Copyright 2004 WH Freeman and Company.
18. Israelachvili JN. J Colloid Interface Sci. 1986;76:2376.
19. Squires TM. Quake SR. Microfluidics: fluid physics at the nanoliter scale. Review in Modern Physics. To appear July 2005.
20. Douglas JM. Conceptual Design of Chemical Processes. New York, NY: McGraw-Hill; 1988.
21. Drexler, KE, Nanosystems: Molecular Machinery, Manufacturing, and Computation. New York, NY: Wiley-Interscience; 1992.
22. Smalley RE. Of chemistry, love, and nanobots. Scientific American. 2001;285:76.
23. Whitesides GM. The once and future nanomachine. Scientific American. 2001;285:78.
24. von Kiedrowski G, Eckardt L-H, Naumann K, Pankau WM, Reimold M, Rein M. Toward replicatable, multifunctional, nanoscaffolded machines. A chemical manifesto. Pure Appl Chem. 2003;75(5):609-619.
25. Park SH, Yin P, Liu Y, Reif JH, LaBean TH, Yan H. Programmable DNA self-assemblies for nanoscale organization of ligands and proteins. Nano Letters. 2005;5(4): 729-733. Image in Figure 2 reprinted with permission. Copyright 2005 American Chemical Society.
26. Whaley SR, English DS, Hu EL, Barbara PF, Belcher AM. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature. 2000;405:665-668.
27. Schlick TL, Ding Z, Kovacs EW, Francis MB. Dualsurface modification of the tobacco mosaic virus. J of the A Chem Soc. 2005; 127:3718-3719.
28. Falker JC, Turner ME, Bosworth JK, Trentler TJ, Johnson JE, Lin T, Colvin VL. Virus crystals as nanocomposite scaffolds. J of the A Chem Soc. 2005; 127:5274-5274.
29. Zhong Z, Wang D, Cui Y, Bockrath MW, Lieber CM. Nanowire crossbar arrays as address decoders for integrated nanosystems. Science. 2003;302:1377-13779. Image in Figure 2 reprinted with permission. Copyright 2003 American Association for the Advancement of Science.
30. Kuykendall T, Pauzauskie PJ, Zhang Y, Goldberger J, Sirbuly D, Denlinger J, Yang P. Crystallographic alignment of high-density gallium nitride nanowire arrays. Nature Materials. 2004;3:524-528.
31. Milliron DJ, Hughes SM, Cui Y, Manna L, Li J, Wang L-W, Alivisatos AP. Colloidal nanocrystal heterostructures with linear and branched topology. Nature. 2004; 430:190-195.
32. Vriezema DM, Aragones MC, Elemans JAA, Cornelissen JJLM, Rowan AE, Nolte RJM. Self-assembled nanoreactors. Chemical Reviews. 2005;105:1445-1490.
33. Lee M, Jang CJ, Ryu J-H. Supramolecular reactor from self-assembly of rod-coil molecule in aqueous environment. J of the A Chem Soc. 2004;126:8082-8083.
34. Bolinger P-Y, Stamou D, Vogel H. Integrated nanoreactor systems: triggering the release and mixing of compounds inside single vesicles. J of the A Chem Soc. 2004;126:8594-8595.
35. Lee M, Lee S-J, Jiang L-H, Stimuli-responsive supramolecular nanocapsules from amphiphilic calixarene assembly. J of the A Chem Soc. 2004;126:12724- 12725.
36. Meijer EW, van Genderen MHP. Chemistry: dendrimers set to self-destruct. Nature. 2003;426(6963): 128-129. Image in Figure 3 reprinted with permission. Copyright 2003 Nature Publishing Group.
37. Leung KC.-F, Aricó F, Cantrill SJ, Stoddart JF. Template-directed dynamic synthesis of mechanically interlocked dendrimers. J of the A Chem Soc. 2005;127:5808-5810.
38. Gillies ER, Jonsson TB, Frechet JMJ. Stimuli-responsive supramolecular assemblies of linear-dendritic copolymers. J of the A Chem Soc. 2004;126:11936-11943.
39. Freemantle M. Blossoming of dendrimers. Chem and Eng News.1999;77\21-35.
40. Fréchet JM. Dendrimers and supramolecular chemistry. Proc of the Natl Academy of Sciences of the United States of America. 2002;99:4782-4792.
41. Conn MM, Rebek Jr J. Self-assembling capsules. Chemical Reviews, 1997;97:1647-1668.
42. Yamanaka M, Shivanyuk A. Rebek Jr J. Kinetics and thermodynamics of hexameric capsule formation. J of the A Chem Soc. 2004;126:2939-2943.
43. Davis AV, Yeh RM, Raymond KN. Supramolecular assembly dynamics. Proc of the Natl Academy of Sciences of the United States of America. 2002;99:4793-4796.
