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

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 country, hairpin formation in unmarried strands and hybridization of pairs of strands to shape duplexes, the 1st time this type of wide selection of homes has been captured by way of a coarse-grained version. The scope and power of the version is verified via 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.

Show description

Read Online or Download Coarse-Grained Modelling of DNA and DNA Self-Assembly PDF

Similar fluid dynamics books

flow of industrial fluids - download pdf or read online

Offers perception to the elemental conception and equations of fluid stream. Emphasizes sensible difficulties and contains precious appendices.

Read e-book online Proceedings of the International Conference Porous Media: PDF

This article covers themes similar to: agreement metric R-harmonic manifolds; hypersurfaces in area varieties with a few consistent curvature services; manifolds of pseudodynamics; cubic kinds generated by way of features on projectively flat areas; and unusual submanifolds of a Sasakian manifold Physics of techniques with part transition in porous media; dynamics of the fluid/fluid interface instability; new versions of two-phase circulate via porous media; stream of froth and non-Newtonian fluids; averaged versions of Navie-Stokes circulation in porous media; homogenization of move via hugely heterogeneous media; groundwater toxins difficulties; inverse difficulties, optimization, parameter estimation

Modern Fluid Dynamics: Basic Theory and Selected - download pdf or read online

This textbook covers the necessities of conventional and sleek fluid dynamics, i. e. , the basics of and easy functions in fluid mechanics and convection warmth move with short tours into fluid-particle dynamics and sturdy mechanics. particularly, the booklet can be utilized to reinforce the information base and talent point of engineering and physics scholars in macro-scale fluid mechanics (see Chapters I-V), by way of an introductory day trip into micro-scale fluid dynamics (see Chapters VI-X).

Extra info for Coarse-Grained Modelling of DNA and DNA Self-Assembly

Sample text

When implementing Langevin dynamics, one has a degree of choice of the form of the friction and damping terms, although they must always be related by a fluctuationdissipation theorem if the equilibrium distribution is to be the correct one. Given the degree of simplification inherent in the simulation, it seems unlikely that being precise about the damping terms will prove significantly beneficial. This reasoning justified the simplifying assumptions about the form of the noise and damping terms, effectively treating each nucleotide as a sphere for dynamical purposes.

12. J. SantaLucia, Jr. and D. Hicks. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. , 33:415–40, 2004. 13. N. Peyret. Prediction of nucleic acid hybridization: parameters and algorithms. PhD thesis, Wayne State University, 2000. 14. D. V. Pyshnyi and E. 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.

When taken in conjunction with stacking, the result is the famous B-DNA double helix. The model reproduces basepairing through the VHB term, which incorporates a radial term dependent on the separation of hydrogen-bonding sites, δrHB . This interaction is modulated by terms that encourage the co-linear alignment of all four backbone and hydrogen-bonding sites (quantified by the angles θ1 , θ2 , and θ3 ). A further factor is included to encourage the planes of bases to be antiparallel (measured by θ4 ).

Download PDF sample

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

by Kenneth

Rated 4.75 of 5 – based on 7 votes