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Chapter and Conference Paper
On Availability of Bit-Narrow Operations in General-Purpose Applications
Program instructions that consume and produce small operands can be executed in hardware circuitry of less than full size. We compare different proposed models of accounting for the usefulness of bit-positions...
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Chapter and Conference Paper
Limits and Graph Structure of Available Instruction-Level Parallelism
We reexamine the limits of parallelism available in programs, using run-time reconstruction of program data-flow graphs. While limits of parallelism have been examined in the context of superscalar and VLIW ma...
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Chapter and Conference Paper
Model Checking Reconfigurable Processor Configurations for Safety Properties
Reconfigurable processors pose unique problems for program safety because of their use of computational approaches that are difficult to integrate into traditional program analyses. The combination of proof-ca...
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Article
A deoxyribozyme-based molecular automaton
We describe a molecular automaton, called MAYA, which encodes a version of the game of tic-tac-toe and interactively competes against a human opponent. The automaton is a Boolean network of deoxyribozymes that...
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Chapter and Conference Paper
Building the Components for a Biomolecular Computer
We propose a new method for amorphous bio-compatible computing using deoxyribozyme logic gates [1] in which oligonucleotides act as enzymes on other oligonucleotides, yielding oligonucleotide products. Moreove...
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Protocol
Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts
Recent development of solution-phase molecular-scale Boolean calculations using deoxyribozymes is potentially an important step toward the development of autonomous therapeutic and diagnostic devices. Here, th...
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Chapter and Conference Paper
Designing Nucleotide Sequences for Computation: A Survey of Constraints
We survey common biochemical constraints useful for the design of DNA code words for DNA computation. We define the DNA Code Constraint Problem and cover biochemistry topics relevant to DNA libraries. We exami...
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Chapter and Conference Paper
Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks
We propose a way of implementing a biomolecular computer in the laboratory using deoxyribozyme logic gates inside a microfluidic reaction chamber. We build upon our previous work, which simulated the operation...
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Chapter and Conference Paper
A Static Heap Analysis for Shape and Connectivity: Unified Memory Analysis: The Base Framework
Modeling the evolution of the state of program memory during program execution is critical to many parallelization techniques. Current memory analysis techniques either provide very accurate information but ru...
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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...
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Chapter and Conference Paper
Identification of Heap–Carried Data Dependence Via Explicit Store Heap Models
Dependence information between program values is extensively used in many program optimization techniques. The ability to identify statements, calls and loop iterations that do not depend on each other enables...
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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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Article
Molecules that reason
DNA reactions can be used to implement simple logic programs.
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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
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
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...
