The Community Atmosphere Model, version 4 (CAM4), was released as part of the Community Climate System Model, version 4 (CCSM4). The finite volume (FV) dynamical core is now the default because of its superior transport and conservation properties. Deep convection parameterization changes include a dilute plume calculation of convective available potential energy (CAPE) and the introduction of convective momentum transport (CMT). An additional cloud fraction calculation is now performed following macrophysical state updates to provide improved thermodynamic consistency. A freeze-drying modification is further made to the cloud fraction calculation in very dry environments (e.g., the Arctic), where cloud fraction and cloud water values were often inconsistent in CAM3. In CAM4 the FV dynamical core further degrades the excessive trade-wind simulation, but reduces zonal stress errors at higher latitudes. Plume dilution alleviates much of the midtropospheric tropical dry biases and reduces the persistent monsoon precipitation biases over the Arabian Peninsula and the southern Indian Ocean. CMT reduces much of the excessive trade-wind biases in eastern ocean basins. CAM4 shows a global reduction in cloud fraction compared to CAM3, primarily as a result of the freeze-drying and improved cloud fraction equilibrium modifications. Regional climate feature improvements include the propagation of stationary waves from the Pacific into midlatitudes and the seasonal frequency of Northern Hemisphere blocking events. A 1° versus 2° horizontal resolution of the FV dynamical core exhibits superior improvements in regional climate features of precipitation and surface stress. Improvements in the fully coupled mean climate between CAM3 and CAM4 are also more substantial than in forced sea surface temperature (SST) simulations.
This paper describes a new version of the University of Washington shallow cumulus parameterization. The new version includes improved treatments of lateral mixing rates into cumulus updrafts, the evaporation of precipitation and of the interaction of cumuli with the underlying subcloud layer, and a treatment of the convective inhibition-based mass-flux closure that is more numerically stable and is suitable for the long time steps of global climate models.The paper also documents its performance when combined with a new moist turbulence parameterization in simulations with version 3.5 of the Community Atmosphere Model (CAM3.5). A single-column simulation of nonprecipitating trade cumulus shows considerable improvements in vertical thermodynamic structure and less resolution sensitivity in the new schemes compared to CAM3.5. In global simulations, the new schemes, combined with an increase of vertical resolution from 26 to 30 levels, produce a significant (7%) reduction in overall climate bias, calculated from root-mean-squared error of the seasonal model climatology compared to a suite of global observations of various fields. Biases in almost all fields, particularly the shortwave cloud radiative forcing, are reduced. Geographical bias patterns in surface rainfall, liquid water path, and surface air temperature are only mildly affected by the model parameterization and vertical resolution changes.
A new moist turbulence parameterization is presented and implemented in the Community Atmosphere Model (CAM). It is derived from Grenier and Bretherton but has been heavily modified to improve its numerical stability and efficiency with the long time steps used in climate models. A goal was to provide a more physically realistic treatment of marine stratocumulus-topped boundary layers than in the current CAM. Key features of the scheme include use of moist-conserved variables, an explicit entrainment closure for convective layers, diagnosis of turbulent kinetic energy (TKE) for computation of turbulent diffusivities, an efficient new formulation of TKE transport as a relaxation to layer-mean TKE, and unified treatment of all turbulent layers in each atmospheric column. The scheme is compared with the default turbulence parameterizations in the CAM using three single-column modeling cases, using both operational and high vertical and time resolution. Both schemes performed comparably well on the dry convective boundary layer case. For a stable boundary layer case, the default CAM overdeepens the boundary layer unless its free-tropospheric mixing length is greatly reduced, whereupon the new scheme and default CAM again both perform well at both tested resolutions. A nocturnal stratocumulus case was much better simulated by the new scheme than the default CAM, with much less resolution sensitivity. Global climate simulations with the new scheme in tandem with a new shallow cumulus parameterization are presented in a companion paper.
ABSTRACT:Results are presented from an intercomparison of single-column and cloud-resolving model simulations of a cold-air outbreak mixed-phase stratocumulus cloud observed during the Atmospheric Radiation Measurement (ARM) programme's Mixed-Phase Arctic Cloud Experiment. The observed cloud occurred in a well-mixed boundary layer with a cloud-top temperature of −15 • C. The average liquid water path of around 160 g m −2 was about two-thirds of the adiabatic value and far greater than the average mass of ice which when integrated from the surface to cloud top was around 15 g m −2 .Simulations of 17 single-column models (SCMs) and 9 cloud-resolving models (CRMs) are compared. While the simulated ice water path is generally consistent with observed values, the median SCM and CRM liquid water path is a factor-of-three smaller than observed. Results from a sensitivity study in which models removed ice microphysics suggest that in many models the interaction between liquid and ice-phase microphysics is responsible for the large model underestimate of liquid water path.Despite this underestimate, the simulated liquid and ice water paths of several models are consistent with observed values. Furthermore, models with more sophisticated microphysics simulate liquid and ice water paths that are in better agreement with the observed values, although considerable scatter exists. Although no single factor guarantees a good simulation, these results emphasize the need for improvement in the model representation of mixed-phase microphysics.
