Papers by Anna Shcherbacheva
Investigating Influential Factors and Effects of Inter-Individual Variability in Silver Birch Phenology with Dense Lidar Time-Series
A study of annual tree-wise LiDAR intensity patterns of boreal species observed using a hyper-temporal laser scanning time series
Remote sensing of environment, May 1, 2024
Wood-Leaf Unsupervised Classification of Silver Birch Trees for Biomass Assessment Using Oblique Point Clouds
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Dec 13, 2023
Unsupervised Statistical Approach for Tree-Level Separation of Foliage and Non-Leaf Components from Point Clouds
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Dec 13, 2023
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Dec 13, 2023
Silver birch (Betula pendula Roth) is a deciduous pioneer tree species with significant economic ... more Silver birch (Betula pendula Roth) is a deciduous pioneer tree species with significant economic and ecological importance due to its rapid growth, high genetic variability and adaptability to diverse climates and environments. In this regard, understanding the factors that influence silver birch tree growth variability and its seasonal patterns has been a subject of research interests, which aim at effective forest management and ecological analyses. Tree size, competition, light availability, and topography has been considered significant factors affecting tree growth patterns. However, their relative contributions are not well understood. This is because, to study the interactions between neighbor trees and their competitive responses requires complex measurements. Accurately measuring tree attributes, such as 3D canopy shape and arrangement, is challenging but has been made possible through advancements in highresolution 3D remote sensing, specifically laser scanning technology. This study shows the potential of high-spatial and temporal resolution LiDAR time-series from a permanent laser scanning setup to detect detailed structural changes and timing in individual tree canopies, focusing on assessment of the structural canopy growth characteristics of silver birch trees. We first investigate how silver birch trees respond to competition and neighboring species. Our results focusing on canopy height increment show that tree size, competition, neighboring species, and water availability affect the rate of vertical (height) growth of the studied silver birch trees. Further, we detect the timing in canopy vertical and horizontal growth using LiDAR time-series. Significant variations of up to one week were detected among trees, providing insights for future studies on growth dynamics of silver birch in coniferous-dominant forests.
Additional file 1 of Agent-based modelling of complex factors impacting malaria prevalence
Additional file 1. From in situ to continous model. This file contains more detailed explanation ... more Additional file 1. From in situ to continous model. This file contains more detailed explanation of the data and likelihood, model calibrations, Regression with simulated ABM outputs, the extension to continuous times and a detailed description of the ABM using the ODD protocol.
Applying fluid mechanics and Kalman filtering to forecasting electricity spot prices
The aim of this work is to apply a nonlinear model from fluid mechanic to simulate electricity sp... more The aim of this work is to apply a nonlinear model from fluid mechanic to simulate electricity spot prices. The specified model is based on the viscous Burgers’ equation, that provides the simplest mathematical model of turbulence in fluid dynamics. The model has been applied to Nord Pool spot market System and Pure Trading prices. Modification of the standart Kalman filter (VEnKF) is employed in order to adjust the model output. After carrying out forecasts it was observed that the model reacts upon the spikes afterward via rapid oscillation with large amplitudes. Lappeenranta University of Technology Department of Mathematics and Physics Anna Shcherbacheva Thesis for the Degree of Master of Science in Technology year 2011 57 pages, 27 figures, 1 tables, 0 appendices Examiners: prof. Ph.D. Tuomo Kauranne and prof. Ph.D. Heikki Haario
J. Multiple Valued Log. Soft Comput., 2017
In the present study the impact of household size together with behavioral alterations caused by ... more In the present study the impact of household size together with behavioral alterations caused by parasite on malaria transmission is investigated using a discrete agent-based model of mosquito host-seeking behavior earlier calibrated against experimental data. The rate of transmission was shown to decrease with the typical size of household. Depending on the assumptions, one can observe different thresholds for a significant decrease of the disease reproduction number.
Malaria Journal, 2021
Background Increasingly complex models have been developed to characterize the transmission dynam... more Background Increasingly complex models have been developed to characterize the transmission dynamics of malaria. The multiplicity of malaria transmission factors calls for a realistic modelling approach that incorporates various complex factors such as the effect of control measures, behavioural impacts of the parasites to the vector, or socio-economic variables. Indeed, the crucial impact of household size in eliminating malaria has been emphasized in previous studies. However, increasing complexity also increases the difficulty of calibrating model parameters. Moreover, despite the availability of much field data, a common pitfall in malaria transmission modelling is to obtain data that could be directly used for model calibration. Methods In this work, an approach that provides a way to combine in situ field data with the parameters of malaria transmission models is presented. This is achieved by agent-based stochastic simulations, initially calibrated with hut-level experimental...
