Dominic J O' Lee

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The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however,(More)
This study revisits the classical x-ray diffraction patterns from hydrated, noncrystalline fibers originally used to establish the helical structure of DNA. We argue that changes in these diffraction patterns with DNA packing density reveal strong azimuthally dependent interactions between adjacent molecules up to approximately 40 A interaxial or(More)
Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While(More)
The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their(More)
We have developed a statistical theory for columnar aggregates of semi-flexible polyelectrolytes. The applicability of previous, simplified theories was limited to polyelectrolytes with unrealistically high effective charge and, hence, with strongly suppressed thermal undulations. To avoid this problem, we utilized more consistent approximations for(More)
The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo(More)
A renormalization-group scheme is developed for the 3-dimensional O(2N)-symmetric Ginzburg-Landau-Wilson model, which is consistent with the use of a 1/N expansion as a systematic method of approximation. It is motivated by an application to the critical properties of superconductors, reported in a separate paper. Within this scheme, the infrared stable(More)
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA--subject to the earlier found unusual, frustrated pair potential (A.A. Kornyshev, S. Leikin, J. Chem. Phys. 107, 3656 (1997))--onto an exotic, unknown variant of the XY(More)
We extend to finite temperature the time-dependent effective theory for the Gold-stone field (the phase of the pair field) θ which is appropriate for a superfluid containing one species of fermions with s-wave interactions, described by the BCS Lagrangian. We show that, when Landau damping is neglected, the effective theory can be written as a local(More)
We extend to finite temperature the time-dependent effective theory for the Goldstone field (the phase of the pair field) θ which is appropriate for superconductors containing one species of charge carrier, described by the BCS Lagrangian. We show that, when Landau damping is neglected, the effective theory can be written as a local time-dependent(More)
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