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1
Duncan, Anna L., Matthieu Chavent, Patrice Rassam, et al. "Nanoscale Protein Interactions Determine the Mesoscale Dynamic Organisation of Biomembranes." Biophysical Journal 114, no. 3 (2018): 391a. http://dx.doi.org/10.1016/j.bpj.2017.11.2163.
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Weijenborg, Chris, Petra Friederichs, and Andreas Hense. "Organisation of potential vorticity on the mesoscale during deep moist convection." Tellus A: Dynamic Meteorology and Oceanography 67, no. 1 (2015): 25705. http://dx.doi.org/10.3402/tellusa.v67.25705.
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Duncan, Anna L., Maximilian A. R. Bandurka, Matthieu G. Chavent, et al. "How Nanoscale Protein Interactions Determine the Mesoscale Dynamic Organisation of Membrane Proteins." Biophysical Journal 116, no. 3 (2019): 365a. http://dx.doi.org/10.1016/j.bpj.2018.11.1984.
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4
Mackay, Michael, Siyu Huo, and Marcus Kaiser. "Spatial organisation of the mesoscale connectome: A feature influencing synchrony and metastability of network dynamics." PLOS Computational Biology 19, no. 8 (2023): e1011349. http://dx.doi.org/10.1371/journal.pcbi.1011349.
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Significant research has investigated synchronisation in brain networks, but the bulk of this work has explored the contribution of brain networks at the macroscale. Here we explore the effects of changing network topology on functional dynamics in spatially constrained random networks representing mesoscale neocortex. We use the Kuramoto model to simulate network dynamics and explore synchronisation and critical dynamics of the system as a function of topology in randomly generated networks with a distance-related wiring probability and no preferential attachment term. We show networks which predominantly make short-distance connections smooth out the critical coupling point and show much greater metastability, resulting in a wider range of coupling strengths demonstrating critical dynamics and metastability. We show the emergence of cluster synchronisation in these geometrically-constrained networks with functional organisation occurring along structural connections that minimise the participation coefficient of the cluster. We show that these cohorts of internally synchronised nodes also behave en masse as weakly coupled nodes and show intra-cluster desynchronisation and resynchronisation events related to inter-cluster interaction. While cluster synchronisation appears crucial to healthy brain function, it may also be pathological if it leads to unbreakable local synchronisation which may happen at extreme topologies, with implications for epilepsy research, wider brain function and other domains such as social networks.
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Lagouvardos, K., V. Kotroni, and E. Defer. "Synoptic environment related to rapid cyclogenesis in the Eastern Mediterranean." Advances in Geosciences 7 (February 14, 2006): 115–19. http://dx.doi.org/10.5194/adgeo-7-115-2006.
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Abstract. This paper presents first results on the investigation of the synoptic conditions that led to the rapid development of a low-pressure system over the Aegean Sea. Indeed, during the period 21–22 January 2004, a very deep cyclone was observed over the Aegean Sea with a minimum central pressure of ~972 hPa, a value which is among the lowest observed over the entire Mediterranean Sea during the last 40 years. The rapid development was associated with a two-trough system that, under the influence of a very intense upper-level jet, was merged in one and then acquired a negative tilting. Additional information on the mesoscale organisation of the system is given, based on lightning data and space borne microwave and infrared observations.
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Duncan, Anna L., Maximillian A. R. Bandurka, Wanling Song та Mark S. P. Sansom. "Modelling the Dynamic Organisation of the β2-Adrenergic Receptor in Crowded Membranes: From the Nano to the Mesoscale". Biophysical Journal 118, № 3 (2020): 17a. http://dx.doi.org/10.1016/j.bpj.2019.11.277.
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Jansa, A., P. Alpert, P. Arbogast, et al. "MEDEX: a general overview." Natural Hazards and Earth System Sciences 14, no. 8 (2014): 1965–84. http://dx.doi.org/10.5194/nhess-14-1965-2014.
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Abstract. The general objective of the international MEDiterranean EXperiment (MEDEX) was the better understanding and forecasting of cyclones that produce high impact weather in the Mediterranean. This paper reviews the motivation and foundation of MEDEX, the gestation, history and organisation of the project, as well as the main products and scientific achievements obtained from it. MEDEX obtained the approval of World Meteorological Organisation (WMO) and can be considered as framed within other WMO actions, such as the ALPine EXperiment (ALPEX), the Mediterranean Cyclones Study Project (MCP) and, to a certain extent, THe Observing System Research and Predictability EXperiment (THORPEX) and the HYdrological cycle in Mediterranean EXperiment (HyMeX). Through two phases (2000–2005 and 2006–2010), MEDEX has produced a specific database, with information about cyclones and severe or high impact weather events, several main reports and a specific data targeting system field campaign (DTS-MEDEX-2009). The scientific achievements are significant in fields like climatology, dynamical understanding of the physical processes and social impact of cyclones, as well as in aspects related to the location of sensitive zones for individual cases, the climatology of sensitivity zones and the improvement of the forecasts through innovative methods like mesoscale ensemble prediction systems.
