The emergence of antibiotic resistance among nosocomial pathogens has reemphasized the need for effective infection control strategies. The spread of resistant pathogens within hospital settings proceeds along various routes of transmission and is characterized by large fluctuations in prevalence, which are typical for small populations. Identification of the most important route of colonization (exogenous by cross-transmission or endogenous caused by the selective pressure of antibiotics) is important for the design of optimal infection control strategies. Such identification can be based on a combination of epidemiological surveillance and costly and laborious as well as time-consuming methods of genotyping. Furthermore, analysis of the effects of interventions is hampered by the natural fluctuations in prevalence. To overcome these problems, we introduce a mathematical algorithm based on a Markov chain description. The input is longitudinal prevalence data only. The output is estimates of the key parameters characterizing the two colonization routes. The algorithm is tested on two longitudinal surveillance data sets of intensive care patients. The quality of the estimates is determined by comparing them to accurate estimates based on additional information obtained by genotyping. The results warrant optimism that this algorithm may help to quantify transmission dynamics and can be used to evaluate the effects of infection control interventions more carefully.

In low-mass binary systems, mass transfer is likely to occur via a slow and dense stellar wind when one of the stars is in the asymptotic giant branch (AGB) phase. Observations show that many binaries that have undergone AGB mass transfer have orbital periods of 1-10 yr, at odds with the predictions of binary population synthesis models. In this paper we investigate the mass-accretion efficiency and angular-momentum loss via wind mass transfer in AGB binary systems and we use these quantities to predict the evolution of the orbit. To do so, we perform 3D hydrodynamical simulations of the stellar wind lost by an AGB star in the time-dependent gravitational potential of a binary system, using the AMUSE framework. We approximate the thermal evolution of the gas by imposing a simple effective cooling balance and we vary the orbital separation and the velocity of the stellar wind. We find that for wind velocities larger than the relative orbital velocity of the system the flow is described by the Bondi-Hoyle-Lyttleton approximation and the angularmomentum loss is modest, which leads to an expansion of the orbit. On the other hand, for low wind velocities an accretion disk is formed around the companion and the accretion efficiency as well as the angular-momentum loss are enhanced, implying that the orbit will shrink. We find that the transfer of angular momentum from the binary orbit to the outflowing gas occurs within a few orbital separations from the center of mass of the binary. Our results suggest that the orbital evolution of AGB binaries can be predicted as a function of the ratio of the terminal wind velocity to the relative orbital velocity of the system, v ∞ /v orb . Our results can provide insight into the puzzling orbital periods of post-AGB binaries and also suggest that the number of stars entering into the common-envelope phase will increase. The latter can have significant implications for the expected formation rates of the end products of low-mass binary evolution, such as cataclysmic binaries, type Ia supernova and double white-dwarf mergers.

We introduce the publicly available code sphray, a smoothed particle hydrodynamics (SPH) ray tracer designed to solve the 3D, time‐dependent, radiative transfer equation for cosmological density fields. The SPH nature of sphray makes the incorporation of separate hydrodynamics and gravity solvers very natural. sphray relies on a Monte Carlo (MC) ray‐tracing scheme that does not interpolate the SPH particles on to a grid but instead integrates directly through the SPH kernels. Given an arbitrary (series of) SPH density field(s) and a description of the sources of ionizing radiation, the code will calculate the non‐equilibrium ionization and temperature state of hydrogen (H i, H ii) and helium (He i, He ii, He iii). The sources of radiation can include point‐like objects, diffuse recombination radiation, and a background field from outside the computational volume. The MC ray‐tracing implementation allows for the quick introduction of new physics and is parallelization‐friendly. A quick Axis Aligned Bounding Box (AABB) test taken from computer graphics applications allows for the acceleration of the ray‐tracing component. We present the algorithms used in sphray and verify the code by performing the test problems detailed in the recent Radiative Transfer Comparison Project of Iliev et. al. The source code for sphray and example SPH density fields are made available on a companion website (http://www.sphray.org).

CO observations in active galactic nuclei and star-bursts reveal high kinetic temperatures. Those environments are thought to be very turbulent due to dynamic phenomena such as outflows and high supernova rates. We investigate the effect of mechanical heating on atomic fine-structure and molecular lines, and their ratios. We try to use those ratios as a diagnostic to constrain the amount of mechanical heating in an object and also study its significance on estimating the H 2 mass. Equilibrium photo-dissociation models (PDRs hereafter) were used to compute the thermal and chemical balance for the clouds. The equilibria were solved for numerically using the optimized version of the Leiden PDR-XDR code. Large velocity gradient calculations were done as post-processing on the output of the PDR models using RADEX. High-J CO line ratios are very sensitive to mechanical heating (Γ mech hereafter). Emission becomes at least one order of magnitude brighter in clouds with n ∼ 10 5 cm −3 and a star formation rate of 1 M yr −1 (corresponding to Γ mech = 2 × 10 −19 erg cm −3 s −1 ). Emission of low-J CO lines is not as sensitive to Γ mech , but they do become brighter in response to Γ mech . Generally, for all of the lines we considered, Γ mech increases excitation temperatures and decreases the optical depth at the line centre. Hence line ratios are also affected, strongly in some cases. Ratios involving HCN are a good diagnostic for Γ mech , where the HCN(1-0)/CO(1-0) increases from 0.06 to 0.25 and the HCN(1-0)/HCO + (1-0) increase from 0.15 to 0.5 for amounts of Γ mech equivelent to 5% of the surface heating rate. Both ratios increase to more than 1 for higher Γ mech , as opposed to being much less than unity in pure PDRs. The first major conclusion is that low-J to high-J intensity ratios will yield a good estimate of the mechanical heating rate (as opposed to only low-J ratios). The second one is that the mechanical heating rate should be taken into account when determing A V or equivalently N H , and consequently the cloud mass. Ignoring Γ mech will also lead to large errors in density and radiation field estimates.

