Time & Place:  CS 191a: Second term, 2007; CS 191b: Third Term, 2007.
Jorgensen 74, Tu 10am-11:55am, Th 10am-10:55am

Grading Policy for CS 191a:
There will be weekly homework sets, a midterm, and a final exam.
Homeworks: The homeworks will consist of two simple questions and will be graded on a {0,1,2} scale.

• 0: Not turned in
• 1: Obviously wrong/little evidence of effort
• 2: Seems mostly correct/clear evidence of effort

Grading Policy for CS 191b:
Your grade will be based on weekly reading and writing assignments, as well as a final project. The final project is due June 1st. Presentations will be 12:00-3pm Monday June 11.

Office hours for CS 191a:
Joseph: Wednesday 1pm-2pm, Moore 210C.
David: Wednesday 7pm-8pm, Moore 204.

Resources: Will be posted as appropriate.

Syllabus: Will be posted soon.

CS 191b Reading List for 2007 (NOTE: These papers are for download by Caltech students for "fair use" only!):

April 12
• A.M. Turing (1937), "On Computable Numbers, With An Application To The Entscheidungsproblem", Proc. London Math Society, 42, 230-265.
  
Available in .pdf here.

• A.W. Burks (1970), "Von Neumann's Self-Reproducing Automata", orignally published in Essays on Cellular Automata, (ed. A.W. Burks) University of Illinois Press, pages 1-52. (This version from taken from Papers of John Von Neumann on Computing and Computer Theory, MIT Press, Cambridge, Massachusetts, 1987) (.pdf) Read pages 491-500, skim 501-529, read 530-540.
April 26
• Stuart Kauffman (1969), "Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets" J. Theoret. Biol. 22: 437-467. (.pdf)
• Aggarwal, Cheng, Goldwasser, Kao, Espanes, Schweller (2005), "Complexities for generalized models of self-assembly" SIAM J. Computing 34: 1493-1515. (.pdf)
May 3
• D. P. Bartel and J. W. Szostak (1993), "Isolation of New Ribozymes from a Large Pool of Random Sequences." Science 261: 1411-1418. (.pdf)
• Dirks, Lin, Winfree, Pierce (2004), "Paradigms for computational nucleic acid design." Nucleic Acids Research 34: 1392-1403. (.pdf)
• [optional] Dan Gillespie (2007), "Stochastic Simulation of Chemical Kinetics" Annu. Rev. Chem. 58: 35-55. (.pdf)
• [optional] Dan Gillespie (1977), "Exact Stochastic Simulation of Coupled Chemical Reactions." Journal of Physical Chemistry 81: 2340-2361. (.pdf)
May 10
• Alan M. Turing (1952), "The Chemical Basis of Morphogenesis." Philosophical Transactions of the Royal Society B, 237: 37-72. (.pdf)
• John J. Hopfield (1982), "Neural networks and physical systems with emergent collective computational abilities." Proc Natl Acad Sci U S A, 79: 2554-2558. (.pdf)
May 17
• B. Wlotzka and J. S. McCaskill (1997), "A Molecular Predator and its Prey: Coupled Isothermal Amplification of Nucleic Acids." Chemistry and Biology, 4: 25-33. (.pdf)
• L. Wolpert (1969), "Positional Information and the Spatial Pattern of Cellular Development" J. Theoret. Biol. 25: 1-47. (.pdf)
May 24
• E. Klavins (2004), "Directed Self-Assembly Using Graph Grammars" Proceedings of FNANO 2004. (.pdf)
• ...and that's it...!

