574 research outputs found
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 within error. In (ii), we find , a value between the 3D
and 2D () 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
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