Context. Multitransition CO observations of galaxy centers have revealed that significant fractions of the dense circumnuclear gas have high kinetic temperatures, which are hard to explain by pure photon excitation, but may be caused by dissipation of turbulent energy. Aims. We aim to determine to what extent mechanical heating should be taken into account while modeling PDRs. To this end, the effect of dissipated turbulence on the thermal and chemical properties of PDRs is explored. Methods. Clouds are modeled as 1D semi-infinite slabs whose thermal and chemical equilibrium is solved for using the Leiden PDR-XDR code, where mechanical heating is added as a constant term throughout the cloud. An extensive parameter space in hydrogen gas density, FUV radiation field and mechanical heating rate is considered, covering almost all possible cases for the ISM relevant to the conditions that are encountered in galaxies. Effects of mechanical heating on the temperature profiles, column densities of CO and H 2 O and column density ratios of HNC, HCN and HCO + are discussed. Results. In a steady-state treatment, mechanical heating seems to play an important role in determining the kinetic temperature of the gas in molecular clouds. Particularly in high-energy environments such as starburst galaxies and galaxy centers, model gas temperatures are underestimated by at least a factor of two if mechanical heating is ignored. The models also show that CO, HCN and H 2 O column densities increase as a function of mechanical heating. The HNC/HCN integrated column density ratio shows a decrease by a factor of at least two in high density regions with n ∼ 10 5 cm −3 , whereas that of HCN/HCO + shows a strong dependence on mechanical heating for this same density range, with boosts of up to three orders of magnitude. Conclusions. The effects of mechanical heating cannot be ignored in studies of the molecular gas excitation whenever the ratio of the star formation rate to the gas density (SFR/n 3/2 ) is close to, or exceeds, 7 × 10 −6 M yr −1 cm 4.5 . If mechanical heating is not included, predicted column densities (such as those of CO) are underestimated, sometimes (as in the case of HCN and HCO + ) even by a few orders of magnitude. As a lower bound to its importance, we determined that it has non-negligible effects already when mechanical heating is as little as 1% of the UV heating in a PDR.

Quasar feedback has most likely a substantial but only partially understood impact on the formation of structure in the universe. A potential direct probe of this feedback mechanism is the Sunyaev‐Zel'dovich (SZ) effect: energy emitted from quasar heats the surrounding intergalactic medium and induces a distortion in the microwave background radiation passing through the region. Here, we examine the formation of such hot quasar bubbles using a cosmological hydrodynamic simulation which includes a self‐consistent treatment of black hole growth and associated feedback, along with radiative gas cooling and star formation. From this simulation, we construct microwave maps of the resulting SZ effect around black holes with a range of masses and redshifts. The size of the temperature distortion scales approximately with black hole mass and accretion rate, with a typical amplitude up to a few micro‐Kelvin on angular scales around 10 arcsec. We discuss prospects for the direct detection of this signal with current and future single‐dish and interferometric observations, including Atacama Large Millimetre Array (ALMA) and Cornell Caltech Atacama Telescope (CCAT). These measurements will be challenging, but will allow us to characterize the evolution and growth of supermassive black holes and the role of their energy feedback on galaxy formation.

Aims. We perform a simulation using the Astrophysical Multipurpose Software Environment of the Orion Trapezium star cluster in which the evolution of the stars and the dynamics of planetary systems are taken into account. Methods. The initial conditions from earlier simulations were selected in which the size and mass distributions of the observed circumstellar disks in this cluster are satisfactorily reproduced. Four, five, or size planets per star were introduced in orbit around the 500 solar-like stars with a maximum orbital separation of 400 au.Results. Our study focuses on the production of free-floating planets. A total of 357 become unbound from a total of 2522 planets in the initial conditions of the simulation. Of these, 281 leave the cluster within the crossing timescale of the star cluster; the others remain bound to the cluster as free-floating intra-cluster planets. Five of these free-floating intra-cluster planets are captured at a later time by another star.Conclusions. The two main mechanisms by which planets are lost from their host star, ejection upon a strong encounter with another star or internal planetary scattering, drive the evaporation independent of planet mass of orbital separation at birth. The effect of small perturbations due to slow changes in the cluster potential are important for the evolution of planetary systems. In addition, the probability of a star to lose a planet is independent of the planet mass and independent of its initial orbital separation. As a consequence, the mass distribution of free-floating planets is indistinguishable from the mass distribution of planets bound to their host star.Article number, page 3 of 17

As a computationally attractive alternative for global large eddy simulations (LESs), we investigate the possibility of using comprehensive three-dimensional LESs as a superparameterization that can replace all traditional parameterizations of atmospheric processes that are currently used in global models. We present the technical design for a replacement of the parameterization for clouds, convection, and turbulence of the global atmospheric model of the European Centre for Medium-Range Weather Forecasts by the Dutch Atmospheric Large Eddy Simulation model. The model coupling consists of bidirectional data exchange between the global model and the high-resolution LES models embedded within the columns of the global model. Our setup allows for selective superparameterization, that is, for applying superparameterization in local regions selected by the user, while keeping the standard parameterization of the global model intact outside this region. Computationally, this setup can result in major geographic load imbalance, because of the large difference in computational load between superparameterized and nonsuperparameterized model columns. To resolve this issue, we use a modular design where the local and global models are kept as distinct model codes and organize the model coupling such that all the local models run in parallel, separate from the global model. First simulation results, employing this design, demonstrate the potential of our approach.