CS 191b Reading List from 2005 (NOTE: These papers are for download by Caltech students for "fair use" only!):

• Week 2: Universal Computation and Construction
  Required reading:
  • A.M. Turing (1937), "On Computable Numbers, With An Application To The Entscheidungsproblem", Proc. London Math Society, 42, 230-265.
    Available in .pdf here or in online form via these links: The Turing Digital Archive (look for entry AMT/B/12), abelard.org.
    Read up to part II, i.e., read pages 230 - 252 (top).
  • John Von Neumann (1951), "The General and Logical Theory of Automata", various sources, including Papers of John Von Neumann on Computing and Computer Theory, MIT Press, Cambridge, Massachusetts, 1987. (.pdf)
    This transcript of a 1948 seminar includes von Neumann's first discussion of self-reproducing machines, and is a good theoretical and philosophical overview of automata theory as it relates to natural organisms. Read also the transcript of the discussion following the seminar. (Beware the MANY transcription errors, especially exponenents in numbers!) The full description of von Neumann's machine appears in the Burks paper below.
  • A.W. Burks (1970), "Von Neumann's Self-Reproducing Automata", orignally published in Essays on Cellular Automata, (ed. A.W. Burks) University of Illinois Press, pages 1-52. (This version from taken from Papers of John Von Neumann on Computing and Computer Theory, MIT Press, Cambridge, Massachusetts, 1987) (.pdf)
    Read pages 491-500, skim 501-529, read 530-540.
  Recommended reading:
  • John Von Neumann, Theory of Self-Reproducing Automata, University of Illinois Press, Urbana, Illinois, 1966.
    Part two of this book is the original reference upon which the A.W. Burks paper is based. This book is available online via the following website: walenz.org.
    Chapters one and two of part two have the most relevance, and note that there are figures which appear at the end of the book.
• Week 3: Tiling, Crystals, and the Origin of Life
  Required reading:
  • L.S. Penrose (1958), "Mechanics of Self-reproduction", Ann. of Human Genetics, 23:59-72. (.pdf)
  • H. Wang (1965), "Games, logic and computers." Scientific American, 213, No. 5, 98-106 (November 1965). (.pdf)
  • A.G. Cairns-Smith (1965), "The Origin of Life and the Nature of the Primitive Gene", J. Theoretical Biology, 10: 53-88. (.pdf)
  Recommended reading:
  • L.S. Penrose and R. Penrose (1957), "A Self-reproducing analogue", Nature, 179:1183 (1957). (.pdf)
  • L.S. Penrose (1959), "Self-reproducing Machines", Scientific American, 200:105-114 (June 1959). (.pdf)
• Week 4: Self-assembly, Morphogenesis, and DNA
  Required reading:
  • D. Soloveichik and E. Winfree (2004), "Complexity of Self-Assembled Shapes", preprint cs.CC/0412096 on arXiv.org. (.pdf)
  • P.W.K. Rothemund, N. Papadakis, E. Winfree (2004), "Algorithmic Self-Assembly of DNA Sierpinski Triangles", PLoS Biology, 2: e424. (.pdf)
  Recommended reading:
  • E. Winfree, F. Liu, L. Wenzler, N.C. Seeman (1998), "Design and self-assembly of two-dimensional DNA crystals", Nature 394: 539-544. (.pdf)
  • C. Mao, T. LaBean, J. Reif, N.C. Seeman (2000), "Logical computation using algorithmic self-assembly of DNA triple-crossover molecules", Nature 407: 493-496. (.pdf)
• Week 5: Physics of Computation
  Required reading:
  • C.H. Bennett (1973), "Logical Reversibility of Computation", IBM J. Res. Develop. 17: 525-532. (.pdf)
  • C.H. Bennett (1982), "The Thermodynamics of Computation -- a Review." Int. J. Theor. Phys. 21: 905-940. (.pdf)
  Recommended reading:
  • R. Landauer (1961), "Irreversibility and Heat Generation in the Computing Process." IBM J. Res. Develop. 3: 183-191. (.pdf)
  • C.H. Bennett, "Time/Space Trade-offs for Reversible Computation", SIAM J. Comput. 18: 766-776 (1989). (.pdf)
  • E. Fredkin and T. Toffoli, "Conservative Logic." Int. J. Theor. Phys. 21: 219-253 (1982). (.pdf)
  • C.H. Bennett and R. Landauer, "The Fundamental Physical Limits of Computation," Scientific American, 253(1):48-56 (July 1985) (.pdf)
    (overlaps with #3 but better figures)
