Browsing by Subject "MONTE-CARLO"

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  • Simola, Umberto; Cisewski-Kehe, Jessi; Gutmann, Michael U.; Corander, Jukka (2021)
    Approximate Bayesian Computation (ABC) methods are increasingly used for inference in situations in which the likelihood function is either computationally costly or intractable to evaluate. Extensions of the basic ABC rejection algorithm have improved the computational efficiency of the procedure and broadened its applicability. The ABC - Population Monte Carlo (ABC-PMC) approach has become a popular choice for approximate sampling from the posterior. ABC-PMC is a sequential sampler with an iteratively decreasing value of the tolerance, which specifies how close the simulated data need to be to the real data for acceptance. We propose a method for adaptively selecting a sequence of tolerances that improves the computational efficiency of the algorithm over other common techniques. In addition we define a stopping rule as a by-product of the adaptation procedure, which assists in automating termination of sampling. The proposed automatic ABC-PMC algorithm can be easily implemented and we present several examples demonstrating its benefits in terms of computational efficiency.
  • Seppa, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti (2017)
    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected-both in experiments and simulations-factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20-60 % rh. Force-distance adhesion studies at humidity levels between 25 % rh and 53 % rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.
  • Makela, Jarmo; Susiluoto, Jouni; Markkanen, Tiina; Aurela, Mika; Järvinen, Heikki; Mammarella, Ivan; Hagemann, Stefan; Aalto, Tuula (2016)
    We examined parameter optimisation in the JSBACH (Kaminski et al., 2013; Knorr and Kattge, 2005; Reick et al., 2013) ecosystem model, applied to two boreal forest sites (Hyytiala and Sodankyla) in Finland. We identified and tested key parameters in soil hydrology and forest water and carbon-exchange-related formulations, and optimised them using the adaptive Metropolis (AM) algorithm for Hyytil with a 5-year calibration period (2000-2004) followed by a 4-year validation period (2005-2008). Sodankyla acted as an independent validation site, where optimisations were not made. The tuning provided estimates for full distribution of possible parameters, along with information about correlation, sensitivity and identifiability. Some parameters were correlated with each other due to a phenomenological connection between carbon uptake and water stress or other connections due to the set-up of the model formulations. The latter holds especially for vegetation phenology parameters. The least identifiable parameters include phenology parameters, parameters connecting relative humidity and soil dryness, and the field capacity of the skin reservoir. These soil parameters were masked by the large contribution from vegetation transpiration. In addition to leaf area index and the maximum carboxylation rate, the most effective parameters adjusting the gross primary production (GPP) and evapotranspiration (ET) fluxes in seasonal tuning were related to soil wilting point, drainage and moisture stress imposed on vegetation. For daily and half-hourly tunings the most important parameters were the ratio of leaf internal CO2 concentration to external CO2 and the parameter connecting relative humidity and soil dryness. Effectively the seasonal tuning transferred water from soil moisture into ET, and daily and half-hourly tunings reversed this process. The seasonal tuning improved the month-to-month development of GPP and ET, and produced the most stable estimates of water use efficiency. When compared to the seasonal tuning, the daily tuning is worse on the seasonal scale. However, daily parametrisation reproduced the observations for average diurnal cycle best, except for the GPP for Sodankyla validation period, where half-hourly tuned parameters were better. In general, the daily tuning provided the largest reduction in model-data mismatch. The models response to drought was unaffected by our parametrisations and further studies are needed into enhancing the dry response in JSBACH.
  • Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka (2012)
  • Lintusaari, Jarno; Gutmann, Michael U.; Dutta, Ritabrata; Kaski, Samuel; Corander, Jukka (2017)
    Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in many other branches of science. It provides a principled framework for dealing with uncertainty and quantifying how it changes in the light of new evidence. For many complex models and inference problems, however, only approximate quantitative answers are obtainable. Approximate Bayesian computation (ABC) refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible. We explain here the fundamentals of ABC, review the classical algorithms, and highlight recent developments.
