Coarse-Grained Modelling of DNA and DNA Self-Assembly

• Main Author: Ouldridge, Thomas E. (Author)
• Corporate Author: SpringerLink (Online service)
• Format: Electronic eBook
• Language: English
• Published: Berlin, Heidelberg : Springer Berlin Heidelberg : Imprint: Springer, 2012.
• Series: Springer Theses, Recognizing Outstanding Ph.D. Research,
• Subjects: Physics.; Polymers.; Amorphous substances.; Complex fluids.; Biophysics.; Biological physics.; Statistical physics.; Dynamical systems.; Nanotechnology.; Biophysics and Biological Physics.; Polymer Sciences.; Statistical Physics, Dynamical Systems and Complexity.; Soft and Granular Matter, Complex Fluids and Microfluidics.
• Physical Description: XII, 176 p. online resource.
• ISBN: 9783642305177
• ISSN: 2190-5053

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.