Browsing by Subject "SIMULATION"

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  • Bergstrom, Martin; Browne, Thomas; Ehlers, Soren; Helle, Inari; Herrnring, Hauke; Khan, Faisal; Kubiczek, Jan; Kujala, Pentti; Korgesaar, Mihkel; Leira, Bernt Johan; Parviainen, Tuuli; Polojarvi, Arttu; Suominen, Mikko; Taylor, Rocky; Tuhkuri, Jukka; Vanhatalo, Jarno; Veitch, Brian (2022)
    While society benefits from Arctic shipping, it is necessary to recognize that ship operations in Arctic waters pose significant risks to people, the environment, and property. To support the management of those risks, this article presents a comprehensive approach addressing both short-term operational risks, as well as risks related to long-term extreme ice loads. For the management of short-term operational risks, an extended version of the Polar Operational Limit Assessment Risk Indexing System (POLARIS) considering the magnitude of the consequences of potential adverse events is proposed. For the management of risks related to long-term extreme ice loads, guidelines are provided for using existing analytical, numerical, and semi-empirical methods. In addition, to support the design of ice class ship structures, the article proposes a novel approach that can be used in the conceptual design phase for the determination of preliminary scantlings for primary hull structural members.
  • Golub, Malgorzata; Thiery, Wim; Marce, Rafael; Pierson, Don; Vanderkelen, Inne; Mercado-Bettin, Daniel; Woolway, R. Iestyn; Grant, Luke; Jennings, Eleanor; Kraemer, Benjamin M.; Schewe, Jacob; Zhao, Fang; Frieler, Katja; Mengel, Matthias; Bogomolov, Vasiliy Y.; Bouffard, Damien; Cote, Marianne; Couture, Raoul-Marie; Debolskiy, Andrey; Droppers, Bram; Gal, Gideon; Guo, Mingyang; Janssen, Annette B. G.; Kirillin, Georgiy; Ladwig, Robert; Magee, Madeline; Moore, Tadhg; Perroud, Marjorie; Piccolroaz, Sebastiano; Vinnaa, Love Raaman; Schmid, Martin; Shatwell, Tom; Stepanenko, Victor M.; Tan, Zeli; Woodward, Bronwyn; Yao, Huaxia; Adrian, Rita; Allan, Mathew; Anneville, Orlane; Arvola, Lauri; Atkins, Karen; Boegman, Leon; Carey, Cayelan; Christianson, Kyle; de Eyto, Elvira; DeGasperi, Curtis; Grechushnikova, Maria; Hejzlar, Josef; Joehnk, Klaus; Jones, Ian D.; Laas, Alo; Mackay, Eleanor B.; Mammarella, Ivan; Markensten, Hampus; McBride, Chris; Ozkundakci, Deniz; Potes, Miguel; Rinke, Karsten; Robertson, Dale; Rusak, James A.; Salgado, Rui; van der Linden, Leon; Verburg, Piet; Wain, Danielle; Ward, Nicole K.; Wollrab, Sabine; Zdorovennova, Galina (2022)
    Empirical evidence demonstrates that lakes and reservoirs are warming across the globe. Consequently, there is an increased need to project future changes in lake thermal structure and resulting changes in lake biogeochemistry in order to plan for the likely impacts. Previous studies of the impacts of climate change on lakes have often relied on a single model forced with limited scenario-driven projections of future climate for a relatively small number of lakes. As a result, our understanding of the effects of climate change on lakes is fragmentary, based on scattered studies using different data sources and modelling protocols, and mainly focused on individual lakes or lake regions. This has precluded identification of the main impacts of climate change on lakes at global and regional scales and has likely contributed to the lack of lake water quality considerations in policy-relevant documents, such as the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC). Here, we describe a simulation protocol developed by the Lake Sector of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) for simulating climate change impacts on lakes using an ensemble of lake models and climate change scenarios for ISIMIP phases 2 and 3. The protocol prescribes lake simulations driven by climate forcing from gridded observations and different Earth system models under various representative greenhouse gas concentration pathways (RCPs), all consistently bias-corrected on a 0.5 degrees x 0.5 degrees global grid. In ISIMIP phase 2, 11 lake models were forced with these data to project the thermal structure of 62 well-studied lakes where data were available for calibration under historical conditions, and using uncalibrated models for 17 500 lakes defined for all global grid cells containing lakes. In ISIMIP phase 3, this approach was expanded to consider more lakes, more models, and more processes. The ISIMIP Lake Sector is the largest international effort to project future water temperature, thermal structure, and ice phenology of lakes at local and global scales and paves the way for future simulations of the impacts of climate change on water quality and biogeochemistry in lakes.