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Callens, S. J. P., R. Burdis, M. Cihova, J. A. Kim, Q. Y. Lau, and M. M. Stevens. "GEOMETRIC CONTROL OF BONE TISSUE GROWTH AND ORGANIZATION." Orthopaedic Proceedings 106-B, SUPP_1 (2024): 65. http://dx.doi.org/10.1302/1358-992x.2024.1.065.
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Cells typically respond to a variety of geometrical cues in their environment, ranging from nanoscale surface topography to mesoscale surface curvature. The ability to control cellular organisation and fate by engineering the shape of the extracellular milieu offers exciting opportunities within tissue engineering. Despite great progress, however, many questions regarding geometry-driven tissue growth remain unanswered.Here, we combine mathematical surface design, high-resolution microfabrication, in vitro cell culture, and image-based characterization to study spatiotemporal cell patterning and bone tissue formation in geometrically complex environments. Using concepts from differential geometry, we rationally designed a library of complex mesostructured substrates (101-103 µm). These substrates were accurately fabricated using a combination of two-photon polymerisation and replica moulding, followed by surface functionalisation. Subsequently, different cell types (preosteoblasts, fibroblasts, mesenchymal stromal cells) were cultured on the substrates for varying times and under varying osteogenic conditions. Using imaging-based methods, such as fluorescent confocal microscopy and second harmonic generation imaging, as well as quantitative image processing, we were able to study early-stage spatiotemporal cell patterning and late-stage extracellular matrix organisation. Our results demonstrate clear geometry-dependent cell patterning, with cells generally avoiding convex regions in favour of concave domains. Moreover, the formation of multicellular bridges and collective curvature-dependent cell orientation could be observed. At longer time points, we found clear and robust geometry-driven orientation of the collagenous extracellular matrix, which became apparent with second harmonic generation imaging after ∼2 weeks of culture.Our results highlight a key role for geometry as a cue to guide spatiotemporal cell and tissue organisation, which is relevant for scaffold design in tissue engineering applications. Our ongoing work aims at understanding the underlying principles of geometry-driven tissue growth, with a focus on the interactions between substrate geometry and mechanical forces.
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Jansa, A., P. Alpert, P. Arbogast, et al. "MEDEX: a general overview." Natural Hazards and Earth System Sciences Discussions 2, no. 1 (2014): 535–80. http://dx.doi.org/10.5194/nhessd-2-535-2014.
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Abstract. The general objective of the international MEDiterranean EXperiment (MEDEX) was the better understanding and forecasting of cyclones that produce high impact weather in the Mediterranean. This paper reviews the motivation and foundation of MEDEX, the gestation, history and organisation of the project, as well as the main products and scientific achievements obtained from it. MEDEX obtained the approval of WMO and can be considered as framed within other WMO actions, such as ALPEX, MCP and, to certain extent, THORPEX and HyMeX. Through two phases (2000–2005 and 2006–2010) MEDEX has produced a specific database, with information about cyclones and high impact weather events, several main reports and a specific field campaign (DTS-MEDEX-2009). The scientific achievements are significant in fields like climatology, dynamical understanding of the physical processes and social impact of cyclones, as well as on aspects related to the location of sensitive zones for individual cases, climatology of sensitivity zones and the improvement of the forecasts through innovative methods like mesoscale ensemble prediction systems.
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Siqueira, José Ricardo, and Valdo da Silva Marques. "Tracking and short-term forecasting of mesoscale convective cloud clusters over southeast Brazil using satellite infrared imagery." Journal of Southern Hemisphere Earth Systems Science 71, no. 1 (2021): 1. http://dx.doi.org/10.1071/es19050.
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This paper presents the tracking and short-term forecasting of mesoscale convective cloud clusters (CCs) that occurred over southeast Brazil and the adjacent Atlantic Ocean during 2009–17. These events produce intense rainfall and severe storms that impact agriculture, defence, hydroelectricity and offshore oil production. To identify, track and forecast CCs, the Geostationary Operational Environmental Satellite infrared imagery and the Forecasting and Tracking the Evolution of Cloud Clusters method are used. The forecast performance is investigated by applying statistical analyses between the observed and forecasted CCs’ physical properties. A total of 7139 mesoscale convective CCs were identified, tracked and selected for the short-term forecasting at their maturation phases. The CC tracking showed a high frequency of CCs over the Atlantic Ocean and mainly over continental and coastal southeast Brazil during the wet season. This indicates an important role played by the cold fronts and convective diurnal forcing on the organisation of convective cloudiness over that region. The majority of the CCs reached their maturation phases within the first 2h of life cycle, which occurred mostly between the late afternoon and evening. The CCs had short lifetimes and were predominantly in meso-β scales, followed by meso-α convective CCs. The CCs showed cloud-top temperatures typical of clouds with strong vertical development and potential to produce rainfall. The short-term forecasting of CCs at their maturation phases revealed different behaviours of the statistical indices with forecast range. For the 30–60-min timeframe, the forecasts performed relatively well. For longer forecast lead times (90–120min), the forecasts overestimated the occurrences, intensities and growth of the CCs and forecasted the CCs to be further north and east of their actual observed locations. Overall, our results may contribute to improving the forecast quality of these intense weather events.
