Browsing by Subject "IRON"

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  • Silvonen, Soila; Niemistö, Juha; Csibrán, Adrián; Jilbert, Tom; Torma, Péter; Krámer, Tamás; Nurminen, Leena; Horppila, Jukka (2021)
    Hypolimnetic withdrawal (HW) is a lake restoration method that is based on the removal of phosphorus (P) along with near-bottom water. While it has often proven to be effective, the method also sets challenges: it is about balancing between effective P removal and maintenance of the thermal stratification of the lake. The success of different HW projects has been reviewed in some studies retrospectively, but scientific literature still lacks studies that use detailed data on the lake biogeochemistry to scale and optimize the method in advance, and to predict the outcomes of the restoration measure. In the current study, we investigated the seasonal biogeochemistry, P stocks and thermal stratification of a eutrophic lake (Lake Kymijarvi/Myllypohja basin, southern Finland) to determine an optimal withdrawal rate, to assess its effects on stratification, and to evaluate the expected success of HW. We found that by adjusting HW with P diffusive fluxes from the sediment (diffusion-adjusted HW), it is possible to remove a notable part of the cycling P without causing major disturbances to the thermal stratification even in a relatively shallow lake. Our results show that HW can have great potential in lake restoration: diffusion-adjusted HW in our study lake could increase the annual P output by 35-46%, shifting the P budget of the lake to negative. We thus propose a novel approach to optimize HW on the basis of the diffusive flux of P from the sediment, with the goal of extracting P continuously at an equivalent rate to the diffusive flux. We finally discuss how this can be achieved more effectively with HW based on a closed-circuit system. (c) 2020 The Authors. Published by Elsevier B.V.
  • De Backer, A.; Domain, C.; Becquart, C. S.; Luneville, L.; Simeone, D.; Sand, A. E.; Nordlund, K. (2018)
    The impacts of ions and neutrons in metals cause cascades of atomic collisions that expand and shrink, leaving microstructure defect debris, i.e. interstitial or vacancy clusters or loops of different sizes. In De Backer et al (2016 Europhys. Lett. 115 26001), we described a method to detect the first morphological transition, i.e. the cascade fragmentation in subcascades, and a model of primary damage combining the binary collision approximation and molecular dynamics (MD). In this paper including W, Fe, Be, Zr and 20 other metals, we demonstrate that the fragmentation energy increases with the atomic number and decreases with the atomic density following a unique power law. Above the fragmentation energy, the cascade morphology can be characterized by the cross pair correlation functions of the multitype point pattern formed by the subcascades. We derive the numbers of pairs of subcascades and observed that they follow broken power laws. The energy where the power law breaks indicates the second morphological transition when cascades are formed by branches decorated by chaplets of small subcascades. The subcascade interaction is introduced in our model of primary damage by adding pairwise terms. Using statistics obtained on hundreds of MD cascades in Fe, we demonstrate that the interaction of subcascades increases the proportion of large clusters in the damage created by high energy cascades. Finally, we predict the primary damage of 500 keV Fe ion in Fe and obtain cluster size distributions when large statistics of MD cascades arc not feasible.
  • Lagerspets, Emi; Valbonetti, Evelyn; Eronen, Aleksi; Repo, Timo (2021)
    We report here novel Cu(I) thiophene carbaldimine catalysts for the selective aerobic oxidation of primary alcohols to their corresponding aldehydes and various diols to lactones or lactols. In the presence of the in situ generated Cu(I) species, a persistent radical (2,2,6,6-tetramethylpiperdine-N-oxyl (TEMPO)) and N-methylimidazole (NMI) as an auxiliary ligand, the reaction proceeds under aerobic conditions and at ambient temperature. Especially the catalytic system of 1-(thiophen-2-yl)-N-(4-(trifluoromethoxy)phenyl)methanimine (ligand L2) with copper(I)-iodide showed high reactivity for all kind of alcohols (benzylic, allylic and aliphatic). In the case of benzyl alcohol even 2.5 mol% of copper loading gave quantitative yield. Beside high activity under aerobic conditions, the catalysts ability to oxidize 1,5-pentadiol to the corresponding lactol (86% in 4 h) and Nphenyldiethanolamine to the corresponding morpholine derivate lactol (86% in 24 h) is particularly noteworthy.
