the proceedings contain 11 papers. the topics discussed include: the topology of scaffold routings on non-spherical mesh wireframe;simplifying chemical reaction network implementations with two-stranded dna building b...
ISBN:
(纸本)9783959771634
the proceedings contain 11 papers. the topics discussed include: the topology of scaffold routings on non-spherical mesh wireframe;simplifying chemical reaction network implementations with two-stranded dna building blocks;composable computation in leaderless, discrete chemical reaction networks;CRNs exposed: a method for the systematic exploration of chemical reaction networks;population-induced phase transitions and the verification of chemical reaction networks;ALCH: an imperative language for chemical reaction network-controlled tile assembly;implementing non-equilibrium networks with active circuits of duplex catalysts;design automation of polyomino set that self-assembles into a desired shape;verification and computation in restricted tile automata;and turning machines.
the proceedings contain 11 papers. the topics discussed include: Turing universality of step-wise and stage assembly at temperature 1;a type system for dnaQL;deterministic function computation with chemical reaction n...
ISBN:
(纸本)9783642322075
the proceedings contain 11 papers. the topics discussed include: Turing universality of step-wise and stage assembly at temperature 1;a type system for dnaQL;deterministic function computation with chemical reaction networks;reachability bounds for chemical reaction networks and strand displacement systems;synthesizing minimal tile sets for complex patterns in the framework of patterned dna self-assembly;a geometric approach to Gibbs energy landscapes and optimal dna codeword design;a dna based molecular logic gate capable of a variety of logical operations;deciding whether a regular language is generated by a splicing system;probabilistic reasoning with a Bayesian dna device based on strand displacement;dna self-assembly and computation studied with a coarse-grained dynamic bonded model;and space and energy efficient computation withdna strand displacement systems.
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 15 papers. the topics discussed include: extending dna-sticker arithmetic to arbitrary size using staples;parallel computation using active self-assembly;dna walker circuits: computational pote...
ISBN:
(纸本)9783319019277
the proceedings contain 15 papers. the topics discussed include: extending dna-sticker arithmetic to arbitrary size using staples;parallel computation using active self-assembly;dna walker circuits: computational potential, design, and verification;leaderless deterministic chemical reaction networks;dna sticky end design and assignment for robust algorithmic self-assembly;dna reservoir computing: a novel molecularcomputing approach;signal transmission across tile assemblies: 3D static tiles simulate active self-assembly by 2D signal-passing tiles;3-color bounded patterned self-assembly;exponential replication of patterns in the signal tile assembly model;modular verification of dna strand displacement networks via serializability analysis;iterative self-assembly with dynamic strength transformation and temperature control;probabilistic reasoning with an enzyme-driven dna device;staged self-assembly and polyomino context-free grammars;and functional analysis of large-scale dna strand displacement circuits.
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.
Motivated by certain coding techniques for reliable dnacomputing, we consider the problem of characterizing nontrivial languages D that are maximal withthe property that D (*) is contained in the subword closure of ...
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Motivated by certain coding techniques for reliable dnacomputing, we consider the problem of characterizing nontrivial languages D that are maximal withthe property that D (*) is contained in the subword closure of a given set S of words of some fixed length k. this closure is simply the set of all words whose subwords of length k must be in S. We provide a deep structural characterization of these languages D, which leads to polynomial time algorithms for computing such languages.
Withthe rapid development of dnacomputing, there are some questions worth study that how to implement the arithmetic operations used in cryptosystem based on dnacomputing models. this paper proposes an improved dna...
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ISBN:
(纸本)9781509050819
Withthe rapid development of dnacomputing, there are some questions worth study that how to implement the arithmetic operations used in cryptosystem based on dnacomputing models. this paper proposes an improved dnacomputing model to calculate modular-multiplication over finite field GF(2(n)). Comparing to related works, both assembly time complexity and space complexity are more optimal. the computation tiles performing 4 different functions assemble into the seed configuration with inputs to figure out the result. It is given that how the computation tiles be bitwise coded and how assembly rules work. the assembly time complexity is theta(n) and the space complexity is theta(n(2)). this model requires 148 types of computation tiles and 8 types of boundary tiles.
Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridizat...
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Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.
Designing a set of dna base sequences for a large-scale molecular circuit is a difficult problem in the field of dnacomputing. A dna circuit frequently suffers from unintended dna strand displacements among strands;t...
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ISBN:
(纸本)9788993215144
Designing a set of dna base sequences for a large-scale molecular circuit is a difficult problem in the field of dnacomputing. A dna circuit frequently suffers from unintended dna strand displacements among strands;this problem can ruin the desired function of a dna circuit. In this study, our aim was to develop a computational tool for the design of dna base sequences by means of an original algorithm based on mismatches in a dna base sequence. Validity of the proposed algorithm is confirmed by practical redesign examples.
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