Browsing by Subject "SIMULATION"

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  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Kadribasic, Fedja; Mirabolfathi, Nader; Nordlund, Kai; Sand, Andrea E.; Holmström, Eero; Djurabekova, Flyura (2018)
    We propose a method using solid state detectors with directional sensitivity to dark matter interactions to detect low-mass weakly interacting massive particles (WIMPs) originating from galactic sources. In spite of a large body of literature for high-mass WIMP detectors with directional sensitivity, no available technique exists to cover WIMPs in the mass range <1 GeV/c(2). We argue that single-electron-resolution semiconductor detectors allow for directional sensitivity once properly calibrated. We examine the commonly used semiconductor material response to these low-mass WIMP interactions.
  • Hemilä, Harri (2017)
    Background: The relative scale has been used for decades in analysing binary data in epidemiology. In contrast, there has been a long tradition of carrying out meta-analyses of continuous outcomes on the absolute, original measurement, scale. The biological rationale for using the relative scale in the analysis of binary outcomes is that it adjusts for baseline variations; however, similar baseline variations can occur in continuous outcomes and relative effect scale may therefore be often useful also for continuous outcomes. The aim of this study was to determine whether the relative scale is more consistent with empirical data on treating the common cold than the absolute scale. Methods: Individual patient data was available for 2 randomized trials on zinc lozenges for the treatment of the common cold. Mossad (Ann Intern Med 125:81-8, 1996) found 4.0 days and 43% reduction, and Petrus (Curr Ther Res 59:595-607, 1998) found 1.77 days and 25% reduction, in the duration of colds. In both trials, variance in the placebo group was significantly greater than in the zinc lozenge group. The effect estimates were applied to the common cold distributions of the placebo groups, and the resulting distributions were compared with the actual zinc lozenge group distributions. Results: When the absolute effect estimates, 4.0 and 1.77 days, were applied to the placebo group common cold distributions, negative and zero (i.e., impossible) cold durations were predicted, and the high level variance remained. In contrast, when the relative effect estimates, 43 and 25%, were applied, impossible common cold durations were not predicted in the placebo groups, and the cold distributions became similar to those of the zinc lozenge groups. Conclusions: For some continuous outcomes, such as the duration of illness and the duration of hospital stay, the relative scale leads to a more informative statistical analysis and more effective communication of the study findings. The transformation of continuous data to the relative scale is simple with a spreadsheet program, after which the relative scale data can be analysed using standard meta-analysis software. The option for the analysis of relative effects of continuous outcomes directly from the original data should be implemented in standard meta-analysis programs.
  • Afonso, Marco Martins; Muratore-Ginanneschi, Paolo; Gama, Silvio M. A.; Mazzino, Andrea (2018)
    We investigate the large-scale transport properties of quasi-neutrally-buoyant inertial particles carried by incompressible zero-mean periodic or steady ergodic flows. We show howto compute large-scale indicators such as the inertial-particle terminal velocity and eddy diffusivity from first principles in a perturbative expansion around the limit of added-mass factor close to unity. Physically, this limit corresponds to the case where the mass density of the particles is constant and close in value to the mass density of the fluid, which is also constant. Our approach differs from the usual over-damped expansion inasmuch as we do not assume a separation of time scales between thermalization and small-scale convection effects. For a general flow in the class of incompressible zero-mean periodic velocity fields, we derive closed-form cell equations for the auxiliary quantities determining the terminal velocity and effective diffusivity. In the special case of parallel flows these equations admit explicit analytic solution. We use parallel flows to show that our approach sheds light onto the behavior of terminal velocity and effective diffusivity for Stokes numbers of the order of unity.
  • Koota, Elina; Kääriäinen, Maria; Melender, Hanna-Leena (2018)
    Introduction: Emergency nurses are expected to adopt evidence-based practice (EBP). The aim of this systematic review was to describe educational interventions promoting EBP and their outcomes among emergency nurses, compared with no education, to inform clinicians and researchers about effective educational interventions suitable for use in emergency departments (EDs). Methods: CINAHL, Cochrane, PubMed and Scopus were systematically searched to identify studies published between January 1, 2006 and October 20, 2016 describing educational interventions designed to promote EBP among emergency nurses. 711 studies were identified and screened; 10 were selected for inclusion and quality assessment. The studies were analyzed using deductive content analysis, and the review's results are presented in accordance with the PRISMA guidelines. Results: Ten relevant studies on nine different self-developed educational interventions were identified. Eight studies had highly significant or significant results. Interventions involving face-to-face contact led to significant or highly significant effects on patient benefits and emergency nurses' knowledge, skills, and behavior. Interventions using written self-directed learning material led to significant improvements in nurses' knowledge of EBP. All the descriptions of the interventions were incomplete, and the reported details varied considerably between the studies. Conclusions: There have been few studies on educational interventions to promote EBP among emergency nurses but the available results are promising.
