Browsing by Subject "SIMULATION"

Sort by: Order: Results:

Now showing items 21-40 of 57
  • Poedts, Stefaan; Lani, Andrea; Scolini, Camilla; Verbeke, Christine; Wijsen, Nicolas; Lapenta, Giovanni; Laperre, Brecht; Millas, Dimitrios; Innocenti, Maria Elena; Chane, Emmanuel; Baratashvili, Tinatin; Samara, Evangelia; Van der Linden, Ronald; Rodriguez, Luciano; Vanlommel, Petra; Vainio, Rami; Afanasiev, Alexandr; Kilpua, Emilia; Pomoell, Jens; Sarkar, Ranadeep; Aran, Angels; Sanahuja, Blai; Paredes, Josep M.; Clarke, Ellen; Thomson, Alan; Rouilard, Alexis; Pinto, Rui F.; Marchaudon, Aurelie; Blelly, Pierre-Louis; Gorce, Blandine; Plotnikov, Illya; Kouloumvakos, Athanasis; Heber, Bernd; Herbst, Konstantin; Kochanov, Andrey; Raeder, Joachim; Depauw, Jan (2020)
    Aims: This paper presents a H2020 project aimed at developing an advanced space weather forecasting tool, combining the MagnetoHydroDynamic (MHD) solar wind and coronal mass ejection (CME) evolution modelling with solar energetic particle (SEP) transport and acceleration model(s). The EUHFORIA 2.0 project will address the geoeffectiveness of impacts and mitigation to avoid (part of the) damage, including that of extreme events, related to solar eruptions, solar wind streams, and SEPs, with particular emphasis on its application to forecast geomagnetically induced currents (GICs) and radiation on geospace. Methods: We will apply innovative methods and state-of-the-art numerical techniques to extend the recent heliospheric solar wind and CME propagation model EUHFORIA with two integrated key facilities that are crucial for improving its predictive power and reliability, namely (1) data-driven flux-rope CME models, and (2) physics-based, self-consistent SEP models for the acceleration and transport of particles along and across the magnetic field lines. This involves the novel coupling of advanced space weather models. In addition, after validating the upgraded EUHFORIA/SEP model, it will be coupled to existing models for GICs and atmospheric radiation transport models. This will result in a reliable prediction tool for radiation hazards from SEP events, affecting astronauts, passengers and crew in high-flying aircraft, and the impact of space weather events on power grid infrastructure, telecommunication, and navigation satellites. Finally, this innovative tool will be integrated into both the Virtual Space Weather Modeling Centre (VSWMC, ESA) and the space weather forecasting procedures at the ESA SSCC in Ukkel (Belgium), so that it will be available to the space weather community and effectively used for improved predictions and forecasts of the evolution of CME magnetic structures and their impact on Earth. Results: The results of the first six months of the EU H2020 project are presented here. These concern alternative coronal models, the application of adaptive mesh refinement techniques in the heliospheric part of EUHFORIA, alternative flux-rope CME models, evaluation of data-assimilation based on Karman filtering for the solar wind modelling, and a feasibility study of the integration of SEP models.
  • Turc, L.; Roberts, O. W.; Archer, M. O.; Palmroth, M.; Battarbee, M.; Brito, T.; Ganse, U.; Grandin, M.; Pfau-Kempf, Y.; Escoubet, C. P.; Dandouras, I. (2019)
    The foreshock, extending upstream of Earth's bow shock, is a region of intense electromagnetic wave activity and nonlinear phenomena, which can have global effects on geospace. It is also the first geophysical region encountered by solar wind disturbances journeying toward Earth. Here, we present the first observations of considerable modifications of the foreshock wave field during extreme events of solar origin called magnetic clouds. Cluster's multispacecraft data reveal that the typical quasi-monochromatic foreshock waves can be completely replaced by a superposition of waves each with shorter correlation lengths. Global numerical simulations further confirm that the foreshock wave field is more intricate and organized at smaller scales. Ion measurements suggest that changes in shock-reflected particle properties may cause these modifications of the wave field. This state of the foreshock is encountered only during extreme events at Earth, but intense magnetic fields are typical close to the Sun or other stars.