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Singh, Shweta, and Norbert Kalthoff. "Process Studies of the Impact of Land-Surface Resolution on Convective Precipitation Based on High-Resolution ICON Simulations." Meteorology 1, no. 3 (2022): 254–73. http://dx.doi.org/10.3390/meteorology1030017.
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This study investigated the relevant processes responsible for differences of convective precipitation caused by land-surface resolution. The simulations were performed with the ICOsahedral Nonhydrostatic model (ICON) with grid spacing of 156 m and Large Eddy Simulation physics. Regions of different orographic complexity, days with weak synoptic forcing and favourable convective conditions were selected. The resolution of land-surface properties (soil type, vegetation) and/or the orography was reduced from 156 to 5000 m. Analyses are based on backward trajectories (Lagrangian Analysis Tool (LAGRANTO)), heat budget and convective organisation potential (COP) calculations. On average, the relative difference of areal mean daily precipitation at 1250 and 5000 m land-surface resolutions compared to 156 m were 6% and 15%, respectively. No consistent dependency of precipitation on orography or land-surface properties was found. Both factors impact convective initiation over areas with embedded mesoscale-sized land-surface heterogeneities. The position of convective precipitation was often influenced by the resolution of orography. Coarsening from 156 to 5000 m considerably changed the location of wind convergence and associated convection initiation. It also affects the onset times of clouds (<20 min) and precipitation (≈1 h). Cloud aggregation and microphysical processes proved to be important for further development towards convective precipitation.
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Masson, V., P. Le Moigne, E. Martin, et al. "The SURFEXv7.2 land and ocean surface platform for coupled or offline simulation of earth surface variables and fluxes." Geoscientific Model Development 6, no. 4 (2013): 929–60. http://dx.doi.org/10.5194/gmd-6-929-2013.
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Abstract. SURFEX is a new externalized land and ocean surface platform that describes the surface fluxes and the evolution of four types of surfaces: nature, town, inland water and ocean. It is mostly based on pre-existing, well-validated scientific models that are continuously improved. The motivation for the building of SURFEX is to use strictly identical scientific models in a high range of applications in order to mutualise the research and development efforts. SURFEX can be run in offline mode (0-D or 2-D runs) or in coupled mode (from mesoscale models to numerical weather prediction and climate models). An assimilation mode is included for numerical weather prediction and monitoring. In addition to momentum, heat and water fluxes, SURFEX is able to simulate fluxes of carbon dioxide, chemical species, continental aerosols, sea salt and snow particles. The main principles of the organisation of the surface are described first. Then, a survey is made of the scientific module (including the coupling strategy). Finally, the main applications of the code are summarised. The validation work undertaken shows that replacing the pre-existing surface models by SURFEX in these applications is usually associated with improved skill, as the numerous scientific developments contained in this community code are used to good advantage.
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Villiger, Leonie, Marina Dütsch, Sandrine Bony, et al. "Water isotopic characterisation of the cloud–circulation coupling in the North Atlantic trades – Part 1: A process-oriented evaluation of COSMOiso simulations with EUREC4A observations." Atmospheric Chemistry and Physics 23, no. 23 (2023): 14643–72. http://dx.doi.org/10.5194/acp-23-14643-2023.
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Abstract. Naturally available, stable, and heavy water molecules such as HDO and H218O have a lower saturation vapour pressure than the most abundant light water molecule H216O; therefore, these heavy water molecules preferentially condense and rain out during cloud formation. Stable water isotope observations thus have the potential to provide information on cloud processes in the trade-wind region, in particular when combined with high-resolution model simulations. In order to evaluate this potential, nested COSMOiso (isotope-enabled Consortium for Small Scale Modelling; Steppeler et al., 2003; Pfahl et al., 2012) simulations with explicit convection and horizontal grid spacings of 10, 5, and 1 km were carried out in this study over the tropical Atlantic for the time period of the EUREC4A (Elucidating the role of clouds-circulation coupling in climate; Stevens et al., 2021) field experiment. The comparison to airborne in situ and remote sensing observations shows that the three simulations are able to distinguish between different mesoscale cloud organisation patterns as well as between periods with comparatively high and low rain rates. Cloud fraction and liquid water content show a better agreement with aircraft observations with higher spatial resolution, because they show strong spatial variations on the scale of a few kilometres. A low-level cold-dry bias, including too depleted vapour in the subcloud and cloud layer and too enriched vapour in the free troposphere, is found in all three simulations. Furthermore, the simulated secondary isotope variable d-excess in vapour is overestimated compared to observations. Special attention is given to the cloud base level, which is the formation altitude of shallow cumulus clouds. The temporal variability of the simulated isotope variables at cloud base agrees reasonably well with observations, with correlations of the flight-to-flight data as high as 0.7 for δ2H and d-excess. A close examination of isotopic characteristics under precipitating clouds, non-precipitating clouds, clear-sky and dry-warm patches at the altitude of cloud base shows that these different environments are represented faithfully in the model with similar frequencies of occurrence, isotope signals, and specific-humidity anomalies as found in the observations. Furthermore, it is shown that the δ2H of cloud base vapour at the hourly timescale is mainly controlled by mesoscale transport and not by local microphysical processes, while the d-excess is mainly controlled by large-scale drivers. Overall, this evaluation of COSMOiso, including the isotopic characterisation of different cloud base environments, suggests that the simulations can be used for investigating the role of atmospheric circulations on different scales for controlling the formation of shallow cumulus clouds in the trade-wind region, as will be done in part 2 of this study.