  • Lu, P.; Cao, X.; Wang, Q.; Leppäranta, M.; Cheng, B.; Li, Z. (2018)
    To investigate the influence of a surface ice lid on the optical properties of a melt pond, a radiative transfer model was employed that includes four plane-parallel layers: an ice lid, a melt pond, the underlying ice, and the ocean beneath the ice. The thickness H-s and the scattering coefficient sigma(s) of the ice lid are altered. Variations in the spectral albedo and transmittance T due to H-s for a transparent ice lid are limited, and scattering in the ice lid has a pronounced impact on the albedo of melt ponds as well as the vertical distribution of spectral irradiance in ponded sea ice. The thickness of the ice lid determines the amount of solar energy absorbed. A 2-cm-thick ice lid can absorb 13% of the incident solar energy, half of the energy absorbed by a 30-cm-deep meltwater layer below the lid. This has an influence on the thermodynamics of melting sea ice. The color and spectral albedo of refreezing melt ponds depend on the value of the dimensionless number sigma(s) H- s. Good agreement between field measurements and our model simulations is found. The number sigma(s) H- s is confirmed to be a good index showing that the influence of an ice lid with sigma(s) H- s Plain Language Summary Melt ponds are pools of open water that form on sea ice in the warm months of the Arctic Ocean, and they will frequently be refrozen due to loss of heat and then covered by an ice lid or snow even in summer. This lid is very important to the optical properties of melt ponds. If the ice lid is very thin, the change in the reflective characteristics of the melt pond is minimal; that is, the influence of the ice lid is negligible. If snow accumulates on the ice lid, the reflective characteristics of the melt pond change completely. How about the situation between the above two extreme cases? In this study, we find that a dimensionless number is a good index to quantify the impact of the ice lid. Visual inspections on the color of refreezing melt ponds also help to judge the significance of the influence of the ice lid. This will allow for an accurate estimation on the role of surface ice lid during field investigations on the optical properties of melt ponds.
  • Ahlgren, Tommy; Heinola, Kalle (2020)
    The application of mean-field rate theory equations have proven to be a versatile method in simulating defect dynamics and temporal changes in the microstructure of materials. The reliability and usefulness of the method, however, depends critically on the defect interaction parameters used. In this study, we show that the main interaction parameter, the sink strength, intrinsically depends on the detrapping, or the dissociation process itself. We present a theory on how to determine the appropriate sink strengths. The correct sink strength required for a detrapping defect, is considerably larger than the values commonly used, and thus should not be neglected.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2018)
    A measurement is presented of the effective leptonic weak mixing angle (sin(2) theta(effl))using the forward- backward asymmetry of Drell-Yan lepton pairs (mu mu and ee) produced in proton-proton collisions at N root s = 8 TeV at the CMS experiment of the LHC. The data correspond to integrated luminosities of 18.8 and 19.6 fb(-1) in the dimuon and dielectron channels, respectively, containing 8.2 million dimuon and 4.9 million dielectron events. With more events and new analysis techniques, including constraints obtained on the parton distribution functions from the measured forward-backward asymmetry, the statistical and systematic uncertainties are significantly reduced relative to previous CMS measurements. The extracted value of sin(2) theta(effl) from the combined dilepton data is sin(2) theta(effl) = 0.23101 +/- 0.00036 (stat) +/- 0.00018 (syst) 0.00016 (theo) +/- 0.00031 (parton distributions in proton) = 0.23101 +/- 0.00053.
  • The ALICE collaboration; Acharya, S.; Brucken, E. J.; Chang, B.; Kim, D. J.; Litichevskyi, V.; Mieskolainen, M. M.; Orava, R.; Rak, J.; Räsänen, S. S.; Saarinen, S.; Slupecki, M.; Snellman, T. W.; Trzaska, W. H.; Vargyas, M.; Viinikainen, J. (2018)
    A measurement of beauty hadron production at mid-rapidity in proton-lead collisions at a nucleon-nucleon centre-of-mass energy root s(NN) = 5.02 TeV is presented. The semi-inclusive decay channel of beauty hadrons into J/psi is considered, where the J/psi mesons are reconstructed in the dielectron decay channel at mid-rapidity down to transverse momenta of 1.3 GeV/c. The bb production cross section at mid-rapidity, d sigma(bb)/dy, and the total cross section extrapolated over full phase space, sigma(bb), are obtained. This measurement is combined with results on inclusive J/psi production to determine the prompt J/psi cross sections. The results in p-Pb collisions are then scaled to expectations from pp collisions at the same centre-of-mass energy to derive the nuclear modification factor R-pPb, and compared to models to study possible nuclear modifications of the production induced by cold nuclear matter effects. RpPb is found to be smaller than unity at low pT for both J/psi coming from beauty hadron decays and prompt J/psi.
