Publications Sept 1998-1999 Supported by the Current Grant
1998-1999 Books (1 Book):
L. F. Landweber and E. B. Baum, eds.. DIMACS Workshop on DNA Based Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, ed. H. Rubin, published Sept. 1998.
Papers Sept 1998-1999 Supported by the Current Grant
Leonard M. Adleman, Paul W. K. Rothemund, Sam Roweis, Erik Winfree. ``On Applying Molecular Computation to the Data Encryption Standard.'' Journal of Computational Biology, 6(1): 53--63, 1999
Eugene Antipov. A Max 1s problem in DNA computing via genetic algorithms. In Wolfgang Banzhaf, A. E. Eiben, Max H. Garzon, Vasant Honavar, Mark Jakiela, and Robert E. Smith, editors, Late-Breaking Papers of the Genetic and Evolutionary Computation Conference, July 13-17, 1999, Orlando, Florida USA., San Francisco, 1999. Morgan Kaufman.
http://www.cis.udel.edu/~wood/BMC/papers/REU.pdfBach, E., A. Condon, E. Glaser, and C. Tanguay, Improved Models and Algorithms for DNA Computation, Proc. 11th Annual IEEE Conference on Computational Complexity, J. Computer and System Sciences, to appear, 1999.
Bancroft,C. C.T. Clelland, V. Risca, Genomic Steganography: Amplifiable Microdots, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Bloom,B., C. Bancroft, Liposomal-Mediated Biomolecular Computation, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Boneh, D., Dunworth, C., Lipton, R.J., and Sgall, J. Making DNA computers Error Resistant. In DNA Based Computers II, L. F. Landweber and E. B. Baum, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 44 pages 165-172, American Mathematical Society. published Sept. 1998.
Brockman, J.M.; Frutos, A.G. and Corn, R.M. "A Multi-Step Chemical Modification Procedure to Create DNA Arrays on Gold Surfaces for the Study of Protein-DNA Interactions with Surface Plasmon Resonance Imaging," J. Am. Chem. Soc., 121 8044-8051 (1999).
Chen, J., E. Antipov, B. Lemieux, W. Cedeno, D.H. Wood, In vitro Selection for a Max 1s DNA Genetic Algorithm, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Clelland, C.T., Risca, V., and C. Bancroft. Genomic Steganography: Amplifiable Microdots. Under review by Nature, 1999.
Cukras, A., Faulhammer, D., Lipton, R., and Landweber, L.F., "Chess games: A model for RNA-based computation", 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998. Invited to special issue of BIOSYSTEMS, 1998.
Junghuei Chen, Eugene Antipov, Bertrand Lemieux, Walter Cedeno, and David Harlan Wood. DNA computing implementing genetic algorithms. In Laura Landweber, Erik Winfree, Richard Lipton, and Stephan Freeland, editors, Preliminary Proceedings DIMACS Workshop on Evolution as Computation, pages 39-49, DIMACS, Piscataway NJ, January 1999.
http://www.cis.udel.edu/~wood/BMC/papers/UDel_DIMACS_99.pdf
J. Chen, D. Wood, "A New DNA Separation Technique with Low Error Rate", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, . published Sept. 1998.
Junghuei Chen, David Wood, "A New DNA Separation Technique with Low Error Rate", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Cukras, A., Faulhammer, D., Lipton, R., and Landweber, L.F. Chess games: a model for RNA-based computation. DIMACS: 4th Annual Workshop on DNA Based Computers. (1998).
Faulhammer, D., A. R. Cukras, R. J. Lipton, L. F. Landweber, When the Knight Falls: On Constructing an RNA Computer, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Faulhammer, D., Cukras, A. R., Lipton, R. J. and L. F. Landweber (in press) Molecular Computation: RNA Solutions to Chess Problems. Proc. Natl. Acad. Sci. USA., to appear 1999.
Brian L. Frey and Robert M. Corn, "Covalent Attachment and Derivatization of Poly-L-Lysine Monolayers on Gold Surfaces as Characterized by Polarization-Modulation FTIR Spectroscopy," Analytical Chem., 68 3187 (1996).
