Algorithms for Coloring Quadtrees

We describe simple linear time algorithms for coloring the squares of balanced and unbalanced quadtrees so that no two adjacent squares are given the same color. If squares sharing sides are defined as adjacent, we color balanced quadtrees with three colors, and unbalanced quadtrees with four colors; these results are both tight, as some quadtrees require this many colors. If squares sharing corners are defined as adjacent, we color balanced or unbalanced quadtrees with six colors; for some quadtrees, at least five colors are required.Comment: 7 pages, 9 figure

Bond-Order Time Series Analysis for Detecting Reaction Events in Ab Initio Molecular Dynamics Simulations.

Ab initio molecular dynamics is able to predict novel reaction mechanisms by directly observing the individual reaction events that occur in simulation trajectories. In this article, we describe an approach for detecting reaction events from simulation trajectories using a physically motivated model based on time series analysis of ab initio bond orders. We found that applying a threshold to the bond order was insufficient for accurate detection, whereas peak finding on the first time derivative resulted in significantly improved accuracy. The model is trained on a reference set of reaction events representing the ideal result given unlimited computing resources. Our study includes two model systems: a heptanylium carbocation that undergoes hydride shifts and an unsaturated iron carbonyl cluster that features CO ligand migration and bridging behavior. The results indicate a high level of promise for this analysis approach to be used in mechanistic analysis of reactive AIMD simulations more generally

Quantum chemical studies of redox properties and conformational changes of a four-center iron CO2 reduction electrocatalyst.

The CO2 reduction electrocatalyst [Fe4N(CO)12]- (abbrev. 1-) reduces CO2 to HCO2- in a two-electron, one-proton catalytic cycle. Here, we employ ab initio calculations to estimate the first two redox potentials of 1- and explore the pathway of a side reaction involving CO dissociation from 13-. Using the BP86 density functional approximation, the redox potentials were computed with a root mean squared error of 0.15 V with respect to experimental data. High temperature Born-Oppenheimer molecular dynamics was employed to discover a reaction pathway of CO dissociation from 13- with a reaction energy of +10.6 kcal mol-1 and an activation energy of 18.8 kcal mol-1; including harmonic free energy terms, this yields ΔGsep = 1.4 kcal mol-1 for fully separated species and ΔG‡ = +17.4 kcal mol-1, indicating CO dissociation is energetically accessible at ambient conditions. The analogous dissociation pathway from 12- has a reaction energy of 22.1 kcal mol-1 and an activation energy of 22.4 kcal mol-1 (ΔGsep = 12.8 kcal mol-1, ΔG‡ = +18.1 kcal mol-1). Our computed harmonic vibrational analysis of [Fe4N(CO)11]3- or 23- reveals a distinct CO-stretching peak red-shifted from the main CO-stretching band, pointing to a possible vibrational signature of dissociation. Multi-reference CASSCF calculations are used to check the assumptions of the density functional approximations that were used to obtain the majority of the results

Avoidance of fisheries-induced evolution: management implications for catch selectivity and limit reference points

I examined how the fitness (r) associated with early- and late-maturing genotypes varies with fishing mortality (F) and age-/size-specific probability of capture. Life-history data on Newfoundland's northern Atlantic cod (Gadus morhua) allowed for the estimation of r for individuals maturing at 4 and 7 year in the absence of fishing. Catch selectivity data associated with four types of fishing gear (trap, gillnet, handline, otter trawl) were then incorporated to examine how r varied with gear type and with F. The resulting fitness functions were then used to estimate the F above which selection would favour early (4 year) rather than delayed (7 year) maturity. This evolutionarily-sensitive threshold, Fevol, identifies a limit reference point somewhat similar to those used to define overfishing (e.g., Fmsy, F0.1). Over-exploitation of northern cod resulted in fishing mortalities considerably greater than those required to effect evolutionary change. Selection for early maturity is reduced by the dome-shaped selectivities characteristic of fixed gears such as handlines (the greater the leptokurtosis, the lower the probability of a selection response) and enhanced by the knife-edged selectivities of bottom trawls. Strategies to minimize genetic change are consistent with traditional management objectives (e.g., yield maximization, population increase). Compliance with harvest control rules guided by evolutionarily-sensitive limit reference points, which may be achieved by adherence to traditional reference points such as Fmsy and F0.1, should be sufficient to minimize the probability of fisheries-induced evolution for commercially exploited species