  • Sievänen, Risto; Raumonen, Pasi; Perttunen, Jari; Nikinmaa, Eero Heikki; Kaitaniemi, Pekka Juhani (2018)
    Background and Aims: Functional-structural plant models (FSPMs) allow simulation of tree crown development as the sum of modular (e.g. shoot-level) responses triggered by the local environmental conditions. The actual process of space filling by the crowns can be studied. Although the FSPM simulations are at organ scale, the data for their validation have usually been at more aggregated levels (whole-crown or whole-tree). Measurements made by terrestrial laser scanning (TLS) that have been segmented into elementary units (internodes) offer a phenotyping tool to validate the FSPM predictions at levels comparable with their detail. We demonstrate the testing of different formulations of crown development of Scots pine trees in the LIGNUM model using segmented TLS data. Methods: We made TLS measurements from four sample trees growing in a forest on a relatively poor soil from sapling size to mature stage. The TLS data were segmented into intenodes. The segmentation also produced information on whether needles were present in the internode. We applied different formulations of crown development (flushing of buds and length of growth of new internodes) in LIGNUM. We optimized the parameter values of each formulation using genetic algorithms to observe the best fit of LIGNUM simulations to the measured trees. The fitness function in the estimation combined both tree-level characteristics (e.g. tree height and crown length) and measures of crown shape (e.g. spatial distribution of needle area). Key Results: Comparison of different formulations against the data indicates that the Extended Borchert- Honda model for shoot elongation works best within LIGNUM. Control of growth by local density in the crown was important for all shoot elongation formulations. Modifying the number of lateral buds as a function of local density in the crown was the best way to accomplish density control. Conclusions: It was demonstrated how segmented TLS data can be used in the context of a shoot-based model to select model components.
  • Herodotou, Herodotos; Chen, Yuxing; Lu, Jiaheng (2020)
    Big data processing systems (e.g., Hadoop, Spark, Storm) contain a vast number of configuration parameters controlling parallelism, I/O behavior, memory settings, and compression. Improper parameter settings can cause significant performance degradation and stability issues. However, regular users and even expert administrators grapple with understanding and tuning them to achieve good performance. We investigate existing approaches on parameter tuning for both batch and stream data processing systems and classify them into six categories: rule-based, cost modeling, simulation-based, experiment-driven, machine learning, and adaptive tuning. We summarize the pros and cons of each approach and raise some open research problems for automatic parameter tuning.
  • Cornell, Stephen J.; Suprunenko, Yevhen F.; Finkelshtein, Dmitri; Somervuo, Panu; Ovaskainen, Otso (2019)
    Individual-based models, 'IBMs', describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of them cannot give the general insights required. Here, we resolve this problem with a general mathematical framework for IBMs containing interactions of an unlimited level of complexity, and derive equations that reliably approximate the effects of space and stochasticity. We provide software, specified in an accessible and intuitive graphical way, so any researcher can obtain analytical and simulation results for any particular IBM without algebraic manipulation. We illustrate the framework with examples from movement ecology, conservation biology, and evolutionary ecology. This framework will provide unprecedented insights into a hitherto intractable panoply of complex models across many scientific fields.
