Search

This study introduces a coupled flow-biology computational model based on scaling methods and dimensionless numbers. The aim is to illustrate the validity of this model for the investigation of vertical migration of colonies of the cyanobacterium Microcystis aeruginosa under turbulent flow conditions and affected by (light-induced) assimilation/respiration processes. This model connects the distinct time scales of turbulence (typically minutes for the integral time scale) and light-induced mass-density changes of cyanobacteria (diurnal). To compute the full Microcystis vertical migration cycles we combine Direct Numerical Simulations (DNS) of turbulence and this scaling approach. The Microcystis colonies are subjected to turbulence and DNS allows computation of their trajectories with a particle tracking algorithm. The latter is based on a simplified version of the Maxey-Riley equation describing the buoyancy and hydrodynamic forces on the colonies and requires knowledge of the smallest turbulent flow scales (down to the Kolmogorov scale, thus requiring DNS). The coupled flow-biology model proves to capture natural diurnal migration of Microcystis colonies. Under very low turbulence conditions Microcystis shows a quasi-periodic daily migration where the Stokes drag and the buoyancy force are predominant. Higher turbulence conditions override such periodicity, and mix the colonies thoroughly through the water column. Our analysis yields the buoyancy Stokes number Stb, which distinguishes the deterministic buoyancy dominated migration over the more chaotic random colony excursions due to turbulence.

The performance of an atmospheric single-column model (SCM) is studied systematically for stably-stratified conditions. To this end, 11 years (2005–2015) of daily SCM simulations were compared to observations from the Cabauw observatory, The Netherlands. Each individual clear-sky night was classified in terms of the ambient geostrophic wind speed with a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1\hbox { m} \hbox { s}^{-1}$$\end{document}1ms-1 bin-width. Nights with overcast conditions were filtered out by selecting only those nights with an average net radiation of less than \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-\,30\hbox { W }\hbox {m}^{-2}$$\end{document}-30Wm-2. A similar procedure was applied to the observational dataset. A comparison of observed and modelled ensemble-averaged profiles of wind speed and potential temperature and time series of turbulent fluxes showed that the model represents the dynamics of the nocturnal boundary layer (NBL) at Cabauw very well for a broad range of mechanical forcing conditions. No obvious difference in model performance was found between near-neutral and strongly-stratified conditions. Furthermore, observed NBL regime transitions are represented in a natural way. The reference model version performs much better than a model version that applies excessive vertical mixing as is done in several (global) operational models. Model sensitivity runs showed that for weak-wind conditions the inversion strength depends much more on details of the land-atmosphere coupling than on the turbulent mixing. The presented results indicate that in principle the physical parametrizations of large-scale atmospheric models are sufficiently equipped for modelling stably-stratified conditions for a wide range of forcing conditions.

The representation of the atmospheric boundary layer is an important part of weather and climate models and impacts many applications such as air quality and wind energy. Over the years, the performance in modeling 2-m temperature and 10-m wind speed has improved but errors are still significant. This is in particular the case under clear skies and low wind speed conditions at night as well as during winter in stably stratified conditions over land and ice. In this paper, the authors review these issues and provide an overview of the current understanding and model performance. Results from weather forecast and climate models are used to illustrate the state of the art as well as findings and recommendations from three intercomparison studies held within the Global Energy and Water Exchanges (GEWEX) Atmospheric Boundary Layer Study (GABLS). Within GABLS, the focus has been on the examination of the representation of the stable boundary layer and the diurnal cycle over land in clear-sky conditions. For this purpose, single-column versions of weather and climate models have been compared with observations, research models, and large-eddy simulations. The intercomparison cases are based on observations taken in the Arctic, Kansas, and Cabauw in the Netherlands. From these studies, we find that even for the noncloudy boundary layer important parameterization challenges remain.

At present a variety of boundary-layer schemes is in use in numerical models and often a large variation of model results is found. This is clear from model intercomparisons, such as organized within the GEWEX Atmospheric Boundary Layer Study (GABLS). In this paper we analyze how the specification of the land-surface temperature affects the results of a boundary-layer scheme, in particular for stable conditions. As such we use a well established column model of the boundary layer and we vary relevant parameters in the turbulence scheme for stable conditions. By doing so, we can reproduce the outcome for a variety of boundary-layer models. This is illustrated with the original set-up of the second GABLS intercomparison study using prescribed geostrophic winds and land-surface temperatures as inspired by (but not identical to) observations of CASES-99 for a period of more than two diurnal cycles. The model runs are repeated using a surface temperature that is calculated with a simple land-surface scheme. In the latter case, it is found that the range of model results in stable conditions is reduced for the sensible heat fluxes, and the profiles of potential temperature and wind speed. However, in the latter case the modelled surface temperatures are rather different than with the original set-up, which also impacts on near-surface air temperature and wind speed. As such it appears that the model results in stable conditions are strongly influenced by non-linear feedbacks in which the magnitude of the geostrophic wind speed and the related land-surface temperature play an important role.