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Poologaindran, A., R. Romero-Garcia, M. Hart, et al. "OS14.4.A The Neuroplastic Potential of the Human Brain before and After Glioma Surgery: Towards “Interventional Neurorehabilitation." Neuro-Oncology 23, Supplement_2 (2021): ii16. http://dx.doi.org/10.1093/neuonc/noab180.052.
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Abstract INTRODUCTION The human brain is a highly neuroplastic ‘complex’ network: it self-organises without a hard blueprint, adapts to evolving circumstances, and can withstand insults. However, similar to other naturally occurring networks, brain networks can only endure a finite amount of damage before cognitive processes are affected. In this study, we first sought to establish the brain networks governing domain-general cognition (DGC) in healthy individuals across the lifespan. We then sought to map, track, and potentially rehabilitate networks governing DGC through connectomics and non-invasive brain stimulation (NIBS) when damaged by low-grade gliomas (LGG) and surgical oncology. METHODS Using MRI and cognitive data from n=629 individuals (aged 18–88, Female= 51%), we assessed the structural, functional, and topological relevance of the spatially-distributed multiple-demand (MD) system for DGC. Next, in n=17 patients undergoing glioma surgery, we longitudinally acquired connectomic and cognitive data at multiple time points: pre-surgery and post-surgery Day 1, Month 3, Month 12. In an independent cohort of n=34 patients, we sought to establish the safety profile for “interventional neurorehabilitation”: connectome-driven NIBS in the acute post-operative period to accelerate cognitive recovery. RESULTS In healthy individuals, the MD system across multiple scales of biological organisation was positively associated with higher-order cognition (Catell’s fluid intelligence). In our patients, pre-operative LGG infiltration into the structural MD system was negatively associated with the number of long-term cognitive deficits, suggesting a functional reorganisation. Mixed-effects modelling demonstrated the resilience of the functional MD system to infiltration and resection, while the early post-operative period was critical for effective neurorehabilitation. Graph analyses revealed increased perioperative modularity can distinguish patients with long-term cognitive improvements at one-year follow-up. Finally, NIBS within two weeks post-craniotomy had a 90% (n=31/34) recruitment rate into the trial. There were no seizures or serious complications due to NIBS in this patient population. Transient headaches and tingling were reported in a minority of patients. CONCLUSION For the first time, we elucidate long-term cognitive and network trajectories following LGG surgery while establishing a positive safety-profile for NIBS in the acute post-operative period. We argue that “mesoscale” brain mapping serves as a robust biomarker for intervention-related plasticity for future clinical trials. While we performed these experiments in the context of neurosurgery, connectomics and NIBS could be adopted across diverse neuro-oncological care pathways (i.e. chemotherapy/radiation).
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Huntrieser, H., H. Schlager, M. Lichtenstern, et al. "NO<sub>x</sub> production by lightning in Hector: first airborne measurements during SCOUT-O3/ACTIVE." Atmospheric Chemistry and Physics Discussions 9, no. 4 (2009): 14361–451. http://dx.doi.org/10.5194/acpd-9-14361-2009.