  • Fiedler, Stephanie; Kinne, Stefan; Huang, Wan Ting Katty; Räisänen, Petri; O'Donnell, Declan; Bellouin, Nicolas; Stier, Philip; Merikanto, Joonas; van Noije, Twan; Makkonen, Risto; Lohmann, Ulrike (2019)
    This study assesses the change in anthropogenic aerosol forcing from the mid-1970s to the mid-2000s. Both decades had similar global-mean anthropogenic aerosol optical depths but substantially different global distributions. For both years, we quantify (i) the forcing spread due to model-internal variability and (ii) the forcing spread among models. Our assessment is based on new ensembles of atmosphere-only simulations with five state-of-the-art Earth system models. Four of these models will be used in the sixth Coupled Model Intercomparison Project (CMIP6; Eyring et al., 2016). Here, the complexity of the anthropogenic aerosol has been reduced in the participating models. In all our simulations, we prescribe the same patterns of the anthropogenic aerosol optical properties and associated effects on the cloud droplet number concentration. We calculate the instantaneous radiative forcing (RF) and the effective radiative forcing (ERF). Their difference defines the net contribution from rapid adjustments. Our simulations show a model spread in ERF from -0.4 to -0.9 W m(-2). The standard deviation in annual ERF is 0.3 W m(-2), based on 180 individual estimates from each participating model. This result implies that identifying the model spread in ERF due to systematic differences requires averaging over a sufficiently large number of years. Moreover, we find almost identical ERFs for the mid-1970s and mid-2000s for individual models, although there are major model differences in natural aerosols and clouds. The model-ensemble mean ERF is -0.54 W m(-2) for the pre-industrial era to the mid-1970s and -0.59 W m(-2) for the pre-industrial era to the mid-2000s. Our result suggests that comparing ERF changes between two observable periods rather than absolute magnitudes relative to a poorly constrained pre-industrial state might provide a better test for a model's ability to represent transient climate changes.
  • Niemi, Riitta; Vilar, Maria J; Dohoo, I.R.; Hovinen, Mari; Simojoki, Heli; Rajala-Schultz, Päivi Johanna (2020)
    Antibiotic dry cow therapy (DCT) is an important part of most mastitis control programs. Updating DCT recommendations is an ongoing topic due to the global problem of antimicrobial resistance. Finland, along with other Nordic countries, has implemented selective DCT for decades. Our study analyzed Dairy Herd Improvement (DHI) information from 241 Finnish farmers who participated in a survey about their drying-off practices. The aim was to evaluate herd-level associations between milk somatic cell count (SCC), milk production, and various antimicrobial DCT approaches both cross-sectionally in 2016 and longitudinally in 2012 - 2016. The three DCT approaches in the study were selective, blanket, and no DCT use. An additional aim was to evaluate whether dynamic changes occurred in herd-average SCC and annual milk production over five years, and whether these potential changes differed between different DCT approaches. The method for the longitudinal analyses was growth modeling with random coefficient models. Differences in SCC and milk production between farms with different DCT approaches were minor. Regardless of the farm's DCT approach, annual milk production increased over the years, while average SCC was reasonably constant. The variability in SCC and milk production across all DCT groups was low between years, and most of the variability was between farms. Compared to other milking systems, farms with automatic milking system (AMS) had higher SCC, and in 2016 higher milk production. The results of this study suggest that it is possible to maintain low herd-average SCC and good milk production when using selective DCT and following the guidelines for prudent antimicrobial use. Average SCC and milk production varied across the herds, suggesting that advice on DCT practices should be herd-specific. The methodology of growth modeling using random coefficient models was applicable in analyzing longitudinal data, in which the time frame was relatively short and the number of herds was limited.
  • Jussila, Vilho; Fälth, Billy; Mäntyniemi, Päivi; Voss, Peter H.; Lund, Björn; Fülöp, Ludovic (2021)
    We present a modeling technique for generating synthetic ground motions, aimed at earthquakes of design significance for critical structures and ground motions at distances corresponding to the engineering near field, in which real data are often missing. We use dynamic modeling based on the finite-difference approach to simulate the rupture process within a fault, followed by kinematic modeling to generate the ground motions. The earthquake source ruptures were modeled using the 3D distinct element code (Itasca, 2013). We then used the complete synthetic program by Spudich and Xu (2002) to simulate the propagation of seismic waves and to obtain synthetic ground motions. In this work, we demonstrate the method covering the frequency ranges of engineering interests up to 25 Hz and quantify the differences in ground motion generated. We compare the synthetic ground motions for distances up to 30 km with a ground-motion prediction equation, which synthesizes the expected ground motion and its randomness based on observations. The synthetic ground motions can be used to supplement observations in the near field for seismic hazard analysis. We demonstrate the hybrid approach to one critical site in the Fennoscandian Shield, northern Europe.