Frutos, A.G.; Weibel, S.C. and Corn, R.M. "Near Infrared Surface Plasmon Resonance Measurements of Ultrathin Films. 2. Fourier Transform SPR Spectroscopy," Analytical Chem., 71 3935-3940 (1999).
Frutos, A.G.; Smith, L. M. and Corn, R.M. "Enzymatic Ligation Reactions of DNA "Words" on Surfaces for DNA Computing," J. Am. Chem. Soc., 120 10277 (1998).
Frutos, A.G.; and Corn, R.M. "Surface Plasmon Resonance Measurements of Ultrathin Organic Films," Analytical Chem., 70 449A (1998).
Anthony G. Frutos, Andrew J. Thiel, Anne E. Condon, Lloyd M. Smith, Robert M. Corn, "DNA Computing at Surfaces: 4 Base Mismatch Word Design", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Frutos, A. G., Liu, Q., Thiel, A. J., Sanner, A. M. W., Condon, A. E., Smith, L. M. and Corn, R. M. Demonstration of a word design strategy for DNA computing on surfaces. Nucleic Acids Res., 25 (23), 4748-4757. 1997.
Anthony G. Frutos, Andrew J. Thiel, Anne E. Condon, Lloyd M. Smith, Robert M. Corn, "DNA Computing at Surfaces: 4 Base Mismatch Word Design", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Frutos, A.G., Smith, L.M. and Corn, R.M. Enzymatic ligation reactions of DNA "words" on surfaces for DNA computing. J. Am. Chem. Soc., 120 (40), 10277-10282. 1998.
Gehani, A., T. H. LaBean, and J.H. Reif, DNA-based Cryptography, 5th DIMACS Workshop on DNA Based Computers, MIT, June, 1999. To appear in DNA Based Computers, V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, (ed. E. Winfree), to be published by the American Mathematical Society, 2000.
www.cs.duke.edu/~reif/paper/DNAcrypt/crypt.ps http://www.cs.duke.edu/~reif/paper/DNAcrypt/crypt.talk/crypt.talk.pdf http://www.cs.duke.edu/~reif/paper/DNAcrypt/crypt.talk/crypt.talk.web/crypt.talk.htmlGillmor, S.D.; Liu, Q.; Thiel, A.J.; Condon, A.E.; Corn, R.M.; Smith, L.M. and Lagally, M.G. "Hydrophobic/Hydrophilic Patterned Surfaces to Create DNA Arrays" to be submitted (to Langmuir), 1999.
Goode Laun,T.E., "Constants and Splicing Systems", Ph.D. Dissertation, Binghamton University, 1999.
Goode Laun,T.E. & D.Pixton, 'Semi-simple splicing systems', invited article for book, Ed. C.Martin-Vide, (to appear in 2000).
Goode Laun,T.E. & D.Pixton, 'Syntactic monoids, simultaneous pumping and H systems', (in preparation).
Goode Laun,T.E. & K.J.Reddy, 'Wet splicing systems', in "DNA Based Computers III", Ed. by H.Rubin & D.H.Wood, DIMACS ser. in Discr. Math. v.48, AMS,Providence RI (1999).
Guarnieri, F., and C. Bancroft. Use of a Horizontal Chain Reaction for DNA-Based Addition. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 4:105-111 (1999).
T.Head, Circular suggestions for DNA computing, in: "Pattern Formation in Biology, Vision and Dynamics", Eds. M.Gromov & A.Carbone, Pattern Formation, World Scientific, invited paper, Singapore and London (to appear 1999).
http://www.math.binghamton.edu/dennis/DARPA/circular.htmlT.Head, M.Yamamura & S.Gal, Aqueous computing: writing on molecules, Proceedings of the Congress on Evolutionary Computing (CEC'99), invited paper, July 6-9, 1999.
http://www.math.binghamton.edu/dennis/DARPA/aqueous.htmlHead,T., 'Writing by methylation proposed for aqueous computing', invited article for book, Ed. C.Martin-Vide, (to appear in 2000).
Head,T., 'Splicing representations of strictly locally testable languages',
Discrete Applied Math., 87(1998)139-147.
Head,T., 'Splicing languages generated with one sided contexts', in: "Biomolecular Computing - Theory and Experiment", Ed. by Gh.Paun,
Springer-Verlag (1998).
