Theory of algorithmic self-assembly

The challenge of programming molecules to manipulate themselves.

[1]  Matthew J. Patitz Simulation of Self-Assembly in the Abstract Tile Assembly Model with ISU TAS , 2011, ArXiv.

[2]  Scott M. Summers Reducing Tile Complexity for the Self-assembly of Scaled Shapes Through Temperature Programming , 2011, Algorithmica.

[3]  M. Kazemi Abstract , 2003 .

[4]  Ashish Goel,et al.  Running time and program size for self-assembled squares , 2001, STOC '01.

[5]  Matthew J. Patitz,et al.  Exact Shapes and Turing Universality at Temperature 1 with a Single Negative Glue , 2011, DNA.

[6]  Matthew J. Patitz,et al.  A Domain-Specific Language for Programming in the Tile Assembly Model , 2009, DNA.

[7]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[8]  Matthew J. Patitz,et al.  Limitations of self-assembly at temperature 1 , 2009, Theor. Comput. Sci..

[9]  Lila Kari,et al.  The power of nondeterminism in self-assembly , 2011, SODA '11.

[10]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[11]  A. Kolmogorov Three approaches to the quantitative definition of information , 1968 .

[12]  Jarkko Kari,et al.  The Undecidability of the Infinite Ribbon Problem: Implications for Computing by Self-Assembly , 2009, SIAM J. Comput..

[13]  John H. Reif,et al.  Local Parallel Biomolecular Computation , 1997, Int. J. Unconv. Comput..

[14]  Erik D. Demaine,et al.  Staged self-assembly: nanomanufacture of arbitrary shapes with O(1) glues , 2008, Natural Computing.

[15]  M AdlemanLeonard Molecular computation of solutions to combinatorial problems , 1994 .

[16]  Pekka Orponen,et al.  Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-assembly , 2011, DNA.

[17]  Sudheer Sahu,et al.  Compact Error-Resilient Computational DNA Tiling Assemblies , 2004, DNA.

[18]  E. Winfree Simulations of Computing by Self-Assembly , 1998 .

[19]  Matthew J. Patitz,et al.  Self-assembly of decidable sets , 2008, Natural Computing.

[20]  Matthew Cook,et al.  Combining self-healing and proofreading in self-assembly , 2008, Natural Computing.

[21]  Ján Manuch,et al.  Step-Assembly with a Constant Number of Tile Types , 2009, ISAAC.

[22]  John H. Reif,et al.  Tile Complexity of Linear Assemblies , 2012, SIAM J. Comput..

[23]  Matthew Cook,et al.  Self-Assembled Circuit Patterns , 2003, DNA.

[24]  Erik Winfree,et al.  Self-healing Tile Sets , 2006, Nanotechnology: Science and Computation.

[25]  Erik D. Demaine,et al.  One-dimensional staged self-assembly , 2012, Natural Computing.

[26]  David Doty,et al.  Randomized Self-Assembly for Exact Shapes , 2009, 2009 50th Annual IEEE Symposium on Foundations of Computer Science.

[27]  Erik D. Demaine,et al.  Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract) , 2010, STACS.

[28]  Satoshi Murata,et al.  Error suppression mechanisms for DNA tile self-assembly and their simulation , 2009, Natural Computing.

[29]  Ashish Goel,et al.  Dimension augmentation and combinatorial criteria for efficient error-resistant DNA self-assembly , 2008, SODA '08.

[30]  Ming-Yang Kao,et al.  Randomized Self-assembly for Approximate Shapes , 2008, ICALP.

[31]  Ashish Goel,et al.  Error Free Self-assembly Using Error Prone Tiles , 2004, DNA.

[32]  Ivan Rapaport,et al.  Self-assemblying Classes of Shapes with a Minimum Number of Tiles, and in Optimal Time , 2006, FSTTCS.

[33]  Erik Winfree,et al.  Complexity of Self-Assembled Shapes , 2004, SIAM J. Comput..

[34]  Erik Winfree,et al.  Programmable Control of Nucleation for Algorithmic Self-Assembly , 2009, SIAM J. Comput..

[35]  Wenyan Liu,et al.  Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced Tile Assembly Model , 2011, Natural Computing.

[36]  Jack H. Lutz,et al.  The Tile Assembly Model is Intrinsically Universal , 2011, 2012 IEEE 53rd Annual Symposium on Foundations of Computer Science.

[37]  Erik Winfree,et al.  Two computational primitives for algorithmic self-assembly: copying and counting. , 2005, Nano letters.

[38]  Erik D. Demaine,et al.  Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM , 2013, STACS.

[39]  Ming-Yang Kao,et al.  Complexities for generalized models of self-assembly , 2004, SODA '04.

[40]  Erik Winfree,et al.  An information-bearing seed for nucleating algorithmic self-assembly , 2009, Proceedings of the National Academy of Sciences.

[41]  Ming-Yang Kao,et al.  Reducing tile complexity for self-assembly through temperature programming , 2006, SODA '06.

[42]  Ján Manuch,et al.  Two Lower Bounds for Self-Assemblies at Temperature 1 , 2009, 2009 3rd International Conference on Bioinformatics and Biomedical Engineering.

[43]  E. Winfree,et al.  Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. , 2008, Nano letters.

[44]  Erik Winfree,et al.  Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly , 2003, DNA.

[45]  M. Sahani,et al.  Algorithmic Self-Assembly of DNA , 2006 .

[46]  A. Turing On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[47]  Matthew J. Patitz,et al.  Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature , 2010, 2010 IEEE 51st Annual Symposium on Foundations of Computer Science.

[48]  Erik Winfree,et al.  The program-size complexity of self-assembled squares (extended abstract) , 2000, STOC '00.

[49]  Jack H. Lutz,et al.  Computability and Complexity in Self-assembly , 2008, Theory of Computing Systems.

[50]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[51]  Florent Becker Pictures worth a thousand tiles, a geometrical programming language for self-assembly , 2009, Theor. Comput. Sci..

[52]  E. Winfree,et al.  Synthesis of crystals with a programmable kinetic barrier to nucleation , 2007, Proceedings of the National Academy of Sciences.

[53]  Erik Winfree,et al.  Complexity of Compact Proofreading for Self-assembled Patterns , 2005, DNA.

[54]  Erik Winfree,et al.  Reducing facet nucleation during algorithmic self-assembly. , 2007, Nano letters.

[55]  John H. Reif,et al.  Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications , 2007, DNA.

[56]  Robert T. Schweller,et al.  Temperature 1 self-assembly: deterministic assembly in 3D and probabilistic assembly in 2D , 2009, SODA '11.

[57]  Ashish Goel,et al.  Combinatorial optimization problems in self-assembly , 2002, STOC '02.

[58]  Ján Manuch,et al.  Two Lower Bounds for Self-Assemblies at Temperature 1 , 2009 .

[59]  Pekka Orponen,et al.  Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly , 2010, DNA.

[60]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.