On the uniform generation of modular diagrams

In this paper we present an algorithm that generates $k$-noncrossing, $\sigma$-modular diagrams with uniform probability. A diagram is a labeled graph of degree $\le 1$ over $n$ vertices drawn in a horizontal line with arcs $(i,j)$ in the upper half-plane. A $k$-crossing in a diagram is a set of $k$ distinct arcs $(i_1, j_1), (i_2, j_2),\ldots,(i_k, j_k)$ with the property $i_1 < i_2 < \ldots < i_k < j_1 < j_2 < \ldots< j_k$. A diagram without any $k$-crossings is called a $k$-noncrossing diagram and a stack of length $\sigma$ is a maximal sequence $((i,j),(i+1,j-1),\dots,(i+(\sigma-1),j-(\sigma-1)))$. A diagram is $\sigma$-modular if any arc is contained in a stack of length at least $\sigma$. Our algorithm generates after $O(n^k)$ preprocessing time, $k$-noncrossing, $\sigma$-modular diagrams in $O(n)$ time and space complexity.Comment: 21 pages, 7 figure

Crossover from one to three dimensions for a gas of hard-core bosons

We develop a variational theory of the crossover from the one-dimensional (1D) regime to the 3D regime for ultra-cold Bose gases in thin waveguides. Within the 1D regime we map out the parameter space for fermionization, which may span the full 1D regime for suitable transverse confinement.Comment: 4 pages, 2 figure

Shapes of topological RNA structures

A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed topological genus there exist only finitely many such shapes. We shall express topological RNA structures as unicellular maps, i.e. graphs together with a cyclic ordering of their half-edges. In this paper we prove a bijection of shapes of topological RNA structures. We furthermore derive a linear time algorithm generating shapes of fixed topological genus. We derive explicit expressions for the coefficients of the generating polynomial of these shapes and the generating function of RNA structures of genus $g$. Furthermore we outline how shapes can be used in order to extract essential information of RNA structure databases.Comment: 27 pages, 11 figures, 2 tables. arXiv admin note: text overlap with arXiv:1304.739

On the formation of current sheets in response to the compression or expansion of a potential magnetic field

The compression or expansion of a magnetic field that is initially potential is considered. It was recently suggested by Janse & Low [2009, ApJ, 690, 1089] that, following the volumetric deformation, the relevant lowest energy state for the magnetic field is another potential magnetic field that in general contains tangential discontinuities (current sheets). Here we examine this scenario directly using a numerical relaxation method that exactly preserves the topology of the magnetic field. It is found that of the magnetic fields discussed by Janse & Low, only those containing magnetic null points develop current singularities during an ideal relaxation, while the magnetic fields without null points relax toward smooth force-free equilibria with finite non-zero current.Comment: Accepted for publication in Ap

Segue Between Favorable and Unfavorable Solvation

Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understood from the perspective of Weeks' theory of solvation [Ann. Rev. Phys. Chem. 2002, 53, 533] and supports theories based upon that perspective.Comment: 8 pages, 7 figure