  • Matt Cook, "Universality in Elementary Cellular Automata," Complex Systems, 15:1-40 (2004) (.pdf)
    or an expanded unpublished draft (.pdf) This is his proof that Wolfram's Rule 110 is universal, including the more complete version of the paper that Wolfram's journal wouldn't publish.
• Week 6: In-vitro Evolution
  Required reading:
  • D. P. Bartel and J. W. Szostak (1993), "Isolation of New Ribozymes from a Large Pool of Random Sequences." Science 261: 1411-1418. (.pdf)
  • M. C. Wright and G. F. Joyce (1997), "Continuous in vitro Evolution of Catalytic Function." Science 276: 614-617. (.pdf)
  • W.K. Johnston, P.J. Unrau, M.S. Lawrence, M.E. Glasner and D.P. Bartel (2001), "RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension." Science 292: 1319-1325. (.pdf)
  Recommended reading:
  • D. R. Mills, R. L. Peterson, and S. Spiegelman (1967), "An Extracellular Darwinian Experiment with a Self-Duplicating Nucleic Acid Molecule." Proc. Natl. Acad. Sci. USA 58: 217-224. (.pdf)
  • M. Eigen (1971), "Selforganization of Matter and Evolution of Biological Macromolecules." Naturwissenschaften. 58 (10): 183-465&&. (.pdf)
• Week 7: DNA Computation and Nanotechnology
  Required reading:
  • L. M. Adleman (1994), "Molecular Computation of Solutions to Combinatorial Problems." Science 266: 1021-1023. (.pdf)
  • K. Sakamoto, H. Gouzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, M. Hagiya (2000), "Molecular Computation by DNA Hairpin Formation." Science 288: 1223-1226. (.pdf)
  • M. Stojanovich and D. Stefanovic (2003), "A Deoxyribozyme-Based Molecular Automaton." Nature Biotechnology 21(9): 1069-1074. (.pdf)
  Recommended reading:
  • D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall (1996), "On the Computational Power of DNA." Discr. Appl. Math. 71: 79-94. (.pdf)
  • R. S. Braich, C. Johnson, P. W. K. Rothemund, D. Hwang, N. Chelyapov, and L. M. Adleman (2000), "Solution of a Satisfiability Problem on a Gel-Based DNA Computer." Proceedings of the Sixth International Meeting on DNA-Based Computers. (.pdf)
  • M. Stojanovich, T. Mitchell and D. Stefanovic (2002), "Deoxyribozyme-Based Logic Gates." J. Am. Chem. Soc. 124: 3555-3561. (.pdf)
  • B. Yurke, A. J. Turberfield, A. P. Mills, Jr., F. G. Simmel, and J. L. Neumann (2000), "A DNA-Fuelled Molecular Machine Made of DNA."  Nature 406: 605-608. (.pdf)
  • A. J. Turberfield, J. C. Mitchell, B. Yurke, A.P. Mills, Jr., M. I. Blakey, F.C. Simmel (2003), "DNA Fuel for Free-Running Nanomachines." Physical Review Letters 90(11): 118102-1 - 118102-4. (.pdf)
• Week 8: Sythetic In-Vitro Systems with Enzymes
  Required reading:
  • B. Wlotzka and J. S. McCaskill (1997), "A Molecular Predator and its Prey: Coupled Isothermal Amplification of Nucleic Acids." Chemistry and Biology January 4: 25-33. (.pdf)
  • M. Levy and A. D. Ellington (2004), "Exponential Growth by Cross-Catalytic Cleavage of Deoxyribozymogens." PNAS Vol 100, no. 11: 6416-6421. (.pdf)
  • Y. Benenson, B. Gil, U. Ben-Dor, R. Adar and E. Shapiro (2004), "An Autonomous Molecular Computer for Logical Control of Gene Expression." Nature 429: 423-429. (.pdf)
  Recommended reading:
  • J. Ackermann, B. Wlotzka, and J.S. McCaskill (1998), "In vitro DNA-based Predator-Prey System with Oscillatory Kinetics" Bulletin of Mathematical Biology 60: 329-353. (.pdf)
  • Y. Benenson, T. Paz-Elizur, R. Adar, E. Keinan, Z. Livneh and E. Shapiro (2004), "Programmable and Autonomous Computing Machine made of Biomolecules." Nature 414: 430-434. (.pdf)
• Week 9: Pi-Calculus and Algorithmic Chemistry
  Required reading:
  • M. Curti, P. Degano, C. Priami, et al (2004), "Modelling Biochemical Pathways Through Enhanced Pi-Calculus." Theoretical Computer Science 325 (1): 111-140. (.pdf)
  • W. Fontana (1992), "Algorithmic Chemistry" Artificial Life II pg 159-211, Addison-Wesley, Redwood City, California, 1992. (.pdf)
  Recommended reading:
  • A. Regev, E. Shapiro (2002), "Cells as Computation." Nature 419: 343-343. (.pdf)
  • R. Adar, Y. Benenson, G. Linshiz, A. Rosner, N. Tishby, E. Shapiro (2002), "Stochastic Computing with Biomolecular Automata" PNAS 101: 9960-9965. (.pdf)