This paper provides a description of the integrated representation for the cloud processes in the Community Atmosphere Model, version 5 (CAM5). CAM5 cloud parameterizations add the following unique characteristics to previous versions: 1) a cloud macrophysical structure with horizontally nonoverlapped deep cumulus, shallow cumulus, and stratus in each grid layer, where each of which has its own cloud fraction, and mass and number concentrations for cloud liquid droplets and ice crystals; 2) stratus–radiation–turbulence interactions that allow CAM5 to simulate marine stratocumulus solely from grid-mean relative humidity without relying on a stability-based empirical formula; 3) prognostic treatment of the number concentrations of stratus liquid droplets and ice crystals, with activated aerosols and detrained in-cumulus condensates as the main sources and with evaporation, sedimentation, and precipitation of stratus condensate as the main sinks; and 4) radiatively active cumulus and snow. By imposing consistency between diagnosed stratus fraction and prognosed stratus condensate, unrealistically empty or highly dense stratus is avoided in CAM5. Because of the activation of the prognostic aerosols and the parameterizations of the radiation and stratiform precipitation production as a function of the cloud droplet size, CAM5 simulates various aerosol indirect effects as well as the direct effects: that is, aerosols affect both the radiation budget and the hydrological cycle. Detailed analysis of various simulations indicates that CAM5 improves upon CAM3/CAM4 in global performance as well as in physical formulation. However, several problems are also identified in CAM5, which can be attributed to deficient regional tuning, inconsistency between various physics parameterizations, and incomplete treatment of physics. Efforts are continuing to further improve CAM5.
A pincer-like benzene-bridged sensor 1 with a pyrene excimer as a signal source and imidazolium as a phosphate anion receptor was synthesized and investigated for ATP sensing. A unique switch of excimer vs monomer pyrene fluorescence of 1 is observed in the presence of ATP due to the charcteristic sandwich pi-pi stacking of pyrene-adenine-pyrene. On the other hand, four other bases of nucleoside triphosphates such as GTP, CTP, UTP, and TTP can interact only from the outside with the already stabilized stacked pyrene-pyrene dimer of 1, resulting in excimer fluorescence quenching. The fluorescent intensity ratio of monomer-to-excimer for 1 upon binding with ATP (I(375)/I(487)) is much larger than that upon binding with ADP and AMP. This difference is large enough to discriminate ATP from ADP and AMP. As one of the biological applications, sensor 1 is successfully applied to the ATP staining experiments. Sensor 1 is also applied to monitor the hydrolysis of ATP and ADP by apyrase. The results indicate that 1 is a useful fluorescent sensor for investigations of ATP-relevant biological processes.
In the body, soft tissues often undergo cycles of stretching and relaxation that may affect cell behaviour without changing matrix rigidity. To determine whether transient forces can substitute for a rigid matrix, we stretched soft pillar arrays. Surprisingly, 1–5% cyclic stretching over a frequency range of 0.01–10 Hz caused spreading and stress fibre formation (optimum 0.1 Hz) that persisted after 4 h of stretching. Similarly, stretching increased cell growth rates on soft pillars comparative to rigid substrates. Of possible factors linked to fibroblast growth, MRTF-A (myocardin-related transcription factor-A) moved to the nucleus in 2 h of cyclic stretching and reversed on cessation; but YAP (Yes-associated protein) moved much later. Knockdown of either MRTF-A or YAP blocked stretch-dependent growth. Thus, we suggest that the repeated pulling from a soft matrix can substitute for a stiff matrix in stimulating spreading, stress fibre formation and growth.
Many nematodes show a stage-specific behavior called nictation in which a worm stands on its tail and waves its head in three dimensions. Here we show that nictation is a dispersal behavior regulated by a specific set of neurons, the IL2 cells, in C. elegans. We established assays for nictation and showed that cholinergic transmission was required for nictation. Cell type-specific rescue experiments and genetic ablation experiments revealed that the IL2 ciliated head neurons were essential for nictation. Intact cilia in IL2 neurons, but not in other ciliated head neurons, were essential, as the restoration of the corresponding wild-type gene activity in IL2 neurons alone in cilia-defective mutants was sufficient to restore nictation. Optogenetic activation of IL2 neurons induced nictation, suggesting that signals from IL2 neurons are sufficient for nictation. Finally, we demonstrated that nictation is required for transmission of C. elegans to a new niche using flies as artificial carriers, suggesting a role of nictation as a dispersal and survival strategy under harsh conditions.
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