Coarse-Grained Modelling of DNA and DNA Self-Assembly by Thomas E. Ouldridge

By Thomas E. Ouldridge

This thesis provides a unique coarse-grained version of DNA, within which bases are represented as inflexible nucleotides. The version is proven to quantitatively reproduce many phenomena, together with elastic homes of the double-stranded nation, hairpin formation in unmarried strands and hybridization of pairs of strands to shape duplexes, the 1st time one of these wide selection of houses has been captured via a coarse-grained version. The scope and strength of the version is established by means of simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker — the 1st time that coarse-grained modelling has been utilized to dynamic DNA nanotechnology.

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I. Model and thermodynamics. J. Chem. , 134(16):165103– 165116, 2011. 127. T. J. Schmitt and T. A. Knotts IV. Thermodynamics of DNA hybridization on surfaces. J. Chem. , 134, 205105–205113, 2011. 128. M. J. Hoefert, E. J. Sambriski, and J. J. de Pablo. Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides. Soft Matter, 7:560–566, 2011. 129. S. Pitchiaya and Y. Krishnan. First blueprint, now bricks: DNA as construction material on the nanoscale. Chem. Soc. , 35:1111–1121, 2006.

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