  • Jussila, Vilho; Fälth, Billy; Mäntyniemi, Päivi; Voss, Peter H.; Lund, Björn; Fülöp, Ludovic (2021)
    We present a modeling technique for generating synthetic ground motions, aimed at earthquakes of design significance for critical structures and ground motions at distances corresponding to the engineering near field, in which real data are often missing. We use dynamic modeling based on the finite-difference approach to simulate the rupture process within a fault, followed by kinematic modeling to generate the ground motions. The earthquake source ruptures were modeled using the 3D distinct element code (Itasca, 2013). We then used the complete synthetic program by Spudich and Xu (2002) to simulate the propagation of seismic waves and to obtain synthetic ground motions. In this work, we demonstrate the method covering the frequency ranges of engineering interests up to 25 Hz and quantify the differences in ground motion generated. We compare the synthetic ground motions for distances up to 30 km with a ground-motion prediction equation, which synthesizes the expected ground motion and its randomness based on observations. The synthetic ground motions can be used to supplement observations in the near field for seismic hazard analysis. We demonstrate the hybrid approach to one critical site in the Fennoscandian Shield, northern Europe.
  • Herranen, Touko; Laurson, Lasse (2017)
    We study field-driven magnetic domain wall dynamics in garnet strips by large-scale three-dimensional micromagnetic simulations. The domain wall propagation velocity as a function of the applied field exhibits a low-field linear part terminated by a sudden velocity drop at a threshold field magnitude, related to the onset of excitations of internal degrees of freedom of the domain wall magnetization. By considering a wide range of strip thicknesses from 30 nm to 1.89 mu m, we find a nonmonotonic thickness dependence of the threshold field for the onset of this instability, proceeding via nucleation and propagation of Bloch lines within the domain wall. We identify a critical strip thickness above which the velocity drop is due to nucleation of horizontal Bloch lines, while for thinner strips and depending on the boundary conditions employed, either generation of vertical Bloch lines, or close-to-uniform precession of the domain wall internal magnetization takes place. For strips of intermediate thicknesses, the vertical Bloch lines assume a deformed structure due to demagnetizing fields at the strip surfaces, breaking the symmetry between the top and bottom faces of the strip, and resulting in circulating Bloch line dynamics along the perimeter of the domain wall.
  • Kulig, Waldemar; Mikkolainen, Heikki; Olzynska, Agnieszka; Jurkiewicz, Piotr; Cwiklik, Lukasz; Hof, Martin; Vattulainen, Ilpo; Jungwirth, Pavel; Rog, Tomasz (2018)
    Translocation of sterols between cellular membrane leaflets is of key importance in membrane organization, dynamics, and signaling. We present a novel translocation mechanism that differs in a unique manner from the established ones. The bobbing mechanism identified here is demonstrated for tail-oxidized sterols, but is expected to be viable for any molecule containing two polar centers at the opposite sides of the molecule. The mechanism renders translocation across a lipid membrane possible without a change in molecular orientation. For tail-oxidized sterols, the bobbing mechanism provides an exceptionally facile means to translocate these signaling molecules across membrane structures and may thus represent an important pathway in the course of their biological action.
  • Oleynik, Philipp; Vainio, Rami; Punkkinen, Arttu; Dudnik, Oleksiy; Gieseler, Jan; Hedman, Hannu-Pekka; Hietala, Heli; Hæggström, Edward; Niemelä, Petri; Peltonen, Juhani; Praks, Jaan; Punkkinen, Risto; Säntti, Tero; Valtonen, Eino (2020)
    RADMON is a small radiation monitor designed and assembled by students of University of Turku and University of Helsinki. It is flown on-board Aalto-1, a 3-unit CubeSat in low Earth orbit at about 500 km altitude. The detector unit of the instrument consists of two detectors, a Si solid-state detector and a CsI(Tl) scintillator, and utilizes the Delta E-E technique to determine the total energy and species of each particle hitting the detector. We present the results of the on-ground and in-flight calibration campaigns of the instrument, as well as the characterization of its response through extensive simulations within the Geant4 framework. The overall energy calibration margin achieved is about 5%. The full instrument response to protons and electrons is presented and the issue of proton contamination of the electron channels is quantified and discussed. (C) 2019 COSPAR. Published by Elsevier Ltd. All rights reserved.
