Computer Science ETDs

Author

Dandan Mo

Publication Date

7-1-2016

Abstract

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized re- actions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi- spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, and NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.

Language

English

Keywords

molecular circuits, molecular spiders, continuous time Markov chain, kinetic Monte Carlo simulation

Document Type

Dissertation

Degree Name

Computer Science

Level of Degree

Doctoral

Department Name

Department of Computer Science

First Advisor

Stefanovic, Darko

First Committee Member (Chair)

Stefanovic, Darko

Second Committee Member

Lakin, Matthew

Third Committee Member

Stojanovic, Milan

Fourth Committee Member

Luan, Shuang

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