  • Polley, Anirban; Orlowski, Adam; Danne, Reinis; Gurtovenko, Andrey A.; de la Serna, Jorge Bernardino; Eggeling, Christian; Davis, Simon J.; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Proteins embedded in the plasma membrane mediate interactions with the cell environment and play decisive roles in many signaling events. For cell-cell recognition molecules, it is highly likely that their structures and behavior have been optimized in ways that overcome the limitations of membrane tethering. In particular, the ligand binding regions of these proteins likely need to be maximally exposed. Here we show by means of atomistic simulations of membrane-bound CD2, a small cell adhesion receptor expressed by human T-cells and natural killer cells, that the presentation of its ectodomain is highly dependent on membrane lipids and receptor glycosylation acting in apparent unison. Detailed analysis shows that the underlying mechanism is based on electrostatic interactions complemented by steric interactions between glycans in the protein and the membrane surface. The findings are significant for understanding the factors that render membrane receptors accessible for binding and signaling.
  • Lankinen, Kaisu; Smeds, Eero; Tikka, Pia; Pihko, Elina; Hari, Riitta; Koskinen, Miika (2016)
    Observation of another person's actions and feelings activates brain areas that support similar functions in the observer, thereby facilitating inferences about the other's mental and bodily states. In real life, events eliciting this kind of vicarious brain activations are intermingled with other complex, ever-changing stimuli in the environment. One practical approach to study the neural underpinnings of real-life vicarious perception is to image brain activity during movie viewing. Here the goal was to find out how observed haptic events in a silent movie would affect the spectator's sensorimotor cortex. The functional state of the sensorimotor cortex was monitored by analyzing, in 16 healthy subjects, magnetoencephalographic (MEG) responses to tactile finger stimuli that were presented once per second throughout the session. Using canonical correlation analysis and spatial filtering, consistent single-trial responses across subjects were uncovered, and their waveform changes throughout the movie were quantified. The long-latency (85-175 ms) parts of the responses were modulated in concordance with the participants' average moment-by-moment ratings of own engagement in the haptic content of the movie (correlation r=0.49; ratings collected after the MEG session). The results, obtained by using novel signal-analysis approaches, demonstrate that the functional state of the human sensorimotor cortex fluctuates in a fine-grained manner even during passive observation of temporally varying haptic events. Hum Brain Mapp 37:4061-4068, 2016. (c) 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
  • Sand, Andrea E.; Ullah, Rafi; Correa, Alfredo A. (2019)
    The effects of incident energetic particles, and the modification of materials under irradiation, are governed by the mechanisms of energy losses of ions in matter. The complex processes affecting projectiles spanning many orders of magnitude in energy depend on both ion and electron interactions. Developing multi-scale modeling methods that correctly capture the relevant processes is crucial for predicting radiation effects in diverse conditions. In this work, we obtain channeling ion ranges for tungsten, a prototypical heavy ion, by explicitly simulating ion trajectories with a method that takes into account both the nuclear and the electronic stopping power. The electronic stopping power of self-ion irradiated tungsten is obtained from first-principles time-dependent density functional theory (TDDFT). Although the TDDFT calculations predict a lower stopping power than SRIM by a factor of three, our result shows very good agreement in a direct comparison with ion range experiments. These results demonstrate the validity of the TDDFT method for determining electronic energy losses of heavy projectiles, and in turn its viability for the study of radiation damage.
  • Pfau-Kempf, Y.; Palmroth, M.; Johlander, A.; Turc, L.; Alho, M.; Battarbee, M.; Dubart, M.; Grandin, M.; Ganse, U. (2020)
    Dayside magnetic reconnection at the magnetopause, which is a major driver of space weather, is studied for the first time in a three-dimensional (3D) realistic setup using a hybrid-Vlasov kinetic model. A noon-midnight meridional plane simulation is extended in the dawn-dusk direction to cover 7 Earth radii. The southward interplanetary magnetic field causes magnetic reconnection to occur at the subsolar magnetopause. Perturbations arising from kinetic instabilities in the magnetosheath appear to modulate the reconnection. Its characteristics are consistent with multiple, bursty, and patchy magnetopause reconnection. It is shown that the kinetic behavior of the plasma, as simulated by the model, has consequences on the applicability of methods such as the four-field junction to identify and analyze magnetic reconnection in 3D kinetic simulations.
