DNA Computing and Molecular Programming
19th International Conference, DNA 19, Tempe, AZ, USA, September 22-27, 2013. Proceedings
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Chapter and Conference Paper
Complexity of Self-assembled Shapes
The connection between self-assembly and computation suggests that a shape can be considered the output of a self-assembly “program,” a set of tiles that fit together to create a shape. It seems plausible that...
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Chapter and Conference Paper
Complexity of Compact Proofreading for Self-assembled Patterns
Fault-tolerance is a critical issue for biochemical computation. Recent theoretical work on algorithmic self-assembly has shown that error correcting tile sets are possible, and that they can achieve exponenti...
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Article
Combining self-healing and proofreading in self-assembly
Molecular self-assembly is a promising approach to bottom-up fabrication of complex structures. A major impediment to the practical use of self-assembly to create complex structures is the high rate of error u...
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Article
Computation with finite stochastic chemical reaction networks
A highly desired part of the synthetic biology toolbox is an embedded chemical microcontroller, capable of autonomously following a logic program specified by a set of instructions, and interacting with its ce...
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Chapter and Conference Paper
DNA as a Universal Substrate for Chemical Kinetics
We show that a DNA-based chemical system can be constructed such that it closely approximates the dynamic behavior of an arbitrary system of coupled chemical reactions. Using strand displacement reactions as a...
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Chapter and Conference Paper
Time-Complexity of Multilayered DNA Strand Displacement Circuits
Recently we have shown how molecular logic circuits with many components arranged in multiple layers can be built using DNA strand displacement reactions. The potential applications of this and similar technol...
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Chapter
Programmability of Chemical Reaction Networks
Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting ...
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Chapter and Conference Paper
Efficient Turing-Universal Computation with DNA Polymers
Bennett’s proposed chemical Turing machine is one of the most important thought experiments in the study of the thermodynamics of computation. Yet the sophistication of molecular engineering required to physic...
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Chapter and Conference Paper
Deterministic Function Computation with Chemical Reaction Networks
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming...
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Book and Conference Proceedings
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Chapter and Conference Paper
Erratum to: DNA Computing and Molecular Programming
Erratum to: D. Soloveichik and B. Yurke (Eds.) DNA Computing and Molecular Programming DOI: 10.1007/978-3-319-01928-4
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Article
Programmable chemical controllers made from DNA
Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications su...
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Chapter and Conference Paper
Probability 1 Computation with Chemical Reaction Networks
The computational power of stochastic chemical reaction networks (CRNs) varies significantly with the output convention and whether or not error is permitted. Focusing on probability 1 computation, we demonstr...
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Chapter and Conference Paper
Speed Faults in Computation by Chemical Reaction Networks
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. Assuming a fixed molecular population size and bimolecular reactions, CRNs are formally equivalent to population protocols, ...
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Article
Deterministic function computation with chemical reaction networks
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming...
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Chapter and Conference Paper
Leakless DNA Strand Displacement Systems
While current experimental demonstrations have been limited to small computational tasks, DNA strand displacement systems (DSD systems) [25] hold promise for sophisticated information processing within chemical o...
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Chapter and Conference Paper
Stable Leader Election in Population Protocols Requires Linear Time
A population protocol stably elects a leader if, for all n, starting from an initial configuration with n agents each in an identical state, with probability 1 it reaches a configuration y that is correct (exactl...
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Article
Preface
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Chapter and Conference Paper
Robustness of Expressivity in Chemical Reaction Networks
We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard definiti...
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Article
Probability 1 computation with chemical reaction networks
The computational power of stochastic chemical reaction networks (CRNs) varies significantly with the output convention and whether or not error is permitted. Focusing on probability 1 computation, we demonstr...
