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

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

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds

Normal-mode analysis of infrared and Raman spectra of poly(vinyl fluoride)

Infrared and Raman spectra of samples of poly(vinyl fluoride) (PVF) have been recorded. The vibrational spectra have been analyzed by means of normal-mode calculations. A force field was derived by using 2-fluorobutane as a model compound. Crowder's force field for hydrofluorocarbons was employed as a starting point and subsequently refined in application to secondary fluorides. A planar zigzag, syndiotactic single-chain model of crystalline PVF was submitted to be analyzed by this scheme. A comparison of observed infrared and Raman bands with frequencies calculated for syndiotactic PVF shows that PVF produced by conventional free radical polymerization has an atactic structure, supporting the 19F-NMR results and conclusions reached by Koenig and Boerio. Band assignments in terms of atactic structure are proposed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30156/1/0000533.pd

Hamiltonian dynamics of the two-dimensional lattice phi^4 model

The Hamiltonian dynamics of the classical $\phi^4$ model on a two-dimensional square lattice is investigated by means of numerical simulations. The macroscopic observables are computed as time averages. The results clearly reveal the presence of the continuous phase transition at a finite energy density and are consistent both qualitatively and quantitatively with the predictions of equilibrium statistical mechanics. The Hamiltonian microscopic dynamics also exhibits critical slowing down close to the transition. Moreover, the relationship between chaos and the phase transition is considered, and interpreted in the light of a geometrization of dynamics.Comment: REVTeX, 24 pages with 20 PostScript figure

The merger of vertically offset quasi-geostrophic vortices

We examine the critical merging distance between two equal-volume, equal-potential-vorticity quasi-geostrophic vortices. We focus on how this distance depends on the vertical offset between the two vortices, each having a unit mean height-to-width aspect ratio. The vertical direction is special in the quasi-geostrophic model (used to capture the leading-order dynamical features of stably stratified and rapidly rotating geophysical flows) since vertical advection is absent. Nevertheless vortex merger may still occur by horizontal advection. In this paper, we first investigate the equilibrium states for the two vortices as a function of their vertical and horizontal separation. We examine their basic properties together with their linear stability. These findings are next compared to numerical simulations of the nonlinear evolution of two spheres of potential vorticity. Three different regimes of interaction are identified, depending on the vertical offset. For a small offset, the interaction differs little from the case when the two vortices are horizontally aligned. On the other hand, when the vertical offset is comparable to the mean vortex radius, strong interaction occurs for greater horizontal gaps than in the horizontally aligned case, and therefore at significantly greater full separation distances. This perhaps surprising result is consistent with the linear stability analysis and appears to be a consequence of the anisotropy of the quasi-geostrophic equations. Finally, for large vertical offsets, vortex merger results in the formation of a metastable tilted dumbbell vortex.Publisher PDFPeer reviewe

Geometry of dynamics, Lyapunov exponents and phase transitions

The Hamiltonian dynamics of classical planar Heisenberg model is numerically investigated in two and three dimensions. By considering the dynamics as a geodesic flow on a suitable Riemannian manifold, it is possible to analytically estimate the largest Lyapunov exponent in terms of some curvature fluctuations. The agreement between numerical and analytical values for Lyapunov exponents is very good in a wide range of temperatures. Moreover, in the three dimensional case, in correspondence with the second order phase transition, the curvature fluctuations exibit a singular behaviour which is reproduced in an abstract geometric model suggesting that the phase transition might correspond to a change in the topology of the manifold whose geodesics are the motions of the system.Comment: REVTeX, 10 pages, 5 PostScript figures, published versio

Diagrams for Symmetric Product Orbifolds

We develop a diagrammatic language for symmetric product orbifolds of two-dimensional conformal field theories. Correlation functions of twist operators are written as sums of diagrams: each diagram corresponds to a branched covering map from a surface where the fields are single-valued to the base sphere where twist operators are inserted. This diagrammatic language facilitates the study of the large N limit and makes more transparent the analogy between symmetric product orbifolds and free non-abelian gauge theories. We give a general algorithm to calculate the leading large N contribution to four-point correlators of twist fields.Comment: 43 pages, 19 figures, v2: references adde

Adsorption Isotherms of Hydrogen: The Role of Thermal Fluctuations

It is shown that experimentally obtained isotherms of adsorption on solid substrates may be completely reconciled with Lifshitz theory when thermal fluctuations are taken into account. This is achieved within the framework of a solid-on-solid model which is solved numerically. Analysis of the fluctuation contributions observed for hydrogen adsorption onto gold substrates allows to determine the surface tension of the free hydrogen film as a function of film thickness. It is found to decrease sharply for film thicknesses below seven atomic layers.Comment: RevTeX manuscript (3 pages output), 3 figure

Exact 2-point function in Hermitian matrix model

J. Harer and D. Zagier have found a strikingly simple generating function for exact (all-genera) 1-point correlators in the Gaussian Hermitian matrix model. In this paper we generalize their result to 2-point correlators, using Toda integrability of the model. Remarkably, this exact 2-point correlation function turns out to be an elementary function - arctangent. Relation to the standard 2-point resolvents is pointed out. Some attempts of generalization to 3-point and higher functions are described.Comment: 31 pages, 1 figur