Browsing by Subject "DIFFUSION"

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  • Barmaki, Samineh; Obermaier, Daniela; Kankuri, Esko; Vuola, Jyrki; Franssila, Sami; jokinen, Ville (2020)
    A hypoxic (low oxygen level) microenvironment and nitric oxide paracrine signaling play important roles in the control of both biological and pathological cell responses. In this study, we present a microfluidic chip architecture for nitric oxide delivery under a hypoxic microenvironment in human embryonic kidney cells (HEK-293). The chip utilizes two separate, but interdigitated microfluidic channels. The hypoxic microenvironment was created by sodium sulfite as the oxygen scavenger in one of the channels. The nitric oxide microenvironment was created by sodium nitroprusside as the light-activated nitric oxide donor in the other channel. The solutions are separated from the cell culture by a 30 µm thick gas-permeable, but liquid-impermeable polydimethylsiloxane membrane. We show that the architecture is preliminarily feasible to define the gaseous microenvironment of a cell culture in the 100 µm and 1 mm length scales.
  • Zhang, Chao; Vehkamäki, Marko; Pietikäinen, Mika; Leskelä, Markku; Ritala, Mikko (2020)
    Novel area-selective molecular layer deposition (AS-MLD) of polyimide (PI) on Cu versus native SiO2 was studied. By use of 1,6-diaminohexane (DAH) and pyromellitic dianhydride (PMDA) as precursors, PI films can be selectively deposited on the Cu surface at 200-210 degrees C with a rate around 7.8 A/cycle while negligible growth takes place on SiO2. The selectivity was successfully demonstrated also on Cu/SiO2 patterns at 200 degrees C; after 180 MLD cycles, around 140 nm thick PI was deposited on Cu regions while
  • Mason, D. R.; Sand, A. E.; Dudarev, S. L. (2019)
    We describe the development of a new object kinetic Monte Carlo (kMC) code where the elementary defect objects are off-lattice atomistic configurations. Atomic-level transitions are used to transform and translate objects, to split objects and to merge them together. This gradually constructs a database of atomic configurations-a set of relevant defect objects and their possible events generated on-the-fly. Elastic interactions are handled within objects with empirical potentials at short distances, and between spatially distinct objects using the dipole tensor formalism. The model is shown to evolve mobile interstitial clusters in tungsten faster than an equivalent molecular dynamics (MD) simulation, even at elevated temperatures. We apply the model to the evolution of complex defects generated using MD simulations of primary radiation damage in tungsten. We show that we can evolve defect structures formed in cascade simulations to experimentally observable timescales of seconds while retaining atomistic detail. We conclude that the first few nanoseconds of simulation following cascade initiation would be better performed using MD, as this will capture some of the near-temperature-independent evolution of small highly-mobile interstitial clusters. For the 20keV cascade annealing simulations considered here, we observe internal relaxations of sessile objects. These relaxations would be difficult to capture using conventional object kMC, yet are important as they establish the conditions for long timescale evolution.
  • Kindler, Oliver; Pulkkinen, Otto; Cherstvy, Andrey G.; Metzler, Ralf (2019)
    Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called "autoinducers") and themselves sense the autoinducer concentration in their vicinity. Once-due to increased local cell density inside a "cluster" of the growing colony-the concentration of autoinducers exceeds a threshold value, cells in this clusters get "induced" into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
  • Hurmekoski, Elias; Sjolie, Hanne K. (2018)
    Scenario analyses are widely used in forest sector foresight studies, being typically based on either qualitative or quantitative approaches. As scenario analyses are used for informing decision-makers, it is of interest to contrast the similarities and differences between the scenario processes and outcomes using quantitative and qualitative approaches and to explore the underlying causes of differences. This paper uses the output from a qualitative scenario study to design forest sector model (FSM) scenarios and compares the results from the two approaches. We analyse two cases on wood products markets in Norway: i) Wood products suppliers establish a developer firm specializing on wood construction to boost demand, and ii) Levying a carbon tax while reducing CO2 emissions in cement production. Comparing the qualitative studies (innovation diffusion analysis, backcasting and Delphi) and FSM analyses (NorFor model), the results resemble for case ii) but deviate strongly for case i). Notably, the strategy aiming to boost the demand for domestic wood products leads in NorFor mainly to an increase in imports with limited impact on Norwegian sawnwood production. Causes of the discrepancies are discussed. Despite the challenges of combining the two frameworks, we believe that the method where assumptions based on stakeholder input or other qualitative research approaches are elaborated in a FSM and compared, should be more explored. Importantly, applying various methods and frameworks allows for complementing and diversifying the picture, and thus improving the knowledge base. (C) 2017 Department of Forest Economics, Swedish University of Agricultural Sciences, Umea. Published by Elsevier GmbH.
