This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker - the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.
Coarse-Grained Modelling of DNA and DNA Self-Assembly
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This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker - the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.
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...
This book presents three types of synthetically cooperative DNA recognizing assemblies, in order to advance the development of programmable DNA-binding pyrrole-imidazole polyamides (PIPs). PIPs...
Theoretical Computer Science.- Molecular Biology.- Word Design for DNA Computing.- Non-Autonomous DNA Models.- Autonomous DNA Models.- Cellular DNA Computing.
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