  • Granberg, Fredric; Byggmästar, Jesper; Nordlund, Kai (2019)
    In order to understand the effect of irradiation on the material properties, we need to look into the atomistic evolution of the system during the recoil event. The nanoscale features formed due to irradiation will ultimately affect the macroscopic properties of the material. The defect production in pristine materials have been subject to investigation previously, but as the dose increases, overlap will start to happen. This effect of cascades overlapping with pre-existing debris has only recently been touched, and mainly been investigated for interstitial-type defects. We focus on vacancy-type defect clusters in BCC Fe and start a recoil event in their near vicinity. The final defect number as well as the transformation of the defect clusters are investigated, and their behaviour is related to the distance between the defect and the cascade centre. We found that for vacancy-type defects, the suppression of defect production is not as strong as previously observed for interstitial-type defects. The cascade-induced transformation, such as change in Burgers vector or creation of dislocations, was determined for all initial defect structures.
  • Nousiainen, Katri Ilona; Mäkelä, Teemu Olavi; Peltonen, Juha (2022)
    Objective Phantoms are often used to estimate the geometric accuracy in magnetic resonance imaging (MRI). However, the distortions may differ between anatomical and phantom images. This study aimed to investigate the applicability of a phantom-based and a test-subject-based method in evaluating geometric distortion present in clinical head-imaging sequences. Materials and methods We imaged a 3D-printed phantom and test subjects with two MRI scanners using two clinical head-imaging 3D sequences with varying patient-table positions and receiver bandwidths. The geometric distortions were evaluated through nonrigid registrations: the displaced acquisitions were compared against the ideal isocenter positioning, and the varied bandwidth volumes against the volume with the highest bandwidth. The phantom acquisitions were also registered to a computed tomography scan. Results Geometric distortion magnitudes increased with larger table displacements and were in good agreement between the phantom and test-subject acquisitions. The effect of increased distortions with decreasing receiver bandwidth was more prominent for test-subject acquisitions. Conclusion Presented results emphasize the sensitivity of the geometric accuracy to positioning and imaging parameters. Phantom limitations may become an issue with some sequence types, encouraging the use of anatomical images for evaluating the geometric accuracy.
  • Chrbolková, Kateřina; Brunetto, Rosario; Ďurech, Josef; Kohout, Tomáš; Mizohata, Kenichiro; Malý, Petr; Dědič, Václav; Lantz, Cateline; Penttilä, Antti; Trojánek, František; Maturilli, Alessandro (2021)
    Context. Space weathering is a process that changes the surface of airless planetary bodies. Prime space weathering agents are solar wind irradiation and micrometeoroid bombardment. These processes alter planetary reflectance spectra and often modify their compositional diagnostic features. Aims. In this work we focused on simulating and comparing the spectral changes caused by solar wind irradiation and by micrometeoroid bombardment to gain a better understanding of these individual space weathering processes. Methods. We used olivine and pyroxene pellets as proxies for planetary materials. To simulate solar wind irradiation we used hydrogen, helium, and argon ions with energies from 5 to 40 keV and fluences of up to 10(18) particles cm(-2). To simulate micrometeoroid bombardment we used individual femtosecond laser pulses. We analysed the corresponding evolution of different spectral parameters, which we determined by applying the Modified Gaussian Model, and we also conducted principal component analysis. Results. The original mineralogy of the surface influences the spectral evolution more than the weathering agent, as seen from the diverse evolution of the spectral slope of olivine and pyroxene upon irradiation. The spectral slope changes seen in olivine are consistent with observations of A-type asteroids, while the moderate to no slope changes observed in pyroxene are consistent with asteroid (4) Vesta. We also observed some differences in the spectral effects induced by the two weathering agents. Ions simulating solar wind have a smaller influence on longer wavelengths of the spectra than laser irradiation simulating micrometeoroid impacts. This is most likely due to the different penetration depths of ions and laser pulses. Our results suggest that in some instances it might be possible to distinguish between the contributions of the two agents on a weathered surface.
