640 research outputs found
Multi-layer model for the web graph
This paper studies stochastic graph models of the WebGraph. We present a new model that describes the WebGraph as an ensemble of different regions generated by independent stochastic processes (in the spirit of a recent paper by Dill et al. [VLDB 2001]). Models such as the Copying Model [17] and Evolving Networks Model [3] are simulated and compared on several relevant measures such as degree and clique distribution
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
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
Slow energy relaxation of macromolecules and nano-clusters in solution
Many systems in the realm of nanophysics from both the living and inorganic
world display slow relaxation kinetics of energy fluctuations. In this paper we
propose a general explanation for such phenomenon, based on the effects of
interactions with the solvent. Within a simple harmonic model of the system
fluctuations, we demonstrate that the inhomogeneity of coupling to the solvent
of the bulk and surface atoms suffices to generate a complex spectrum of decay
rates. We show for Myoglobin and for a metal nano-cluster that the result is a
complex, non-exponential relaxation dynamics.Comment: 5 pages, 3 figure
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
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
The Local Minority Game
Ecologists and economists try to explain collective behavior in terms of
competitive systems of selfish individuals with the ability to learn from the
past. Statistical physicists have been investigating models which might
contribute to the understanding of the underlying mechanisms of these systems.
During the last three years one intuitive model, commonly referred to as the
Minority Game, has attracted broad attention. Powerful yet simple, the minority
game has produced encouraging results which can explain the temporal behaviour
of competitive systems. Here we switch the interest to phenomena due to a
distribution of the individuals in space. For analyzing these effects we modify
the Minority Game and the Local Minority Game is introduced. We study the
system both numerically and analytically, using the customary techniques
already developped for the ordinary Minority Game
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
- …