New insights on growth mechanisms of protein clusters at surfaces: an AFM and simulation study

Despite its relevance to a wide range of technological and fundamental areas, a quantitative understanding of protein surface clustering dynamics is often lacking. In inorganic crystal growth, surface clustering of adatoms is well described by diffusion-aggregation models. In such models, the statistical properties of the aggregate arrays often reveal the molecular scale aggregation processes. We investigate the potential of these theories to reveal hitherto hidden facets of protein clustering by carrying out concomitant observations of lysozyme adsorption onto mica surfaces, using atomic force microscopy. and Monte Carlo simulations of cluster nucleation and growth. We find that lysozyme clusters diffuse across the substrate at a rate that varies inversely with size. This result suggests which molecular scale mechanisms are responsible for the mobility of the proteins on the substrate. In addition the surface diffusion coefficient of the monomer can also be extracted from the comparison between experiments and simulations. While concentrating on a model system of lysozyme-on-mica, this 'proof of concept' study successfully demonstrates the potential of our approach to understand and influence more biomedically applicable protein-substrate couples.

Numerical simulation of the 12 May 1997 CME Event: The role of magnetic reconnection

We perform a numerical study of the evolution of a Coronal Mass Ejection (CME) and its interaction with the coronal magnetic field based on the 12 May 1997, CME event using a global MagnetoHydroDynamic (MHD) model for the solar corona. The ambient solar wind steady-state solution is driven by photospheric magnetic field data, while the solar eruption is obtained by superimposing an unstable flux rope onto the steady-state solution. During the initial stage of CME expansion, the core flux rope reconnects with the neighboring field, which facilitates lateral expansion of the CME footprint in the low corona. The flux rope field also reconnects with the oppositely orientated overlying magnetic field in the manner of the breakout model. During this stage of the eruption, the simulated CME rotates counter-clockwise to achieve an orientation that is in agreement with the interplanetary flux rope observed at 1 AU. A significant component of the CME that expands into interplanetary space comprises one of the side lobes created mainly as a result of reconnection with the overlying field. Within 3 hours, reconnection effectively modifies the CME connectivity from the initial condition where both footpoints are rooted in the active region to a situation where one footpoint is displaced into the quiet Sun, at a significant distance (≈1R ) from the original source region. The expansion and rotation due to interaction with the overlying magnetic field stops when the CME reaches the outer edge of the helmet streamer belt, where the field is organized on a global scale. The simulation thus offers a new view of the role reconnection plays in rotating a CME flux rope and transporting its footpoints while preserving its core structure.

Simulation of crop yields using ERA-40: Limits to skill and nonstationarity in weather-yield relationships

Reanalysis data provide an excellent test bed for impacts prediction systems. because they represent an upper limit on the skill of climate models. Indian groundnut (Arachis hypogaea L.) yields have been simulated using the General Large-Area Model (GLAM) for annual crops and the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-yr reanalysis (ERA-40). The ability of ERA-40 to represent the Indian summer monsoon has been examined. The ability of GLAM. when driven with daily ERA-40 data, to model both observed yields and observed relationships between subseasonal weather and yield has been assessed. Mean yields "were simulated well across much of India. Correlations between observed and modeled yields, where these are significant. are comparable to correlations between observed yields and ERA-40 rainfall. Uncertainties due to the input planting window, crop duration, and weather data have been examined. A reduction in the root-mean-square error of simulated yields was achieved by applying bias correction techniques to the precipitation. The stability of the relationship between weather and yield over time has been examined. Weather-yield correlations vary on decadal time scales. and this has direct implications for the accuracy of yield simulations. Analysis of the skewness of both detrended yields and precipitation suggest that nonclimatic factors are partly responsible for this nonstationarity. Evidence from other studies, including data on cereal and pulse yields, indicates that this result is not particular to groundnut yield. The detection and modeling of nonstationary weather-yield relationships emerges from this study as an important part of the process of understanding and predicting the impacts of climate variability and change on crop yields.