  • Keuters, Meike Hedwig; Keksa-Goldsteine, Velta; Dhungana, Hiramani; Huuskonen, Mikko T.; Pomeshchik, Yuriy; Savchenko, Ekaterina; Korhonen, Paula K.; Singh, Yajuvinder; Wojciechowski, Sara; Lehtonen, Sarka; Kanninen, Katja M.; Malm, Tarja; Sirviö, Jouni; Muona, Anu; Koistinaho, Milla; Goldsteins, Gundars; Koistinaho, Jari (2021)
    Lipid peroxidation-initiated ferroptosis is an iron-dependent mechanism of programmed cell death taking place in neurological diseases. Here we show that a condensed benzo[b]thiazine derivative small molecule with an arylthiazine backbone (ADA-409-052) inhibits tert-Butyl hydroperoxide (TBHP)-induced lipid peroxidation (LP) and protects against ferroptotic cell death triggered by glutathione (GSH) depletion or glutathione peroxidase 4 (GPx4) inhibition in neuronal cell lines. In addition, ADA-409-052 suppresses pro-inflammatory activation of BV2 microglia and protects N2a neuronal cells from cell death induced by pro-inflammatory RAW 264.7 macrophages. Moreover, ADA-409-052 efficiently reduces infarct volume, edema and expression of pro-inflammatory genes in a mouse model of thromboembolic stroke. Targeting ferroptosis may be a promising therapeutic strategy in neurological diseases involving severe neuronal death and neuroinflammation.
  • Ousaaid, Driss; Ghouizi, Asmae El; Laaroussi, Hassan; Bakour, Meryem; Mechchate, Hamza; Es-safi, Imane; Kamaly, Omkulthom Al; Saleh, Asmaa; Conte, Raffaele; Lyoussi, Badiaa; El Arabi, Ilham (2022)
    This study aims to examine the ability of apple vinegar on phenylhydrazine (PHZ)-induced hemolytic anemia in Wistar rats. In vitro, phenolic and flavonoid content and antioxidant activity were determined. In vivo, phenylhydrazine (10 mg/kg) was injected intravenously into rats for 4 days and then treated with apple vinegar daily by gavage (1 mL/kg) for five weeks. high level of polyphenols and flavonoids (90 +/- 1.66 mg GAE/100 mL and 7.29 +/- 0.23 mg QE/100 mL, respectively) were found in the apple vinegar which gives it a good ability to scavenge free radicals (TAC = 4.22 +/- 0.18 mg AAE/100 mL and DPPH, IC50 = 0.49 +/- 0.004 mu L/ml). The phytochemical composition of apple vinegar revealed the presence of numerous bioactive compounds including arbutin, apigenin, sinapic, ferulic and trans-ferulic acids. The major antioxidant components in apple vinegar were ferulic and trans-ferulic acids (40% and 43%, respectively). PHZ treatment induced changes in platelets, blood cell count, mean corpuscular volume, hemoglobin concentration and mean capsulated hemoglobin. However, the co-administration of apple vinegar revealed its capacity to ameliorate the changes induced by phenylhydrazine. Therefore, apple vinegar use could have a positive impact on the prevention of hemolytic anemia induced by phenylhydrazine due to the antioxidant properties of its major components.