44. Leung DH, Fiedler D, Bergman RG, Raymond KN. Selective C-H bond activation by a supramolecular host-guest assembly. Angewandte Chemie Intl Ed. 2004;43: 963-966.
45. Vignon SA, Jarrosson T, Iijima T, Tseng H-R, Sanders JKM, Stoddart JF. Switchable netural bistable rotaxanes. J of the A Cheml Soc. 2004;126:9884-9885.
46. Altieri A, Gatti FG, Kay ER, Leigh DA, Martel D, Paolucci F, Slawin AMZ, Wong JKY. Electrochemically switchable hydrogen-bonded molecular shuttles. J of the A Chem Soc. 2003;125:8644-8654.
47. Katz E, Lioubashevsky O, Willner I. Electromechanics of a redox-active rotaxane in a monolayer assembly on an electrode. J of the A Chem Soc. 2004;126:15520-15532.
48. Jang YH, Hwang S, Kim Y-H, Jang S S, Goddart III WA. Density functional theory studies of the [2]rotaxane component of the Stoddart-Heath molecular switch. J of the A Chem Soc. 2004;126:12636-12645.
49. Jang YH, Jang SS, Goddart III WA. Molecular dynamics simulation study on a monolayer of half [2]rotaxane self-assembled on Au(111). J of the A Chem Soc. 2005;127: 4959-4964.
50. Cantrill SJ, Chichak KS, Peters AJ, Stoddart JF. Nanoscale borromean rings. Accounts of Chem Res. 2005;38:1-9.
51. Hooker JM, Kovacs EW, Francis MB. Interior surface modification of bacteriophage MS2. J of the A Chem Soc. 2004;126:3718-3719.
52. Hess H, Clemmens J, Brunner C, Doot R, Luna S, Ernst K-H, Vogel V. "Molecular self-assembly of "nanowires" and " nanospools" using active transport. Nano Letts. 2005; 5:629-633.
53. Sherman WB, Seeman NC. A precisely controlled DNA biped walking device," Nano Letts. 2004;4:1203-1207. Image in Figure 2 reprinted with permission. Copyright 2004 American Chemical Society.
54. Chen Y, Mao C. Putting a brake on an autonomous DNA nanomotor. J of the A Chem Soc. 2004;126:8626-8627.
55. Badjic JD, Balzani V, Credi A, Silvi S, Stoddart JF. A molecular elevator. Science. 2004;303:1845-1849.
56. Pérez EM, Dryden DTF, Leigh DA, Teobaldi G, Zerbetto F. A generic basis for some simple light-operated mechanical molecular machine. J of the A Chem Soc. 2004;126: 12210-12211.
57. Tian Y, Mao C. Molecular gears: A pair of DNA circles continuously rolls against each other. J of the A Chem Soc. 2004;126:11410-11411.
58. + channels. J of the A Chem Soc. 2004; 126:15944-15945.
59. Sidorov V, Kotch FW, Kuebler JL, Lam Y-F, Davis JT. Chloride transport across lipid bilayers and transmembrane potential induction by an oligophenoxyacetamide. J of the A Chem Soc. 2003;125:2840-2841.
60. Kalra A, Garde S, Hummer G. Osmotic water transport through carbon nanotube membranes. Proc of the Natl Academy of Sciences of the United States of America. 2003;100:10175-10180.
61. Hummer G, Rasaiah JC, Noworyta JP. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 2001;414:188-190.
62. Zhu F, Schulten K. Water and proton conduction through carbon nanotubes as models for biological channels. Biophysical J. 2003;85:236-244.
63. Skoulidas AI, Ackerman DM, Johnson JK, Sholl DS. Rapid transport of gases in carbon nanotubes. Physical Review Letts. 2002;89:185901.
64. Sakai N, Sorde N, Matile S. Synthetic catalytic pores. J of the A Chem Soc. 2003;125:7776-7777.
65. Balzani V, Credi A, Venturi M. Light-powered molecular-scale machines. Pure and Appl Chem. 2003;75:541-547.
66. Baskaran D, Mays JW, Zhang XP, Bratcher MS. Carbon nanotubes with covalently linked porphyrin antennae: photoinduced electron transfer. J of the A Chem Soc 2005;127:6916-6917.
67. Mao C, Sun W, Shen Z, Seeman NC. A nanomechanical device based on the B-Z transition of DNA. Nature. 1999; 397:144-146.
68. Elizarov AM, Chiu S-H, Stoddart JF. An acid-base switchable [2]rotaxane. J of Organic Chemistry. 2002;67:9175-9181.
69. Liu Y, Flood AH, Stoddard JF. Thermally and electro-chemically controllable self-complexing molecular switches. J of the A Chem Soc. 2004;126:9150-9151.