Understanding advances in the simulation of intraseasonal variability in the ECMWF model. Part II: the application of process-based diagnostics

In Part I of this study it was shown that moving from a moisture-convergent- to a relative-humidity-dependent organized entrainment rate in the formulation for deep convection was responsible for significant advances in the simulation of the Madden – Julian Oscillation (MJO) in the ECMWF model. However, the application of traditional MJO diagnostics were not adequate to understand why changing the control on convection had such a pronounced impact on the representation of the MJO. In this study a set of process-based diagnostics are applied to the hindcast experiments described in Part I to identify the physical mechanisms responsible for the advances in MJO simulation. Increasing the sensitivity of the deep convection scheme to environmental moisture is shown to modify the relationship between precipitation and moisture in the model. Through dry-air entrainment, convective plumes ascending in low-humidity environments terminate lower in the atmosphere. As a result, there is an increase in the occurrence of cumulus congestus, which acts to moisten the mid troposphere. Due to the modified precipitation – moisture relationship more moisture is able to build up, which effectively preconditions the tropical atmosphere for the t ransition t o d eep convection. R esults from this study suggest that a tropospheric moisture control on convection is key to simulating the interaction between the convective heating and the large-scale wave forcing associated with the MJO.

Comparison of the open-closed separatrix in a global magnetospheric simulation with observations: the role of the ring current

The development of global magnetospheric models, such as Space Weather Modeling Framework (SWMF), which can accurately reproduce and track space weather processes has high practical utility. We present an interval on 5 June 1998, where the location of the polar cap boundary, or open-closed field line boundary (OCB), can be determined in the ionosphere using a combination of instruments during a period encompassing a sharp northward to southward interplanetary field turning. We present both point- and time-varying comparisons of the observed and simulated boundaries in the ionosphere and find that when using solely the coupled ideal magnetohydrodynamic magnetosphere-ionosphere model, the rate of change of the OCB to a southward turning of the interplanetary field is significantly faster than that computed from the observational data. However, when the inner magnetospheric module is incorporated, the modeling framework both qualitatively, and often quantitatively, reproduces many elements of the studied interval prior to an observed substorm onset. This result demonstrates that the physics of the inner magnetosphere is critical in shaping the boundary between open and closed field lines during periods of southward interplanetary magnetic field (IMF) and provides significant insight into the 3-D time-dependent behavior of the Earth's magnetosphere in response to a northward-southward IMF turning. We assert that during periods that do not include the tens of minutes surrounding substorm expansion phase onset, the coupled SWMF model may provide a valuable and reliable tool for estimating both the OCB and magnetic field topology over a wide range of latitudes and local times.

Unsteady flow simulation of a vertical axis augmented wind turbine: a two-dimensional study

As the integration of vertical axis wind turbines in the built environment is a promising alternative to horizontal axis wind turbines, a 2D computational investigation of an augmented wind turbine is proposed and analysed. In the initial CFD analysis, three parameters are carefully investigated: mesh resolution; turbulence model; and time step size. It appears that the mesh resolution and the turbulence model affect result accuracy; while the time step size examined, for the unsteady nature of the flow, has small impact on the numerical results. In the CFD validation of the open rotor with secondary data, the numerical results are in good agreement in terms of shape. It is, however, observed a discrepancy factor of 2 between numerical and experimental data. Successively, the introduction of an omnidirectional stator around the wind turbine increases the power and torque coefficients by around 30–35% when compared to the open case; but attention needs to be given to the orientation of the stator blades for optimum performance. It is found that the power and torque coefficients of the augmented wind turbine are independent of the incident wind speed considered.

The plasticity of the mirror system: how reward learning modulates cortical motor simulation of others

Cortical motor simulation supports the understanding of others' actions and intentions. This mechanism is thought to rely on the mirror neuron system (MNS), a brain network that is active both during action execution and observation. Indirect evidence suggests that alpha/beta suppression, an electroencephalographic (EEG) index of MNS activity, is modulated by reward. In this study we aimed to test the plasticity of the MNS by directly investigating the link between alpha/beta suppression and reward. 40 individuals from a general population sample took part in an evaluative conditioning experiment, where different neutral faces were associated with high or low reward values. In the test phase, EEG was recorded while participants viewed videoclips of happy expressions made by the conditioned faces. Alpha/beta suppression (identified using event-related desynchronisation of specific independent components) in response to rewarding faces was found to be greater than for non-rewarding faces. This result provides a mechanistic insight into the plasticity of the MNS and, more generally, into the role of reward in modulating physiological responses linked to empathy.