References: The following books may be useful in understanding the ideas in this course. None of them are required, but all of them will be useful for various sections of the course.

• G. G. Hammes, Thermodynamics and Kinetics for the Biological Sciences, John Wiley & Sons, New York, 2000.
• A. Fersht, Structure and Mechanism in Protein Science, W.H. Freeman and Company, New York, 1999.
• C. Branden and J. Tooze, Introduction to Protein Science, Garland Publishing, Inc., New York and London, 1991.
• A. Kornberg and T. Baker, DNA Replication, W.H. Freeman and Company, New York, 1992.
• V. Bloomfield, D. Crothers and I. Tinoco, Jr, Nucleic Acids, University Science Books, Sausalito, California, 2000.
• M. Minsky, Computation: Finite and Infinite Machines, Prentice-Hall, Inc., Englewood Cliffs, N.J., 1967.
• J. Savage, Models of Computation: Exploring the Power of Computing, Addison Wesley Longman, Inc., Berkeley, California, 1998.
• R. Feynman, Feynman Lectures on Computation, Addison-Wesley Publishing Company, Inc., Reading, Massachusetts, 1996.
• Jan L.A. van de Snepscheut, What Computing Is All About, Springer-Verlag, New York, 1993.
• S. Strogatz, Nonlinear Dynamics and Chaos, Addison-Wesley Publishing Company, Reading, Massachusetts, 1994.

Physics of Computation

• R. Landauer, "Irreversibility and Heat Generation in the Computing Process." IBM J. Res. Develop. 3: 183-191 (1961).
• C. H. Bennett, "Logical Reversibility of Computation."  IBM J. Res. Develop. 17: 525-532 (1973).
• C. H. Bennett, "The Thermodynamics of Computation -- a Review." Int. J. Theor. Phys. 21: 905-940 (1982). .pdf
• E. Fredkin and T. Toffoli, "Conservative Logic." Int. J. Theor. Phys. 21: 219-253 (1982).
• C. H. Bennett, "Time/Space Trade-offs for Reversible Computation." SIAM J. Comput. 18: 766-776 (1989).
• (overlaps with #3 but better figures) C. H. Bennett and Rolf Landauer, "The Fundamental Physical Limits of Computation," Scientific American, (198?)

• J. von Neumann, "Probabilistic Logics and the Synthesis of Reliable Organisms from Unreliable Components." In Automata Studies, C. Shannon (ed), 1956. .pdf
• N. Pippenger, "Developments in "The Synthesis of Reliable Organisms from Unreliable Components." In Proc. of Symposia in Pure Mathematics vol 50, 1990. .pdf
• M. Arbib, "Automata that Construct as well as Compute." In Brains, Machines, and Mathematics, pp. 143-161, 1987.

