Complex trajectory method in time-dependent WKB

We present a significant improvement to a time-dependent WKB (TDWKB) formulation developed by Boiron and Lombardi [JCP {\bf108}, 3431 (1998)] in which the TDWKB equations are solved along classical trajectories that propagate in the complex plane. Boiron and Lombardi showed that the method gives very good agreement with the exact quantum mechanical result as long as the wavefunction does not exhibit interference effects such as oscillations and nodes. In this paper we show that this limitation can be overcome by superposing the contributions of crossing trajectories. We also demonstrate that the approximation improves when incorporating higher order terms in the expansion. These improvements could make the TDWKB formulation a competitive alternative to current time-dependent semiclassical methods

An exactly solvable model for driven dissipative systems

We introduce a solvable stochastic model inspired by granular gases for driven dissipative systems. We characterize far from equilibrium steady states of such systems through the non-Boltzmann energy distribution and compare different measures of effective temperatures. As an example we demonstrate that fluctuation-dissipation relations hold, however with an effective temperature differing from the effective temperature defined from the average energy.Comment: Some further clarifications. No changes in results or conclusion

Cooperative Wireless Sensor Network Positioning via Implicit Convex Feasibility

We propose a distributed positioning algorithm to estimate the unknown positions of a number of target nodes, given distance measurements between target nodes and between target nodes and number of reference nodes at known positions. Based on a geometric interpretation, we formulate the positioning problem as an implicit convex feasibility problem in which some of the sets depend on the unknown target positions, and apply a parallel projection onto convex sets approach to estimate the unknown target node positions. The proposed technique is suitable for parallel implementation in which every target node in parallel can update its position and share the estimate of its location with other targets. We mathematically prove convergence of the proposed algorithm. Simulation results reveal enhanced performance for the proposed approach compared to available techniques based on projections, especially for sparse networks

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia)

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the 'isolation with migration' model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide–resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an “action at a distance” on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps

Haploinsufficiency of Activation-Induced Deaminase for Antibody Diversification and Chromosome Translocations both In Vitro and In Vivo

The humoral immune response critically relies on the secondary diversification of antibodies. This diversification takes places through somatic remodelling of the antibody genes by two molecular mechanisms, Class Switch Recombination (CSR) and Somatic Hypermutation (SHM). The enzyme Activation Induced Cytidine Deaminase (AID) initiates both SHM and CSR by deaminating cytosine residues on the DNA of immunoglobulin genes. While crucial for immunity, AID-catalysed deamination is also the triggering event for the generation of lymphomagenic chromosome translocations. To address whether restricting the levels of AID expression in vivo contributes to the regulation of its function, we analysed mice harbouring a single copy of the AID gene (AID+/−). AID+/− mice express roughly 50% of normal AID levels, and display a mild hyperplasia, reminiscent of AID deficient mice and humans. Moreover, we found that AID+/− cells have an impaired competence for CSR and SHM, which indicates that AID gene dose is limiting for its physiologic function. We next evaluated the impact of AID reduction in AID+/− mice on the generation of chromosome translocations. Our results show that the frequency of AID-promoted c-myc/IgH translocations is reduced in AID+/− mice, both in vivo and in vitro. Therefore, AID is haploinsufficient for antibody diversification and chromosome translocations. These findings suggest that limiting the physiologic levels of AID expression can be a regulatory mechanism that ensures an optimal balance between immune proficiency and genome integrity

Optimized Spectral Energy Distribution for Seyfert Galaxies

The temperature predicted by photoionization models for the Narrow Line Region of Seyfert 2 galaxies is lower than the value inferred from the observed [O III] {\lambda}4363A/{\lambda}5007A line ratio. We explore the possibility of considering a harder ionizing continuum than typically assumed. The spectral ionizing energy distribution, which can generate the observed {\lambda}4363A/{\lambda}5007A ratio, is characterized by a secondary continuum peak at 200 eV.Comment: 17 pages, 4 figures, accepted for publication in Revista Mexicana de Astronom\'ia y Astrof\'isic

An Extended Eddy-Diffusivity Mass-Flux Scheme for Unified Representation of Subgrid-Scale Turbulence and Convection

Large-scale weather forecasting and climate models are beginning to reach horizontal resolutions of kilometers, at which common assumptions made in existing parameterization schemes of subgrid-scale turbulence and convection—such as that they adjust instantaneously to changes in resolved-scale dynamics—cease to be justifiable. Additionally, the common practice of representing boundary-layer turbulence, shallow convection, and deep convection by discontinuously different parameterizations schemes, each with its own set of parameters, has contributed to the proliferation of adjustable parameters in large-scale models. Here we lay the theoretical foundations for an extended eddy-diffusivity mass flux (EDMF) scheme that has explicit time-dependence and memory of subgrid-scale variables and is designed to represent all subgrid-scale turbulence and convection, from boundary layer dynamics to deep convection, in a unified manner. Coherent up- and downdrafts in the scheme are represented as prognostic plumes that interact with their environment and potentially with each other through entrainment and detrainment. The more isotropic turbulence in their environment is represented through diffusive fluxes, with diffusivities obtained from a turbulence kinetic energy budget that consistently partitions turbulence kinetic energy between plumes and environment. The cross-sectional area of up- and downdrafts satisfies a prognostic continuity equation, which allows the plumes to cover variable and arbitrarily large fractions of a large-scale grid box and to have life cycles governed by their own internal dynamics. Relatively simple preliminary proposals for closure parameters are presented and are shown to lead to a successful simulation of shallow convection, including a time-dependent life cycle