  • Jeon, Yunsuk; Lakanmaa, Riitta-Liisa; Meretoja, Riitta; Leino-Kilpi, Helena (2017)
    Purpose: To identify competence assessment instruments in perianesthesia nursing care and to describe the validity and reliability of the instruments. Design: A scoping review in a systematic manner. Methods: A search in CINAHL, MEDLINE, and ERIC was carried out to identify empirical studies from 1994 to 2015. A narrative synthesis approach was undertaken to analyze the data. Findings: Nine competence assessment instruments in perianesthesia nursing care were identified. The instruments used three types of data collection methods: Self-report, observation, and written examinations. The most commonly reported validity method was content validity involving expert panels and reliability tests for internal consistency and inter-rater's consistency. Conclusions: Integrating more than one data collection method may give support to overcoming some of the limitations, such as lack of objectivity and misinterpretation of the assessment results. In an ever-changing environment, perianesthesia nursing competence requires constant reassessment from the perspective of content validity, scoring methods, and reliability.
  • Valiev, R. R. (2020)
    The effect of the nonadiabatic electronic state-mixing between the S-1 and S-2 states in tetraoxa[8]circulene is investigated computationally. The calculations show that the nonadiabatic electronic state-mixing effect on the fluorescence of tetraoxa[8]circulene is one million times weaker than the Herzberg-Teller vibronic effect. Analysis of the promotive modes of the S-0 -> S-1 and S-1 -> S-0 transitions shows that they are same for both absorption and emission. Also, the Duschinsky effect is found to be very weak for the S-0 -> S-1 and S-1 -> S-0 transitions. The Jahn-Teller symmetry breaking of the S-2 state leads to an energy splitting of similar to 1500 cm(-1) between the two components of the S-2 state.
  • Haapanen, Outi; Reidelbach, Marco; Sharma, Vivek (2020)
    Respiratory complex I (NADH:quinone oxidoreductase) plays a central role in generating the proton electrochemical gradient in mitochondrial and bacterial membranes, which is needed to generate ATP. Several high-resolution structures of complex I have been determined, revealing its intricate architecture and complementing the biochemical and biophysical studies. However, the molecular mechanism of long-range coupling between ubiquinone (Q) reduction and proton pumping is not known. Computer simulations have been applied to decipher the dynamics of Q molecule in the similar to 30 angstrom long Q tunnel. In this short report, we discuss the binding and dynamics of Q at computationally predicted Q binding sites, many of which are supported by structural data on complex I. We suggest that the binding of Q at these sites is coupled to proton pumping by means of conformational rearrangements in the conserved loops of core subunits.
  • Lanne, Markku; Luoto, Jani Pentti (2018)
    We propose imposing data-driven identification constraints to alleviate the multimodality problem arising in the estimation of poorly identified dynamic stochastic general equilibrium models under non-informative prior distributions. We also devise an iterative procedure based on the posterior density of the parameters for finding these constraints. An empirical application to the Smets and Wouters () model demonstrates the properties of the estimation method, and shows how the problem of multimodal posterior distributions caused by parameter redundancy is eliminated by identification constraints. Out-of-sample forecast comparisons as well as Bayes factors lend support to the constrained model.
  • Djurabekova, F.; Fridlund, C.; Nordlund, K. (2020)
    We present molecular dynamics simulations of atomic mixing over a Si/SiO2 heterostructure interface, induced by focused Ne+ and broad Si(+ )ion-beam irradiations, using a speed-up scheme that significantly reduces the relaxation time of the cascading recoils. To assess the qualitative reliance of the chosen method, two different potential models for Si-O, Si-Si, and O-O interactions were used: the Stillinger-Weber-like Watanabe-Samela potential and the Tersoff-like Munetoh potential. Furthermore, the molecular dynamics simulations were assessed by simulating a similar case, at a total fluence of 1 x10(15) cm(-2), with the binary collision approximation. The same general atomic density profile distributions were achieved with both models; however, the binary collision approach showed shallower penetration of Si into the SiO(2 )layer. Coordination analysis of the molecular dynamics results provides strong evidence that ion mixing at high fluences leads to coordination defects, which will affect the electronic properties of the structures unless removed with annealing.