Dessins, their delta-matroids and partial duals

Given a map $\mathcal M$ on a connected and closed orientable surface, the delta-matroid of $\mathcal M$ is a combinatorial object associated to $\mathcal M$ which captures some topological information of the embedding. We explore how delta-matroids associated to dessins d'enfants behave under the action of the absolute Galois group. Twists of delta-matroids are considered as well; they correspond to the recently introduced operation of partial duality of maps. Furthermore, we prove that every map has a partial dual defined over its field of moduli. A relationship between dessins, partial duals and tropical curves arising from the cartography groups of dessins is observed as well.Comment: 34 pages, 20 figures. Accepted for publication in the SIGMAP14 Conference Proceeding

Statistical-mechanical lattice models for protein-DNA binding in chromatin

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat

A remark on the three approaches to 2D Quantum gravity

The one-matrix model is considered. The generating function of the correlation numbers is defined in such a way that this function coincide with the generating function of the Liouville gravity. Using the Kontsevich theorem we explain that this generating function is an analytic continuation of the generating function of the Topological gravity. We check the topological recursion relations for the correlation functions in the $p$-critical Matrix model.Comment: 11 pages. Title changed, presentation improve

Universal geometrical factor of protein conformations as a consequence of energy minimization

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A)) of the van der Waals volume V to the surface area A and average atomic radius of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.Comment: 6 pages, 1 table, 4 figure

Strings from Feynman Graph counting : without large N

A well-known connection between n strings winding around a circle and permutations of n objects plays a fundamental role in the string theory of large N two dimensional Yang Mills theory and elsewhere in topological and physical string theories. Basic questions in the enumeration of Feynman graphs can be expressed elegantly in terms of permutation groups. We show that these permutation techniques for Feynman graph enumeration, along with the Burnside counting lemma, lead to equalities between counting problems of Feynman graphs in scalar field theories and Quantum Electrodynamics with the counting of amplitudes in a string theory with torus or cylinder target space. This string theory arises in the large N expansion of two dimensional Yang Mills and is closely related to lattice gauge theory with S_n gauge group. We collect and extend results on generating functions for Feynman graph counting, which connect directly with the string picture. We propose that the connection between string combinatorics and permutations has implications for QFT-string dualities, beyond the framework of large N gauge theory.Comment: 55 pages + 10 pages Appendices, 23 figures ; version 2 - typos correcte

Modelling stochastic bivariate mortality

Stochastic mortality, i.e. modelling death arrival via a jump process with stochastic intensity, is gaining increasing reputation as a way to represent mortality risk. This paper represents a first attempt to model the mortality risk of couples of individuals, according to the stochastic intensity approach. On the theoretical side, we extend to couples the Cox processes set up, i.e. the idea that mortality is driven by a jump process whose intensity is itself a stochastic process, proper of a particular generation within each gender. Dependence between the survival times of the members of a couple is captured by an Archimedean copula. On the calibration side, we fit the joint survival function by calibrating separately the (analytical) copula and the (analytical) margins. First, we select the best fit copula according to the methodology of Wang and Wells (2000) for censored data. Then, we provide a sample-based calibration for the intensity, using a time-homogeneous, non mean-reverting, affine process: this gives the analytical marginal survival functions. Coupling the best fit copula with the calibrated margins we obtain, on a sample generation, a joint survival function which incorporates the stochastic nature of mortality improvements and is far from representing independency.On the contrary, since the best fit copula turns out to be a Nelsen one, dependency is increasing with age and long-term dependence exists

8-hydroxyquinoline-2-carboxylic acid as possible molybdophore: A multi-technique approach to define its chemical speciation, coordination and sequestering ability in aqueous solution

8-hydroxyquinoline-2-carboxylic acid (8-HQA) has been found in high concentrations (0.5–5.0 mmol·dm−3) in the gut of Noctuid larvae (and in a few other lepidopterans), in which it is proposed to act as a siderophore. Since it is known that many natural siderophores are also involved in the uptake and metabolism of other essential elements than iron, this study reports some results on the investigation of 8-HQA interactions with molybdate (MoO42−, i.e., the main molybdenum form in aqueous environments), in order to understand the possible role of this ligand as molybdophore. A multi-technique approach has been adopted, in order to derive a comprehensive set of information necessary to assess the chemical speciation of the 8-HQA/MoO42− system, as well as the coordination behavior and the sequestering ability of 8-HQA towards molybdate. Chemical speciation studies have been performed in KCl(aq) at I = 0.2 mol·dm−3 and T = 298.15 K by ISE-H+ (glass electrode) potentiometric and UV/Vis spectrophotometric titrations. CV (Cyclic Voltammetry), DP-ASV (Differential Pulse-Anodic Stripping Voltammetry), ESI-MS experiments and quantum mechanical calculations have been also performed to derive information about the nature and possible structure of species formed. These results are also compared with those reported for the 8-HQA/Fe3+ system in terms of chemical speciation and sequestering ability of 8HQA