The performance of diagnostic equations for the stable boundary layer height h is evaluated with four observational datasets that represent a broad range of latitudes, land use, and surface roughness. In addition, large-eddy simulation results are used. Special care is given to data-quality selection.The performance of diagnostic equations for the stable boundary layer height h is evaluated with four observational datasets that represent a broad range of latitudes, land use, and surface roughness. In addition, large-eddy simulation results are used. Special care is given to data-quality selection. The diagnostic equations evaluated are so-called multilimit equations as derived by Zilitinkevich and coworkers in a number of papers. It appears that these equations show a serious negative bias, especially for It

The cause of persistent cyanobacteria scum formation in lakes is an unresolved subject. Scum refers to the event in which cyanobacteria are at the water surface of a lake. Factors like low turbulence levels, long day-light, high water temperatures and the buoyant capacity of cyanobacterial cells play a role in theoccurrence of scums. However, they do not explain why scums are observed at periods during the day when according to theory they should have disappeared into the deeper water layers. In this study, we present an alternative explanation. The hypothesis we present here is that irreversible buoyancy of cyanobacteria colonies is created by the growth of gas bubbles on or within the mucilage of the colonies. These bubbles grow under oxygen super-saturated conditions. At low wind speed and high chlorophyll levels, the dissolved oxygen (DO) produced during photosynthesis by cyanobacteria, cannot escape sufficiently fast to the atmosphere hence a DO supersaturated condition arises in the water. At this stage, growth of oxygen bubbles may occur inside or attached to the mucilage. We present results of compression experiments to support our hypothesis. In a chamber, the pressure on lake water containing a natural cyanobacteria population is increased. At 3x10^5 and 4x10^5 Pa the cyanobacteria colonies were not able to float anymore and sank. This pressure is lower than the 10^6 Pa needed to collapse all gas vacuoles inside the cyanobacteria cells (Walsby, 1994). The observed change from floating to sinking colonies due to increased water pressure suggests that gas bubbles were present inside the colonies. In lakes, these gas bubbles may lead to permanent buoyancy, i.e. a persistent scum.

The performance of the Scintec displaced-beam small aperture scintillometer (DBSAS) in the stable boundary layer (SBL) is investigated using data gathered during the CASES-99 experiment in Kansas, U.S.A. The DBSAS is superior to the eddy-covariance method in determining vertical fluxes of sensible heat and momentum close to the ground and/or over short (< 1 min) averaging intervals. Both aspects are of importance in the shallow and non-stationary SBL. The friction velocity, u*, the temperature scale, θ*, and from these the sensible heat flux, H, were calculated from the indirectly determined dissipation rate, ε, and the structure parameter of temperature, CT2, by the DBSAS, which was operated over a path length of 112 m. All these variables are compared with eddy-covariance data for 10-minute time averages. Previously reported systematic errors in the DBSAS, overestimation of u* for low u* values and underestimation of u* for high u* values, have in part been dealt with by adjusting the beam displacement distance from 2.7 mm to 2.6 mm in the calculations. The latter adjustment is presented as a working hypothesis, not a general solution.

In the stable boundary layer it is often observed that turbulence is not continuous in space and time. This discontinuous, intermittent turbulence causes alterations from the mean evolution of the stratified atmospheric boundary layer, which may result in an oscillatory type of behavior of the near-surface wind speed and temperature. This paper focuses on an intermittency generating mechanism that arises from a direct interaction of the lower atmosphere (first tens of meters) with the vegetation surface, without interaction with the air aloft. This atmosphere–surface intermittency (ASI) is associated with the essential elements of the stable boundary layer (SBL): strong surface cooling, the supply of mechanical energy by the synoptic pressure gradient, and the limiting effect of stratification on mixing efficiency. In Part I it is shown that the essence of ASI can be captured by a system of three coupled nonlinear differential equations. This simplified system shows both intermittent and nonintermittent flow regimes for different circumstances. In the present paper, this system is studied analytically, following a system dynamics approach. The transition between the different flow regimes is identified as a Hopf bifurcation. This property is used to derive a dimensionless parameter, which is a function of external parameters, such as radiative forcing and pressure gradient. With this dimensionless parameter the equilibrium behavior of the system (i.e., intermittent or nonintermittent) can be predicted exactly. As such this parameter is used to classify SBL regimes. It is shown that the proposed classification parameter provides different information about the state of the SBL than other typical SBL classification parameters such as z/L and Ri.