  • Lindford, Andrew; Juteau, Susanna; Jaks, Viljar; Klaas, Mariliis; Lagus, Heli; Vuola, Jyrki; Kankuri, Esko (2021)
    We describe a case of Lichtenberg Figures (LFs) following an electrical injury from a high-voltage switchgear in a 47 year-old electrician. LFs, also known as ferning pattern or keraunographic markings, are a pathognomonic skin sign for lightning strike injuries. Their true pathophysiology has remained a mystery and only once before described following an electical injury. The aim was to characterise the tissue response of LFs by performing untargeted non-labelled proteomics and immunohistochemistry on paraffin-embedded sections of skin biopsies taken from the area of LFs at presentation and at 3 months follow-up. Our results demonstrated an increase in dermal T-cells and greatly increased expression of the iron-binding glycoprotein lactoferrin by keratinocytes and lymphocytes. These changes in the LF-affected skin were associated with extravasation of red blood cells from dermal vessels. Our results provide an initial molecular and cellular insight into the tissue response associated with LFs.
  • Byggmästar, J; Granberg, F; Sand, A E; Pirttikoski, A; Alexander, Rebecca; Marinica, M. C.; Nordlund, K (2019)
    Overlap of collision cascades with previously formed defect clusters become increasingly likely at radiation doses typical for materials in nuclear reactors. Using molecular dynamics, we systematically investigate the effects of different pre-existing self-interstitial clusters on the damage produced by an overlapping cascade in bcc iron and tungsten. We find that the number of new Frenkel pairs created in direct overlap with an interstitial cluster is reduced to essentially zero, when the size of the defect cluster is comparable to that of the disordered cascade volume. We develop an analytical model for this reduced defect production as a function of the spatial overlap between a cascade and a defect cluster of a given size. Furthermore, we discuss cascade-induced changes in the morphology of self-interstitial clusters, including transformations between 1/2<111> and <100> dislocation loops in iron and tungsten, and between C15 clusters and dislocation loops in iron. Our results provide crucial new cascade-overlap effects to be taken into account in multi-scale modelling of radiation damage in bcc metals.
  • Skarp-de Haan, Caroline P. A.; Culebro, Alejandra; Schott, Thomas; Revez, Joana; Schweda, Elke K. H.; Hänninen, Marja-Liisa; Rossi, Mirko (2014)
  • Hollingsworth, A.; Barthe, M-F; Lavrentiev, M. Yu; Derlet, P. M.; Dudarev, S. L.; Mason, D. R.; Hu, Z.; Desgardin, P.; Hess, J.; Davies, S.; Thomas, B.; Salter, H.; Shelton, E. F. J.; Heinola, K.; Mizohata, K.; De Backer, A.; Baron-Wiechec, A.; Jepu, I.; Zayachuk, Y.; Widdowson, A.; Meslin, E.; Morellec, A. (2022)
    Self-ion irradiation of pure tungsten with 2 MeV W ions provides a way of simulating microstructures generated by neutron irradiation in tungsten components of a fusion reactor. Transmission electron microscopy (TEM) has been used to characterize defects formed in tungsten samples by ion irradiation. It was found that tungsten irradiated to 0.85 dpa at relatively low temperatures develops a characteristic microstructure dominated by dislocation loops and black dots. The density and size distribution of these defects were estimated. Some of the samples exposed to self-ion irradiation were then implanted with deuterium. Thermal Desorption Spectrometry (TDS) analysis was performed to estimate the deuterium inventory as a function of irradiation damage and deuterium release as a function of temperature. Increase of inventory with increasing irradiation dose followed by slight decrease above 0.1 dpa was found. Application of Positron Annihilation Spectroscopy (PAS) to self-irradiated but not deuterium implanted samples enabled an assessment of the density of irradiation defects as a function of exposure to highenergy ions. The PAS results show that the density of defects saturates at doses in the interval from 0.085 to 0.425 displacements per atom (dpa). These results are discussed in the context of recent theoretical simulations exhibiting the saturation of defect microstructure in the high irradiation exposure limit. The saturation of damage found in PAS agrees with the simulation data described in the paper. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
  • Murros, Kari E.; Huynh, Anh Vy; Takala, Timo M.; Saris, Per E. J. (2021)
    Parkinson's disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein alpha-synuclein, a neuronal protein, aggregates to form toxic structures in nerve cells. The cause of Parkinson's disease (PD) remains unknown. Intestinal dysfunction and changes in the gut microbiota, common symptoms of PD, are evidently linked to the pathogenesis of PD. Although a multitude of studies have investigated microbial etiologies of PD, the microbial role in disease progression remains unclear. Here, we show that Gram-negative sulfate-reducing bacteria of the genus Desulfovibrio may play a potential role in the development of PD. Conventional and quantitative real-time PCR analysis of feces from twenty PD patients and twenty healthy controls revealed that all PD patients harbored Desulfovibrio bacteria in their gut microbiota and these bacteria were present at higher levels in PD patients than in healthy controls. Additionally, the concentration of Desulfovibrio species correlated with the severity of PD. Desulfovibrio bacteria produce hydrogen sulfide and lipopolysaccharide, and several strains synthesize magnetite, all of which likely induce the oligomerization and aggregation of alpha-synuclein protein. The substances originating from Desulfovibrio bacteria likely take part in pathogenesis of PD. These findings may open new avenues for the treatment of PD and the identification of people at risk for developing PD.
