26,503 research outputs found
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions
Genetic regulatory networks (GRNs) have been widely studied, yet there is a
lack of understanding with regards to the final size and properties of these
networks, mainly due to no network currently being complete. In this study, we
analyzed the distribution of GRN structural properties across a large set of
distinct prokaryotic organisms and found a set of constrained characteristics
such as network density and number of regulators. Our results allowed us to
estimate the number of interactions that complete networks would have, a
valuable insight that could aid in the daunting task of network curation,
prediction, and validation. Using state-of-the-art statistical approaches, we
also provided new evidence to settle a previously stated controversy that
raised the possibility of complete biological networks being random and
therefore attributing the observed scale-free properties to an artifact
emerging from the sampling process during network discovery. Furthermore, we
identified a set of properties that enabled us to assess the consistency of the
connectivity distribution for various GRNs against different alternative
statistical distributions. Our results favor the hypothesis that highly
connected nodes (hubs) are not a consequence of network incompleteness.
Finally, an interaction coverage computed for the GRNs as a proxy for
completeness revealed that high-throughput based reconstructions of GRNs could
yield biased networks with a low average clustering coefficient, showing that
classical targeted discovery of interactions is still needed.Comment: 28 pages, 5 figures, 12 pages supplementary informatio
Geometrical resonance in spatiotemporal systems
We generalize the concept of geometrical resonance to perturbed sine-Gordon,
Nonlinear Schrödinger and Complex Ginzburg-Landau equations. Using this
theory we can control different dynamical patterns. For instance, we can
stabilize breathers and oscillatory patterns of large amplitudes successfully
avoiding chaos. On the other hand, this method can be used to suppress
spatiotemporal chaos and turbulence in systems where these phenomena are
already present. This method can be generalized to even more general
spatiotemporal systems.Comment: 2 .epl files. Accepted for publication in Europhysics Letter
Non-Markovian Quantum Optics with Three-Dimensional State-Dependent Optical Lattices
Quantum emitters coupled to structured photonic reservoirs experience
unconventional individual and collective dynamics emerging from the interplay
between dimensionality and non-trivial photon energy dispersions. In this work,
we systematically study several paradigmatic three dimensional structured baths
with qualitative differences in their bath spectral density. We discover
non-Markovian individual and collective effects absent in simplified
descriptions, such as perfect subradiant states or long-range anisotropic
interactions. Furthermore, we show how to implement these models using only
cold atoms in state-dependent optical lattices and show how this unconventional
dynamics can be observed with these systems.Comment: 39 pages, 17 figures. Accepted versio
Purely Long-Range Coherent Interactions in Two-Dimensional Structured Baths
In this work we study the quantum dynamics emerging when quantum emitters
exchange excitations with a two-dimensional bosonic bath with hexagonal
symmetry. We show that a single quantum emitter spectrally tuned to the middle
of the band relaxes following a logarithmic law in time due to the existence of
a singular point with vanishing density of states, i.e., the Dirac point.
Moreover, when several emitters are coupled to the bath at that frequency,
long-range coherent interactions between them appear which decay inversely
proportional to their distance without exponential attenuation. We analyze both
the finite and infinite system situation using both perturbative and
non-perturbative methods.Comment: 18 pages, 7 figures. Text restructured. Extended discussion on
experimental consideration
Interplay of Coulomb and electron-phonon interactions in graphene
We consider mutual effect of the electron-phonon and strong Coulomb
interactions on each other by summing up leading logarithmic corrections via
the renormalization group approach. We find that the Coulomb interaction
enhances electron coupling to the intervalley A1 optical phonons, but not to
the intravalley E2 phonons
ALICE experience with GEANT4
Since its release in 1999, the LHC experiments have been evaluating GEANT4 in
view of adopting it as a replacement for the obsolescent GEANT3 transport
MonteCarlo. The ALICE collaboration has decided to perform a detailed physics
validation of elementary hadronic processes against experimental data already
used in international benchmarks. In one test, proton interactions on different
nuclear targets have been simulated, and the distribution of outgoing particles
has been compared to data. In a second test, penetration of quasi-monoenergetic
low energy neutrons through a thick shielding has been simulated and again
compared to experimental data. In parallel, an effort has been put on the
integration of GEANT4 in the AliRoot framework. An overview of the present
status of ALICE GEANT4 simulation and the remaining problems will be presented.
This document will describe in detail the results of these tests, together with
the improvements that the GEANT4 team has made to the program as a result of
the feedback received from the ALICE collaboration. We will also describe the
remaining problems that have been communicated to GEANT4 but not yet addressed.Comment: 8 pages, 12 figures, for the CHEP03 conference proceeding
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