Titlebook: Mathematics of DNA Structure, Function and Interactions; Craig John Benham,Stephen Harvey,David Swigon Conference proceedings 2009 Springe

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Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotincluding gene regulation, DNA replication, and recombination. The biological importance of DNA loop formation is underscored by an abundance of architectural proteins in cells such as HU, IHF, and HMGs, which facilitate looping by bending the intervening DNA between cognate protein-binding sites. W

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Micromechanics of Single Supercoiled DNA Molecules,e semiflexible polymer including the effect of torsional stress, and for the free energy of plectonemic supercoils, a theory of coexisting plectonemic and extended DNA is constructed and shown to produce phenomena observed experimentally. Analytical results for DNA extension and torque are presented

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Flexibility Of Nucleosomes On Topologically Constrained DNA,ational flexibility, its molecular mechanism and its functional relevance. Our initial approach combined both empirical measurement and theoretical simulation of the topological properties of single particles reconstituted on DNA minicircles. Two types of particles were studied in addition to the co

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Paradox Regained: a Topological Coupling of Nuclesomal DNA Wrapping and Chromatin Fibre Coiling,s have elucidated many of the mechanistic elaborations that regulate this process, the underlying mechanical basis of the folding transitions is poorly understood. Here I present a novel solution to the so-called ‘linking number paradox‘ problem (Finch et al., 1977) and show that this solution impli

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Statistical-Mechanical Analysis of Enzymatic Topological Transformations in DNA Molecules,in unknown, and therefore different models of the reactions require critical testing. A great help in such testing comes from computer simulation. The computational approach, described in the review, allows simulating the distribution of the reaction products for a chosen model of the enzyme action.

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Correction to: The Mathematics of DNA Structure, Mechanics, and Dynamics,

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Mathematics of DNA Structure, Function and Interactions

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