E. Winfree, F. Liu, L.A. Wenzler, and N.C. Seeman, "Design and Self-Assembly of Two-Dimensional DNA Crystals," Nature, vol. 394, pp. 539--544, 1998. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
The Minimum-Model DNA Computation on a Sequence of Probe Arrays - Ogihara, Ray (2002) (Correct)
.... [15, 5] the sticker DNA PNA model proposed by Roweis et al. 28, 4] the hairpin DNA model of Sakamoto et al. 29] the surface DNA model of Liu et al. 16] the enzymatic model of Rothemund [27] and of Benenseon et al. 3] and the two dimensional DNA self assembly model of Seeman and Winfree [33]. The objective of this paper is to explore further the minimum DNA computation model proposed and studied in our earlier papers [17, 19] The study of the minimum DNA computation model is motivated by the desire to clarify what computational power DNA has when the set of permissible operations ....
E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman. Design and self-assembly of twodimensional DNA crystals. Nature, 394:539-544, 1998. 11
Towards Molecular Programming - Hagiya (2002) (Correct)
....at two points. Therefore, the tile is composed of four single stranded DNA molecules that self assemble. Double crossover molecules have four sticky ends, which each hybridize with the sticky end of another molecule (Fig. 3, right) Therefore, they can self assemble and form a planar structure [42]. This process of self assembly corresponds to allowing square tiles with colored edges to hybridize only if adjacent edges are of the same color (Fig. 3, upper left) As mentioned below, the process of tiling square tiles with colored edges is universal [43] because it can simulate execution of ....
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals, Nature 394, 539-544 (1998)
Algorithmic Self-Assembly of DNA Tiles and its.. - Pelletier, Weimerskirch (2002) (Correct)
....that edges of the same color have to face each other [15] This can be intuitively understood by thinking of a given row of tiles as representing a state of the Turing machine while the color encoding plays the role of the matching rules. This shows that computing using Wang tiles is universal [16, 13]. 2.2 Physical Implementation of Wang Tiles Recent advances in the eld of materials science have enabled the experimental study of algorithmic selfassembly (abbreviated as ASA in the following) The rst system, studied by Rothemund [12] was made of tiles whose edges were coated with materials ....
E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman. Design and Self-Assembly of two-dimensional DNA Crystals. Nature, vol. 394, pages 539-544, 1998.
Combinatorial Optimization Problems in Self-Assembly - Adleman, Cheng, Goel.. (2002) (3 citations) (Correct)
....automata were formed with an error rates of 2.8 . DNA systems, more technologically interesting than the plastic tile systems because of their size, are being actively pursued by at least two research groups and the problems of errors and controlled nucleation are being emphasized. Winfree et al. [22] demonstrated that (i) DNA strands can self assemble into 13 nanometers 4 nm 2 nm DNA tiles and (ii) that these tiles can further selfassemble into periodic crystals of approximately a quarter million tiles and several microns in size. Mao et al. 13] have reported the creation of small ....
E. Winfree, F. Liu, L. Wenzler, N. Seeman. Design and self-assembly of two-dimensional DNA crystals, 6 pages. (Nature 394, 539-544 (Aug. 6, 1998) Article)
DNA Self-Assembly For Constructing 3D Boxes - Kao, Ramachandran (2001) (Correct)
....New Haven, CT 06520 8285, USA, kao ming yang cs.yale.edu. ## Supported by a 2001 National Defense Science and Engineering Graduate Fellowship. Combining these two technologies, several researchers have demonstrated the power of DNA self assembly in nanostructure fabrication. Winfree et al. [13] investigated how to use self assembly of DX molecules to build 2D lattice DNA crystals. Rothemund and Winfree [7] further proposed a mathematical model and a complexity measure for building such 2D structures. A natural extension of the seminal 2D results of Winfree et al. 13] and Rothemund and ....
....Winfree et al. 13] investigated how to use self assembly of DX molecules to build 2D lattice DNA crystals. Rothemund and Winfree [7] further proposed a mathematical model and a complexity measure for building such 2D structures. A natural extension of the seminal 2D results of Winfree et al. [13] and Rothemund and Winfree [7] would be the creation of 3D nanostructures using tiling. To initiate such an extension, this paper (1) proposes a general mathematical model for constructing 3D structures from 2D tiles; 2) identifies a set of biological and algorithmic issues basic to the ....
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.
Running Time and Program Size for Self-assembled Squares - Adleman, Cheng, Goel, Huang (2001) (2 citations) (Correct)
....such as computer circuits from inexpensive components such as DNA and inorganic nanocrystals. Despite its importance, self assembly is poorly understood. Recently, work related to DNA computation has led to experimental systems for the investigation of self assembly and its relation to computation [8, 5, 3, 2]. In addition certain theoretical aspects of self assembly have been considered. Winfree [8, 9] proved that self assembling tile systems in a plane are capable of doing universal computation, and when restricted to a line are exactly as powerful as discrete finite automata. Adleman [1] proposed a ....