  • Auvinen, Piritta; Mäntyselkä, Pekka; Koponen, Hannu; Kautiainen, Hannu; Korniloff, Katariina; Ahonen, Tiina; Vanhala, Mauno (2018)
    Background: Restless legs syndrome is a sensorimotor disorder associated with several mental illnesses particularly depression. Methods: A cross-sectional study of primary care patients. The prevalence of restless legs symptoms was studied in 706 patients with depressive symptoms and 426 controls without a psychiatric diagnosis by using a structured questionnaire. The depressive symptoms were evaluated with the BDI and the psychiatric diagnosis was confirmed by means of a diagnostic interview (M.I.N.I.). The subjects with elevated depressive symptoms were divided into two groups subjects with depressive symptoms with and without clinical depression. Results: The prevalence of restless legs symptoms was 24.8% in the controls, 50.0% in the patients with clinical depression and 42.4% in the patients with depressive symptoms. CRP value was significantly higher (p =.003) in the clinically depressed patients than in the other groups. There was a higher concentration of TNF-alpha in the subjects with restless legs symptoms (7.4 ng/l +/- 3.2) compared with the subjects without symptoms (6.7 ng/1 +/- 2.3)(p Conclusions: TNF-alpha level was associated with restless legs symptoms only among subjects with depressive symptoms whether they had clinical depression or not. We suggest that TNF-alpha could be an underlying factor between restless legs symptoms and comorbidities.
  • Sissala, Niina; Mustaniemi, Sanna; Kajantie, Eero; Vääräsmäki, Marja; Koivunen, Peppi (2022)
    Incidence of gestational diabetes (GDM) has increased rapidly. It poses significant risks for both mother and fetus affecting also negatively their longer-term metabolic heath. We asked whether early pregnancy maternal hemoglobin (Hb) levels, indicative for tissue oxygenation, would affect mother's metabolic health and fetal outcome. We assessed in FinnGeDi, a Finnish multicenter case-control study for GDM (n = 1828), association of maternal 1st trimester Hb levels with metabolic parameters and perinatal outcome. Our data show that mothers with GDM had higher Hb levels compared to controls (mean difference 1.746 g/L). Hb levels associated positively with pre-pregnancy body mass index (BMI), fasting glucose levels and glucose levels in a glucose tolerance test and systolic and diastolic blood pressure (bp) levels. When assessed in quartiles the highest Hb quartile had more chronic and gestational hypertension and the most adverse outcome of the metabolic parameters, dose-dependency seen in bp, BMI and glucose levels. In a multivariable regression analysis Hb levels remained an independently associated parameter for GDM after adjusting for key covariates (OR 1.019, 95% CI [1.007; 1.031]). In conclusion, higher maternal Hb levels within the normal variation are an independent risk factor for GDM in this population but have little effect on perinatal outcome.
