Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output. Big efforts are devoted to develop methods for effective selection of the relevant experimental data, before taking the quantitative analysis of bond parameters. Here we present a methodology which is based on the application of graph theory. The force-distance curves corresponding to repeated pulling events are mapped onto their correlation network (mathematical graph). On these graphs the groups of similar curves appear as topological modules, which are identified using the spectral analysis of graphs. We demonstrate the approach by analyzing a large ensemble of the force-distance curves measured on: ssDNA-ssDNA, peptide-RNA (system from HIV1), and peptide-Au surface. Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought together and/or pulling speeds. This demonstrates the sensitivity of the method to the spatial degrees of freedom, suggesting potential applications in the case of large molecular complexes and situations with multiple binding sites

Power-Law Scaling in the Internal Variability of Cumulus Cloud Size Distributions due to Subsampling and Spatial Organization

In this study, the spatial structure of cumulus cloud populations is investigated using three-dimensional snapshots from large-domain LES experiments. The aim is to understand and quantify the internal variability in cloud size distributions due to subsampling effects and spatial organization. A set of idealized shallow cumulus cases is selected with varying degrees of spatial organization, including a slowly organizing marine precipitating case and five more quickly organizing diurnal cases over land. A subdomain analysis is applied, yielding cloud number distributions at sample sizes ranging from severely undersampled to nearly complete. A strong power-law scaling is found in the relation between cloud number variability and subdomain size, reflecting an inverse linear relation. Scaling subdomain size by cloud size yields a data collapse across time points and cases, highlighting the role played by cloud spacing in controlling the stochastic variability. Spatial organization acts on top of this baseline model by increasing the maximum cloud size and by enhancing the variability in the number of smallest clouds. This reflects that the smaller clouds start to live on top of larger-scale thermodynamic structures, such as cold pools, which favor or inhibit their formation. Compositing all continental cumulus cases suggests the existence of a prototype diurnal time dependence in the spatial organization. A simple stochastic expression for cloud number variability is proposed that is formulated in terms of two dimensionless groups, which allows objective estimation of the degree of spatial organization in simulated and observed cumulus cloud populations

Factors Controlling Stratocumulus Cloud Lifetime Over Coastal Land

The breakup of stratocumulus clouds over coastal land areas is studied using a combination of large-eddy simulations (LESs) and mixed-layer models (MLMs) with a focus on mechanisms regulating the timing of the breakup. In contrast with stratocumulus over ocean, strong sensible heat flux over land prevents the cloud layer from decoupling during day. As the cloud thins during day, turbulence generated by surface flux becomes larger than turbulence generated by longwave cooling across the cloud layer. To capture this shift in turbulence generation in the MLM, an existing entrainment parameterization is extended. The MLM is able to mimic cloud evolution for a variety of Bowen ratios, but only after this modification of the entrainment parameterization. Cloud lifetime depends on a combination of the cloud-top entrainment flux, the Bowen ratio of the surface, and the strength of advection of cool ocean air by the sea breeze. For dry land surface conditions, the authors’ MLM suggests a breakup time a few hours after sunrise. For relatively wet land surface conditions, the cloud layer briefly breaks into partly cloudy conditions during midday, and the stratocumulus cloud reforms in the evening

Factors Controlling Stratocumulus Cloud Lifetime Over Coastal Land

The breakup of stratocumulus clouds over coastal land areas is studied using a combination of large-eddy simulations (LESs) and mixed-layer models (MLMs) with a focus on mechanisms regulating the timing of the breakup. In contrast with stratocumulus over ocean, strong sensible heat flux over land prevents the cloud layer from decoupling during day. As the cloud thins during day, turbulence generated by surface flux becomes larger than turbulence generated by longwave cooling across the cloud layer. To capture this shift in turbulence generation in the MLM, an existing entrainment parameterization is extended. The MLM is able to mimic cloud evolution for a variety of Bowen ratios, but only after this modification of the entrainment parameterization. Cloud lifetime depends on a combination of the cloud-top entrainment flux, the Bowen ratio of the surface, and the strength of advection of cool ocean air by the sea breeze. For dry land surface conditions, the authors’ MLM suggests a breakup time a few hours after sunrise. For relatively wet land surface conditions, the cloud layer briefly breaks into partly cloudy conditions during midday, and the stratocumulus cloud reforms in the evening

