A major challenge in practical dna tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through ab...
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ISBN:
(纸本)9783319019284;9783319019277
A major challenge in practical dna tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through abstract tile set design. In this paper, we instead investigate the effects of "sticky end" sequence choices in systems using the kinetic model along withthe nearest-neighbor model of dna interactions. We show that boththe sticky end sequences present in a system and their positions in the system can significantly affect error rates, and propose algorithms for sequence design and assignment.
the simple-sticker model uses robotic processing of dna strands contained in a fixed number of tubes to implement massively-parallel processing of bit strings. the bits whose value are '1' are recorded by shor...
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ISBN:
(纸本)9783319019284;9783319019277
the simple-sticker model uses robotic processing of dna strands contained in a fixed number of tubes to implement massively-parallel processing of bit strings. the bits whose value are '1' are recorded by short dna "stickers" that hybridize at specific places on the strand. Other dna models, like folded origami, use "staples" that hybridize to disjoint portions of a single strand. this paper proposes an extended-sticker paradigm that uses staples to hybridize to contiguous portions of two substrands, forming virtual strands. the problem of redundant bits is solved by blotting out old values. As an example of the novel extended-sticker paradigm, a log-time summation algorithm outperforms (with an ideal implementation) any electronic supercomputer conceivable in the near future for large data sets. JavaScript and CUDA simulations validate the theoretical operation of the proposed algorithm.
A surface chemical reaction network (sCRN, Qian and Winfree in dnacomputing and molecularprogramming: 20thinternationalconference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an...
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A surface chemical reaction network (sCRN, Qian and Winfree in dnacomputing and molecularprogramming: 20thinternationalconference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an emergent paradigm for molecularprogramming, in which a chemical molecule is placed at each site of a lattice, and each molecule may undergo either bi-molecular reactions associated with one of the nearest molecules or uni-molecular reactions autonomously. the lattice structure as well as the localized reactions between molecules facilitate an effective formalization of sCRNs in the framework of cellular automata. this formalism not only allows a systematic evaluation of the complexity of a sCRN, but also enables a formal approach to reduce the model's complexity for the sake of improving its effectiveness. To this end, this paper proposes a new sCRN model that has less complexity measured in terms of the numbers of both cell states and transition rules. Especially, universality of computations will be shown by implementing all asynchronous circuits, including the well-known full-adder, into the sCRN. the decreased complexity may enhance the feasibility of the proposed sCRN model for physical implementation.
We present a method for the analysis of functional properties of large-scale dna strand displacement (DSD) circuits based on Satisfiability Modulo theories that enables us to prove the functional correctness of dna ci...
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ISBN:
(纸本)9783319019284;9783319019277
We present a method for the analysis of functional properties of large-scale dna strand displacement (DSD) circuits based on Satisfiability Modulo theories that enables us to prove the functional correctness of dna circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together withthe components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.
this book constitutes the refereed proceedings of the 19th international conference on dna computing and molecular programming, dna19, held in Tempe, AZ, USA, in September 2013. the 14 full papers presented were care...
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ISBN:
(数字)9783319019284
ISBN:
(纸本)9783319019277
this book constitutes the refereed proceedings of the 19th international conference on dna computing and molecular programming, dna19, held in Tempe, AZ, USA, in September 2013. the 14 full papers presented were carefully selected from 29 submissions. the papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.
In this paper, we report a novel solid-state nanopore sensor with small-sized graphene cage-structured nanopore prepared by using nanopore processing technology combined with two-dimensional thin film materials. We co...
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ISBN:
(纸本)9798350359848;9798350359831
In this paper, we report a novel solid-state nanopore sensor with small-sized graphene cage-structured nanopore prepared by using nanopore processing technology combined with two-dimensional thin film materials. We compare the differences between graphene nanopores and graphene cage-structured nanopores in dna detection results. the results show that the reverse dna molecule capture rate of graphene-caged nanopores is about 1.5 times higher than that of graphene nanopores at 600 mV. the simulation analysis shows that there is a significant difference in the potential distribution of the caged nanopores with different structures. this study is expected to further enrich the single-molecule detection means of solid-state nanopores and provide new ideas for different detection needs.
We present a biomolecular probabilistic model driven by the action of a dna toolbox made of a set of dna templates and enzymes that is able to perform Bayesian inference. the model will take single-stranded dna as inp...
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ISBN:
(纸本)9783319019284;9783319019277
We present a biomolecular probabilistic model driven by the action of a dna toolbox made of a set of dna templates and enzymes that is able to perform Bayesian inference. the model will take single-stranded dna as input data, representing the presence or absence of a specific molecular signal (the evidence). the program logic uses different dna templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (dna polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded dna species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes' law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagnosis. thanks to the inherent amplification capability of this dna toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.
molecular beacons have the advantages of simple structure, high sensitivity and quick response etc.. dnacomputing is a new method of simulating bio-molecular structure and computing using molecule biology technology,...
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ISBN:
(纸本)9781424438655
molecular beacons have the advantages of simple structure, high sensitivity and quick response etc.. dnacomputing is a new method of simulating bio-molecular structure and computing using molecule biology technology, and creates a precedent in using bio-chemical reaction as the calculating tools. It is a novel way to solve a class of problems that are difficult to calculate NP-complete problem. In this paper the corresponding dnacomputing of implicit enumeration is given using the advantages of molecular beacons based on previous studies.
We present a process algebra for dnacomputing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into dna structures.
ISBN:
(纸本)9783642106033
We present a process algebra for dnacomputing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into dna structures.
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