  • Grandin, Maxime; Battarbee, Markus; Osmane, Adnane; Ganse, Urs; Pfau-Kempf, Yann; Turc, Lucile; Brito, Thiago; Koskela, Tuomas; Dubart, Maxime; Palmroth, Minna (2019)
    Particle precipitation plays a key role in the coupling of the terrestrial magnetosphere and ionosphere by modifying the upper atmospheric conductivity and chemistry, driving field-aligned currents, and producing aurora. Yet quantitative observations of precipitating fluxes are limited, since ground-based instruments can only provide indirect measurements of precipitation, while particle telescopes aboard spacecraft merely enable point-like in situ observations with an inherently coarse time resolution above a given location. Further, orbit timescales generally prevent the analysis of whole events. On the other hand, global magnetospheric simulations can provide estimations of particle precipitation with a global view and higher time resolution. We present the first results of auroral (similar to 1-30 keV) proton precipitation estimation using the Vlasiator global hybrid-Vlasov model in a noon-midnight meridional plane simulation driven by steady solar wind with a southward interplanetary magnetic field. We first calculate the bounce loss-cone angle value at selected locations in the simulated nightside magnetosphere. Then, using the velocity distribution function representation of the proton population at those selected points, we study the population inside the loss cone. This enables the estimation of differential precipitating number fluxes as would be measured by a particle detector aboard a low-Earth-orbiting (LEO) spacecraft. The obtained differential flux values are in agreement with a well-established empirical model in the midnight sector, as are the integral energy flux and mean precipitating energy. We discuss the time evolution of the precipitation parameters derived in this manner in the global context of nightside magnetospheric activity in this simulation, and we find in particular that precipitation bursts of
  • Gutmann, Michael U.; Dutta, Ritabrata; Kaski, Samuel; Corander, Jukka (2018)
    Increasingly complex generative models are being used across disciplines as they allow for realistic characterization of data, but a common difficulty with them is the prohibitively large computational cost to evaluate the likelihood function and thus to perform likelihood-based statistical inference. A likelihood-free inference framework has emerged where the parameters are identified by finding values that yield simulated data resembling the observed data. While widely applicable, a major difficulty in this framework is how to measure the discrepancy between the simulated and observed data. Transforming the original problem into a problem of classifying the data into simulated versus observed, we find that classification accuracy can be used to assess the discrepancy. The complete arsenal of classification methods becomes thereby available for inference of intractable generative models. We validate our approach using theory and simulations for both point estimation and Bayesian inference, and demonstrate its use on real data by inferring an individual-based epidemiological model for bacterial infections in child care centers.
  • Angileri, A.; Sardini, P.; Beaufort, D.; Amiard, G.; Beaufort, M. F.; Nicolai, J.; Siitari-Kauppi, M.; Descostes, M. (2020)
    In highly permeable sedimentary rock formations, U extraction by in-situ leaching techniques (ISR - In-Situ Recovery) is generally considered to have a limited environmental impact at ground level. Significantly, this method of extraction produces neither mill tailings nor waste rocks. Underground, however, the outcome for U-238 daughter elements in aquifers is not well known because of their trace concentrations in the host rocks. Thus, understanding the in-situ mobility of these elements remains a challenge. Two samples collected before and after six months of ISR experiments (Dulaan Uul, Mongolia) were studied with the help of a digital autoradiography technique (DA) of alpha particles, bulk alpha spectrometry, and complementary petrographic observation methods. These techniques demonstrate that before and after leaching, the radioactivity is concentrated in altered and microporous Fe-Ti oxides. Most of the daughter elements of U remain trapped in the rock after the leaching process. DA confirms that the alpha activity of the Fe-Ti oxides remains high after uranium leaching, and the initial secular equilibrium of the U-238 series for Th-230 to Po-210 daughter elements (including Ra-226) of the fresh rocks is maintained after leaching. While these findings should be confirmed by more systematic studies, they already identify potential mechanisms explaining why the U-daughter concentrations in leaching water are low.