Atmospheric impact of Arctic Sea ice loss in a coupled ocean–atmosphere simulation

The atmospheric response to an idealized decline in Arctic sea ice is investigated in a novel fully coupled climate model experiment. In this experiment two ensembles of single-year model integrations are performed starting on 1 April, the approximate start of the ice melt season. By perturbing the initial conditions of sea ice thickness (SIT), declines in both sea ice concentration and SIT, which result in sea ice distributions that are similar to the recent sea ice minima of 2007 and 2012, are induced. In the ice loss regions there are strong (~3 K) local increases in sea surface temperature (SST); additionally, there are remote increases in SST in the central North Pacific and subpolar gyre in the North Atlantic. Over the central Arctic there are increases in surface air temperature (SAT) of ~8 K due to increases in ocean–atmosphere heat fluxes. There are increases in SAT over continental North America that are in good agreement with recent changes as seen by reanalysis data. It is estimated that up to two-thirds of the observed increase in SAT in this region could be related to Arctic sea ice loss. In early summer there is a significant but weak atmospheric circulation response that projects onto the summer North Atlantic Oscillation (NAO). In early summer and early autumn there is an equatorward shift of the eddy-driven jet over the North Atlantic as a result of a reduction in the meridional temperature gradients. In winter there is no projection onto a particular phase of the NAO.

Understanding advances in the simulation of the Madden-Julian Oscillation in a numerical weather prediction model.

The Madden-Julian Oscillation (MJO) is the dominant mode of intraseasonal variability in the Trop- ics. It can be characterised as a planetary-scale coupling between the atmospheric circulation and organised deep convection that propagates east through the equatorial Indo-Pacific region. The MJO interacts with weather and climate systems on a near-global scale and is a crucial source of predictability for weather forecasts on medium to seasonal timescales. Despite its global signifi- cance, accurately representing the MJO in numerical weather prediction (NWP) and climate models remains a challenge. This thesis focuses on the representation of the MJO in the Integrated Forecasting System (IFS) at the European Centre for Medium-Range Weather Forecasting (ECMWF), a state-of-the-art NWP model. Recent modifications to the model physics in Cycle 32r3 (Cy32r3) of the IFS led to ad- vances in the simulation of the MJO; for the first time the observed amplitude of the MJO was maintained throughout the integration period. A set of hindcast experiments, which differ only in their formulation of convection, have been performed between May 2008 and April 2009 to asses the sensitivity of MJO simulation in the IFS to the Cy32r3 convective parameterization. Unique to this thesis is the attribution of the advances in MJO simulation in Cy32r3 to the mod- ified convective parameterization, specifically, the relative-humidity-dependent formulation for or- ganised deep entrainment. Increasing the sensitivity of the deep convection scheme to environmen- tal moisture is shown to modify the relationship between precipitation and moisture in the model. Through dry-air entrainment, convective plumes ascending in low-humidity environments terminate lower in the atmosphere. As a result, there is an increase in the occurrence of cumulus congestus, which acts to moisten the mid-troposphere. Due to the modified precipitation-moisture relationship more moisture is able to build up which effectively preconditions the tropical atmosphere for the transition to deep convection. Results from this thesis suggest that a tropospheric moisture control on convection is key to simulating the interaction between the physics and large-scale circulation associated with the MJO.

A process-based evaluation of dust-emitting winds in the CMIP5 simulation of HadGEM2-ES

Despite the importance of dust aerosol in the Earth system, state-of-the-art models show a large variety for North African dust emission. This study presents a systematic evaluation of dust emitting-winds in 30 years of the historical model simulation with the UK Met Office Earth-system model HadGEM2-ES for the Coupled Model Intercomparison Project Phase 5. Isolating the effect of winds on dust emission and using an automated detection for nocturnal low-level jets (NLLJs) allow an in-depth evaluation of the model performance for dust emission from a meteorological perspective. The findings highlight that NLLJs are a key driver for dust emission in HadGEM2-ES in terms of occurrence frequency and strength. The annually and spatially averaged occurrence frequency of NLLJs is similar in HadGEM2-ES and ERA-Interim from the European Centre for Medium-Range Weather Forecasts. Compared to ERA-Interim, a stronger pressure ridge over northern Africa in winter and the southward displaced heat low in summer result in differences in location and strength of NLLJs. Particularly the larger geostrophic winds associated with the stronger ridge have a strengthening effect on NLLJs over parts of West Africa in winter. Stronger NLLJs in summer may rather result from an artificially increased mixing coefficient under stable stratification that is weaker in HadGEM2-ES. NLLJs in the Bodélé Depression are affected by stronger synoptic-scale pressure gradients in HadGEM2-ES. Wintertime geostrophic winds can even be so strong that the associated vertical wind shear prevents the formation of NLLJs. These results call for further model improvements in the synoptic-scale dynamics and the physical parametrization of the nocturnal stable boundary layer to better represent dust-emitting processes in the atmospheric model. The new approach could be used for identifying systematic behavior in other models with respect to meteorological processes for dust emission. This would help to improve dust emission simulations and contribute to decreasing the currently large uncertainty in climate change projections with respect to dust aerosol.