Intrinsic Absorption in the Spectrum of NGC 7469: Simultaneous Chandra, FUSE, and STIS Observations

We present simultaneous X-ray, far-ultraviolet, and near-ultraviolet spectra of the Seyfert 1 galaxy NGC 7469 obtained with the Chandra X-Ray Observatory, the Far Ultraviolet Spectroscopic Explorer, and the Space Telescope Imaging Spectrograph on the Hubble Space Telescope. Previous non-simultaneous observations of this galaxy found two distinct UV absorption components, at -560 and -1900 km/s, with the former as the likely counterpart of the X-ray absorber. We confirm these two absorption components in our new UV observations, in which we detect prominent O VI, Ly alpha, N V, and C IV absorption. In our Chandra spectrum we detect O VIII emission, but no significant O VIII or O VII absorption. We also detect a prominent Fe K alpha emission line in the Chandra spectrum, as well as absorption due to hydrogen-like and helium-like neon, magnesium, and silicon at velocities consistent with the -560 km/s UV absorber. The FUSE and STIS data reveal that the H I and C IV column densities in this UV- and X-ray- absorbing component have increased over time, as the UV continuum flux decreased. We use measured H I, N V, C IV, and O VI column densities to model the photoionization state of both absorbers self-consistently. We confirm the general physical picture of the outflow in which the low velocity component is a highly ionized, high density absorber with a total column density of 10^20 cm^-2, located near the broad emission line region, although due to measurable columns of N V and C IV, we assign it a somewhat smaller ionization parameter than found previously, U~1. The high velocity UV component is of lower density, log N=18.6, and likely resides farther from the central engine as we find its ionization parameter to be U=0.08.Comment: Minor correction to abstract; STScI eprint #1683; 50 pages, incl. 19 figures, 4 tables; Accepted to Ap

Implications of fisheries-induced evolution for stock rebuilding and recovery

Worldwide depletion of fish stocks has led fisheries managers to become increasingly concerned about rebuilding and recovery planning. To succeed, factors affecting recovery dynamics need to be understood, including the role of fisheries-induced evolution. Here we investigate a stock's response to fishing followed by a harvest moratorium by analyzing an individual-based evolutionary model parameterized for Atlantic cod Gadus morhua from its northern range, representative of long-lived, late-maturing species. The model allows evolution of life-history processes including maturation, reproduction, and growth. It also incorporates environmental variability, phenotypic plasticity, and density-dependent feedbacks. Fisheries-induced evolution affects recovery in several ways. The first decades of recovery were dominated by demographic and density-dependent processes. Biomass rebuilding was only lightly influenced by fisheries-induced evolution, whereas other stock characteristics such as maturation age, spawning stock biomass, and recruitment were substantially affected, recovering to new demographic equilibria below their preharvest levels. This is because genetic traits took thousands of years to evolve back to preharvest levels, indicating that natural selection driving recovery of these traits is weaker than fisheries-induced selection was. Our results strengthen the case for proactive management of fisheries-induced evolution, as the restoration of genetic traits altered by fishing is slow and may even be impractical

Life-history evolution and elevated natural mortality in a population of Atlantic cod (Gadus morhua)

Fisheries-induced evolution has been hypothesized to delay the recovery of collapsed fish stocks through effects on their productivity. The cod stock in the southern Gulf of St. Lawrence (SGSL) collapsed in the early 1990s and has shown no recovery since then, due mainly to high natural mortality of adult cod. Age and size at maturation of SGSL cod decreased sharply over time in cohorts produced in the 1950s and 1960s, likely reflecting an evolutionary response to intensified fishing, and have remained low since then, despite severe reductions in fishing mortality over the past 15 years. A predicted consequence of early maturation is increased natural mortality due to higher costs to reproduction. Early maturation may be a cause of increases in natural mortality of SGSL cod in the 1970s but does not appear to be related to the much larger increases since then. Instead, the current high natural mortality of SGSL cod appears to be primarily a cause, rather than a consequence, of the continued early maturation in this population, now replacing fishing mortality as the agent of selection favouring early maturity. This striking example of the failure to reverse fisheries-induced evolution by relaxing fishing pressure emphasizes the need for management strategies that minimize the chances of harvest-induced genetic change

Intrinsic Absorption in the Spectrum of Mrk 279: Simultaneous Chandra, FUSE, and STIS Observations