....its importance, self assembly is poorly understood. Recently, work related to DNA computation has led to experimental systems for the investigation of self assembly and its relation to computation [8, 5, 3, 2] In addition certain theoretical aspects of self assembly have been considered. Winfree [8, 9] proved that self assembling tile systems in a plane are capable of doing universal computation, and when restricted to a line are exactly as powerful as discrete finite automata. Adleman [1] proposed a mathematical model of self assembly and analyzed the time complexity of linear polymerization. ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, and Nadrian C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539-544, 1998.
Computationally Inspired Biotechnologies: Improved DNA.. - Reif, LaBean (2000) (1 citation) (Correct)
....provide EC strands which most closely match the error profiles for probe DNA synthesized on a chip. Other mutagenisis Methods used for more general computations are given in [KG98] DNA Self Assembly. It is also, in principle, possible to construct EC strands using a self assembly method [R97, WLW 98, WYS96, LYK 00, LWR99, RLS00, MLR 00] involving a universal base pairing nucleotide like inosine to generate diverse populations of prefixes. 3 Adapting to Biotechnology VQ Methods Used in Computer Science 3.1 VQ Coding Methods Used in Computer Science We next consider information theoretic ....
Winfree, E., F. Liu, Lisa A. Wenzler, N. C. Seeman, "Design and SelfAssembly of Two Dimensional DNA Crystals", Nature 394: 539--544, 1998. (1998).
Toward a Mathematical Theory of Self-Assembly (Extended Abstract) - Adleman (1999) (Correct)
....complexity will shed light on aspects of catalysis, self replication, thermodynamics and computation. 1. The Irreversible Model The fundamental objects of our study will be square tiles on the in nite two dimensional plane. Each side of each tile will be covered with a speci c glue [Winfree98, Rothemund99]. By speci c, we mean that each type of glue will have a set of glues to which it can stick and which can stick to it and a disjoint set of glues to which it cannot stick and which cannot stick to it. Tiles can be thought to have a north side, south side, east side and west side. Formally, a tile ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, and Nadrian C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539-544, 1998.
2D DNA Self-Assembly for Satisfiability - Lagoudakis, LaBean (Correct)
....proposed by Winfree [Win98a] for O(1) DNA computations. Basic components for DNA tiling have been prototyped and tested by Seeman and colleagues. In particular, double crossover molecules have been shown to be rigid and able to form planar lattices containing hundreds of thousands of tiles [WLWS98] Winfree has shown how to solve the Hamiltonian Path problem using 2 dimensional DNA tiling [Win98a] Further, LaBean, Winfree and Reif [LWR99] have been experimenting with parallel XOR and addition operations using DNA tiling. 2.2. 2D DNA Self Assembly for Satisfiability. The main goal of the ....
....bound for instances that can be solved on a conventional computer. 6. Future Work It is an open question whether the design(s) will work well in practice or not, a fact that can be verified only experimentally. Encouragement comes from the recent investigations of several DNA tile structures [WLWS98] In particular, TAO35 (see figure 1) is a general DNA tile that is currently being investigated for use in self assembly computations [LWR99] Moreover, it was recently demonstrated by LaBean, Winfree and Reif that input layers like the ones we use can be constructed relatively easily using a ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, and Nadrian C. Seeman, Design and self-assembly of two-dimensional DNA crystals, Nature 394 (1998), 539--544.
Local Parallel Biomolecular Computation - Reif (1999) (4 citations) (Correct)
....Winfree, et al. [WYS96] also provided a very valuable experimental test validating the preferential pairing of matching DNA tiles over partially non matching DNA tiles, but did not at that time experimentally demonstrate a DNA self assembly for a (non trivial) computation. Erik Winfree, et al. [WLW 98] recently experimentally constructed the first large (involving thousands of individual times) two dimensional arrays of DNA crystals by self assembly of nearly identical DNA tiles. The tiles consisted of two double crossovers (DX) which self assemble into a periodic 2D lattice. They produced ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, Nadrian C. Seeman, Design and Self-Assembly of Two Dimensional DNA Crystals, Nature 394: 539--544, 1998. (1998).
Paradigms for Biomolecular Computation - Reif (1998) (3 citations) (Correct)
....the preferential pairing of matching DNA tiles over partially non matching DNA tiles. Winfree [Win98a] made computer simulations of computing by selfassembly of DNA tiles, with a detailed simulation model of the kenetics of annealing during the self assembly of DNA tiles. Erik Winfree, et al. [WLW 98] recently experimentally constructed the first large (involving thousands of individual times) two dimensional arrays of DNA crystals by self assembly of nearly identical DNA tiles. The tiles consisted of two double crossovers (DX) which self assemble into a periodic 2D lattice. They produced ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, Nadrian C. Seeman, Design and Self-Assembly of Two Dimensional DNA Crystals, Nature 394: 539--544, 1998. (1998).
