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

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

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

Origin of passivation in hole-selective transition metal oxides for crystalline silicon heterojunction solar cells

Transition metal oxides (TMOs) have recently demonstrated to be a good alternative to boron/phosphorous doped layers in crystalline silicon heterojunction solar cells. In this work, the interface between n-type c-Si (n-Si) and three thermally evaporated TMOs (MoO3, WO3, and V2O5) was investigated by transmission electron microscopy, secondary ion-mass, and x-ray photoelectron spectroscopy. For the oxides studied, surface passivation of n-Si was attributed to an ultra-thin (1.9–2.8 nm) SiOx~1.5 interlayer formed by chemical reaction, leaving oxygen-deficient species (MoO, WO2, and VO2) as by-products. Carrier selectivity was also inferred from the inversion layer induced on the n-Si surface, a result of Fermi level alignment between two materials with dissimilar electrochemical potentials (work function difference ¿¿ = 1 eV). Therefore, the hole-selective and passivating functionality of these TMOs, in addition to their ambient temperature processing, could prove an effective means to lower the cost and simplify solar cell processing.Postprint (author's final draft

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