  • Seppälä, Anniina; Puhakka, Eini; Olin, Markus (2016)
    The swelling and cation exchange properties of montmorillonite are fundamental in a wide range of applications ranging from nanocomposites to catalytic cracking of hydrocarbons. The swelling results from several factors and, though widely studied, information on the effects of a single factor at a time is lacking. In this study, density functional theory (DFT) calculations were used to obtain atomic-level information on the swelling of montmorillonite. Molecular dynamics (MD) was used to investigate the swelling properties of montmorillonites with different layer charges and interlayer cationic compositions. Molecular dynamics calculations, with CLAYFF force field, consider three layer charges (-1.0, -0.66 and -0.5 e per unit cell) arising from octahedral substitutions and interlayer counterions of Na, K and Ca. The swelling curves obtained showed that smaller layer charge results in greater swelling but the type of the interlayer cation also has an effect. The DFT calculations were also seen to predict larger d values than MD. The formation of 1, 2 and 3 water molecular layers in the interlayer spaces was observed. Finally, the data from MD calculations were used to predict the self-diffusion coefficients of interlayer water and cations in different montmorillonites and in general the coefficient increased with increasing water content and with decreasing layer charge.
  • Wilkosz, Natalia; Rissanen, Sami; Cyza, Malgorzata; Szybka, Renata; Nowakowska, Maria; Bunker, Alex; Rog, Tomasz; Kepczynski, Mariusz (2017)
    Uptake of piroxicam, a non-steroidal anti-inflammatory drug, from the intestines after oral intake is limited due to its low solubility and its wide use is associated with several side effects related to the gastrointestinal tract. In this study, all-atom molecular dynamics (MD) simulations and fluorescent spectroscopy were employed to investigate the interaction of piroxicam in neutral, zwitterionic, and cationic forms with lipid bilayers composed of phosphatidylcholine, cholesterol, and PEGylated lipids. Our study was aimed to assess the potential for encapsulation of piroxicam in liposomal carriers and to shed more light on the process of gastrointestinal tract injury by the drug. Through both the MD simulations and laser scanning confocal microscopy, we have demonstrated that all forms of piroxicam can associate with the lipid bilayers and locate close to the water-membrane interface. Conventional liposomes used in drug delivery are usually stabilized by the addition of cholesterol and have their bloodstream lifetime extended through the inclusion of PEGylated lipids in the formulation to create a protective polymer corona. For this reason, we tested the effect of these two modifications on the behavior of piroxicam in the membrane. When the bilayer was PEGylated, piroxicam localize to the PEG layer and within the lipid headgroup region. This suggests that PEGylated liposomes are capable of carrying a larger quantity of piroxicam than the conventional ones. (C) 2017 Elsevier B.V. All rights reserved.
  • Euclid Collaboration; Ilbert, O.; Gozaliasl, G.; Keihänen, E.; Kurki-Suonio, H.; Väliviita, J.; Kirkpatrick, C. C. (2021)
    The analysis of weak gravitational lensing in wide-field imaging surveys is considered to be a major cosmological probe of dark energy. Our capacity to constrain the dark energy equation of state relies on an accurate knowledge of the galaxy mean redshift z. We investigate the possibility of measuring z with an accuracy better than 0.002 (1+z) in ten tomographic bins spanning the redshift interval 0.2 99.8%. The zPDF approach can also be successful if the zPDF is de-biased using a spectroscopic training sample. This approach requires deep imaging data but is weakly sensitive to spectroscopic redshift failures in the training sample. We improve the de-biasing method and confirm our finding by applying it to real-world weak-lensing datasets (COSMOS and KiDS+VIKING-450).
  • 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.