  • Jilbert, Tom; Jokinen, Sami; Saarinen, Timo; Mattus-Kumpunen, Ulpu; Simojoki, Asko; Saarni, Saija; Salminen, Sarianna; Niemist, Juha; Horppila, Jukka (2020)
    Using biogeochemical analyses of sediments and porewaters, we investigate the legacy of a brief, intense period of eutrophication on sedimentary phosphorus (P) cycling in a boreal lake (Enonselka basin, Lake Vesijarvi, Finland). Point-source sewage inputs in the twentieth century caused deoxygenation of the lake and accelerated the focusing of iron (Fe) and manganese (Mn) oxides into deeper areas. Early diagenesis under Fe-Mn-rich conditions now favors rapid burial of P in these areas, likely as a combination of both oxide-bound P phases and authigenic manganous vivianite. A new P budget for Enonselka basin shows that P burial causes an annual drawdown of 1.2% (+/- 0.2%) of the surface sediment P inventory, supporting a long-term trend towards recovery since the construction of a wastewater treatment plant in the mid-1970s. However, remineralization of organic matter and associated dissolution of Fe-Mn oxides continues to regenerate P from a deep reactive layer (20-60 cm depth) deposited at the height of past eutrophication, leading to an upwards diffusive flux of dissolved phosphate towards the surface sediments. The magnitude of this flux is similar to that of external P loading to the lake. The combined incoming fluxes of P are likely to retard the complete recovery from eutrophication by decades, despite ongoing restoration actions.
  • Myllykangas, Jukka-Pekka; Rissanen, Antti J.; Hietanen, Susanna; Jilbert, Tom (2020)
    Methane is produced microbially in vast quantities in sediments throughout the world's oceans. However, anaerobic oxidation of methane (AOM) provides a near-quantitative sink for the produced methane and is primarily responsible for preventing methane emissions from the oceans to the atmosphere. AOM is a complex microbial process that involves several different microbial groups and metabolic pathways. The role of different electron acceptors in AOM has been studied for decades, yet large uncertainties remain, especially in terms of understanding the processes in natural settings. This study reports whole-core incubation methane oxidation rates along an estuarine gradient ranging from near fresh water to brackish conditions, and investigates the potential role of different electron acceptors in AOM. Microbial community structure involved in different methane processes is also studied in the same estuarine system using high throughput sequencing tools. Methane oxidation in the sediments was active in three distinct depth layers throughout the studied transect, with total oxidation rates increasing seawards. We find extensive evidence of non-sulphate AOM throughout the transect. The highest absolute AOM rates were observed below the sulphate-methane transition zone (SMTZ), strongly implicating the role of alternative electron acceptors (most likely iron and manganese oxides). However, oxidation rates were ultimately limited by methane availability. ANME-2a/b were the most abundant microbial phyla associated with AOM throughout the study sites, followed by ANME-2d in much lower abundances. Similarly to oxidation rates, highest abundances of microbial groups commonly associated with AOM were found well below the SMTZ, further reinforcing the importance of non-sulphate AOM in this system.
  • Kiani, Mina; Tammeorg, Priit; Niemistö, Juha; Simojoki, Asko; Tammeorg, Olga (2020)
    Mankind is taking advantage of numerous services by small shallow lakes such as drinking water supply, irrigation, and recreational function; however, many of these lakes suffer from eutrophication. Given the key role of phosphorus (P) in eutrophication process, one of the effective restoration methods especially for small shallow lakes is removal of sediments enriched with nutrients. In our study, we used interannual, seasonal, and spatial data to examine the changes in sediment P mobility after removal of sediments in 2016 from a 1-ha highly eutrophic lake. We measured the sediment redox potential, analyzed soluble reactive P (SRP) in the pore water and P fractional composition of the surface sediments, and calculated the P diffusive flux in three locations in two continuous years (2017 and 2018) after the excavation. Similar measurements were done before sediment removal at central site of the lake in 2015. Removing nutrient-rich sediment also removed 6400 kg of P, and thus the potential for release of P from sediments decreased on a long-term scale. However, a large pool of releasable P was rebuilt soon after the sediment removal due to high external P loading, resulting in extensive anoxia of sediment surface and associated internal P loading as high as 1450 mg m−2 summer−1. Moreover, the Fe-P and labile P fractions were the most important sources of P release, as evidenced by their considerable seasonal and interannual changes after the sediment removal. The sediment total Fe negatively correlated with sediment P diffusive flux, pore water SRP, and near-bottom water total P and SRP concentrations which indicated a strong linkage between sediment P dynamics and Fe after the restoration. Sediment removal could be a beneficial restoration approach, but the effects on lake water quality remain only short-term unless there is an adequate control on external loading to the lake.