• D. Bray, "Protein Molecules as Computational Elements in Living Cells." Nature. 376: 307-312 (1995).
• D. C. Hauri and J. Ross, "A Model of Excitation and Adaptation in Bacterial Chemotaxis." Biophysical Journal 68: 708-722 (1995).
• P. B. Detwiler, S. Ramanathan, A. Sengupta, B. I. Shraiman, "Engineering Aspects of Enzymatic Signal Transduction: Photoreceptors in the Retina." Biophysical Journal, 79: 2801-2817 (2000). .pdf
• M. O. Magnasco, "Chemical Kinetics is Turing Universal." Phys. Rev. Let. 78: 1190-1193 (1997). .pdf
• A. Hjelmfelt, E. D. Weinberger, and J. Ross, "Chemical Implementation of Neural Networks and Turing Machines." Proc. Natl. Acad. Sci. USA88: 10983-10987 (1991). .pdf
• A. Hjelmfelt and J. Ross, "Chemical Implementation and Thermodynamics of Collective Neural Networks." Proc. Natl. Acad. Sci. USA 89: 388-391 (1992). .pdf

• M. A. Shae, G. K. Ackers, "The Or Control System of Bacteriophage Lambda: A Physical-Chemical Model for Gene Regulation." J. Mol. Biol. 181: 211-230 (1985).
• E. Mjolsness, D. H. Sharp, J. Reinitz, "A Connectionist Model of Development." J. Theoretical Biology 152: 429-453 (1991).
• R. Weiss, G. H. Homsy, and T. F. Knight, Jr., "Toward in vivo Digital Circuits."  Proceedings of DIMACS Workshop on Evolution as Computation (1999). .pdf
• M. B. Elowitz and S. Leibler, "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403: 335-338 (2000). .pdf
• T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a Genetic Toggle Switch in Escherichia coli." Nature 403: 339-342(2000). .pdf
• R. Weiss and T. F. Knight, Jr., "Engineerings Communications for Microbial Robotics." Proceedings of the Sixth International Meeting on DNA-Based Computers (2000). .pdf
• C. H. Yuh, H. Bolouri, and E. H. Davidson, "Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene." Science279: 1896-1902 (1998). .pdf
• A. Sengupta, M. Djordjevic, B. I. Shraiman, "Specificity and robustness in transcription control networks." PNAS 99:2072-2077 (2002). .pdf
• S. Shen-Orr, R. Milo, S. Mangan, U. Alon, "Network Motifs in the transcriptional regulation network of Escherichia coli." Nature Genetics 31:64-68 (2002). .pdf supplemental.pdf
• M. A. Savageau, "Design principles for elementary gene circuits: Elements, methods, and examples." Chaos 11:142-159-68 (2002). .pdf

• A. Arnold, M. Siemann, K. Scharnweber, M. Werner, S. Baumann, M. Reuss, "Kinetic Modeling and Simulation of In Vitro Transcription by Phage T7 RNA Polymerase." Biotechnology and Bioengineering72: 548-561 (2001). .pdf
• B. Wlotzka and J. S. McCaskill, "A Molecular Predator and Its Prey: Coupled Isothermal Amplification of Nucleic Acids." Chemistry and Biology 4: 25-33 (1997). .pdf
• J. Ackermann, B. Wlotzka, and J. S. McCaskill, "In vitro DNA-based Predator-Prey Systems with Oscillatory Kinetics."  Bull. Math. Biol. 60: 329-353 (1998). .pdf
• Y. Benenson, T. Paz-Elizur, R. Adar, E. Keinan, Z. Livneh, E. Shapiro, "Programmable and autonomous computing machine made of biomolecules." Nature 414: 430-434 (2002). .pdf

• H. H. McAdams and A. Arkin, "Stochastic Mechanisms in Gene Expression." Proc. Natl. Acad. Sci. USA 94: 814-819 (1997). .pdf
• N. Barkai and S. Leibler, "Circadian Clocks Limited by Noise." Nature403: 267-268 (2000). .pdf
• J. Vilar, H. Kueh, N. Barkai and S. Leibler, "Mechanisms of noise-resistance in genetic oscillators." PNAS99: 5988-5992 (2002). .pdf
• M. A. Gibson and J. Bruck, "Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels." J. Phys. Chem. A 104: 1876-1889 (2000). .pdf
• W. Bialek, "Stability and Noise in Biochemical Switches." (2000) .pdf
• D. Gonze, J. Halloy, A, Goldbeter, "Robustness of circadian rhythms with respect to molecular noise." PNAS 99: 673-678 (2002). .pdf supplemental-info.pdf caption.html

