New PDF release: Coarse-Grained Modelling of DNA and DNA Self-Assembly

By Thomas E. Ouldridge

ISBN-10: 3642305164

ISBN-13: 9783642305160

ISBN-10: 3642305172

ISBN-13: 9783642305177

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 houses 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 capability of the version is tested by way 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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Extra info for Coarse-Grained Modelling of DNA and DNA Self-Assembly

Example text

Ouldridge et al. The self-assembly of DNA Holliday junctions studied with a minimal model. J. Chem. , 130:065101, 2009. 3. J. Malo, et al. Engineering a 2D protein-DNA crystal. Angew. Chem. Int. , 44:3057–3061, 2005. 4. J. Bois et al. Topological constraints in nucleic acid hybridization kinetics. Nucl. , 33(13):4090–4095, 2005. 5. S. A. Harris, C. A. Laughton, and T. B. Liverpool. Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucl. , 36(1):21–29, 2008.

C. Linak and K. Dorfman. Analysis of a DNA simulation model through hairpin melting experiments. J. Chem. , 133(12):125101–125112, 2010. 118. S. Niewieczerzał and M. Cieplak. Stretching and twisting of the DNA duplexes in coarsegrained dynamical models. J. Phys. Condens. Matter, 21(47):474221, 2009. 119. T. A. Knotts et al. A coarse grain model for DNA. J. Chem. , 126, 084901, 2007. 120. F. B. Bombelli et al. DNA closed nanostructures: a structural and Monte Carlo simulation study. J. Phys. Chem.

M. Ivanova. Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides. Russ. Chem. B+, 51:1145–1155, 2002. 15. D. V. Pyshnyi and E. M. Ivanova. The influence of nearest neighbors on the efficiency of coaxial stacking at contiguous stacking hybridization of oligodeoxyribonucleotides. Nucleos. Nucleot. , 23(6–7):1057–1064, 2004. 16. M. J. Lane et al. The thermodynamic advantage of DNA oligonucleotide ‘stacking hybridization’ reactions: Energetics of a DNA nick.

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

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