the proceedings contain 16 papers. the topics discussed include: improving efficiency of 3-SAT-solving tile systems;optimizing tile concentrations to minimize errors and time for dna tile self-assembly systems;scalabl...
ISBN:
(纸本)9783642183041
the proceedings contain 16 papers. the topics discussed include: improving efficiency of 3-SAT-solving tile systems;optimizing tile concentrations to minimize errors and time for dna tile self-assembly systems;scalable, time-responsive, digital, energy-efficient molecular circuits using dna strand displacement;negative interactions in irreversible self-assembly;search and validation of short genome-wide biomarkers for bacterial biological phylogenies;high-fidelity dna hybridization using programmable moleculardna devices;synthesizing minimal tile sets for patterned dna self-assembly;operation of a dna-based autocatalytic network in serum;triangular tile self-assembly systems;randomized self assembly of rectangular nano structures;design of a functional nanomaterial with recognition ability for constructing light-driven nanodevices;efficient Turing-universal computation withdna polymers;and simple evolution of complex crystal species.
the proceedings contain 16 papers. the topics discussed include: filter position in networks of evolutionary processors does not matter: a direct proof;strand algebras for dnacomputing;a domain-specific language for ...
ISBN:
(纸本)364210603X
the proceedings contain 16 papers. the topics discussed include: filter position in networks of evolutionary processors does not matter: a direct proof;strand algebras for dnacomputing;a domain-specific language for programming in the tile assembly model;advancing the deoxyribozyme-based logic gate design process;dna chips for species identification and biological phylogenies;renewable, time-responsive dna logic gates for scalable digital circuits;self-assembly of the discrete Sierpinski carpet and related fractals;automatic design of dna logic gates based on kinetic simulation;design of a biomolecular device that executes process algebra;the effect of malformed tiles on tile assemblies within kTAM;positional state representation and its transition control for photonic dna automation;construction of AND gate for RTRACS withthe capacity of extension to NAND gate;and time-complexity of multilayered dna strand displacement circuits.
the proceedings contain 16 papers. the special focus in this conference is on dnacomputing and molecularprogramming. the topics include: Automated, constraint-based analysis of tethered dna nanostructures;dna-templa...
ISBN:
(纸本)9783319667980
the proceedings contain 16 papers. the special focus in this conference is on dnacomputing and molecularprogramming. the topics include: Automated, constraint-based analysis of tethered dna nanostructures;dna-templated synthesis optimization;ruleset optimization on isomorphic oritatami systems;unknotted strand routings of triangulated meshes;the design space of strand displacement cascades with toehold-size clamps;a stochastic molecular scheme for an artificial cell to infer its environment from partial observations;complexities for high-temperature two-handed tile self-assembly;a dna neural network constructed from molecular variable gain amplifiers;a stochastic approach to shortcut bridging in programmable matter;a minimal requirement for self-assembly of lines in polylogarithmic time;robust detection in leak-prone population protocols;inferring parameters for an elementary step model of dna structure kinetics with locally context-dependent arrhenius rates;simplifying analyses of chemical reaction networks for approximate majority;chemical boltzmann machines;a general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities and thermodynamic binding networks.
this paper proposes how to use self-assembly of dna tiles to calculate integer power over finite field GF(2n) with less assembly processing time. Two key functional components accomplish the computing process. One of ...
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ISBN:
(纸本)9781538666142
this paper proposes how to use self-assembly of dna tiles to calculate integer power over finite field GF(2n) with less assembly processing time. Two key functional components accomplish the computing process. One of them computes modular-multiplication and modularsquare in parallel, and the other one calculates modularsquare and transmits intermediate result. It achieves better performance than previous work for its optimized assembly rules. this tile assembly model requires 5316 types of computation tiles and 12 types of boundary tiles.
dna catalysts have been developed as methods of amplifying single-stranded nucleic acid signals. the maximum turnover (gain) of these systems, however, often varies based on strand and complex purities, and has so far...
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ISBN:
(纸本)9783642183041
dna catalysts have been developed as methods of amplifying single-stranded nucleic acid signals. the maximum turnover (gain) of these systems, however, often varies based on strand and complex purities, and has so far not been well-controlled. Here we introduce methods for controlling the asymptotic turnover of strand displacement-based dna catalysts and show how these could be used to construct linear classifier systems.
the potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of dna-based chemical amplifiers that can operate in bodily fluids. As a...
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ISBN:
(纸本)9783642183041
the potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of dna-based chemical amplifiers that can operate in bodily fluids. As a first step toward this goal, we have tested the operation of a dna-based autocatalytic network in human serum and mouse serum. Withthe addition of sodium dodecyl sulfate to prevent degradation by nuclease activity, the network was found to operate successfully with bothdna and RNA catalysts.
In this paper, we report a scheme for reversible state-transition of the automaton responding to a single kind of a photonic signal. the state is encoded into the conformation of hairpin-dnas tethered with azobenzene,...
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ISBN:
(纸本)9783642183041
In this paper, we report a scheme for reversible state-transition of the automaton responding to a single kind of a photonic signal. the state is encoded into the conformation of hairpin-dnas tethered with azobenzene, which is responsive to visible and UV light irradiation. the reversible behavior is realized by carrying out a sequence of conformation-change of the hairpin-dna in a stepwise manner. Experimental results demonstrate that the state can be changed reversibly according to photonic signals.
dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacemen...
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ISBN:
(纸本)9783642183041
dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacement reactions. To facilitate consideration of spurious reactions during the design process, one common strategy is to subdivide dna strands into domains, continuous nucleic acid bases that can be abstracted to act as a unit in hybridization and dissociation. Here, considerations for domain-based sequence design are discussed, and heuristics are presented for the sequence design of domains. Based on these heuristics, a randomized algorithm is implemented for sequence design.
Implementing dnacomputing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered ci...
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Implementing dnacomputing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered circuits is far more challenging than for solution-phase circuits, because molecular geometry must be taken into account when deciding whether two tethered species may interact. Here, we tackle this issue by translating a tethered molecular circuit into a constraint problem that encodes the possible physical configurations of the components, using a simple biophysical model. We use a satisfaction modulo theories solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry. We apply this technique to example structures from the literature, and discuss how this approach could be integrated with a reaction enumerator to enable fully automated analysis of tethered molecularcomputing systems. this paper is a significantly revised and extended version of a conference publication: Lakin and Phillips (in Brijder and Qian (eds) Proceedings of the 23rd internationalconference on dnacomputing and molecularprogramming. Lecture Notes in Computer Science, vol 10467, pp 1-16, 2017).
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models...
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Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we discuss a method to implement arbitrary (abstract) CRNs in a test tube using dna. Finally, we discuss relationships between CRNs and other models of computation.
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