1,403 research outputs found
Three-dimensional numerical simulation of 1GeV/Nucleon U92+ impact against atomic hydrogen
The impact of 1GeV/Nucleon U92+ projectiles against atomic hydrogen is
studied by direct numerical resolution of the time-dependent wave equation for
the atomic electron on a three-dimensional Cartesian lattice. We employ the
fully relativistic expressions to describe the electromagnetic fields created
by the incident ion. The wave equation for the atom interacting with the
projectile is carefully derived from the time-dependent Dirac equation in order
to retain all the relevant terms.Comment: 12 pages and 7 figures included in the tex
Phase transitions in systems of self-propelled agents and related network models
An important characteristic of flocks of birds, school of fish, and many
similar assemblies of self-propelled particles is the emergence of states of
collective order in which the particles move in the same direction. When noise
is added into the system, the onset of such collective order occurs through a
dynamical phase transition controlled by the noise intensity. While originally
thought to be continuous, the phase transition has been claimed to be
discontinuous on the basis of recently reported numerical evidence. We address
this issue by analyzing two representative network models closely related to
systems of self-propelled particles. We present analytical as well as numerical
results showing that the nature of the phase transition depends crucially on
the way in which noise is introduced into the system.Comment: Four pages, four figures. Submitted to PR
Perturbation propagation in random and evolved Boolean networks
We investigate the propagation of perturbations in Boolean networks by
evaluating the Derrida plot and modifications of it. We show that even small
Random Boolean Networks agree well with the predictions of the annealed
approximation, but non-random networks show a very different behaviour. We
focus on networks that were evolved for high dynamical robustness. The most
important conclusion is that the simple distinction between frozen, critical
and chaotic networks is no longer useful, since such evolved networks can
display properties of all three types of networks. Furthermore, we evaluate a
simplified empirical network and show how its specific state space properties
are reflected in the modified Derrida plots.Comment: 10 pages, 8 figure
The dynamics of critical Kauffman networks under asynchronous stochastic update
We show that the mean number of attractors in a critical Boolean network
under asynchronous stochastic update grows like a power law and that the mean
size of the attractors increases as a stretched exponential with the system
size. This is in strong contrast to the synchronous case, where the number of
attractors grows faster than any power law.Comment: submitted to PR
Regulation of Ace2-dependent genes requires components of the PBF complex in schizosaccharomyces pombe
The division cycle of unicellular yeasts is completed with the activation of a cell separation program that results in the dissolution of the septum assembled during cytokinesis between the 2 daughter cells, allowing them to become independent entities. Expression of the eng1+ and agn1+ genes, encoding the hydrolytic enzymes responsible for septum degradation, is activated at the end of each cell cycle by the transcription factor Ace2. Periodic ace2+ expression is regulated by the transcriptional complex PBF (PCB Binding Factor), composed of the forkhead-like proteins Sep1 and Fkh2 and the MADS box-like protein Mbx1. In this report, we show that Ace2-dependent genes contain several combinations of motifs for Ace2 and PBF binding in their promoters. Thus, Ace2, Fkh2 and Sep1 were found to bind in vivo to the eng1+ promoter. Ace2 binding was coincident with maximum level of eng1+ expression, whereas Fkh2 binding was maximal when mRNA levels were low, supporting the notion that they play opposing roles. In addition, we found that the expression of eng1+ and agn1+ was differentially affected by mutations in PBF components. Interestingly, agn1+ was a major target of Mbx1, since its ectopic expression resulted in the suppression of Mbx1 deletion phenotypes. Our results reveal a complex regulation system through which the transcription factors Ace2, Fkh2, Sep1 and Mbx1 in combination control the expression of the genes involved in separation at the end of the cell division cycle
Canalizing Kauffman networks: non-ergodicity and its effect on their critical behavior
Boolean Networks have been used to study numerous phenomena, including gene
regulation, neural networks, social interactions, and biological evolution.
Here, we propose a general method for determining the critical behavior of
Boolean systems built from arbitrary ensembles of Boolean functions. In
particular, we solve the critical condition for systems of units operating
according to canalizing functions and present strong numerical evidence that
our approach correctly predicts the phase transition from order to chaos in
such systems.Comment: to be published in PR
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