Head,T., 'Hamiltonian paths and double stranded DNA', in: "Biomolecular
Computing - Theory and Experiment", Ed. by Gh.Paun, Springer-Verlag
(1998)80-92.
Head,T., 'Communication by documents in communities of organisms', Millennium III, Issue #4, (to appear winter 1999).
Head,T., 'Relativised code properties amd multi-tube DNA dictionaries', invited article for book, Ed. by Gh.Paun (to appear in 2000).
Head,T., 'Biomolecular realizations of a well grounded parallel architecture', invited article for book on biomolecular computing, Ed. By J.Reif, (to appear 2000).
Head,T., 'Writing by methylation proposed for aqueous computing', invited article for book, Ed. C.Martin-Vide, (to appear in 2000).
Head,T., G.Rozenberg, R. Bladergroen, C.K.D.Breek, P.H.M.Lommerse & H.Spaink, 'The plasmid alternative for biomolecular computing', (to be
submitted)
Head,T., 'M.Yamamura & S.Gal, Aqueous computing: writing on molecules', in: Proc. Congr. Evolut. Comput. 1999, IEEE Service Center, Piscataway, NJ (1999)1006-1010.
Kari, L., L. F. Landweber, Computational Power of Gene Rearrangement, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Joshua P. Klien, Thomas H. Leete, and Harvey Rubin. A biomolecular implementation of logically reversible computation with minimal energy dissipation. Extended version of DNA4 and CEC99 papers. BioSystems, to appear.
http://www.cis.udel.edu/~wood/BMC/papers/BioSystems.pdfJoshua P. Klien, Thomas H. Leete, and Harvey Rubin. A biomolecular implementation of logically reversible computation with minimal energy dissipation. In Peter J. Angeline, Zbyszek Michalewicz, Marc Schoenauer, Xin Yao, and Ali Zalzala, editors, 1999 Congress on Evolutionary Computation. IEEE Computer Society Press, New York, to appear, 1999
http://www.cis.udel.edu/~wood/BMC/papers/cec99.pdf
Kari, L. and L. F. Landweber. (1999) Computing with DNA. Methods Mol. Biol. 132: 413-430.
L.Kari, J.Kari, L.Landweber. Reversible molecular computation in cili-ates. In Jewels are Forever, Karhumaki, J.; Maurer, H.; Paun, G.; Rozenberg, G., (Eds). Springer-Verlag 1999, pp.353-363.
Klein, JP., Leete, TH. & Rubin H. A Biomolecular Implementation of Logically Reversible Computation with Minimal Energy Dissipation. BioSystems 52, 15-23, 1999.
Knight, R. D. and L. F. Landweber. (1998) Rhyme or Reason: RNA-Arginine Interactions and the Genetic Code. Chemistry and Biology. 5: R215-220.
LaBean, T. H., E. Winfree, J. H. Reif, Experimental Progress in Computation by Self-Assembly of DNA Tilings, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree,, to be published by the American Mathematical Society, 2000.
http://www.cs.duke.edu/~thl/tilings/labean.ps http://www.cs.duke.edu/~thl/tilings/TileTalkSlides.hqx
Thomas H. LaBean, Hao Yan, Jens Kopatsch, Furong Liu, Erik Winfree, John H. Reif, Nadrian C. Seeman. ``Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes.'' Journal of the American Chemical Society, in press. 1999.
L. F. Landweber and E. B. Baum, eds.. DIMACS Workshop on DNA Based Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, ed. H. Rubin, published Sept. 1998.
Landweber, L. F. and R. J. Lipton. DNA2DNA Computations: A potential 'killer app'? In 24th International Colloquium on Automata, Languages and Programming (ICALP), Lecture Notes in Computer Science, pages 672-683, Springer-Verlag.1998. In DNA Based Computers III, H. Rubin and D.H. Wood, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, vol 48, 161-172.
Lagoudakis, M. G., T. H. LaBean, 2D DNA Self-Assembly for Satisfiability, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.44, American Mathematical Society, ed. E. Winfree, (1999).
Landweber, L. F. and L. Kari. (1998) The Evolution of DNA Computing: Nature's Solution to a Path Problem. 1998 Genetic Programming Conference Proceedings, John Koza et al., eds., Morgan Kaufmann Publishers, Inc., 700-708.
