Andrzej Pekalski networks of scientific interests with internal degrees of freedom through self-citation analysis

Old and recent theoretical works by Andrzej Pekalski (APE) are recalled as possible sources of interest for describing network formation and clustering in complex (scientific) communities, through self-organisation and percolation processes. Emphasis is placed on APE self-citation network over four decades. The method is that used for detecting scientists field mobility by focusing on author's self-citation, co-authorships and article topics networks as in [1,2]. It is shown that APE's self-citation patterns reveal important information on APE interest for research topics over time as well as APE engagement on different scientific topics and in different networks of collaboration. Its interesting complexity results from "degrees of freedom" and external fields leading to so called internal shock resistance. It is found that APE network of scientific interests belongs to independent clusters and occurs through rare or drastic events as in irreversible "preferential attachment processes", similar to those found in usual mechanics and thermodynamics phase transitions.Comment: 7 pages, 1 table, 44 references, submitted to Int J Mod Phys

The Structure of Isothermal, Self-gravitating Gas Spheres for Softened Gravity

A theory for the structure of isothermal, self-gravitating gas spheres in pressure equilibrium in a softened gravitational field is developed. The one parameter spline softening proposed by Hernquist & Katz (1989) is used. We show that the addition of this extra scale parameter implies that the set of equilibrium solutions constitute a one-parameter family, rather than the one and only one isothermal sphere solution for Newtonian gravity. We demonstrate the perhaps somewhat surprising result that for any finite choice of softening length and temperature, it is possible to deposit an arbitrarily large mass of gas in pressure equilibrium and with a non-singular density distribution inside of r_0 for any r_0 > 0. The theoretical predictions of our models are compared with the properties of the small, massive, quasi-isothermal gas clumps which typically form in numerical Tree-SPH simulations of 'passive' galaxy formation of Milky Way sized galaxies. We find reasonable agreement despite the neglect of rotational support in the models. We comment on whether the hydrodynamical resolution in our numerical simulation of galaxy formation is sufficient, and finally we conclude that one should be cautious, when comparing results of numerical simulations involving gravitational softening and hydrodynamical smoothing, with reality.Comment: 22 pages Latex + 12 figure

The Observability of Metal Lines Associated with the Lyman-alpha Forest

We develop a prescription for characterizing the strengths of metal lines associated with Lyman-alpha forest absorbers (LYFAs) of a given neutral hydrogen column density N_HI and metallicity [Fe/H]. This Line Observability Index (LOX) is line-specific and translates, for weak lines, into a measure of the equivalent width. It can be evaluated quickly for thousands of transitions within the framework of a given model of the Lyman-alpha forest, providing a ranking of the lines in terms of their strengths and enabling model builders to select the lines that should be detectable in observed spectra of a given resolution and signal-to-noise ratio. We compute the LOX for a large number of elements and transitions in two cosmological models of the Lyman-alpha forest at z=3 derived from a hydrodynamic simulation of structure formation, and we discuss how the LOX depends on redshift and on model parameters such as the mean baryonic density and radiation field. We find that the OVI (1032,1038) doublet is the best probe of the metallicity in low column density LYFAs N_{HI} \approx 10^{14.5} cm^{-2}). Metallicities down to [O/H] \sim -3 ([Fe/H] \sim -3.5 with the assumed [O/Fe] ratio) yield OVI absorption features that should be detectable in current high-quality spectra, provided that the expected position of the OVI feature is not contaminated by HI absorption. The strongest transitions in lower ionisation states of oxygen are OV(630), OIV(788), and OIII(833), and are likely to be detected with next generation UV instruments. Of the lines with rest wavelengths \lambda_r > 1216, which can potentially be observed redwards of the \lya forest, the CIV(1548,1551) doublet is expected to dominate in all LYFAs, regardless of the value of N_HI.Comment: Substantially revised version: larger line database, additional cosmological model analyzed. Accepted for Ap

Studying the WHIM Content of the Galaxy Large-Scale Structures along the Line of Sight to H 2356-309