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Abstract. During the SCOUT-O3/ACTIVE field phase in November–December 2005 airborne in situ measurements were performed inside and in the vicinity of thunderstorms over northern Australia with several research aircraft (German Falcon, Russian M55 Geophysica, and British Dornier-228). Here a case study from 19 November is presented in large detail on the basis of airborne trace gas measurements (NO, NOy, CO, O3) and stroke measurements from the German LIghtning Location NETwork (LINET), set up in the vicinity of Darwin during the field campaign. The anvil outflow from three different types of thunderstorms was probed by the Falcon aircraft: 1) a continental thunderstorm developing in a tropical airmass near Darwin, 2) a mesoscale convective system (MCS) developing within the tropical maritime continent (Tiwi Islands) known as Hector, and 3) a continental thunderstorm developing in a subtropical airmass ~200 km south of Darwin. For the first time detailed measurements of NO were performed in the Hector outflow. The highest NO mixing ratios were observed in Hector with peaks up to 7 nmol mol−1 in the main anvil outflow at ~11.5–12.5 km altitude. The mean NOx (=NO+NO2) mixing ratios during these penetrations (~100 km width) varied between 2.2 and 2.5 nmol mol−1. The NOx contribution from the boundary layer (BL), transported upward with the convection, to total anvil-NOx was found to be minor (<10%). On the basis of Falcon measurements, the mass flux of lightning-produced NOx (LNOx) in the well-developed Hector system was estimated to 0.6–0.7 kg(N) s−1. The highest average stroke rate of the probed thunderstorms was observed in the Hector system with 0.2 strokes s−1 (here only strokes with peak currents ≥10 kA contributing to LNOx were considered). The LNOx mass flux and the stroke rate were combined to estimate the LNOx production rate in the different thunderstorm types. For a better comparison with other studies, LINET strokes were scaled with Lightning Imaging Sensor (LIS) flashes. The LNOx production rate per LIS flash was estimated to 4.1–4.8 kg(N) for the well-developed Hector system, and to 5.4 and 1.7 kg(N) for the continental thunderstorms developing in subtropical and tropical airmasses, respectively. If we assume, that these different types of thunderstorms are typical thunderstorms globally (LIS flash rate ~44 s−1), the annual global LNOx production rate based on Hector would be ~5.7–6.6 Tg(N) a−1 and based on the continental thunderstorms developing in subtropical and tropical airmasses ~7.6 and ~2.4 Tg(N) a−1, respectively. The latter thunderstorm type produced much less LNOx per flash compared to the subtropical and Hector thunderstorms, which may be caused by the shorter mean flash component length observed in this storm. It is suggested that the vertical wind shear influences the horizontal extension of the charged layers, which seems to play an important role for the flash lengths that may originate. In addition, the horizontal dimension of the anvil outflow and the cell organisation within the thunderstorm system are probably important parameters influencing flash length and hence LNOx production per flash.
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Huntrieser, H., H. Schlager, M. Lichtenstern, et al. "NO<sub>x</sub> production by lightning in Hector: first airborne measurements during SCOUT-O3/ACTIVE." Atmospheric Chemistry and Physics 9, no. 21 (2009): 8377–412. http://dx.doi.org/10.5194/acp-9-8377-2009.
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Abstract. During the SCOUT-O3/ACTIVE field phase in November–December 2005, airborne in situ measurements were performed inside and in the vicinity of thunderstorms over northern Australia with several research aircraft (German Falcon, Russian M55 Geophysica, and British Dornier-228. Here a case study from 19 November is presented in detail on the basis of airborne trace gas measurements (NO, NOy, CO, O3) and stroke measurements from the German LIghtning Location NETwork (LINET), set up in the vicinity of Darwin during the field campaign. The anvil outflow from three different types of thunderstorms was probed by the Falcon aircraft: (1) a continental thunderstorm developing in a tropical airmass near Darwin, (2) a mesoscale convective system (MCS), known as Hector, developing within the tropical maritime continent (Tiwi Islands), and (3) a continental thunderstorm developing in a subtropical airmass ~200 km south of Darwin. For the first time detailed measurements of NO were performed in the Hector outflow. The highest NO mixing ratios were observed in Hector with peaks up to 7 nmol mol−1 in the main anvil outflow at ~11.5–12.5 km altitude. The mean NOx (=NO+NO2) mixing ratios during these penetrations (~100 km width) varied between 2.2 and 2.5 nmol mol−1. The NOx contribution from the boundary layer (BL), transported upward with the convection, to total anvil-NOx was found to be minor (<10%). On the basis of Falcon measurements, the mass flux of lightning-produced NOx (LNOx) in the well-developed Hector system was estimated to 0.6–0.7 kg(N) s−1. The highest average stroke rate of the probed thunderstorms was observed in the Hector system with 0.2 strokes s−1 (here only strokes with peak currents ≥10 kA contributing to LNOx were considered). The LNOx mass flux and the stroke rate were combined to estimate the LNOx production rate in the different thunderstorm types. For a better comparison with other studies, LINET strokes were scaled with Lightning Imaging Sensor (LIS) flashes. The LNOx production rate per LIS flash was estimated to 4.1–4.8 kg(N) for the well-developed Hector system, and to 5.4 and 1.7 kg(N) for the continental thunderstorms developing in subtropical and tropical airmasses, respectively. If we assume, that these different types of thunderstorms are typical thunderstorms globally (LIS flash rate ~44 s−1), the annual global LNOx production rate based on Hector would be ~5.7–6.6 Tg(N) a−1 and based on the continental thunderstorms developing in subtropical and tropical airmasses ~7.6 and ~2.4 Tg(N) a−1, respectively. The latter thunderstorm type produced much less LNOx per flash compared to the subtropical and Hector thunderstorms, which may be caused by the shorter mean flash component length observed in this storm. It is suggested that the vertical wind shear influences the horizontal extension of the charged layers, which seems to play an important role for the flash lengths that may originate. In addition, the horizontal dimension of the anvil outflow and the cell organisation within the thunderstorm system are probably important parameters influencing flash length and hence LNOx production per flash.