70. Gianneschi NC, Nguyen ST, Mirkin CA. Signal amplification and detection via a supramolecular allosteric catalyst. J of the A Chem Soc. 2005; 127:1644-1645. Image in Figure 3 reprinted with permission. Copyright 2005 American Chemical Society.
71. Lee JY, Kim SK, Jung JH, Kim JS. Bifunctional fluorescent calix[4]arene chemosensor for both a cation and an anion. J of Organic Chemistry. 2005;70:1463-1466.
72. Petitjean A, Khoury RG, Kyritsakas N, Lehn J-M. Dynamic devices. Shape switching and substrate binding in ion-controlled nanomechanical molecular tweezers. J of the A Chem Soc. 2004; 126:6637-6647.
73. Muraoka T, Kinbara K, Kobayashi Y, Aida T. Light-driven open-close motion of chiral molecular scissors. J of the A Chem Soc. 2003;125:5612-5613.
74. Kobayashi K, Ishii K, Sakamoto S, Shirasaka T, Yamaguchi K. Guest-induced assembly of tetracarboxyl-cavitand and tetra(3-pyridyl)-cavitand into a heterodimeric capsule via hydrogen bonds and CH-halogen and/or CH-π interaction: control of the orientation of the encapsulated guest. J of the A Chem Soc. 2003;125:10615-10624.
75. Hernandez R, Tseng H-R, Wong JW, Stoddard JF, Zing JI. An operational supramolecular nanovalve. J of the A Chem Soc. 2004;126:3370-3371.
76. Ashkenasy G, Jagasia R, Yadav M, Ghadiri MR. Design of a directed molecular network. Proc of the Natl Academy of Sciences of the United States of America. 2004; 101:10872-10877.
77. Ashkenasy G, Ghadiri MR. Boolean logic functions of a synthetic peptide network. J of the A Chem Soc. 2004;126:11140-11141. Image in Figure 4 reprinted with permission. Copyright 2004 American Chemical Society.
78. Von Neumann J. Theory of Self-Reproducing Automata. Burks AW. ed; University of Illinois Press; 1966:388.
79. Rothemund P, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E. Design and characterization of programmable DNA nanotubes. J of the A Chem Soc. 2004;126:16344-16352.
80. Klavins E. Directed self-assembly using graph grammars. Foundations of Nanoscience: Self Assembled Architectures and Devices; Snowbird, UT: 2004.
81. Grunbaum B, Sphephard GC. Tilings' and Patterns. Freeman, New York; 1986.
82. Chopard B, Droz M. Cellular Automata Modeling of Physical Systems. Cambridge University Press, UK: 1998.
83. Troisi A, Wong V, Ratner MA. An agent-based approach for modeling molecular self-organization. Proc of the Natl Academy of Sciences of the United States of America, 2005;102:255-260.
84. Buchanan M. Small World: uncovering nature's hidden networks. Weidenfeld & Nicholson;2002.
85. Klavins E. Toward the Control of Self-Assembling Systems in Bicchi A, Christensen H, Prattichizzo D, eds. Control Problems in Robotics. Vol 4. Springer Tracts in Advanced Robotics. Springer; 2003:153-168.
86. Bishop J, Burden S, Klavins E, Kreisberg R, Malone W, Napp N, Nguyen T. Self-Organizing Programmable Parts, in Intl Conf on Intelligent Robots and Systems. IEEE/RSJ Robotics and Automation Society; 2005. Image in Figure 5 used with author's permission.
87. Richeter S, Rebek Jr J. Catalysis by a Synthetic Receptor Sealed at One End and Functionalized at the Other. J of the A Chem Soc. 2004;126:16280-16281. Images in Figure 2 reprinted with permission. Copyright 2004 American Chemical Society.
88. Kang J, Rebek J. Acceleration of a Diels-Alder reaction by a self-assembled molecular capsule. Nature. 1997;385:50-52. Images in Figure 2 reprinted with permission. Copyright 1997 Nature Publishing Group.
89. Balzani V, Credi A, Raymo FM, Stoddart JF. Artificial Molecular Machines. Angewandte Chemie. 2000;39:3348-3391. Image in Figure 2 reprinted with permission. Copyright 2000 Wiley.
90. Blau WJ, Fleming AJ. Designer Nanotubes by Molecular Self-Assembly. Science 2004;304:1457-1458. Image in Figure 2 reprinted with permission. Copyright 2004 American Association for the Advancement of Science.
91. Rothemund PWK. Using lateral capillary forces to compute by self-assembly. Proc of the Natl Academy of Sciences of the United States of America. 2000;97:984-989. Image in Figure 6 reprinted with permission. Copyright 2000 National Academy of Sciences, U.S.A.