TileSoft: Sequence Optimization Software for.. - Yin, Guo.. (2004) Self-citation (Winfree) (Correct)
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E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman. Design and self-assembly of two-dimensional DNA crystalsnature. Nature, 394:539--544, 1998.
Overview of New Structures for DNA-Based.. - LaBean, Yan.. Self-citation (Liu) (Correct)
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Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N.C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544 (1998).
Experimental Progress in Computation by Self-Assembly of.. - LaBean, Winfree, Reif (1999) (1 citation) Self-citation (Winfree) (Correct)
....neighboring tiles. DX complexes have been shown to be sufficiently rigid to avoid formation of circular structures as seen with the more flexible dsDNA [LYQS96] Recently, 2D lattices consisting of hundreds of thousands of DX units have been constructed and observed by atomic force microscopy [WLWS98] and DX complexes and lattices have been used successfully as substrate for enzymatic reactions including cleavage and ligation [LSS99] 1.0.3. Parallelism, Speed and Tiling Depth. The massive parallelism inherent in DNA based computers has, since its inception, driven thinking in the field. In ....
Erik Winfree, Furong Liu, Lisa A. Wenzler, and Nadrian C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539--544, 1998.
Molecular Electronics: Devices, Systems and Tools for.. - Butts, DeHon, al. (2002) (Correct)
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E. Winfree, F. Liu, L.A. Wenzler, and N.C. Seeman, "Design and Self-Assembly of Two-Dimensional DNA Crystals," Nature, vol. 394, pp. 539--544, 1998.
Claytronics: A Scalable Basis for Future Robots - Goldstein, Mowry (2004) (Correct)
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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.
Biosensors and Bioelectronics 20 (2004) 606--619 - Electronic Manipulation Of (2004) (Correct)
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Winfree, E., Liu, F.R., Wenzler, L.A., Seeman, N.C., 1998. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-- 544.
Electronic manipulation of DNA and proteins - For Potential Nano-Bio (2004) (Correct)
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E. Winfree, F. Liu, L. Wenzler, N. Seeman, "Design and Self-assembly of Two-dimensional DNA Crystals", Nature, 394, pp. 539-544, 1998.
DNA-Based Cryptography - Gehani, LaBean, Reif (1999) (1 citation) (Correct)
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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.
Molecular Computing Machines - Yaakov Benenson Ehud (Correct)
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Winfree, E.; Liu, F.; Wenzler, L.; Seeman, N.C. Design and self-assembly of two-dimensional DNA crystals. Nature 1998, 394(66934 539 -- 544.
Invadable Self-Assembly: Combining Robustness with Eciency - Ho-Lin Chen Qi (2004) (1 citation) (Correct)
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E. Winfree, F. Liu, L. Wenzler, and N. Seeman. Design and self-assembly of two-dimensional dna crystals, 6 pages. Nature, (394):539--544, Aug 1998.
Optimal Self-Assembly of Counters at - Temperature Two Qi (Correct)
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E. Winfree, F. Liu, L. Wenzler, and N. Seeman. Design and self-assembly of twodimensional dna crystals, 6 pages. Nature, (394):539--544, Aug 1998.
DNA-Based Cryptography - Ashish Gehani Thomas (1999) (1 citation) (Correct)
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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.
Invadable Self-Assembly: Combining Robustness with Eciency - Ho-Lin Chen Qi (2004) (1 citation) (Correct)
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E. Winfree, F. Liu, L. Wenzler, and N. Seeman. Design and self-assembly of two-dimensional dna crystals, 6 pages. Nature, (394):539--544, Aug 1998.
Running Time and Program Size for Self-assembled Squares - Leonard Adleman University (2001) (2 citations) (Correct)
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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. 21
Design of an Autonomous DNA Nanomechanical Device.. - Yin, Turberfield.. (Correct)
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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.
Linear Self-Assemblies: Equilibria, - Entropy And Convergence (Correct)
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Erik Winfree, Furong Liu, Lisa A. Wenzler, and Nadrian C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539-544, 1998.
Error Free Self-Assembly using Error Prone Tiles - Ho-Lin Chen Ashish (Correct)
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E. Winfree, F. Liu, L. Wenzler, and N. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, (394):539--544, Aug 1998.
Compact Error-Resilient Computational DNA Tiling Assemblies - John Reif Sudheer (Correct)
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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.
Designs for Autonomous Unidirectional Walking DNA Devices - Yin, Turberfield, Reif (2004) (Correct)
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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.
A DNA Sequence Compiler - Feldkamp, Banzhaf, Rauhe (2000) (3 citations) (Correct)
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) Erik Winfree, Furong Liu, Lisa A. Wenzler, Nadrian C. Seeman, Design and self-assembly of two-dimensional DNA crystals. Nature, 394, 539-544, (1998)
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