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O'Malley, Brendan, David J. Moore, Massimo Noro, et al. "Towards a Mechanical Model of Skin: Insights into Stratum Corneum Mechanical Properties from Hierarchical Models of Lipid Organisation." MRS Proceedings 844 (2004). http://dx.doi.org/10.1557/proc-844-y5.7.
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ABSTRACTThe stratum corneum (SC), the outermost layer of the skin, provides the body with a physiologically essential barrier to unregulated water loss and the influx of exogenous substances. Furthermore, the 10–20 micron thick SC, composed of overlapping protein-rich corneocytes surrounded by a heterogeneous multilamellar lipid matrix, displays tremendous mechanical cohesion and thermal integrity. To understand the contribution of these components to SC mechanical properties requires building a complete mechanical model of the skin. In this study we focus on modelling the hierarchical microstructure of the lipid phase and its relation to mechanical properties using a combination of atomistic and mesoscale simulations. The modelling approaches are parameterised with experimental data from FT-IR spectroscopy, X-ray scattering and, in the case of the mesoscale simulations, with detailed density profiles derived from atomic models. The atomistic models are used to probe the role of specific lipid species in maintaining the thermal and structural stability of the SC extracellular lipid matrix and to investigate the role of hydrogen bonding networks in SC lipid cohesion. Mesoscale models are used to investigate domain formation and lipid bilayer organisation on length and time scales inaccessible with atomistic models. These coarse grained models display transitions between ordered hexagonal gel phases and fluid phases, reproducing the experimentally observed ordering of the hydrophilic and hydrophobic regions.
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Chavent, Matthieu, Anna L. Duncan, Patrice Rassam, et al. "How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins." Nature Communications 9, no. 1 (2018). http://dx.doi.org/10.1038/s41467-018-05255-9.
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Brient, Florent, Fleur Couvreux, Catherine Rio, and Rachel Honnert. "Coherent subsiding structures in large eddy simulations of atmospheric boundary layers." Quarterly Journal of the Royal Meteorological Society, November 21, 2023. http://dx.doi.org/10.1002/qj.4625.
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AbstractCoherent structures are characterized in high‐resolution simulations of three atmospheric boundary layers: dry convection, marine cumulus, and stratocumulus. Based on radioactive‐decaying tracers emitted at different altitudes (surface, top of well‐mixed layer, and cloud top), a object‐oriented methodology allows individual characterization of coherent tridimensional plumes within the flow.Each boundary layer shows updraft structures surrounded by subsiding shells that have similar thermodynamical characteristics. Well‐mixed downdrafts are located relatively close to updrafts and entrain dry, warm air from the free troposphere. Identified in all boundary layers, these subsiding structures are triggered by air mass convergence linked to updrafts' divergence and are thus part of an overturning circulation in well‐mixed layers. Close to the surface, downdrafts' divergence constrain updrafts' locations and thus shape a mesoscale cellular organisation with cell sizes scaling with the boundary‐layer height (aspect ratio of around 2).Active cumulus formation does not strongly perturb the spatial organisation of the sub‐cloud well‐mixed layer. The stratocumulus‐topped boundary layer also shares similarities with the overturning circulation despite having condensation and cloud‐radiation diabatic effects within the mixed layer. However, the visible mesoscale organisation of stratocumulus shows larger cells than the boundary‐layer depth (aspect ratio > 10) that suggest deviations from the clear‐sky conceptual view. The boundary‐layer decoupling influences mass fluxes of coherent structures and thus potentially play a role in shaping the spatial organisation.Since well‐mixed downdrafts contribute to a significant part of resolved flux of heat and moisture, our results suggest that downdraft properties in well mixed layers should be represented at the subgrid scale in climate models through non‐local mass‐flux parameterizations.This article is protected by copyright. All rights reserved.
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Vedechkina, Maria, Duncan E. Astle, and Joni Holmes. "Dimensions of early life adversity and their associations with functional brain organisation." Imaging Neuroscience, 2024. http://dx.doi.org/10.1162/imag_a_00145.