We address the problem of identifying the evaporation rates for neutral molecular clusters from s... more We address the problem of identifying the evaporation rates for neutral molecular clusters from synthetic (computer-simulated) cluster concentrations. We applied Bayesian parameter estimation using a Markov chain Monte Carlo (MCMC) algorithm to determine cluster evaporation/fragmentation rates from synthetic cluster distributions generated by the Atmospheric Cluster Dynamics Code (ACDC) and based on gas kinetic collision rate coefficients and evaporation rates obtained using quantum chemical calculations and detailed balances. The studied system consisted of electrically neutral sulfuric acid and ammonia clusters with up to five of each type of molecules. We then treated the concentrations generated by ACDC as synthetic experimental data. With the assumption that the collision rates are known, we tested two approaches for estimating the evaporation rates from these data. First, we studied a scenario where time-dependent cluster distributions are measured at a single temperature before the system reaches a steady state. In the second scenario, only steady-state cluster distributions are measured but at several temperatures. Additionally, in the latter case, the evaporation rates were represented in terms of cluster formation enthalpies and entropies. This reparameterization reduced the number of unknown parameters, since several evaporation rates depend on the same cluster formation enthalpy and entropy values. We also estimated the evap-oration rates using previously published synthetic steadystate cluster concentration data at one temperature and compared our two cases to this setting. Both the time-dependent and the two-temperature steady-state concentration data allowed us to estimate the evaporation rates with less variance than in the steady-state single-temperature case. We show that temperature-dependent steady-state data outperform single-temperature time-dependent data for parameter estimation, even if only two temperatures are used. We can thus conclude that for experimentally determining evaporation rates, cluster distribution measurements at several temperatures are recommended over time-dependent measurements at one temperature.
Improved identification of evaporation rates and thermodynamic data by Monte-Carlo method
<p&amp... more <p>Atmospheric new particle formation and successive cluster growth to aerosol particles is an important field of research, in particular due to climate change phenomena and air quality monitoring. Recent developments in the instrumentation have enabled quantification of ionic clusters formed in the gas phase at the first steps of particle formation under atmospherically relevant mixing ratios. However, electrically neutral clusters are prevalent in atmospheric conditions, and thus must be charged prior to detection by mass spectrometer. The charging process can lead to cluster fragmentation and thus alter the measured cluster composition.</p><p>Even when the cluster composition can be measured directly, this does not quantify individual cluster-level properties, such as cluster collision and evaporation rates. Collision rates contain relatively small uncertainties in comparison to evaporation rates, which are computed using detailed balance assumption together with the free energies of cluster formation, which can in turn be obtained from Quantum chemistry (QC) methods. As evaporation rates depend exponentially on the free energies, even difference by several kcal/mol between different QC methods results in orders of magnitude differences in evaporation rates.</p><p>On the other hand, in spite of the error margins associated with the evaporation rates, simulations of cluster populations, which incorporate collision and evaporation rates as free parameters (such as Becker-Döring models), have demonstrated good qualitative agreement with experimental data. The Becker-Döring equations are a system of Ordinary Differential equations (ODE) which account for cluster birth and death processes, as well as external sinks and sources. In mathematical terms, prediction of cluster concentrations using kinetic simulations with given cluster collision and evaporation rates is called a forward problem.