DNA Computing and Molecular Programming
18th International Conference, DNA 18, Aarhus, Denmark, August 14-17, 2012. Proceedings
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Darko Stefanovic
Computational Biology/Bioinformatics
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Reference Work Entry In depth
Molecular Automata
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Chapter and Conference Paper
Scalable Design of Logic Circuits Using an Active Molecular Spider System
As spatial locality leads to advantages of computation speed-up and sequence reuse in molecular computing, molecular walkers that exhibit localized reactions are of interest for implementing logic computations...
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Chapter and Conference Paper
Supervised Learning in an Adaptive DNA Strand Displacement Circuit
The development of DNA circuits capable of adaptive behavior is a key goal in DNA computing, as such systems would have potential applications in long-term monitoring and control of biological and chemical sys...
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Chapter and Conference Paper
Iterative Self-assembly with Dynamic Strength Transformation and Temperature Control
We propose an iterative approach to constructing regular shapes by self-assembly. Unlike previous approaches, which construct a shape in one go, our approach constructs a final shape by alternating the steps o...
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Chapter and Conference Paper
Modular Verification of DNA Strand Displacement Networks via Serializability Analysis
DNA strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand di...
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Chapter and Conference Paper
DNA Reservoir Computing: A Novel Molecular Computing Approach
We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps th...
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Book and Conference Proceedings
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Chapter and Conference Paper
Towards a Biomolecular Learning Machine
Learning and generalisation are fundamental behavioural traits of intelligent life. We present a synthetic biochemical circuit which can exhibit non-trivial learning and generalisation behaviours, which is a f...
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Chapter and Conference Paper
Multiple Molecular Spiders with a Single Localized Source—The One-Dimensional Case
Molecular spiders are nanoscale walkers made with DNA enzyme legs attached to a common body. They move over a surface of DNA substrates, cleaving them and leaving behind product DNA strands, which they are abl...
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Chapter and Conference Paper
Multivalent Random Walkers — A Model for Deoxyribozyme Walkers
We propose a stochastic model for molecular transport at the nanoscale that describes the motion of two-dimensional molecular assemblies called multivalent random walkers (MVRWs). This walker model is an abstr...
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Chapter and Conference Paper
Advancing the Deoxyribozyme-Based Logic Gate Design Process
We previously described a tic-tac-toe playing molecular auto- maton, MAYA-II, constructed from a molecular array of deoxyribozyme- based logic gates, that uses oligonucleotides as inputs and outputs. We are no...