  • Murtola, Tiina; Aalto, Atte; Malinen, Jarmo; Aalto, Daniel; Vainio, Martti (2018)
    During voiced speech, vocal folds interact with the vocal tract acoustics. The resulting glottal source-resonator coupling has been observed using mathematical and physical models as well as in in vivo phonation. We propose a computational time-domain model of the full speech apparatus that contains a feedback mechanism from the vocal tract acoustics to the vocal fold oscillations. It is based on numerical solution of ordinary and partial differential equations defined on vocal tract geometries that have been obtained by magnetic resonance imaging. The model is used to simulate rising and falling pitch glides of [alpha, i] in the fundamental frequency (f(o)) interval [145 Hz, 315 Hz]. The interval contains the first vocal tract resonance f(R1) and the first formant F-1 of [i] as well as the fractions of the first resonance f(R1)/5, f(R1)/4, and f(R1)/3 of [alpha]. The glide simulations reveal a locking pattern in the f(o) trajectory approximately at f(R1) of [i]. The resonance fractions of [alpha] produce perturbations in the pressure signal at the lips but no locking.
  • Kuva, J.; Voutilainen, M.; Mattila, K. (2019)
    The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions.
  • Lopez-Cazalilla, Alvaro; Ilinov, Andrew; Nordlund, Kai; Djurabekova, Flyura (2019)
    Long time ion irradiation of surfaces under tilted incidence causes formation of regular nanostructures known as surface ripples. The nature of mechanisms leading to ripples is still not clear, this is why computational methods can shed the light on such a complex phenomenon and help to understand which surface processes are mainly responsible for it. In this work, we analyse the surface response of two materials, a semiconductor (silicon) and a metal (aluminium) under irradiation with the 250 eV and 1000 eV Ar ions focused at 70° from the normal to the surface. We simulate consecutive ion impacts by the means of molecular dynamics to investigate the effect on ripple formation. We find that the redistribution mechanism seems to be the main creator of ripples in amorphous materials, while the erosion mechanism is the leading origin for the pattern formation in crystalline metals.
  • Heinola, K.; Ahlgren, T.; Brezinsek, S.; Vuoriheimo, T.; Wiesen, S. (2019)
    Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate.
  • Svensson, Urban; Voutilainen, Mikko; Muuri, Eveliina; Ferry, Michel; Gylling, Björn (2019)
    A numerical reactive transport model for crystalline rocks is developed and evaluated. The model is based on mineral maps generated by X-ray micro computed tomography (X-μCT); the maps used have a resolution of approximately 30 μm and the rock samples are on the cm scale. A computational grid for the intergranular space is generated and a micro-DFN (Discrete Fracture Network) model governs the grid properties. A particle tracking method (Time Domain Random Walk) is used for transport simulations. The basic concept of the model can now be formulated as follows; “when a particle is close to a reactive mineral surface it has a certain probability to get sorbed during a certain time span. Once sorbed it will remain so a certain time”. The model requires a number of input parameters that represent the sorption properties of the reactive minerals. Attempts are made to relate the parameters to traditional distribution parameters. The model is evaluated by comparisons with recent laboratory experimental data. These experiments consider two rock types (veined gneiss and pegmatitic granite) and two radionuclides (cesium and barium). It is concluded that the new reactive transport model can simulate the experimental data in a consistent and realistic way.