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Abstract Early life adversity is associated with differences in brain function and an elevated risk for poor mental health. Using data from children aged 10 (N=5,798) from the ABCD cohort we investigated how adversity relates to functional brain organisation using a network neuroscience approach. We derived four data-driven categories of adversity by fitting a mixed graphical model: household/community instability, physical/sexual abuse, parental neglect, and financial difficulties. Analyses revealed that multiple forms of adversity were associated with reduced clustering and increased assortativity across the entire brain and that these local measures of organisation captured greater adversity-related variance than mesoscale measures like modularity. The most pronounced effects were in the somatosensory and subcortical networks. Financial difficulties showed the strongest and most widespread associations with brain organisation, with evidence of a mediating effect of assortativity on the association between financial difficulties and internalising symptoms. Adding race as a covariate attenuated most brain-adversity relationships, suggesting that experiences of adversity are strongly related to race/ethnicity in the ABCD sample. These results demonstrate that different forms of adversity are associated with both shared and unique variations in functional brain organisation, highlighting its potential significance for explaining individual differences in mental health outcomes following early life adversity.
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Head, Louise C., Claire Doré, Ryan R. Keogh, et al. "Spontaneous self-constraint in active nematic flows." Nature Physics, January 18, 2024. http://dx.doi.org/10.1038/s41567-023-02336-5.
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AbstractActive processes drive biological dynamics across various scales and include subcellular cytoskeletal remodelling, tissue development in embryogenesis and the population-level expansion of bacterial colonies. In each of these, biological functionality requires collective flows to occur while self-organised structures are protected. However, the mechanisms by which active flows can spontaneously constrain their dynamics to preserve structure are not known. Here, by studying collective flows and defect dynamics in active nematic films, we demonstrate the existence of a self-constraint, namely a two-way, spontaneously arising relationship between activity-driven isosurfaces of flow boundaries and mesoscale nematic structures. We show that self-motile defects are tightly constrained to viscometric surfaces, which are contours along which the vorticity and the strain rate are balanced. This in turn reveals that self-motile defects break mirror symmetry when they move along a single viscometric surface. This is explained by an interdependence between viscometric surfaces and bend walls, which are elongated narrow kinks in the orientation field. These findings indicate that defects cannot be treated as solitary points. Instead, their associated mesoscale deformations are key to the steady-state coupling to hydrodynamic flows. This mesoscale cross-field self-constraint offers a framework for tackling complex three-dimensional active turbulence, designing dynamic control into biomimetic materials and understanding how biological systems can employ active stress for dynamic self-organisation.
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Gillot, Camille, Guilhem Dif-Pradalier, Yanick Sarazin, et al. "The problem of capturing marginality in model reductions of turbulence." Plasma Physics and Controlled Fusion, March 8, 2023. http://dx.doi.org/10.1088/1361-6587/acc276.
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Abstract Reduced quasilinear (QL) and nonlinear (gradient-driven) models with scale separations, commonly used to interpret experiments and to forecast turbulent transport levels in magnetised plasmas are tested against nonlinear models without scale separations (flux-driven). Two distinct regimes of turbulence --either far above threshold or near marginal stability-- are investigated with Boltzmann electrons. The success of reduced models especially hinges on the reproduction of nonlinear fluxes. Good agreement between models is found above threshold whilst reduced models would significantly underpredict fluxes near marginality, overlooking mesoscale flow organisation and turbulence self-advection. Constructive prescriptions whereby to improve reduced models is discussed.
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Hof, Lotta, Till Moreth, Michael Koch, et al. "Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis." BMC Biology 19, no. 1 (2021). http://dx.doi.org/10.1186/s12915-021-00958-w.
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Abstract Background Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days. Results We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures. Conclusion Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.
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Richardson, Robin A., Benjamin S. Hanson, Daniel J. Read, Oliver G. Harlen, and Sarah A. Harris. "Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis." Quarterly Reviews of Biophysics 53 (2020). http://dx.doi.org/10.1017/s0033583520000062.
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Abstract Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject to explicit thermal noise, we have quantified the constraints on the range of molecular conformations that can be explored by dynein-c within the crowded architecture of the axoneme. We subsequently assess the influence of crowding on the 3D exploration of microtubule-binding sites, and specifically on the axial step length. Our calculations combine experimental information on the shape, flexibility and environment of dynein-c from three distinct sources; negative stain electron microscopy, cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET). Our FFEA simulations show that the super-macromolecular organisation of multiple protein complexes into higher-order structures can have a significant influence on the effective flexibility of the individual molecular components, and may, therefore, play an important role in the physical mechanisms underlying their biological function.
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"Preface." Journal of Physics: Conference Series 2718, no. 1 (2024): 011001. http://dx.doi.org/10.1088/1742-6596/2718/1/011001.