  • Murros, Kari; Wasiljeff, Joonas; Macías-Sánchez, Elena; Faivre, Damien; Soinne, Lauri; Valtonen, Jussi; Pohja, Marjatta; Saari, Pekka; Pesonen, Lauri J.; Salminen, Johanna M. (2019)
    Magnetic iron oxide nanoparticles, magnetite/maghemite, have been identified in human tissues, including the brain, meninges, heart, liver, and spleen. As these nanoparticles may play a role in the pathogenesis of neurodegenerative diseases, a pilot study explored the occurrence of these particles in the cervical (neck) skin of 10 patients with Parkinson's disease and 10 healthy controls. Magnetometry and transmission electron microscopy analyses revealed magnetite/maghemite nanoparticles in the skin samples of every study participant. Regarding magnetite/maghemite concentrations of the single-domain particles, no significant between-group difference was emerged. In low-temperature magnetic measurement, a magnetic anomaly at similar to 50 K was evident mainly in the dermal samples of the Parkinson group. This anomaly was larger than the effect related to the magnetic ordering of molecular oxygen. The temperature range of the anomaly, and the size-range of magnetite/maghemite, both refute the idea of magnetic ordering of any iron phase other than magnetite. We propose that the explanation for the finding is interaction between clusters of superparamagnetic and single-domain-sized nanoparticles. The source and significance of these particles remains speculative.
  • Takamiya, Masanari; Xu, Feng; Suhonen, Heikki; Gourain, Victor; Yang, Lixin; Nga Yu Ho, [Tuntematon]; Helfen, Lukas; Schroeck, Anne; Etard, Christelle; Grabher, Clemens; Rastegar, Sepand; Schlunck, Guenther; Reinhard, Thomas; Baumbach, Tilo; Straehle, Uwe (2016)
    Altered levels of trace elements are associated with increased oxidative stress that is eventually responsible for pathologic conditions. Oxidative stress has been proposed to be involved in eye diseases, including cataract formation. We visualized the distribution of metals and other trace elements in the eye of zebrafish embryos by micro X-ray fluorescence (mu-XRF) imaging. Many elements showed highest accumulation in the retinal pigment epithelium (RPE) of the zebrafish embryo. Knockdown of the zebrafish brown locus homologues tyrp1a/b eliminated accumulation of these elements in the RPE, indicating that they are bound by mature melanosomes. Furthermore, albino (slc45a2) mutants, which completely lack melanosomes, developed abnormal lens reflections similar to the congenital cataract caused by mutation of the myosin chaperon Unc45b, and an in situ spin trapping assay revealed increased oxidative stress in the lens of albino mutants. Finally transplanting a wildtype lens into an albino mutant background resulted in cataract formation. These data suggest that melanosomes in pigment epithelial cells protect the lens from oxidative stress during embryonic development, likely by buffering trace elements.
