dna automaton is utilized as a processing core of a nanoscale processor that can deal withmolecular information directly. We are studying on photonic dna automaton in which light and dna are used as information carri...
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ISBN:
(纸本)9783642106033
dna automaton is utilized as a processing core of a nanoscale processor that can deal withmolecular information directly. We are studying on photonic dna automaton in which light and dna are used as information carriers. In the automaton, the internal states are represented as the conformation of dna, or the spatial position of the specific bases in the dna strand, and the state-transition is induced by an external optical signal. this paper focuses on a method for state representation and state transition control based on the conformation of dna. An implementation using hairpin-dna is experimentally demonstrated to verify the proposed scheme.
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 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.
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.
We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific location...
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ISBN:
(纸本)9783642236372
We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels withthe fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.
Unlike their traditional, silicon counterparts, dna computers have natural interfaces with both chemical and biological systems. these can be used for a number of applications, including the precise arrangement of mat...
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Unlike their traditional, silicon counterparts, dna computers have natural interfaces with both chemical and biological systems. these can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, dna strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in dna 'walker' systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions and forming composable circuits. We find that systems of multiple walkers have severely limited potential for parallel circuit evaluation. dna walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of dna walker 'circuits' based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness. this analysis aids in the design of reliable and efficient dna walker circuits.
We study the computational complexity of the recently proposed nubots model of molecular-scale self-assembly. the model generalises asynchronous cellular automata to have non-local movement where large assemblies of m...
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We study the computational complexity of the recently proposed nubots model of molecular-scale self-assembly. the model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be moved around, analogous to millions of molecular motors in animal muscle effecting the rapid movement of macroscale arms and legs. We show that nubots is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time. In computational complexity terms, we show that any problem from the complexity class NC is solved in polylogarithmic expected time on nubots that use a polynomial amount of workspace. Along the way, we give fast parallel algorithms for a number of problems including line growth, sorting, Boolean matrix multiplication and space-bounded Turing machine simulation, all using a constant number of nubot states (monomer types). Circuit depth is a well-studied notion of parallel time, and our result implies that nubots is a highly parallel model of computation in a formal sense. Asynchronous cellular automata are not capable of such parallelism, and our result shows that adding a movement primitive to such a model, to get the nubots model, drastically increases parallel processing abilities.
Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic pi-calculus;at ...
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ISBN:
(纸本)9783642106033
Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic pi-calculus;at the molecular scale by providing a design for a dna-based biomolecular device that simulates a process algebraic machine. Our design of the molecular stochastic pi-calculus system makes use of a modified form of Whiplash-PCR (WPCR) machines. In this design, we connect (via a tethering dna nanostructure) a number of dna strands, each of which corresponds to a WPCR. machine. this collection of WPCR machines are used to execute distinct concurrent processes, each with its own distinct program. Furthermore, their close proximity enables computation to proceed via communication.
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.
Chemical reaction networks (CRNs) and dna strand displacement systems (DSDs) are widely-studied and useful models of molecularprogramming. In this tutorial, we introduce the models, illustrating the expressive power ...
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