Simple analytic approximate solutions arepresented for the set of equations that follows fromthe Monin–Obukhov flux-profile relationships using thestability functions of Dyer (unstable case) andBeljaars–Holtslag (stable case). Several publicationsare devoted to the same subject, however the currentapproach contains some new features, namely: (a) itappears to be more accurate for unstable situationsand (b) it applies also to the general case where windspeed (u) and potential temperature(¿) are given at different levels. In order toillustrate the accuracy of the approach a comparisonwith the actual solutions is presented for someselected combinations of ¿ and u levelstypical for various practical applications.

In this work the dynamic behaviour of the wind in the nocturnal boundary layer is studied, with a particular focus on systematic behaviour of the near-surface wind. Recently, an extension of the well-known Blackadar model for frictionless inertial oscillations above the nocturnal boundary layer was proposed by Van de Wiel et al., which accounts for frictional effects within the nocturnal boundary layer. It appears that the nocturnal wind velocity profile tends to perform an inertial oscillation around an equilibrium wind profile, rather than around the geostrophic wind vector (as in the Blackadar model). In the present study we propose the concept of ‘composite hodographs’ to evaluate the ideas and assumptions of the aforementioned analytical model. Composite hodographs are constructed based on a large observational dataset from the Cabauw observatory. For comparison and deeper analysis, this method is also applied to single-column model simulations that represent the same dataset. From this, it is shown that winds in the middle and upper part of the nocturnal boundary layer closely follow the dynamics predicted by the model by Van de Wiel et al. In contrast, the near-surface wind shows more complex behaviour that can be described by two different stages: (1) a decelerating phase where the wind decreases rapidly in magnitude due to enlarged stress divergence in the transition period near sunset (an aspect not included in the analytical model), and (2) a regular type of inertial oscillation, but with relatively small amplitude as compared to the oscillations in the middle and upper parts of the nocturnal boundary layer. Copyright © 2011 Royal Meteorological Society

In this research we introduce a coupled column model to simulate the vertical migration of Microcystis aeruginosa in natural lakes. M. aeruginosa is a unicellular cyanobacteria that form colonies. They produce toxins and therefore become a potential threat to water quality and human health. Understanding the distribution of this species in space and time is important for improving water management strategies. The model we propose includes both hydrodynamics and physiological responses including explicitly buoyancy regulation in Microcystis cells. Our model applies the Langevin–Fokker–Planck approach to simulate the total colony number concentration along the water column. This approach allows the description of sinking and rising velocities of colonies of different sizes and compositions subjected to turbulent mixing. The model is first applied to the 30 m deep Lake Vlietland in the Netherlands for the summer of 2009. During this summer, the lake showed high blooms of Microcystis which eventually led to scum formation along the shore. The simulations show the preferential distribution of M. aeruginosa through the water column and their strong dependency on colony size. On a daily cycle, small colonies (50–200 μm) do not remain near the surface but are highly concentrated in the middle of the epilimnion, whereas large colonies (≥800 μm) are able to migrate to greater depths and concentrate only temporarily near the surface. For comparing our computer model with available measurements of Microcystis concentration distributions we applied it to Lakes IJsselmeer and Vinkeveen. The results show a good agreement with the observations of diurnal changes in buoyancy status.

This paper addresses the possible role of unresolved terrain drag, relative to the turbulent drag on the development of the stable atmospheric boundary layer over land. Adding a first-order estimate for terrain drag to the turbulent drag appears to provide drag that is similar to the enhanced turbulent drag obtained with the so-called long-tail mixing functions. These functions are currently used in many operational models for weather and climate, although they lack a clear physical basis. Consequently, a simple and practical quasi-empirical parameterization of terrain drag divergence for use in large-scale models is proposed and is tested in a column mode. As an outcome, the cross-isobaric mass flow (a measure for cyclone filling) with the new scheme, using realistic turbulent drag, appears to be equal to what is found with the unphysical long-tail scheme. At the same time, the new scheme produces a much more realistic less-deep boundary layer than is obtained by using the long-tail mixing function.