Landweber, L. F. and L. Kari. (1998) The Evolution of DNA Computing: Nature's Solution to a Computational Problem. 1998 Proceedings of Symposia on Intelligence and Systems '98, May 21-23, 1998. IEEE Computer Society Press, 133-139. Invited to special issue of BIOSYSTEMS, 1999.
L.Landweber, L.Kari. Universal molecular computation in ciliates. InEvolution as Computation, L.Landweber, E,Winfree, Eds., Springer Verlag, 1999.
Landweber, L. F. (1999) RNA Based Computing. In DNA Based Computers II, L. F. Landweber and E. B. Baum, eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society, 181-189.
Laura Landweber, Lila Kari, "The evolution of cellular computing: Nature's solution to a computational problem", 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998. Invited to special issue of BIOSYSTEMS, 1999.
Landweber, L. F. and Winfree, E., eds. (in press) Evolution as Computation. Springer-Verlag.
Landweber, L.F. and I. D. Pokrovskaya. (1999) Emergence of a Dual Catalytic RNA with Metal Specific Cleavage and Ligase Activities: The Spandrels of RNA Evolution. Proc. Natl. Acad. Sci.USA 96: 173-178.
Landweber, L.F., Simon, P.J., and T.A. Wagner. Ribozyme Design and Early Evolution. BioScience 48: 94-103., (1998)
Laura F. Landweber, Richard Lipton (Invited paper), "DNA 2 DNA Computations: A Potential `Killer App'?", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Landweber, L.F. and Kreitman, M. Producing Single-Stranded DNA in Polymerase Chain Reaction for Direct Genomic Sequencing. Methods Enzymol. 218: 17-26, (1993)
Elizabeth Laun, Kalluru J. Reddy, "Wet Splicing Systems", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Thomas H. Leete, Joshua Klein, Jerome S. Salem, Harvey Rubin, Bit Operations Using a DNA Template", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Leete, TH., Schwartz, MD., Williams, WM., Wood, DH., Salem, JS. & Rubin, H. Massively Parallel DNA Computation: Expansion of Symbolic Determinants.in DNA Based Computers II (DIMACS) Workshop, June 10-12, 1996. Amer. Math. Soc. 1998.
F. Liu, H. Wang and N.C. Seeman, Short Extensions to Sticky Ends for DNA Nanotechnology and DNA-Based Computation, Nanobiology 4, 257-262 (1999).
F. Liu, R. Sha and N.C. Seeman, Modifying the Surface Features of Two-Dimensional DNA Crystals, J. Am. Chem. Soc. 121, 917-922 (1999).
F. Liu, M.F. Bruist and N.C. Seeman, Parallel Helical Domains in DNA Branched Junctions Containing 5', 5' and 3', 3' Linkages, Biochemistry 38, 2832-2841 (1999).
Qinghua Liu, Andrew J. Thiel, Anthony G. Frutos, Robert M. Corn, Lloyd M. Smith, "Surface-Based DNA Computation: Hybridization and Destruction", DIMACS Workshop on DNA Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. H. Rubin, (1998).
Liu, Q., A. G. Frutos, L. Wang, A. E. Condon, R. M. Corn, L. M. Smith, DNA Computing on Surfaces, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
Qinghua Liu, Andrew J. Thiel, Anthony G. Frutos, Robert M. Corn, Lloyd M. Smith, "Surface-Based DNA Computation: Hybridization and Destruction", DIMACS Workshop on DNA Based Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, ed. H. Rubin, published Sept. 1998.
Qinghua Liu, Anthony Frutos, Liman Wang, Andrew Thiel, Susan Gillmor, Todd Strother, Anne Condon, Robert Corn, Max Lagally, Lloyd Smith "Progress towards demonstration of a surface based DNA computation: A one word approach to solve a model satisfiability ", 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998. Invited to special issue of BIOSYSTEMS, 1999.
Liu, Q., Frutos, A.G., Wang, L., Condon, A.E., Corn, R.M. and Smith, L.M. 1999. DNA computing on surfaces. Nature, in press.1999.
