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Mission Statement

The Center for Molecular Cybernetics is an NSF Chemical Bonding Center (CBC) that concentrates on developing the theoretical and experimental tools to program and to observe the autonomous behavior of individual molecules or complexes that traverse, interrogate, and modify surface landscapes.

Papers

2007

  • Engineering entropy-driven reactions and networks catalyzed by DNA. Zhang DY, Turberfield AJ, Yurke B, Winfree E. Science, 318:1121-1125, 2007.p
  • An autonomous polymerization motor powered by DNA hybridization. Venkatarman S, Dirks RM, Rothemund PWKR, Winfree E, Pierce NA. Nature Nanotechnology, 2(8):490-494, 2007.p
  • Molecular spiders with memory. Antal T, Krapivsky PL. Phys. Rev. 2007.p
  • Molecular spiders in one dimension. Antal T, Krapivsky PL, Mallick K. J. Stat. Mech. 2007.p

2006

  • Enzyme-free nucleic acid logic circuits. Seelig G, Soloveichik D, Zhang DY, Winfree E. Science, 314(5805):1585-1588, 2006. xx
  • Medium scale integration of molecular logic gates in an automaton. Macdonald J, Li Y, Sutovic M, Lederman H, Pendri K, Lu W, Andrews BL, Stefanovic D, Stojanovic MN. Nano Letters, 6(11):2598-603, 2006. xx
  • Behavior of polycatalytic assemblies in a substrate-displaying matrix. Pei R, Taylor SK, Stefanovic D, Rudchenko S, Mitchell TE, Stojanovic MN. Journal of the American Chemical Society, 128(39):12693-9, 2006. xx
  • Characterization of transverse channel concentration profiles obtainable with a class of microfluidic networks. Sager J, Young M, Stefanovic D. Langmuir, 22(9):4452-4455, 2006. xx
  • Solution-phase molecular-scale computation with deoxyribozyme-based logic gates and fluorescent readouts. Macdonald J, Stefanovic D, Stojanovic MN. In Methods in Molecular Biology, 335: Fluorescent energy transfer nucleic acid probes: designs and protocols (Didenko VV, Ed.) Chapter 22: 343-363. Humana Press Inc., Totowa, NJ. xx
  • Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Lederman H, Macdonald J, Stefanovic D, Stojanovic MN. Biochemistry, 45(4): 1194-1199, 2006. xx

2005

  • Boolean control of aptamer binding states. Kolpashchikov DM, Stojanovic MN. Journal of the American Chemical Society, 127(32): 11348-11351, 2005. xx
  • Binary malachite green aptamer for fluorescent detection of nucleic acids. Kolpashchikov DM. Journal of the American Chemical Society, 127(36): 12442-12443, 2005. xx
  • Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. Farfel J, Stefanovic D.
    DNA11, 11th International Meeting on DNA Computing, London, Ontario, Canada, June 2005. Springer LNCS 3892:38-54, 2006. xx
  • Deoxyribozyme-based ligase logic gates and their initial circuits. Stojanovic MN, Semova S, Kolpashchikov D, Macdonald J, Morgan C, Stefanovic D. Journal of the American Chemical Society, 127(19):6914-6915, 2005. x

Posters

2007

  • DNA-based calculators with 7-segment displays. Macdonald J.
    Presentation, The 13th International Meeting on DNA Computing (cc), Memphis, Tennessee, June 2007.
  • Reaction simulations: a rapid development framework. Calhoun-Lopez M, Stefanovic D. Poster, The 13th International Meeting on DNA Computing (cc), Memphis, Tennessee, June 2007.

2006

  • Oligonucleotide-detecting automata for games and genome analysis. Macdonald J, Li Y, Sutovic M, Stefanovic D, Stojanovic MN. Poster, Genomes to Systems Conference (cc), Manchester, March 2006.
  • Flow cytometry analysis of modular aptameric sensors conjugated to microspheres. Yashin R, Macdonald J, Korkina O, Stojanovic MN, Rudchenko S. Poster, ISAC XXIII International Congress, Québec, Canada, May 2006.