We present a study of the intrinsic X-ray and far-ultraviolet absorption in the Seyfert 1.5 galaxy Markarian 279 using simultaneous observations from the Chandra X-ray Observatory, the Space Telescope Imaging Spectrograph aboard the Hubble Space Telescope, and the Far Ultraviolet Spectroscopic Explorer (FUSE). We also present FUSE observations made at three additional epochs. We detect the Fe K-alpha emission line in the Chandra spectrum, and its flux is consistent with the low X-ray continuum flux level of Mrk 279 at the time of the observation. Due to low signal-to-noise ratios in the Chandra spectrum, no O VII or O VIII absorption features are observable in the Chandra data, but the UV spectra reveal strong and complex absorption from HI and high-ionization species such as O VI, N V, and C IV, as well as from low-ionization species such as C III, N III, C II, and N II in some velocity components. The far-UV spectral coverage of the FUSE data provides information on high-order Lyman series absorption, which we use to calculate the optical depths and line and continuum covering fractions in the intrinsic HI absorbing gas in a self-consistent fashion. The UV continuum flux of Mrk 279 decreases by a factor of ~7.5 over the time spanning these observations and we discuss the implications of the response of the absorption features to this change. From arguments based on the velocities, profile shapes, covering fractions and variability of the UV absorption, we conclude that some of the absorption components, particularly those showing prominent low-ionization lines, are likely associated with the host galaxy of Mrk 279, and possibly with its interaction with a close companion galaxy, while the remainder arises in a nuclear outflow.Comment: To appear in 2004 May ApJS; double-column format; 58 pages, incl. 29 figures, 9 tables; minor changes to tex

The role of Kelvin-Helmholtz instability in the internal structure of relativistic outflows. The case of the jet in 3C 273

Relativistic outflows represent one of the best-suited tools to probe the physics of AGN. Numerical modelling of internal structure of the relativistic outflows on parsec scales provides important clues about the conditions and dynamics of the material in the immediate vicinity of the central black holes in AGN. We investigate possible causes of the structural patterns and regularities observed in the parsec-scale jet of the well-known quasar 3C 273. We present here the results from a 3D relativistic hydrodynamics numerical simulation based on the parameters given for the jet by Lobanov & Zensus (2001), and one in which the effects of jet precession and the injection of discrete components have been taken into account. We compare the model with the structures observed in 3C 273 using very long baseline interferometry and constrain the basic properties of the flow. We find growing perturbation modes in the simulation with similar wavelengths to those observed, but with a different set of wave speeds and mode identification. If the observed longest helical structure is produced by the precession of the flow, longer precession periods should be expected. Our results show that some of the observed structures could be explained by growing Kelvin-Helmholtz instabilities in a slow moving region of the jet. However, we point towards possible errors in the mode identification that show the need of more complete linear analysis in order to interpret the observations. We conclude that, with the given viewing angle, superluminal components and jet precession cannot explain the observed structures.Comment: Accepted for publication in Astronomy & Astrophysics. 14 pages. Higher resolution plots available on request to [email protected] and at http://www.mpifr-bonn.mpg.de/staff/mperuch

AGN feedback and iron enrichment in the powerful radio galaxy, 4C+55.16

We present a detailed X-ray analysis of 4C+55.16, an unusual and interesting radio galaxy, located at the centre of a cool core cluster of galaxies. 4C+55.16 is X-ray bright (L(cluster)~10^45 erg/s), radio powerful, and shows clear signs of interaction with the surrounding intracluster medium. By combining deep Chandra (100 ks) with 1.4 GHz VLA observations, we find evidence of multiple outbursts from the central AGN, providing enough energy to offset cooling of the ICM (P_bubbles=6.7x10^44 erg/s). Furthermore, 4C+55.16 has an unusual intracluster iron distribution showing a plume-like feature rich in Fe L emission that runs along one of the X-ray cavities. The excess of iron associated with the plume is around 10^7M_sol. The metal abundances are consistent with being Solar-like, indicating that both SNIa and SNII contribute to the enrichment. The plume and southern cavity form a region of cool metal-rich gas, and at the edge of this region, there is a clear discontinuity in temperature (from kT~2.5 keV to kT~5.0 keV), metallicity (from ~0.4 solar to 0.8 solar), and surface brightness distribution, consistent with it being caused by a cold front. However, we also suggest that this discontinuity could be caused by cool metal-rich gas being uplifted from the central AGN along one of its X-ray cavities.Comment: 12 pages, 11 figures, 1 table, Accepted to MNRAS (minor revision