We make use of a 500ks Chandra HRC-S/LETG spectrum of the blazar H2356-309, combined with a lower S/N spectrum of the same target, to search for the presence of warm-hot absorbing gas associated with two Large-Scale Structures (LSSs) crossed by this sightline at z=0.062 (the Pisces-Cetus Supercluster, PCS) and at z=0.128 ("Farther Sculptor Wall", FSW). No statistically significant (>=3sigma) individual absorption is detected from any of the strong He- or H-like transitions of C, O and Ne at the redshifts of the structures. However we are still able to constrain the physical and geometrical parameters of the associated putative absorbing gas, by performing joint spectral fit of marginal detections and upper limits of the strongest expected lines with our self-consistent hybrid ionization WHIM spectral model. At the redshift of the PCS we identify a warm phase with logT=5.35_-0.13^+0.07 K and log N_H =19.1+/-0.2 cm^-2 possibly coexisting with a hotter and less significant phase with logT=6.9^+0.1_-0.8 K and log N_H=20.1^+0.3_-1.7 cm^-2 (1sigma errors). For the FSW we estimate logT=6.6_-0.2^+0.1 K and log N_H=19.8_-0.8^+0.4 cm^-2. Our constraints allow us to estimate the cumulative number density per unit redshifts of OVII WHIM absorbers. We also estimate the cosmological mass density obtaining Omega_b(WHIM)=(0.021^+0.031_-0.018) (Z/Z_sun)^-1, consistent with the mass density of the intergalactic 'missing baryons' for high metallicities.Comment: 29 pages, 8 figures, 4 tables. Accepted for publication in Ap

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

Minority and mode conversion heating in (3He)-H JET plasma

Radio frequency (RF) heating experiments have recently been conducted in JET (He-3)-H plasmas. This type of plasmas will be used in ITER's non-activated operation phase. Whereas a companion paper in this same PPCF issue will discuss the RF heating scenario's at half the nominal magnetic field, this paper documents the heating performance in (He-3)-H plasmas at full field, with fundamental cyclotron heating of He-3 as the only possible ion heating scheme in view of the foreseen ITER antenna frequency bandwidth. Dominant electron heating with global heating efficiencies between 30% and 70% depending on the He-3 concentration were observed and mode conversion (MC) heating proved to be as efficient as He-3 minority heating. The unwanted presence of both He-4 and D in the discharges gave rise to 2 MC layers rather than a single one. This together with the fact that the location of the high-field side fast wave (FW) cutoff is a sensitive function of the parallel wave number and that one of the locations of the wave confluences critically depends on the He-3 concentration made the interpretation of the results, although more complex, very interesting: three regimes could be distinguished as a function of X[He-3]: (i) a regime at low concentration (X[He-3] < 1.8%) at which ion cyclotron resonance frequency (ICRF) heating is efficient, (ii) a regime at intermediate concentrations (1.8 < X[He-3] < 5%) in which the RF performance is degrading and ultimately becoming very poor, and finally (iii) a good heating regime at He-3 concentrations beyond 6%. In this latter regime, the heating efficiency did not critically depend on the actual concentration while at lower concentrations (X[He-3] < 4%) a bigger excursion in heating efficiency is observed and the estimates differ somewhat from shot to shot, also depending on whether local or global signals are chosen for the analysis. The different dynamics at the various concentrations can be traced back to the presence of 2 MC layers and their associated FW cutoffs residing inside the plasma at low He-3 concentration. One of these layers is approaching and crossing the low-field side plasma edge when 1.8 < X[He-3] < 5%. Adopting a minimization procedure to correlate the MC positions with the plasma composition reveals that the different behaviors observed are due to contamination of the plasma. Wave modeling not only supports this interpretation but also shows that moderate concentrations of D-like species significantly alter the overall wave behavior in He-3-H plasmas. Whereas numerical modeling yields quantitative information on the heating efficiency, analytical work gives a good description of the dominant underlying wave interaction physics

Equilibration processes in the Warm-Hot Intergalactic Medium

The Warm-Hot Intergalactic Medium (WHIM) is thought to contribute about 40-50 % to the baryonic budget at the present evolution stage of the universe. The observed large scale structure is likely to be due to gravitational growth of density fluctuations in the post-inflation era. The evolving cosmic web is governed by non-linear gravitational growth of the initially weak density fluctuations in the dark energy dominated cosmology. Non-linear structure formation, accretion and merging processes, star forming and AGN activity produce gas shocks in the WHIM. Shock waves are converting a fraction of the gravitation power to thermal and non-thermal emission of baryonic/leptonic matter. They provide the most likely way to power the luminous matter in the WHIM. The plasma shocks in the WHIM are expected to be collisionless. Collisionless shocks produce a highly non-equilibrium state with anisotropic temperatures and a large differences in ion and electron temperatures. We discuss the ion and electron heating by the collisionless shocks and then review the plasma processes responsible for the Coulomb equilibration and collisional ionisation equilibrium of oxygen ions in the WHIM. MHD-turbulence produced by the strong collisionless shocks could provide a sizeable non-thermal contribution to the observed Doppler parameter of the UV line spectra of the WHIM.Comment: 13 pages, 4 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 8; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke