Inoculum Size Effect in Dimorphic Fungi: Extracellular Control of Yeast-Mycelium Dimorphism in \u3ci\u3eCeratocystis ulmi\u3c/i\u3e

We studied the inoculum size effect in Ceratocystis ulmi, the dimorphic fungus that causes Dutch elm disease. In a defined glucose-proline-salts medium, cells develop as budding yeasts when inoculated at \u3e106 spores per ml and as mycelia when inoculated at type, age of the spores, temperature, pH, oxygen availability, trace metals, sulfur source, phosphorous source, or the concentration of glucose or proline. Similarly, it was not influenced by added adenosine, reducing agents, methyl donors, amino sugars, fatty acids, or carbon dioxide. Instead, growing cells excreted an unknown quorum-sensing factor that caused a morphological shift from mycelia to budding yeasts. This yeast-promoting effect is abolished if it is extracted with an organic solvent such as ethyl acetate. The quorum-sensing activity acquired by the organic solvent could be added back to fresh medium in a dosedependent fashion. The quorum-sensing activity in C. ulmi spent medium was specific for C. ulmi and had no effect on the dimorphic fungus Candida albicans or the photomorphogenic fungus Penicillium isariaeforme. In addition, farnesol, the quorum-sensing molecule produced by C. albicans, did not inhibit mycelial development of C. ulmi when present at concentrations of up to 100 μM. We conclude that the inoculum size effect is a manifestation of a quorum-sensing system that is mediated by an excreted extracellular molecule, and we suggest that quorum sensing is a general phenomenon in dimorphic fungi

Evolution of forced shear flows in polytropic atmospheres: A comparison of forcing methods and energetics

Shear flows are ubiquitous in astrophysical objects including planetary and stellar interiors, where their dynamics can have significant impact on thermo-chemical processes. Investigating the complex dynamics of shear flows requires numerical calculations that provide a long time evolution of the system. To achieve a sufficiently long lifetime in a local numerical model the system has to be forced externally. However, at present, there exist several different forcing methods to sustain large-scale shear flows in local models. In this paper we examine and compare various methods used in the literature in order to resolve their respective applicability and limitations. These techniques are compared during the exponential growth phase of a shear flow instability, such as the Kelvin-Helmholtz (KH) instability, and some are examined during the subsequent non-linear evolution. A linear stability analysis provides reference for the growth rate of the most unstable modes in the system and a detailed analysis of the energetics provides a comprehensive understanding of the energy exchange during the system's evolution. Finally, we discuss the pros and cons of each forcing method and their relation with natural mechanisms generating shear flows

Energy- and flux-budget (EFB) turbulence closure model for the stably stratified flows. Part I: Steady-state, homogeneous regimes

We propose a new turbulence closure model based on the budget equations for the key second moments: turbulent kinetic and potential energies: TKE and TPE (comprising the turbulent total energy: TTE = TKE + TPE) and vertical turbulent fluxes of momentum and buoyancy (proportional to potential temperature). Besides the concept of TTE, we take into account the non-gradient correction to the traditional buoyancy flux formulation. The proposed model grants the existence of turbulence at any gradient Richardson number, Ri. Instead of its critical value separating - as usually assumed - the turbulent and the laminar regimes, it reveals a transition interval, 0.1< Ri <1, which separates two regimes of essentially different nature but both turbulent: strong turbulence at Ri<<1; and weak turbulence, capable of transporting momentum but much less efficient in transporting heat, at Ri>1. Predictions from this model are consistent with available data from atmospheric and lab experiments, direct numerical simulation (DNS) and large-eddy simulation (LES).Comment: 40 pages, 6 figures, Boundary-layer Meteorology, resubmitted, revised versio

Global Intermittency and Collapsing Turbulence in the Stratified Planetary Boundary Layer

Direct numerical simulation of the turbulent Ekman layer over a smooth wall is used to investigate bulk properties of a planetary boundary layer under stable stratification. Our simplified configuration depends on two non-dimensional parameters: a Richardson number characterizing the stratification and a Reynolds number characterizing the turbulence scale separation. This simplified configuration is sufficient to reproduce global intermittency, a turbulence collapse, and the decoupling of the surface from the outer region of the boundary layer. Global intermittency appears even in the absence of local perturbations at the surface; the only requirement is that large-scale structures several times wider than the boundary-layer height have enough space to develop. Analysis of the mean velocity, turbulence kinetic energy, and external intermittency is used to investigate the large-scale structures and corresponding differences between stably stratified Ekman flow and channel flow. Both configurations show a similar transition to the turbulence collapse, overshoot of turbulence kinetic energy, and spectral properties. Differences in the outer region resulting from the rotation of the system lead, however, to the generation of enstrophy in the non-turbulent patches of the Ekman flow. The coefficient of the stability correction function from Monin-Obukhov similarity theory is estimated as (Formula presented.) in agreement with atmospheric observations, theoretical considerations, and results from stably stratified channel flows. Our results demonstrate the applicability of this set-up to atmospheric problems despite the intermediate Reynolds number achieved in our simulations. © 2014 The Author(s)

Energy- and flux-budget turbulence closure model for stably stratified flows. Part II: the role of internal gravity waves

We advance our prior energy- and flux-budget turbulence closure model (Zilitinkevich et al., 2007, 2008) for the stably stratified atmospheric flows and extend it accounting for additional vertical flux of momentum and additional productions of turbulent kinetic energy, turbulent potential energy (TPE) and turbulent flux of potential temperature due to large-scale internal gravity waves (IGW). Main effects of IGW are following: the maximal value of the flux Richardson number (universal constant 0.2-0.25 in the no-IGW regime) becomes strongly variable. In the vertically homogeneous stratification, it increases with increasing wave energy and can even exceed 1. In the heterogeneous stratification, when IGW propagate towards stronger stratification, the maximal flux Richardson number decreases with increasing wave energy, reaches zero and then becomes negative. In other words, the vertical flux of potential temperature becomes counter-gradient. IGW also reduce anisotropy of turbulence and increase the share of TPE in the turbulent total energy. Depending on the direction (downward or upward), IGW either strengthen or weaken the total vertical flux of momentum. Predictions from the proposed model are consistent with available data from atmospheric and laboratory experiments, direct numerical simulations and large-eddy simulations.Comment: 37 pages, 5 figures, revised versio

Application of the Large-Eddy Approach to the Simulation of Turbulence in Uniform Shear Flow

In the Rogallo approach to the simulation of homogeneous turbulence in uniform shear flow, the equations of motion are solved in a reference frame that is moving with the mean flow. This choice of reference frame allows the application of periodic boundary conditions to the fluctuating velocity components and the use of a highly accurate spectral scheme for the spatial discretization. However, as time is advanced, the reference frame becomes more and more skewed and a regridding of the computational domain using the periodic structure of the velocity components is required. This regridding procedure introduces aliasing errors that are removed in direct numerical simulation. This study addresses the application of this approach to large-eddy simulation of turbulence in uniform shear flow. Results are compared between direct numerical simulation and large-eddy simulation

Large-Eddy Simulation of Homogeneous Shear Flows With Several Subgrid-Scale Models

In this article, large eddy simulation is used to simulate homogeneous shear flows. The spatial discretization is accomplished by the spectral collocation method and a third-order Runge–Kutta method is used to integrate the time-dependent terms. For the estimation of the subgrid-scale stress tensor, the Smagorinsky model, the dynamic model, the scale-similarity model and the mixed model are used. Their predicting performance for homogeneous shear flow is compared accordingly. The initial Reynolds number varies from 33 to 99 and the initial shear number is 2. Evolution of the turbulent kinetic energy, the growth rate, the anisotropy component and the subgrid-scale dissipation rate is presented. In addition, the performance of several filters is examined

On multiscale acceleration statistics in rotating and sheared homogeneous turbulence

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