In vitro evolution of DNA and RNA

• D. R. Mills, R. L. Peterson, and S. Spiegelman, "An Extracellular Darwinian Experiment with a Self-Duplicating Nucleic Acid Molecule." Proc. Natl. Acad. Sci. USA 58: 217-224 (1967).
• D. P. Bartel and J. W. Szostak, "Isolation of New Ribozymes from a Large Pool of Random Sequences." Science 261: 1411-1418 (1993).
• W. P. C. Stemmer, "DNA Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution." Proc. Natl. Acad. Sci. USA 91: 10747-10751 (1994). .pdf
• R. R. Breaker and G. F. Joyce, "Emergence of a Replicating Species from an in vitro RNA Evolution Reaction."  Proc. Natl. Acad. Sci. USA 91: 6093-6097 (1994). .pdf
• M. C. Wright and G. F. Joyce, "Continuous in vitro Evolution of Catalytic Function." Science 276: 614-617 (1997). .pdf
• R. R. Breaker and G. F. Joyce, "A DNA Enzyme that Cleaves RNA." Chemistry and Biology 1: 223-229 (1994).
• W. K. Johnston, P. J. Unrau, M. S. Lawrence, M. E. Glasner, D. P. Bartel, "RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension." Science 292:1319-1325 (2001). .pdf
• M. Eigen, J. McCaskill, and P. Schuster, "Molecular Quasi-Species." J. Phys. Chem. 92: 6881-6891 (1988).

• L. M. Adleman, "Molecular Computation of Solutions to Combinatorial Problems." Science266: 1021-1023 (1994).
• D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall, "On the Computational Power of DNA." Discr. Appl. Math. 71: 79-94 (1996).
• R. S. Braich, C. Johnson, P. W. K. Rothemund, D. Hwang, N. Chelyapov, and L. M. Adleman, "Solution of a Satisfiability Problem on a Gel-Based DNA Computer." Proceedings of the Sixth International Meeting on DNA-Based Computers (2000). .pdf
• R. S. Braich, N. Chelyapov, C. Johnson, P. W. K. Rothemund, L. Adleman, "Solution of a 20-Variable 3-SAT Problem on a DNA Computer." Science April, 2002. .pdf
• K. Chen and E. Winfree, "Error Correction in DNA Computing: Misclassification and Strand Loss."  Pages 49-63 in E. Winfree, D. Gifford (eds.) DNA Based Computers V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Providence, RI. American Mathematical Society (2000). .ps .pdf
• K. Chen and V. Ramachandran, "A Space-Efficient Randomized DNA Algorithm for k-SAT." Proceedings of the Sixth International Meeting on DNA-Based Computers (2000).

• J. SantaLucia, Jr., "A Unified View of Polymer, Dumbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics."   Proc. Natl. Acad. Sci. USA 95: 1460-1465 (1998). .pdf
• B. Yurke and A. Mills, Jr., "Toehold-Enhanced DNA Strand Exchange: Fuel for Nanomachines."  Preprint (1998).
• M. Zuker and P. Stiegler, "Optimal Computer Folding of Large RNA Sequences using Thermodynamics and Euxiliary Information."  Nucleic Acids Research 9: 133-148 (1981).
• C. Flamm, W. Fontana, I. L. Hofacker, P. Schuster, "RNA Folding at Elementary Step Resolution."  RNA 6: 325-338 (2000). .pdf
• I. Biswas, A. Yamamoto, and P. Hsieh, "Branch Migration Through DNA Sequence Heterology."  J. Mol. Biol. 279: 795-806 (1998). .pdf

