1,721,292 research outputs found
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots
No full textThe configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases
Angular structure of lacunarity, and the renormalization group
No full textWe formulate the angular structure of lacunarity in fractals, in terms of a symmetry reduction of the three point correlation function. This provides a rich probe of universality, and first measurements yield new evidence in support of the equivalence between self-avoiding walks (SAW’s) and percolation perimeters in two dimensions. We argue that the lacunarity reveals much of the renormalization group in real space. This is supported by exact calculations for random walks and measured data for percolation clusters and SAW’s. Relationships follow between exponents governing inward and outward propagating perturbations, and we also find a very general test for the contribution of long-range interactions. © 2000 The American Physical Society
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