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2023 International Conference on Frontiers of Ocean Science and Technology (ICFOST), sponsored by the College of Meteorology and Oceanology, National University of Defense Technology, was held successfully in Jiusuo Hotel Changsha from October 13 to 15, 2023. The Organizing Committees have invited experts in Marine science, Marine technology, Marine engineering, Marine resource exploration and application, Marine equipment R&D and manufacturing, etc. for academic exchanges. The Conference includes discussions on topics such as ocean circulation, air-sea interaction and ocean climate, ocean mesoscale and small-scale processes, ocean remote sensing and data analysis, ocean prediction, ocean environmental safety and support, ocean exploration technology, artificial intelligence oceanography, underwater acoustics, underwater acoustics signal processing, and oceanography teaching skills with a view to promoting the common development of industries, universities and research institutes in the field of ocean science and technologies. This year, ICFOST 2023 will consist of 10 oral sessions, 4 keynote talks from Prof. Juncheng Wang (National Engineering and Technology Research Center for Ocean Monitoring Equipment, China), Prof. Wenju Cai (Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia), Prof. Fangli Qiao (First Institute of Oceanography, Ministry of Natural Resources, China), Prof. Lianglong Da (Naval Submarine Academy, China), as well as 45 invited talks given by distinguished scholars and researchers from the related academic field. It will be a golden opportunity for the students, researchers and engineers to interact among themselves to get better views on technical development and trends for the near future. On behalf of the organizing committees, we’d like to express our sincere gratitude to everyone who has contributed to ICFOST 2023 as its success could have only been achieved through a team effort. Our special thanks go to all the conference speakers for their insightful reviews on many emerging research topics. We would like to thank the program chairs and the session chairs, for their support to the conference; as well as all the technical committee members and reviewers for their excellent work in promoting the conference and reviewing the papers. Finally, we are grateful to all the authors and presenters of the papers as well as all the attendees for their contributions to this wonderful conference. Warmest regards, ICFOST 2023 Organizing Committees List of Conference Committees are available in this Pdf.
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Short, Ewan, Todd P. Lane, and Claire L. Vincent. "Objectively Diagnosing Characteristics of Mesoscale Organization from Radar Reflectivity and Ambient Winds." Monthly Weather Review, November 30, 2022. http://dx.doi.org/10.1175/mwr-d-22-0146.1.
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Abstract In the classical model of mesoscale convective systems (MCSs), a system generates new convective cells on the down-shear side of its cold pool, with the cells fed at low levels from the front, and the stratiform cloud trailing behind the system in the up-shear direction, where “front” and “behind” typically refer to the system’s ground-relative velocity. In this study we present an algorithm for identifying and tracking MCSs in radar reflectivity data, and objectively diagnosing organisational characteristics related to the classical model, namely the offset of stratiform cloud from convective cloud relative to system velocity, the low-level inflow direction, and the shear-relative tilt and propagation directions. When applied to the 15 year radar record covering the Darwin region of northern Australia, the algorithm indicates 65–80% of MCS observations are consistent with the classical model, at least when the four classifications can be made unambiguously. However, these observed characteristics occur almost entirely in the drier phases of the Australian monsoon. During the humid, active monsoon phase, observed characteristics consistent with the classical model are rare, and most systems exhibit non-classical up-shear propagation.
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Abubakar, Eleojo Oluwaseun, and Niall Cunningham. "Small-area estimation and analysis of HIV/AIDS indicators for precise geographical targeting of health interventions in Nigeria. a spatial microsimulation approach." International Journal of Health Geographics 22, no. 1 (2023). http://dx.doi.org/10.1186/s12942-023-00341-8.
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Abstract Background Precise geographical targeting is well recognised as an indispensable intervention strategy for achieving many Sustainable Development Goals (SDGs). This is more cogent for health-related goals such as the reduction of the HIV/AIDS pandemic, which exhibits substantial spatial heterogeneity at various spatial scales (including at microscale levels). Despite the dire data limitations in Low and Middle Income Countries (LMICs), it is essential to produce fine-scale estimates of health-related indicators such as HIV/AIDS. Existing small-area estimates (SAEs) incorporate limited synthesis of the spatial and socio-behavioural aspects of the HIV/AIDS pandemic and/or are not adequately grounded in international indicator frameworks for sustainable development initiatives. They are, therefore, of limited policy-relevance, not least because of their inability to provide necessary fine-scale socio-spatial disaggregation of relevant indicators. Methods The current study attempts to overcome these challenges through innovative utilisation of gridded demographic datasets for SAEs as well as the mapping of standard HIV/AIDS indicators in LMICs using spatial microsimulation (SMS). Results The result is a spatially enriched synthetic individual-level population of the study area as well as microscale estimates of four standard HIV/AIDS and sexual behaviour indicators. The analysis of these indicators follows similar studies with the added advantage of mapping fine-grained spatial patterns to facilitate precise geographical targeting of relevant interventions. In doing so, the need to explicate socio-spatial variations through proper socioeconomic disaggregation of data is reiterated. Conclusions In addition to creating SAEs of standard health-related indicators from disparate multivariate data, the outputs make it possible to establish more robust links (even at individual levels) with other mesoscale models, thereby enabling spatial analytics to be more responsive to evidence-based policymaking in LMICs. It is hoped that international organisations concerned with producing SDG-related indicators for LMICs move towards SAEs of such metrics using methods like SMS.