Liu, Q.; Wang, L. and Smith, L.M. "Identification of DNA Molecules on Surfaces by Array Hybridization for DNA Computing" (in preparation), 1999.
Liu, Q., Frutos, A. G., Thiel, A. J., Corn, R. M. and Smith, L. M. 1998. DNA computing on surfaces: encoding information at the single base level. J. Comp. Biology, 5 (2), 269-278.
F. Liu, R. Sha and N.C. Seeman, Modifying the Surface Features of Two-Dimensional DNA Crystals, Journal of the American Chemical Society 121, 917-922 (1999).
C. Mao, W. Sun, Z. Shen and N.C. Seeman, A DNA Nanomechanical Device Based on the B-Z Transition, Nature 397, 144-146 (1999).
C. Mao, W. Sun and N.C. Seeman, Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy, J. Am. Chem. Soc. 121, 5437-5443 (1999).
Marathe,A., A. E. Condon, R. M. Corn, On Combinatorial DNA Word Design, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999). To appear in J. Computational Biology.
http://corninfo.chem.wisc.edu/writings/codepaper.htmlBryce P. Nelson, Anthony G. Frutos, Jennifer M. Brockman and Robert M. Corn, "Near Infrared Surface Plasmon Resonance Measurements of Ultrathin Films. 1. Angle Shift and SPR Imaging Experiments," Analytical Chem., 71 3928-3934 (1999).
M. Ogihara and A. Ray, Simulating boolean circuits on DNA computers. In Algorithmica 25 :239--250, 1999.
M. Ogihara and A. Ray, The minimum DNA model and its computational power. In Unconventional Models of Computation, pages 309--322. Springer, Singapore (1998).
M. Ogihara and A. Ray,Biomolecular computing---recent theoretical and experimental advances. SIGACT News 30(2), pages 22-30, 1999.
M. Ogihara and A. Ray,Executing parallel logical operations with DNA .
In Proceedings of the Congress on Evolutionary Computation,
pages 972--979, IEEE Press, Piscataway, NJ, 1999.
M. Ogihara, Relating the minimum model for DNA computation and Boolean circuits. In Proceedings of the Genetic and Evolutionary Computation Conference,
pages 1817--1821, Morgan Kaufman, Publishers, San Francisco, CA, 1999.
http://www.cs.rochester.edu/u/ogihara/research/DNA/gecco.ps.gzM. Ogihara and A. Ray, Circuit evaluation: thoughts on a killer application in DNA computing. In Computing with Bio-Molecules. Theory and Experiments (G. Paun, ed.), pages 111--126, Springer-Verlag, Singapore, 1998.
http://www.cs.rochester.edu/u/ogihara/research/DNA/paun.ps.gzMartin Orlian, Frank Guarnieri, Carter Bancroft, "Parallel Primer Extension Horizontal Chain Reactions as a Paradigm of Parallel DNA-Based Computation", DIMACS Workshop on DNA Based Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, ed. H. Rubin, published Sept. 1998.
Pixton,D., 'Splicing in abstract families of languages', Theor. Computer. Sci., (to appear, April 2000).
Reif, J.H., Local Parallel Biomolecular Computation, DIMACS Workshop on DNA Based Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, ed. H. Rubin, published Sept. 1998. Postscript versions of this paper and its figures are at
http://www.cs.duke.edu/~reif/paper/Assembly.ps http://www.cs.duke.edu/~reif/paper/Assembly.fig.psJohn H. Reif and Ashish Gehani, Microflow Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998. Invited to special issue of BIOSYSTEMS, 1999.
Reif, J.H., Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation,18th Invited paper, International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS98), (December, 1998).
http://www.cs.duke.edu/~reif/paper/altcomp.psReif, J.H., Parallel Molecular Computation: Models and Simulations. Algorithmica, special issue on Computational Biology, to appear, 1999.