Recently, the equilibrium height of the stable boundary layer received much attention in a series of papers by Zilitinkevich and co-workers. In these studies the stable boundary-layer height is derived in terms of inverse interpolation of different boundary-layer height scales, each representing a prototype boundary layer. As an alternative we propose an inverse interpolation of the eddy diffusivities for each prototype before applying the definition of the Ekman layer depth. The new equation for the stable boundary-layer height improves performance in a comparison against four observational datasets

The modeling and prediction of the stable boundary layer over land is a persistent, problematic feature in weather, climate, and air quality topics. Here, the performance of a state-of-the-art single-column boundary layer model is evaluated with observations from the 1999 Cooperative Atmosphere–Surface Exchange Study (CASES-99) field experiment. Very high model resolution in the atmosphere and the soil is utilized to represent three different stable boundary layer archetypes, namely, a fully turbulent night, an intermittently turbulent night, and a radiative night with hardly any turbulence (all at clear skies). Each archetype represents a different class of atmospheric stability. In the current model, the atmosphere is fully coupled to a vegetation layer and the underlying soil. In addition, stability functions (local scaling) are utilized based on in situ observations. Overall it is found that the vertical structure, the surface fluxes (apart from the intermittent character) and the surface temperature in the stable boundary layer can be satisfactorily modeled for a broad stability range (at a local scale) with the current understanding of the physics of the stable boundary layer. This can also be achieved by the use of a rather detailed coupling between the atmosphere and the underlying soil and vegetation, together with high resolution in both the atmosphere and the soil. This is especially true for the very stable nights, when longwave radiative cooling is dominant. Both model outcome and observations show that in the latter case the soil heat flux is a dominant term of the surface energy budget.

In this paper, the degree of scatter in flux–gradient relationships for stably stratified conditions is analyzed. It is generally found that scatter in the dimensionless lapse rate ϕh is larger than in the dimensionless shear ϕm when plotted versus the stability parameter z/Λ (where Λ is the local Obukhov length). Here, this phenomenon is explained to be a result of self-correlation due to the occurrence of the momentum and the heat flux on both axes, measurement uncertainties, and other possibly relevant physical processes left aside. It is shown that the ratio between relative errors in the turbulent fluxes influences the orientation of self-correlation in the flux–gradient relationships. In stable conditions, the scatter in ϕm is largely suppressed by self-correlation while for ϕh this is not the case (vice versa for unstable stratification). An alternative way of plotting is discussed for determining the slope of the linear ϕm function.

The impact of coupling the atmosphere to the surface energy balance is examined for the stable boundary layer, as an extension of the first GABLS (GEWEX Atmospheric Boundary-Layer Study) one-dimensional model intercomparison. This coupling is of major importance for the stable boundary-layer structure and its development because coupling enables a realistic physical description of the interdependence of the surface temperature and the surface sensible heat flux. In the present case, the incorporation of a surface energy budget results in stronger cooling (surface decoupling), and a more stable and less deep boundary layer. The proper representation of this is a problematic feature in large-scale numerical weather prediction and climate models. To account for the upward heat flux from the ice surface beneath, we solve the diffusion equation for heat in the underlying ice as a first alternative. In that case, we find a clear impact of the vertical resolution in the underlying ice on boundary-layer development: coarse vertical resolution in the ice results in stronger surface cooling than for fine resolution. Therefore, because of this impact on stable boundary-layer development, the discretization in the underlying medium needs special attention in numerical modelling studies of the nighttime boundary layer. As a second alternative, a bulk conductance layer with stagnant air near the surface is added. The stable boundary-layer development appears to depend heavily on the bulk conductance of the stagnant air layer. This result re-emphasizes the fact that the interaction with the surface needs special attention in stable boundary-layer studies. Furthermore, we perform sensitivity studies to atmospheric resolution, the length-scale formulation and the impact of radiation divergence on stable boundary-layer structure for weak windy conditions.

