DNA Computing and Molecular Programming
18th International Conference, DNA 18, Aarhus, Denmark, August 14-17, 2012. Proceedings
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Chapter and Conference Paper
Computing Game Strategies
We revisit the problem of constructing strategies for simple position games. We derive a general, executable formalism for describing game rules and desired strategy properties. We present the outcomes for sev...
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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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Living Reference Work Entry In depth
Molecular Automata
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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
Maze Exploration with Molecular-Scale Walkers
Molecular spiders are nanoscale walkers made with catalytic DNA legs attached to a rigid body. They move in a matrix of DNA substrates, cleaving them and leaving behind product DNA strands. Unlike a self-avoid...
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Chapter and Conference Paper
Representing Uniqueness Constraints in Object-Relational Map**
Object-oriented languages model data as transient objects, while relational databases store data persistently using a relational data model. The process of making objects persistent by storing their state as r...
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Reference Work Entry In depth
Molecular Automata
Glossary
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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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Article
Training a molecular automaton to play a game
Research at the interface between chemistry and cybernetics has led to reports of ‘programmable molecules’, but what does it mean to say ‘we programmed a set of solution-phase molecules to do X’? A survey of r...
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Chapter and Conference Paper
Shape Analysis with Reference Set Relations
Tracking subset relations between the contents containers on the heap is fundamental to modeling the semantics of many common programing idioms such as applying a function to a subset of objects and maintainin...
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Article
Molecules that reason
DNA reactions can be used to implement simple logic programs.
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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...
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Reference Work Entry In depth
Molecular Automata
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Chapter and Conference Paper
Efficient Context-Sensitive Shape Analysis with Graph Based Heap Models
The performance of heap analysis techniques has a significant impact on their utility in an optimizing compiler. Most shape analysis techniques perform interprocedural dataflow analysis in a context-sensitive ...
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Chapter
Emerging Models of Computation: Directions in Molecular Computing
Computing as we have known it for 60 years is based on the von Neumann stored-program concept and its ubiquitous implementation in the form of electronic instruction processors. For the past four decades, proc...
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Chapter
Nanocomputing
Nanocomputing encompasses any submicron devices and technologies applied to any computational or related tasks. A brief survey is given, and emphasis is placed on biomolecular devices that use nucleic acids as...
