Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields

Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a simple Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the type of knot and on the electric field intensity was investigated. The results are in qualitative agreement with electrophoretic experiments done under conditions of low and high electric fields: especially the inversion of the behavior from low to high electric field could be reproduced. The knot topology imposes on the problem the constrain of self-avoidance, which is the final cause of the observed behavior in strong electric field.Comment: 17 pages, 5 figure

The role of the Berry Phase in Dynamical Jahn-Teller Systems

The presence/absence of a Berry phase depends on the topology of the manifold of dynamical Jahn-Teller potential minima. We describe in detail the relation between these topological properties and the way the lowest two adiabatic potential surfaces get locally degenerate. We illustrate our arguments through spherical generalizations of the linear T x h and H x h cases, relevant for the physics of fullerene ions. Our analysis allows us to classify all the spherical Jahn-Teller systems with respect to the Berry phase. Its absence can, but does not necessarily, lead to a nondegenerate ground state.Comment: revtex 7 pages, 2 eps figures include

Warm and Cold Denaturation in the Phase Diagram of a Protein Lattice Model

Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied our model of solvation to a 16-monomer chain constrained on a two-dimensional lattice. We compute a phase diagram function of the temperature and a solvent parameter which is related to the pH of the solution. It exhibits a native state in which the chain coalesces into a unique compact conformation as well as a denatured state. Under certain solvation conditions, both warm and cold denaturations occur between the native and the denatured states. A good agreement is found with the data obtained from calorimetric experiments, thereby validating the proposed model.Comment: 7 pages, 2 figure

Bethe approximation for self-interacting lattice trees

In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for instance, in the enumeration of spanning trees. Moreover, the expressions we obtain for the asymptotic number of spanning trees and lattice trees on a graph coincide with analogous expressions derived through different approaches. We study the phase diagram of lattice trees with nearest-neighbour attraction and branching energies. We find a collapse transition at a tricritical theta point, which separates an expanded phase from a compact phase. We compare our results for the theta transition in two and three dimensions with available numerical estimates.Comment: 10 pages, 3 figures, to be published in Europhysics Letter

Preliminary Measurements of Be-10/Be-7 Ratio in Rainwater for Atmospheric Transport Analysis

The meteoric cosmogenic beryllium has been used as an essential geophysical tracer in the analysis of atmospheric flows and erosion soils since 1960. The first measurements Be-7 and Be-10 concentrations in rainwater from Mexico, have been carried out by using gamma decay spectroscopy and AMS techniques, respectively for each isotope. With this it was possible to report a preliminar value for the Be-10/Be-7 isotopic ratio in such environmental samples. The present work described preliminary results related to rainwater collected at mountain and metropolitan areas. Results are compared with predictions and previous measurements for both radioisotopes, observing a very sensible behavior particularly for the case of Be-7 activities

Solvent-induced micelle formation in a hydrophobic interaction model

We investigate the aggregation of amphiphilic molecules by adapting the two-state Muller-Lee-Graziano model for water, in which a solvent-induced hydrophobic interaction is included implicitly. We study the formation of various types of micelle as a function of the distribution of hydrophobic regions at the molecular surface. Successive substitution of non-polar surfaces by polar ones demonstrates the influence of hydrophobicity on the upper and lower critical solution temperatures. Aggregates of lipid molecules, described by a refinement of the model in which a hydrophobic tail of variable length interacts with different numbers of water molecules, are stabilized as the length of the tail increases. We demonstrate that the essential features of micelle formation are primarily solvent-induced, and are explained within a model which focuses only on the alteration of water structure in the vicinity of the hydrophobic surface regions of amphiphiles in solution.Comment: 11 pages, 10 figures; some rearrangement of introduction and discussion sections, streamlining of formalism and general compression; to appear in Phys. Rev.

Model for the hydration of non-polar compounds and polymers

We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are neglected. Analytical results show that an effective strengthening of hydrogen bonds in the presence of the solute, together with a geometric reorganization of water molecules, are enough to yield hydrophobic behavior. We extend our model to describe a non-polar homopolymer in aqueous solution, obtaining a clear evidence of both ``cold'' and ``warm'' swelling transitions. This suggests that our model could be relevant to describe some features of protein folding.Comment: REVTeX, 6 pages, 3 figure

De la mitigación de desastres a la interrupción de trampas de riesgo: la experiencia de aprendizajeacción de clima sin riesgo

RESUMEN: En las últimas décadas hemos asistido a una profunda reformulación de cómo entender las condiciones de riesgo en el contexto urbano. Sin embargo, aún enfrentamos significativos desafíos para capturar conceptual, metodológica y empíricamente los círculos viciosos de reproducción de riesgos que configuran ‘trampas de riesgo urbano’ frecuentemente invisibilizadas. Entendemos a las trampas de riesgo como el resultado de la reproducción de riesgos cotidianos y de desastres repetitivos y frecuentes de pequeña escala, que afectan en forma desproporcional a los sectores empobrecidos en forma altamente localizada. A partir de cLIMA sin Riesgo - un proyecto de investigación-acción desarrollado por los autores en el contexto de Lima - este artículo explora las condiciones que producen y reproducen estas trampas, cómo y dónde se materializan, quié- nes son afectados y con qué consecuencias para aquellos que viven en barrios tugurizados y/o asentamientos informales y marginalizados. La discusión examina cómo el conocimiento espacial de la urbanización en riesgo y la evaluación critica de las inversiones y los esfuerzos de mitigación realizados por parte de pobladores y agencias estatales permiten avanzar hacia una apreciación más precisa del impacto de dichas trampas a lo largo del tiempo, así como hacia estrategias de acción para su interrupción. ABSTRACT: The last decades have witnessed a profound change in our understanding of the conditions of risk in urban contexts. However, we still face significant conceptual, methodological and empirical challenges in capturing the vicious cycles of risk accumulation that often render so-called ‘urban risk traps’ invisible. We define risk traps as the result of the reproduction of everyday risks and frequent small-scale disasters, which have highly localized impacts and disproportionately affect impoverished inhabitants. Based on the action-research project cLIMA without Risk (cLIMA sin riesgo), which was conducted by the authors in the context of two marginalized areas in the centre and periphery of Lima, Peru, this article explores the conditions that produce and reproduce these risk traps and it analyses how and where they materialize, who they affect and with what consequences. The discussion examines how spatial knowledge of urbanization at risk together with a critical evaluation of inhabitants’ and state agencies’ investments in mitigation efforts allows us to move towards a more accurate assessment of the impact of these risk traps over time, which is required for developing transformative strategies to disrupt them

Fractal Dimension and Localization of DNA Knots

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the three-dimensional (3D) configuration, and of (ii) weak binding, that permits (partial) relaxation on the surface. In (i) the gyration radius of the adsorbed DNA knot scales with the 3D Flory exponent $\nu\approx 0.58$ within error. In (ii), we find $\nu\approx 0.66$, a value between the 3D and 2D ($\nu=3/4$) exponents, indicating an incomplete 2D relaxation or a different polymer universality class. Compelling evidence is also presented for the localization of the knot crossings in 2D.Comment: 4 pages, 3 figure