• K. E. Drexler, "Molecular Engineering: An Approach to the Development of General Capabilities for Molecular Manipulation." Proc. Natl. Acad. Sci. USA 78: 5275-5278 (1981).
• G. M. Whitesides, J. P. Mathias, C. T. Seto, "Molecular Self-Assembly and Nanochemistry: A Chemical Strategy for the Synthesis of Nanostructures." Science 254: 1312-1319 (1991).
• N. Seeman et. al., "New Motifs in DNA Nanotechnology." Nanotechnology 9: 257-273 (1998). .pdf
• G. Bonnet, S. Tyagi, A. Libchaber, and F. R. Kramer, "Thermodynamic Basis of the Enhanced Specificity of Structures DNA Probes." Proc. Natl. Acad. Sci. USA 96: 6171-6176 (1999). .pdf
• A. J. Turberfield, B. Yurke, and A. P. Mills, Jr., "DNA Hybridization Catalysts and Molecular Tweezers." Pages 171-182 in E. Winfree, D. Gifford (eds.) DNA Based Computers V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Providence, RI. American Mathematical Society (2000). .ps .pdf
• B. Yurke, A. J. Turberfield, A. P. Mills, Jr., F. G. Simmel, and J. L. Neumann, "A DNA-Fuelled Molecular Machine Made of DNA."  Nature 406: 605-608 (2000). .pdf

• E. Winfree, "Whiplash PCR for O(1) Computing."  Proceedings of the Fourth International Meeting on DNA-Based Computers (1998). .ps .pdf
• K. Komiya, K. Sakamoto, H. Gouzu, S. Yokoyama, M. Arita, A. Nishikawa, and M. Hagiya, "Successive State Transitions with I/O Interface by Molecules." Proceedings of the Sixth International Meeting on DNA-Based Computers (2000).
• K. Sakamoto, H. Gouzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, and M. Hagiya, "Molecular Computation by DNA Hairpin Formation."  Science 288: 1223-1226 (2000). .pdf
• E. Winfree, F. Liu, Lisa A. Wenzler, and N. C. Seeman, "Design and Self-Assembly of Two-Dimensional DNA Crystals."  Nature 394: 539-544 (1998). .pdf
• M. G. Lagoudakis and T. H. LaBean, "2D DNA Self-Assembly for Satisfiability." Pages 141-154 in E. Winfree, D. Gifford (eds.) DNA Based Computers V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Providence, RI. American Mathematical Society (2000). .ps .pdf
• C. Mao, T. H. LaBean, J. H. Reif, and N. C. Seeman, "Logical Computation using Algorithmic Self-Assembly of DNA Triple-Crossover Molecules."  Nature 407: 493-496 (2000). .pdf
• R. M. Robinson, "Undecidability and Nonperiodicity for Tilings of the Plane."  Inventiones Math. 12: 177-209 (1971).
• W. P. C. Stemmer, A. Crameri, K. D. Ha, T. M. Brennan, and H. L. Heyneker, "Single-Step Assembly of a Gene and Entire Plasmid from Large Numbers of Oligodeoxyribonucleotides."  Gene 164: 49-53 (1995).

• N. Pippenger, "Developments in "The Synthesis of Reliable Organisms from Unreliable Components." .pdf
• C. H. Bennett, "The Thermodynamics of Computation -- a Review." .pdf
• M. A. Gibson and J. Bruck, "Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels." .pdf
• D. Gonze, J. Halloy, A, Goldbeter, "Robustness of circadian rhythms with respect to molecular noise." .pdf supplemental-info.pdf caption.html
• J. Vilar, H. Kueh, N. Barkai and S. Leibler, "Mechanisms of noise-resistance in genetic oscillators." .pdf
• S. Shen-Orr, R. Milo, S. Mangan, U. Alon, "Network Motifs in the transcriptional regulation network of Escherichia coli." .pdf supplemental.pdf
• M. A. Savageau, "Design principles for elementary gene circuits: Elements, methods, and examples." .pdf
• W. K. Johnston, P. J. Unrau, M. S. Lawrence, M. E. Glasner, D. P. Bartel, "RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension." .pdf
• R. S. Braich, N. Chelyapov, C. Johnson, P. W. K. Rothemund, L. Adleman, "Solution of a 20-Variable 3-SAT Problem on a DNA Computer." .pdf