DNA Based Self-Assembly and Nanorobotic: Theory and Experiments
Abstract
We study the following fundamental questions in DNA based self-assembly and nanorobotics:
How to control errors in self-assembly? How to construct complex nanoscale objects
in simpler ways? How to transport nanoscale objects in programmable manner?Fault tolerance
in self-assembly: Fault tolerant self-assembly is important for nanofabrication and
nanocomputing applications. It is desirable to design compact error-resilient schemes
that do not result in the increase in the original size of the assemblies. We present
a comprehensive theory of compact error-resilient schemes for algorithmic self-assembly
in two and three dimensions, and discuss the limitations and capabilities of redundancy
based
compact error correction schemes.New and powerful self-assembly model:
We develop a reversible self-assembly model in which the glue strength between two
juxtaposed tiles is a function of the time they have been in neighboring positions.
Under our time-dependent glue model, we can rigorously study and demonstrate catalysis
and self-replication in the tile assembly. We can assemble thin rectangles of size
k×N using O(logN/loglogN) types of tiles in our model.Modeling DNA based Nanorobotical
Devices: We design a framework for a discrete event simulator for DNA based nanorobotical
systems. It has two major components: a physical model and a kinetic model. The physical
model captures the conformational changes in molecules, molecular motions and molecular
collisions. The kinetic model
governs the modeling of various reactions in a DNA nanorobotical systems including
hybridization, dehybridization and strand displacement.DNA-based molecular devices
using DNAzyme: We design a class of nanodevices that are autonomous, programmable,
and require no protein enzymes. Our DNAzyme based designs include (1) DNAzyme FSA,
a finite state automata device , (2) DNAzyme router for programmable routing of
nanostructures on two-dimensional DNA addressable lattice, and (3) DNAzyme doctor,
a medical-related application that respond to the under-expression or over-expression
of various RNAs, by releasing an RNA.Nanomotor Powered by Polymerase: We, for the
first time, attempt to harness the
mechanical energy of a polymerase φ29 to construct a polymerase based nanomotor that
pushes a cargo on a DNA track. Polymerase based nanomotor has advantage of high speeds
of polymerase.
Type
DissertationDepartment
Computer ScienceSubject
Computer SciencePermalink
https://hdl.handle.net/10161/443Citation
Sahu, Sudheer (2007). DNA Based Self-Assembly and Nanorobotic: Theory and Experiments. Dissertation, Duke University. Retrieved from https://hdl.handle.net/10161/443.Collections
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