A steepest descent calculation of RNA pseudoknots

We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure

An Algorithmic Approach to Limit Cycles of Nonlinear Differential Systems: the Averaging Method Revisited

This paper introduces an algorithmic approach to the analysis of bifurcation of limit cycles from the centers of nonlinear continuous differential systems via the averaging method. We develop three algorithms to implement the averaging method. The first algorithm allows to transform the considered differential systems to the normal formal of averaging. Here, we restricted the unperturbed term of the normal form of averaging to be identically zero. The second algorithm is used to derive the computational formulae of the averaged functions at any order. The third algorithm is based on the first two algorithms that determines the exact expressions of the averaged functions for the considered differential systems. The proposed approach is implemented in Maple and its effectiveness is shown by several examples. Moreover, we report some incorrect results in published papers on the averaging method.Comment: Proc. 44th ISSAC, July 15--18, 2019, Beijing, Chin

Manning condensation in two dimensions

We consider a macroion confined to a cylindrical cell and neutralized by oppositely charged counterions. Exact results are obtained for the two-dimensional version of this problem, in which ion-ion and ion-macroion interactions are logarithmic. In particular, the threshold for counterion condensation is found to be the same as predicted by mean-field theory. With further increase of the macroion charge, a series of single-ion condensation transitions takes place. Our analytical results are expected to be exact in the vicinity of these transitions and are in very good agreement with recent Monte-Carlo simulation data.Comment: 4 pages, 4 figure

The me in memory:the role of the self in autobiographical memory development

This paper tests the hypothesis that self development plays a role in the offset of childhood amnesia; assessing the importance of both the capacity to anchor a memory to the self-concept, and the strength of the self-concept as an anchor. We demonstrate for the first time that the volume of 3- to 6-year-old’s specific autobiographical memories is predicted by both the volume of their self-knowledge, and their capacity for self-source monitoring within self-referencing paradigms (N =186). Moreover, there is a bidirectional relationship between self and memory, such that autobiographical memory mediates the link between self-source monitoring and self-knowledge. These predictive relationships suggests that the self memory system is active in early childhood

Real symmetric random matrices and replicas

Various ensembles of random matrices with independent entries are analyzed by the replica formalism in the large-N limit. A result on the Laplacian random matrix with Wigner-rescaling is generalized to arbitrary probability distribution.Comment: 17 page

Enumeration of RNA structures by Matrix Models

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed. We analyze the distribution of the genus of pseudoknots as a function of the total number of nucleotides along the phosphate-sugar backbone.Comment: RevTeX, 4 pages, 2 figure

Are better conducting molecules more rigid?

We investigate the electronic origin of the bending stiffness of conducting molecules. It is found that the bending stiffness associated with electronic motion, which we refer to as electro-stiffness, $\kappa_{e}$, is governed by the molecular orbital overlap $t$ and the gap width $u$ between HOMO and LUMO levels, and behaves as $\kappa_{e}\sim t^{2}/\sqrt{u^2+t^{2}}$. To study the effect of doping, we analyze the electron filling-fraction dependence on $\kappa_{e}$ and show that doped molecules are more flexible. In addition, to estimate the contribution of $\kappa_{e}$ to the total stiffness, we consider molecules under a voltage bias, and study the length contraction ratio as a function of the voltage. The molecules are shown to be contracted or dilated, with $\kappa_{e}$ increasing nonlinearly with the applied bias