  • Zhou, Guo-Wei; Yang, Xiao-Ru; Rønn, Regin; Su, Jian-Qiang; Cui, Li; Zheng, Bang-Xiao; Zhu, Yong-Guan (2019)
    Microorganisms capable of anaerobic nitrate-dependent Fe(II) (ferrous iron) oxidation (ANDFO) contribute significantly to iron and nitrogen cycling in various environments. However, lab efforts in continuous cultivation of ANDFO strains suffer from loss of activity when ferrous iron is used as sole electron donor. Here we used a novel strain of nitrate-dependent Fe(II)-oxidizing bacterium Bacillus ferroxidians as a model and focused on physiological activity of cells during ANDFO. It was shown that B. ferroxidans entered a metabolically inactive state during ANDFO. B. ferrooxidans exhibited nitrate reduction coupled with Fe(II) oxidation, and the activity gradually declined and was hardly detected after 48-h incubation. Propidium monoazide (PMA) assisted 16S rRNA gene real-time PCR suggested that large number of B. ferrooxidans cells were alive during incubation. However, 2H(D)-isotope based Raman analysis indicated that the cells were metabolically inactive after 120-h of ANDFO. These inactive cells re-awakened in R2A medium and were capable of growth and reproduction, which was consistent with results in Raman analysis. Scanning electron microscopy (SEM) observation and x-ray diffraction (XRD) revealed the formation of Fe minerals in close proximity of cells in the Fe(II)-oxidizing medium after Fe(II) oxidation. Overall, our results demonstrated that continued ANDFO can induce a metabolically inactive state in B. ferrooxidans, which was responsible for the loss of activity during ANDFO. This study provides insight into the ANDFO process and its contribution to iron and nitrogen cycling in the environments.
  • Baibuz, Ekaterina; Vigonski, Simon; Lahtinen, Jyri; Zhao, Junlei; Jansson, Ville; Zadin, Vahur; Djurabekova, Flyura (2018)
    Abstract Atomistic rigid lattice Kinetic Monte Carlo is an efficient method for simulating nano-objects and surfaces at timescales much longer than those accessible by molecular dynamics. A laborious part of constructing any Kinetic Monte Carlo model is, however, to calculate all migration barriers that are needed to give the probabilities for any atom jump event to occur in the simulations. One of the common methods of barrier calculations is Nudged Elastic Band. The number of barriers needed to fully describe simulated systems is typically between hundreds of thousands and millions. Calculations of such a large number of barriers of various processes is far from trivial. In this paper, we will discuss the challenges arising during barriers calculations on a surface and present a systematic and reliable tethering force approach to construct a rigid lattice barrier parameterization of face-centred and body-centred cubic metal lattices. We have produced several different barrier sets for Cu and for Fe that can be used for KMC simulations of processes on arbitrarily rough surfaces. The sets are published as Data in Brief articles and available for the use.
  • Vaalama, Anu; Hartikainen, Helina; Vallius, Henry; Lukkari, Kaarina (2019)
    Phosphorus (P) exchange in clayey mud sediments was investigated with desorption-sorption isotherms at 22 coastal sites in the eutrophied brackish Gulf of Finland, the Baltic Sea. The aim was to gain information on P sorption potential and pattern of oxygenated surface sediments and to elucidate factors explaining them. Modified Freundlich equation was fitted to the isotherm data and used for calculation of the P exchange parameters EPC0 (equilibrium P concentration at zero net sorption), k(E)(PC0), k(15) and k(100) (P buffering capacities at early, middle and high sorption stages, respectively). They were further used to assess the P sorption potential and pattern of the sediments. Sediment properties explaining the P sorption potential at different sorption stages were identified.The greatest sorption potentials were recorded in originally poorly oxic sediments in the inner archipelago with accumulated fine particulate material, high in adsorbents for P, transported from the watersheds. After oxygenation, they were high in amorphous Fe-oxyhydroxides, which explained their efficient P sorption (k(EPC0) > 1.32 I g(-1)). Poorer P sorption (k(EPC0) 0.45-0.84 I g(-1)) was recorded in fine sediments abundant in Al-oxyhydroxides, presumably due to their higher original P occupation degree. The lowest sorption potentials were found in the outer archipelago sediments. Their lowest specific surface areas and highest original P contents referred to scarcity of adsorbents and high occupation degree of the existing ones. These results suggest that the coastal clayey mud sediments investigated possess high P sorption potential, which can be markedly diminished by eutrophication-induced hypoxia but recovered if oxygen conditions improve.