In this paper a classification of stable boundary layer regimes is presented based on observations of near-surface turbulence during the Cooperative Atmosphere¿Surface Exchange Study-1999 (CASES-99). It is found that the different nights can be divided into three subclasses: a turbulent regime, an intermittent regime, and a radiative regime, which confirms the findings of two companion papers that use a simplified theoretical model (it is noted that its simpliflied structure limits the model generality to near-surface flows). The papers predict the occurrence of stable boundary layer regimes in terms of external forcing parameters such as the (effective) pressure gradient and radiative forcing. The classification in the present work supports these predictions and shows that the predictions are robust in a qualitative sense. As such, it is, for example, shown that intermittent turbulence is most likely to occur in clear-sky conditions with a moderately weak effective pressure gradient. The quantitative features of the theoretical classification are, however, rather sensitive to (often uncertain) local parameter estimations, such as the bulk heat conductance of the vegetation layer. This sensitivity limits the current applicability of the theoretical classification in a strict quantitative sense, apart from its conceptual value

In the stable boundary layer (SBL) it is observed often that turbulence is not continuous in space and time. This discontinuous, intermittent turbulence causes alternations from the mean evolution of the stratified atmospheric boundary layer, which may result in an oscillatory type of behavior of the near-surface wind speed and temperature. It is well known that intermittent turbulence in the SBL can be generated by various mechanisms. This paper focuses on an intermittency generating mechanism that arises from a direct interaction of the lower atmosphere (first tens of meters) with the vegetation surface, without interaction with the air aloft. It is shown that the essence of this mechanism can be captured by a 1D bulk model of three coupled nonlinear differential equations. In the present paper, numerical runs with the model show that intermittent turbulence is most likely to occur over land surfaces with low vegetation during clear-sky conditions in the presence of a moderate to low synoptical pressure gradient. The existence of a vegetation layer has a strong influence on intermittency dynamics. Due to its small heat capacity, the vegetation temperature is able to quickly respond to rapidly changing conditions. This in turn affects the stability of the lower atmosphere, causing an important feedback mechanism. In addition, it was found that intermittent behavior of SBL models occurs for various first-order closure schemes with different stability functions. However, stability functions that allow turbulent transport beyond the critical Richardson number effectively suppress intermittent–oscillatory behavior. Currently, the latter type of formulations is often used in numerical weather prediction to prevent excessive SBL cooling in very stable conditions. The advantage of using a simplified SBL model, as proposed in the present paper, is that it allows an analytical study of the system, which, in turn, allows theoretical predictions about the occurrence of intermittent SBL behavior (see the companion paper).

The main objective of this thesis is to contribute to further understanding of the stable boundary layer (SBL) over land, and its representation in atmospheric models. A SBL develops during night due to radiative surface cooling. Observations in the SBL are difficult since many different physical processes can play a role. These processes are turbulent mixing, radiative transport, a coupling with the vegetation and underlying soil, drainage flows, gravity waves, fog, and aspects of land use heterogeneity. Therefore, the understanding and the representation of the SBL in weather forecast and climate models is relatively poor, especially for calm nights. In this thesis, a detailed column model of the atmosphere-land surface system is used to represent the atmospheric boundary layer over land and ice. As such, LES results and CASES99 field observations are used for comparison and model evaluation. It turns out that the degree of land-surface coupling plays a key role in forecasting the SBL. Also, the sensitivity of the radiation transfer model to vertical resolution is examined. It is found that the SBL can be satisfactorily modelled (except for the low-level jet (LLJ) and intermittency of the turbulence) if the geostrophic wind speed, advection, subsidence, and vegetation and soil properties are known, and if relatively high vertical resolution is used near the surface (both in the soil and in the atmosphere). The column model is used to study the nighttime 2m temperature increase due to additional CO2 as function of wind speed. Observations show that the temperature increase is similar for windy and calm nights, although this is somewhat counterintuitive. Model results confirm that the temperature increase is indeed similar for windy and calm nights. Next an intercomparison study of limited area weather forecast models (COAMPS, MM5, HIRLAM) is performed for CASES-99. Large errors occur in the forecasted minimum temperature, SBL height and diurnal temperature range. Models that account for a realistic interaction with the land surface are advantageous. A sufficient large domain is required to forecast the LLJ, and the forecasted surface cooling is very sensitive to the choice of the radiation scheme, especially for calm nights. Overall it is possible to upgrade the model performance by using the lessons learnt with the column model. In the thesis, also the role of orographic drag on the SBL is explored. It is shown that orography of 10 m amplitude can produce drag as large as the turbulent drag. Accounting for this in a model gave sufficient cyclone filling and a better forecast of the SBL structure and LLJ. The thesis concludes with studies of the SBL height. Dimensional analysis is used to derive a new and robust formulation for the SBL height for a broad range of latitude land-use conditions.