  • Alexandridis, Nikolaos; Marion, Glenn; Chaplin-Kramer, Rebecca; Dainese, Matteo; Ekroos, Johan; Grab, Heather; Jonsson, Mattias; Karp, Daniel S.; Meyer, Carsten; O'Rourke, Megan E.; Pontarp, Mikael; Poveda, Katja; Seppelt, Ralf; Smith, Henrik G.; Martin, Emily A.; Clough, Yann (2021)
    Natural control of invertebrate crop pests has the potential to complement or replace conventional insecticide based practices, but its mainstream application is hampered by predictive unreliability across agroecosystems. Inconsistent responses of natural pest control to changes in landscape characteristics have been attributed to ecological complexity and system-specific conditions. Here, we review agroecological models and their potential to provide predictions of natural pest control across agricultural landscapes. Existing models have used a multitude of techniques to represent specific crop-pest-enemy systems at various spatiotemporal scales, but less wealthy regions of the world are underrepresented. A realistic representation of natural pest control across systems appears to be hindered by a practical trade-off between generality and realism. Nonetheless, observations of context-sensitive, trait-mediated responses of natural pest control to land-use gradients indicate the potential of ecological models that explicitly represent the underlying mechanisms. We conclude that modelling natural pest control across agroecosystems should exploit existing mechanistic techniques towards a framework of contextually bound generalizations. Observed similarities in causal relationships can inform the functional grouping of diverse agroecosystems worldwide and the development of the respective models based on general, but context-sensitive, ecological mechanisms. The combined use of qualitative and quantitative techniques should allow the flexible integration of empirical evidence and ecological theory for robust predictions of natural pest control across a wide range of agroecological contexts and levels of knowledge availability. We highlight challenges and promising directions towards developing such a general modelling framework.
  • Correia, Cristiana; Ferreira, Abigail; Santos, Joana; Lapa, Rui; Yliperttula, Marjo; Urtti, Arto; Vale, Nuno (2021)
    Pharmacokinetic (PK) studies improve the design of dosing regimens in preclinical and clinical settings. In complex diseases like cancer, single-agent approaches are often insufficient for an effective treatment, and drug combination therapies can be implemented. In this work, in silico PK models were developed based on in vitro assays results, with the goal of predicting the in vivo performance of drug combinations in the context of cancer therapy. Combinations of reference drugs for cancer treatment, gemcitabine and 5-fluorouracil (5-FU), and repurposed drugs itraconazole, verapamil or tacrine, were evaluated in vitro. Then, two-compartment PK models were developed based on the previous in vitro studies and on the PK profile reported in the literature for human patients. Considering the quantification parameter area under the dose-response-time curve (AUC(effect)) for the combinations effect, itraconazole was the most effective in combination with either reference anticancer drugs. In addition, cell growth inhibition was itraconazole-dose dependent and an increase in effect was predicted if itraconazole administration was continued (24-h dosing interval). This work demonstrates that in silico methods and AUC(effect) are powerful tools to study relationships between tissue drug concentration and the percentage of cell growth inhibition over time.
  • Yang, Yu; Leppäranta, Matti; Cheng, Bin; Li, Zhijun (2012)
  • Lopez-Cazalilla, A.; Chowdhury, D.; Ilinov, A.; Mondal, S.; Barman, P.; Bhattacharyya, S. R.; Ghose, D.; Djurabekova, F.; Nordlund, K.; Norris, S. (2018)
    The effect of low energy irradiation, where the sputtering is imperceptible, has not been deeply studied in the pattern formation. In this work, we want to address this question by analyzing the nanoscale topography formation on a Si surface, which is irradiated at room temperature by Arthorn ions near the displacement threshold energy, for incidence angles ranging from 0 degrees to 85 degrees. The transition from the smooth to ripple patterned surface, i.e., the stability/instability bifurcation angle is observed at 55 degrees, whereas the ripples with their wave-vector is parallel to the ion beam projection in the angular window of 60 degrees-70 degrees, and with 90 degrees rotation with respect to the ion beam projection at the grazing angles of incidence. A similar irradiation setup has been simulated by means of molecular dynamics, which made it possible, first, to quantify the effect of the irradiation in terms of erosion and redistribution using sequential irradiation and, second, to evaluate the ripple wavelength using the crater function formalism. The ripple formation results can be solely attributed to the mass redistribution based mechanism, as erosion due to ion sputtering near or above the threshold energy is practically negligible. Published by AIP Publishing.