730 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
Statistical Analysis of Genealogical Trees for Polygamic Species
Repetitions within a given genealogical tree provides some information about
the degree of consanguineity of a population. They can be analyzed with
techniques usually employed in statistical physics when dealing with fixed
point transformations. In particular we show that the tree features strongly
depend on the fractions of males and females in the population, and also on the
offspring probability distribution. We check different possibilities, some of
them relevant to human groups, and compare them with simulations.Comment: 2 eps figs, Fig.2 changed to meet cond-mat size criteri
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
Levy-Nearest-Neighbors Bak-Sneppen Model
We study a random neighbor version of the Bak-Sneppen model, where "nearest
neighbors" are chosen according to a probability distribution decaying as a
power-law of the distance from the active site, P(x) \sim |x-x_{ac
}|^{-\omega}. All the exponents characterizing the self-organized critical
state of this model depend on the exponent \omega. As \omega tends to 1 we
recover the usual random nearest neighbor version of the model. The pattern of
results obtained for a range of values of \omega is also compatible with the
results of simulations of the original BS model in high dimensions. Moreover,
our results suggest a critical dimension d_c=6 for the Bak-Sneppen model, in
contrast with previous claims.Comment: To appear on Phys. Rev. E, Rapid Communication
Critical exponents of the anisotropic Bak-Sneppen model
We analyze the behavior of spatially anisotropic Bak-Sneppen model. We
demonstrate that a nontrivial relation between critical exponents tau and
mu=d/D, recently derived for the isotropic Bak-Sneppen model, holds for its
anisotropic version as well. For one-dimensional anisotropic Bak-Sneppen model
we derive a novel exact equation for the distribution of avalanche spatial
sizes, and extract the value gamma=2 for one of the critical exponents of the
model. Other critical exponents are then determined from previously known
exponent relations. Our results are in excellent agreement with Monte Carlo
simulations of the model as well as with direct numerical integration of the
new equation.Comment: 8 pages, three figures included with psfig, some rewriting, + extra
figure and table of exponent
Uncovering the topology of configuration space networks
The configuration space network (CSN) of a dynamical system is an effective
approach to represent the ensemble of configurations sampled during a
simulation and their dynamic connectivity. To elucidate the connection between
the CSN topology and the underlying free-energy landscape governing the system
dynamics and thermodynamics, an analytical soluti on is provided to explain the
heavy tail of the degree distribution, neighbor co nnectivity and clustering
coefficient. This derivation allows to understand the universal CSN network
topology observed in systems ranging from a simple quadratic well to the native
state of the beta3s peptide and a 2D lattice heteropolymer. Moreover CSN are
shown to fall in the general class of complex networks describe d by the
fitness model.Comment: 6 figure
Finding instabilities in the community structure of complex networks
The problem of finding clusters in complex networks has been extensively
studied by mathematicians, computer scientists and, more recently, by
physicists. Many of the existing algorithms partition a network into clear
clusters, without overlap. We here introduce a method to identify the nodes
lying ``between clusters'' and that allows for a general measure of the
stability of the clusters. This is done by adding noise over the weights of the
edges of the network. Our method can in principle be applied with any
clustering algorithm, provided that it works on weighted networks. We present
several applications on real-world networks using the Markov Clustering
Algorithm (MCL).Comment: 4 pages, 5 figure
The Anisotropic Bak-Sneppen model
The Bak-Sneppen model is shown to fall into a different universality class with the introduction of a preferred direction, mirroring the situation in spin systems. This is first demonstrated by numerical simulations and subsequently confirmed by analysis of the multitrait version of the model, which admits exact solutions in the extremes of zero and maximal anisotropy. For intermediate anisotropies, we show that the spatiotemporal evolution of the avalanche has a power law `tail' which passes through the system for any non-zero anisotropy but remains fixed for the isotropic case, thus explaining the crossover in behaviour. Finally, we identify the maximally anisotropic model which is more tractable and yet more generally applicable than the isotropic system
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