Numerical Simulation Of Sediment Transport And Bedmorphology Around A Hydraulic Structure On A River

Scour around hydraulic structures is a critical problem in hydraulic engineering. Under prediction of scour depth may lead to costly failures of the structure, while over prediction might result in unnecessary costs. Unfortunately, up-to-date empirical scour prediction formulas are based on laboratory experiments that are not always able to reproduce field conditions due to complicated geometry of rivers and temporal and spatial scales of a physical model. However, computational fluid dynamics (CFD) tools can perform using real field dimensions and operating conditions to predict sediment scour around hydraulic structures. In Korea, after completing the Four Major Rivers Restoration Project, several new weirs have been built across Han, Nakdong, Geum and Yeongsan Rivers. Consequently, sediment deposition and bed erosion around such structures have became a major issue in these four rivers. In this study, an application of an open source CFD software package, the TELEMAC-MASCARET, to simulate sediment transport and bed morphology around Gangjeong weir, which is the largest multipurpose weir built on Nakdong River. A real bathymetry of the river and a geometry of the weir have been implemented into the numerical model. The numerical simulation is carried out with a real hydrograph at the upstream boundary. The bedmorphology obtained from the numerical results has been validated against field observation data, and a maximum of simulated scour depth is compared with the results obtained by empirical formulas of Hoffmans. Agreement between numerical computations, observed data and empirical formulas is judged to be satisfactory on all major comparisons. The outcome of this study does not only point out the locations where deposition and erosion might take place depending on the weir gate operation, but also analyzes the mechanism of formation and evolution of scour holes after the weir gates.

Extension And Testing Of A 2D Hydrodynamic Model For Direct Rainfall Runoff Simulation

While the simulation of flood risks originating from the overtopping of river banks is well covered within continuously evaluated programs to improve flood protection measures, flash flooding is not. Flash floods are triggered by short, local thunderstorm cells with high precipitation intensities. Small catchments have short response times and flow paths and convective thunder cells may result in potential flooding of endangered settlements. Assessing local flooding and pathways of flood requires a detailed hydraulic simulation of the surface runoff. Hydrological models usually do not incorporate surface runoff at this detailedness but rather empirical equations are applied for runoff detention. In return 2D hydrodynamic models usually do not allow distributed rainfall as input nor are any types of soil/surface interaction implemented as in hydrological models. Considering several cases of local flash flooding during the last years the issue emerged for practical reasons but as well as research topics to closing the model gap between distributed rainfall and distributed runoff formation. Therefore, a 2D hydrodynamic model, depth-averaged flow equations using the finite volume discretization, was extended to accept direct rainfall enabling to simulate the associated runoff formation. The model itself is used as numerical engine, rainfall is introduced via the modification of waterlevels at fixed time intervals. The paper not only deals with the general application of the software, but intends to test the numerical stability and reliability of simulation results. The performed tests are made using different artificial as well as measured rainfall series as input. Key parameters of the simulation such as losses, roughness or time intervals for water level manipulations are tested regarding their impact on the stability.

Economic viability and selection of irrigation systems using simulation and stochastic dominance

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Two dimensional computer simulation of plasma immersion ion implantation

The biggest advantage of plasma immersion ion implantation (PIII) is the capability of treating objects with irregular geometry without complex manipulation of the target holder. The effectiveness of this approach relies on the uniformity of the incident ion dose. Unfortunately, perfect dose uniformity is usually difficult to achieve when treating samples of complex shape. The problems arise from the non-uniform plasma density and expansion of plasma sheath. A particle-in-cell computer simulation is used to study the time-dependent evolution of the plasma sheath surrounding two-dimensional objects during process of plasma immersion ion implantation. Before starting the implantation phase, steady-state nitrogen plasma is established inside the simulation volume by using ionization of gas precursor with primary electrons. The plasma self-consistently evolves to a non-uniform density distribution, which is used as initial density distribution for the implantation phase. As a result, we can obtain a more realistic description of the plasma sheath expansion and dynamics. Ion current density on the target, average impact energy, and trajectories of the implanted ions were calculated for three geometrical shapes. Large deviations from the uniform dose distribution have been observed for targets with irregular shapes. In addition, effect of secondary electron emission has been included in our simulation and no qualitative modifications to the sheath dynamics have been noticed. However, the energetic secondary electrons change drastically the plasma net balance and also pose significant X-ray hazard. Finally, an axial magnetic field has been added to the calculations and the possibility for magnetic insulation of secondary electrons has been proven.

A New Approach to Reducing Search Space and Increasing Efficiency in Simulation Optimization Problems via the Fuzzy-DEA-BCC

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)