</p><p>In the present study, we focus on the so-called inverse problem of how to derive the evaporation rates and thermodynamic data (enthalpy change and entropy change due to addition or removal of molecule) from available measurements, rather than on the forward problem. We do this by Delayed Rejection Adaptive Monte Carlo (DRAM) method for the system containing sulfuric acid and ammonia with the maximal size of the pentamer. Initially, we tested the method on the synthetic data created from Atmospheric Cluster Dynamic Code (ACDC) simulations. By so doing, we identify the combination of fitted parameters and concentration measurements, which leads to the best identification of the evaporation rates. Additionally, we demonstrated that the temperature-dependent data yield better estimates of the evaporation rates as compared to the time-dependent data measured before the system has reached the steady state.</p><p>Next, we apply the technique to improve the identification of the evaporation rates from CLOUD chamber data, which contain cluster concentrations and new particle formation rates measured at different temperatures and a wide range of atmospherically relevant sulfuric acid and ammonia concentrations. As a result, we were able to obtain the probability density functions (PDFs) that show small standard variations for thermodynamic data. By using the values from the PDFs as parameters in the ACDC model, we achieve a fair agreement with the measured NPFs and cluster concentrations for a wide range of temperatures.</p>
The Journal of Physical Chemistry A, 2019
. Geometries of the reactants and products at the M06-2X/aug-cc-pVTZ (black), ωB97X-D/6-31++G** (... more . Geometries of the reactants and products at the M06-2X/aug-cc-pVTZ (black), ωB97X-D/6-31++G** (blue), ωB97X-D/aug-cc-pVTZ (orange), MP2/aug-cc-pVTZ (purple) and CCSD(T)/aug-cc-pVTZ (dark yellow) levels of theory as compared with the experimentally determined structures (green: CH3OH 1 , syn-HCOOH 2 , CH3CHO 3 , H2O 4 and CH2O 5 ). 1.41 Products CH3OH+syn-HCOOH to CH3OCHO+H2O syn-HCOOH to anti-HCOOH CH2O+H2O to CH2(OH)2 MAE* (%) ATcT** -19.0 16.4 -34.9 -ωB97X-D/6-31++G** -17.1 20.0 -47.5 22.68 CCSD(T)/aug-cc-pVTZ//wB97X-D/6-311++G** -20.8 16.7 -34.1 4.50 MPWB1K/aug-cc-pVTZ -16.8 17.1 -49.4 19.15 wB97X-D/aug-cc-pVTZ -17.2 16.4 -39.5 7.53 CBS-QB3 -26.2 15.7 -9.3 38.47 M06-2X/aug-cc-pVTZ -18.5 17.5 -50.1 17.64 MP2/aug-cc-pVTZ -22.5 16.8 -34.5 7.33 CCSD(T)/aug-cc-pVTZ NA*** 16.6 NA -CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ -21.0 16.8 -35.1 4.54 DLPNO-CCSD(T)/aug-cc-pVTZ// ωB97X-D/6-31++G** -21.0 16.8 -34.1 5.05 M06-2X/6-311++G** -17.9 19.6 -49.2 22.06 * Mean Absolute Error ** Active Thermochemical Tables (version 1.122d); *** Not available Section S.A. The Cartesian coordinates of the geometries optimized at the ωB97X-D/6-31++G** level.
Advances in Artificial Life, ECAL 2013, 2013
We simulate the swarming behavior of three synthetic animal species that differ only by the degre... more We simulate the swarming behavior of three synthetic animal species that differ only by the degree of perception they have on their fellow animals. The species are called mosquitoes, birds and fish. The swarms that comprise many individuals of each species in turn move randomly in a rugged potential landscape. The mosquitoes pay no heed to one another. The birds follow a bunch of their nearest neighbours in front, based on strictly limited visibility. The fish, in turn, sense also far-away neighbors through their lateral line, as modeled by an exponentially decaying perception function. The simulations show that such local differences in perception by swarming individuals have global macroscopic consequences to the geometry of the corresponding swarms. These consequences are of persistent nature across many simulations with each species.
Mathematical biosciences, Jan 12, 2017
The efficiency of spatial repellents and long-lasting insecticide-treated nets (LLINs) is a key r... more The efficiency of spatial repellents and long-lasting insecticide-treated nets (LLINs) is a key research topic in malaria control. Insecticidal nets reduce the mosquito-human contact rate and simultaneously decrease mosquito populations. However, LLINs demonstrate dissimilar efficiency against different species of malaria mosquitoes. Various factors have been proposed as an explanation, including differences in insecticide-induced mortality, flight characteristics, or persistence of attack. Here we present a discrete agent-based approach that enables the efficiency of LLINs, baited traps and Insecticide Residual Sprays (IRS) to be examined. The model is calibrated with hut-level experimental data to compare the efficiency of protection against two mosquito species: Anopheles gambiae and Anopheles arabiensis. We show that while such data does not allow an unambiguous identification of the details of how LLINs alter the vector behavior, the model calibrations quantify the overall impa...
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Papers by Anna Shcherbacheva