Reconciling and Validating the Cloud Thickness and Liquid Water Path Tendencies

A detailed derivation of stratocumulus cloud thickness and liquid water path tendencies as a function of the well-mixed boundary layer mass, heat, and moisture budget equations is presented. The derivation corrects an error in the cloud thickness tendency equation derived by R. Wood to make it consistent with the liquid water path tendency equation derived by J. J. van der Dussen et al. The validity of the tendency equations is then tested against the output of large-eddy simulations of a typical stratocumulus-topped boundary layer case and is found to be in good agreement

Monitoring core temperature of firefighters to validate a wearable non-invasive core thermometer in different types of protective clothing:Concurrent in-vivo validation

This study aims (1) to test the validity of a new non-invasive core thermometer, Cosinuss°, in rest and (2) during firefighting simulation tasks, against invasive temperature pill and inner-ear temperature and (3) to compare the change in core temperature of firefighters when working in two types of protective clothing (traditional turnout gear versus new concept). 11 active firefighters performed twice a selection of tasks during their periodic preventive medical examination and a fire-extinguishing task. Without correction no correlation between the Cosinuss° and thermometer pill (ICC≤0.09, p ≥ 0.154, LoA≥1.37) and a moderate correlation between Cosinuss° and inner-ear infrared (ICC = 0.40, p = 0.044, LoA±1.20) was observed. With individual correction both correlations were excellent (ICC≥0.84, p = 0.000, LoA≤0.30). However, during and after working all correlations were poor and non-significant (ICC≤0.38, p ≥ 0.091, LoA≥1.71). During firefighting tasks, the Cosinuss° is invalid for measuring the core temperature. No differences in heat development in the two types of protective clothing was proven

Marine Low Cloud Sensitivity to An Idealized Climate Change: The CGILS LES Intercomparison

Subtropical marine low cloud sensitivity to an idealized climate change is compared in six large-eddy simulation (LES) models as part of CGILS. July cloud cover is simulated at three locations over the subtropical northeast Pacific Ocean, which are typified by cold sea surface temperatures (SSTs) under well-mixed stratocumulus, cool SSTs under decoupled stratocumulus, and shallow cumulus clouds overlying warmer SSTs. The idealized climate change includes a uniform 2 K SST increase with corresponding moist-adiabatic warming aloft and subsidence changes, but no change in free-tropospheric relative humidity, surface wind speed, or CO2. For each case, realistic advective forcings and boundary conditions are generated for the control and perturbed states which each LES runs for 10 days into a quasi-steady state. For the control climate, the LESs correctly produce the expected cloud type at all three locations. With the perturbed forcings, all models simulate boundary-layer deepening due to reduced subsidence in the warmer climate, with less deepening at the warm-SST location due to regulation by precipitation. The models do not show a consistent response of liquid water path and albedo in the perturbed climate, though the majority predict cloud thickening (negative cloud feedback) at the cold-SST location and slight cloud thinning (positive cloud feedback) at the cool-SST and warm-SST locations. In perturbed climate simulations at the cold-SST location without the subsidence decrease, cloud albedo consistently decreases across the models. Thus, boundary-layer cloud feedback on climate change involves compensating thermodynamic and dynamic effects of warming and may interact with patterns of subsidence change

Marine Low Cloud Sensitivity to An Idealized Climate Change: The CGILS LES Intercomparison

Subtropical marine low cloud sensitivity to an idealized climate change is compared in six large-eddy simulation (LES) models as part of CGILS. July cloud cover is simulated at three locations over the subtropical northeast Pacific Ocean, which are typified by cold sea surface temperatures (SSTs) under well-mixed stratocumulus, cool SSTs under decoupled stratocumulus, and shallow cumulus clouds overlying warmer SSTs. The idealized climate change includes a uniform 2 K SST increase with corresponding moist-adiabatic warming aloft and subsidence changes, but no change in free-tropospheric relative humidity, surface wind speed, or CO2. For each case, realistic advective forcings and boundary conditions are generated for the control and perturbed states which each LES runs for 10 days into a quasi-steady state. For the control climate, the LESs correctly produce the expected cloud type at all three locations. With the perturbed forcings, all models simulate boundary-layer deepening due to reduced subsidence in the warmer climate, with less deepening at the warm-SST location due to regulation by precipitation. The models do not show a consistent response of liquid water path and albedo in the perturbed climate, though the majority predict cloud thickening (negative cloud feedback) at the cold-SST location and slight cloud thinning (positive cloud feedback) at the cool-SST and warm-SST locations. In perturbed climate simulations at the cold-SST location without the subsidence decrease, cloud albedo consistently decreases across the models. Thus, boundary-layer cloud feedback on climate change involves compensating thermodynamic and dynamic effects of warming and may interact with patterns of subsidence change