  • Jeon, Jae-Hyung; Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf; Vattulainen, Ilpo (2016)
    Biomembranes are exceptionally crowded with proteins with typical protein-to-lipid ratios being around 1:50 - 1:100. Protein crowding has a decisive role in lateral membrane dynamics as shown by recent experimental and computational studies that have reported anomalous lateral diffusion of phospholipids and membrane proteins in crowded lipid membranes. Based on extensive simulations and stochastic modeling of the simulated trajectories, we here investigate in detail how increasing crowding by membrane proteins reshapes the stochastic characteristics of the anomalous lateral diffusion in lipid membranes. We observe that correlated Gaussian processes of the fractional Langevin equation type, identified as the stochastic mechanism behind lipid motion in noncrowded bilayer, no longer adequately describe the lipid and protein motion in crowded but otherwise identical membranes. It turns out that protein crowding gives rise to a multifractal, non-Gaussian, and spatiotemporally heterogeneous anomalous lateral diffusion on time scales from nanoseconds to, at least, tens of microseconds. Our investigation strongly suggests that the macromolecular complexity and spatiotemporal membrane heterogeneity in cellular membranes play critical roles in determining the stochastic nature of the lateral diffusion and, consequently, the associated dynamic phenomena within membranes. Clarifying the exact stochastic mechanism for various kinds of biological membranes is an important step towards a quantitative understanding of numerous intramembrane dynamic phenomena.
  • Holland-Moritz, Henry; Ilinov, Andrey; Djurabekova, Flyura; Nordlund, Kai; Ronning, Carsten (2017)
    Ion beam processing of surfaces is well known to lead to sputtering, which conventionally is associated only with erosion of atoms from the material. We show here, by combination of experiments and a newly developed Monte Carlo algorithm, that in the case of nanoparticles in a regular two-dimensional array on surfaces, the redeposition of sputtered atoms may play a significant role on the system development. The simulations are directly compared to in situ experiments obtained using a dual focused Ga+ ion beam system and high resolution scanning electron microscopy, and explain the size evolution by a combination of sputtering and redeposition of sputtered material on neighboring particles. The effect is found to be dependent on the size of the nanoparticles: if the nanoparticle size is comparable to the ion range, the reposition is negligible. For larger nanoparticles the redeposition becomes significant and is able to compensate up to 20% of the sputtered material, effectively reducing the process of sputtering. The redeposition may even lead to significant growth: this was seen for the nanoparticles with the sizes much smaller than the ion range. Furthermore, the algorithm shows that significant redeposition is possible when the large size neighboring nanoparticles are present.
  • The ALICE collaboration; Acharya, S.; Brucken, E. J.; Chang, B.; Kim, D. J.; Litichevskyi, V.; Mieskolainen, M. M.; Orava, R.; Rak, J.; Räsänen, S. S.; Saarinen, S.; Slupecki, M.; Snellman, T. W.; Trzaska, W. H.; Vargyas, M.; Viinikainen, J. (2018)
    The correlations between event-by-event fluctuations of anisotropic flow harmonic amplitudes have been measured in Pb-Pb collisions at root s(NN) = 2.76 TeV with the ALICE detector at the Large Hadron Collider. The results are reported in terms of multiparticle correlation observables dubbed symmetric cumulants. These observables are robust against biases originating from nonflow effects. The centrality dependence of correlations between the higher order harmonics (the quadrangular v(4) and pentagonal v(5) flow) and the lower order harmonics (the elliptic v(2) and triangular v(3) flow) is presented. The transverse momentum dependences of correlations between v(3) and v(2) and between v(4) and v(2) are also reported. The results are compared to calculations from viscous hydrodynamics and a multiphase transport (AMPT) model calculations. The comparisons to viscous hydrodynamic models demonstrate that the different order harmonic correlations respond differently to the initial conditions and the temperature dependence of the ratio of shear viscosity to entropy density (eta/s). Asmall average value of eta/s is favored independent of the specific choice of initial conditions in the models. The calculations with the AMPT initial conditions yield results closest to the measurements. Correlations among the magnitudes of v(2), v(3), and v(4) show moderate p(T) dependence in midcentral collisions. This might be an indication of possible viscous corrections to the equilibrium distribution at hadronic freeze-out, which might help to understand the possible contribution of bulk viscosity in the hadronic phase of the system. Together with existing measurements of individual flow harmonics, the presented results provide further constraints on the initial conditions and the transport properties of the system produced in heavy-ion collisions.