Postscript and figures are given at
http://www.cs.duke.edu/~reif/paper/Molecular.psReif, J.H., Paradigms for Biomolecular Computation, First International Conference on Unconventional Models of Computation, Auckland, New Zealand, January 1998. Published in Unconventional Models of Computation, edited by C.S. Calude, J. Casti, and M.J. Dinneen, Springer Publishers, 1998, pp 72-93.
http://www.cs.duke.edu/~reif/paper/paradigm.psReif, J.H. and Zheng Sun, Nano-Robotics Motion Planning and Its Applications in Nanotechnology and Biomolecular Computing, NSF Design and Manufacturing Grantees Conference, Jan 5-8, 1999.
http://www.cs.duke.edu/~reif/paper/NanoRobotics.htmlSam Roweis, Erik Winfree. ``On the reduction of errors in DNA computation.'' Journal of Computational Biology, 6(1): 65--75, 1999.
Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman. ``A Sticker-Based Model for DNA Computation.'' Journal of Computational Biology, 5(4): 615--629, 1998
Rubin, H., J. Klein, T. Leete, A biomolecular implementation of logically reversible computation with minimal energy dissipation, To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. . L. Kari, (1999).
Harvey Rubin, Joshua Klein, Thomas Leete, "A biomolecular implementation of logically reversible computation with minimal energy dissipation", 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998. Invited to special issue of BIOSYSTEMS, 1999.
N.C. Seeman, Nucleic Acid Nanostructures and Topology. Angewandte Chemie. 110, 3408-3428 (1998); Angewandte Chemie International Edition 37, 3220-3238 (1998).
N.C. Seeman, DNA Engineering and its Application to Nanotechnology, Trends in Biotech. 17, 437-443 (1999).
R. Sha, F. Liu, M.F. Bruist and N.C. Seeman, Parallel Helical Domains in DNA Branched Junctions Containing 5', 5' and 3', 3' Linkages, Biochemistry 38, 2832-2841 (1999).
L. M. Smith, R. M. Corn, A. E. Condon, M. G. Lagally, A. G. Frutos, Q. Liu, and A. J. Thiel, A Surface-Based Approach to DNA Computation.
J. Computational Biology, 5(2), 255-266. 1998.
W. Sun, C. Mao, F. Liu and N.C. Seeman, Sequence Dependence of Branch Migratory Minima. J. Mol. Biol. 282, 59-70 (1998).
Erik Winfree, Furong Liu, Lisa A. Wenzler, Nadrian C. Seeman (1998) Design and Self-Assembly of Two Dimensional DNA Crystals. Nature 394: 539--544, 1998.
Strother, T.C.; Votruba, P.G.; Corn, R.M.; Hamers, R.J. and Smith, L.M. "Synthesis and Characterization of DNA-Modified Silicon(111) Surfaces" (in preparation), 1999.
Wang, L., Q. Liu, A. Frutos, S. Gillmor, A. Thiel, T. Strother, A. Condon, R. Corn, M. Lagally, L. Smith, Surface-based DNA computing operations: DESTROY and READOUT, To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. L. Kari, (1999).
E. Winfree, F. Liu, L. A. Wenzler, and N.C. Seeman, Design and Self-Assembly of Two-Dimensional DNA Crystals, Nature 394, 539-544 (1998).
E. Winfree, 5th International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
David Harlan Wood, "Applying error correcting codes to DNA computing", Invited to special issue of BIOSYSTEMS, 1999.
David Harlan Wood, Junghuei Chen, Eugene Antipov, Walter Cedeno, and Bertrand Lemieux. A DNA implementation of the Max 1s problem. In Wolfgang Banzhaf, A. E. Eiben, Max H. Garzon, Vasant Honavar, Mark Jakiela, and Robert E. Smith, editors, GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference, July 13-17, 1999, Orlando, Florida USA., San Francisco, 1999. Morgan Kaufman.
http://www.cis.udel.edu/~wood/BMC/papers/gecco-99.pdfYamamura,M., T.Head & S.Gal, 'Boolean satisfiability decided by DNA plasmids', (in progress).
X. Yang, L.A. Wenzler, J. Qi, X. Li and N.C. Seeman, Ligation of DNA Triangles Containing Double Crossover Molecules, J. Am. Chem. Soc. 120, 9779-9786 (1998).
Zhao, X.; Votruba, P.G.; Strother, T.C.; Ellison, M.D.; Smith, L.M. and Hamers, R.J. "Formation of Organic Films on Si(111) Surfaces via Photochemical Reaction" (in preparation), 1999.