  • Boi, S. (2019)
    The Maxey-Riley equation and its simplified versions represent the most widespread tool to investigate dynamics and dispersion of inertial small particles in turbulent flows. The numerical solution of such models is often very challenging, and some of their terms, such as the molecular diffusivity or the Basset history force, are often neglected to reduce the complexity upon suitable approximations. Here, we propose exact results with regard to the rate of transport on large time scales in random shear flows. These can be expediently used as a benchmark to develop and assess algorithms when solving this class of stochastic integrodifferential problems on large time scales.
  • Lamminsalo, Marko; Karvinen, Timo; Subrizi, Astrid; Urtti, Arto; Ranta, Veli-Pekka (2020)
    Purpose To estimate the diffusion coefficients of an IgG antibody (150 kDa) and its antigen-binding fragment (Fab; 50 kDa) in the neural retina (D-ret) and the combined retinal pigment epithelium-choroid (DRPE-cho) with a 3-dimensional (3D) ocular pharmacokinetic (PK) model of the rabbit eye. Methods Vitreous, retina, and aqueous humor concentrations of IgG and Fab after intravitreal injection in rabbits were taken from Gadkar et al. (2015). A least-squares method was used to estimate D(ret)and D(RPE-cho)with the 3D finite element model where mass transport was defined with diffusion and convection. Different intraocular pressures (IOP), initial distribution volumes (V-init), and neural retina/vitreous partition coefficients (K-ret/vit) were tested. Sensitivity analysis was performed for the final model. Results With the final IgG model (IOP 10.1 Torr, V(init)400 mu l, K(ret/vit)0.5), the estimated D(ret)and D(RPE-cho)were 36.8 x 10(-9)cm(2)s(-1)and 4.11 x 10(-9)cm(2)s(-1), respectively, and 76% of the dose was eliminated via the anterior chamber. Modeling of Fab revealed that a physiological model parameter "aqueous humor formation rate" sets constraints that need to be considered in the parameter estimation. Conclusions This study extends the use of 3D ocular PK models for parameter estimation using simultaneously macromolecule concentrations in three ocular tissues.
  • EXTEND Investigator; ECASS-4 Investigator; EPITHET Investigator; Campbell, Bruce C.; Ma, Henry; Curtze, Sami; Donnan, Geoffrey A.; Kaste, Markku (2019)
    Background Stroke thrombolysis with alteplase is currently recommended 0-4.5 h after stroke onset. We aimed to determine whether perfusion imaging can identify patients with salvageable brain tissue with symptoms 4.5 h or more from stroke onset or with symptoms on waking who might benefit from thrombolysis. Methods In this systematic review and meta-analysis of individual patient data, we searched PubMed for randomised trials published in English between Jan 1, 2006, and March 1, 2019. We also reviewed the reference list of a previous systematic review of thrombolysis and searched ClinicalTrials. gov for interventional studies of ischaemic stroke. Studies of alteplase versus placebo in patients (aged =18 years) with ischaemic stroke treated more than 4.5 h after onset, or with wake-up stroke, who were imaged with perfusion-diffusion MRI or CT perfusion were eligible for inclusion. The primary outcome was excellent functional outcome (modified Rankin Scale [mRS] score 0-1) at 3 months, adjusted for baseline age and clinical severity. Safety outcomes were death and symptomatic intracerebral haemorrhage. We calculated odds ratios, adjusted for baseline age and National Institutes of Health Stroke Scale score, using mixed-effects logistic regression models. This study is registered with PROSPERO, number CRD42019128036. Findings We identified three trials that met eligibility criteria: EXTEND, ECASS4-EXTEND, and EPITHET. Of the 414 patients included in the three trials, 213 (51%) were assigned to receive alteplase and 201 (49%) were assigned to receive placebo. Overall, 211 patients in the alteplase group and 199 patients in the placebo group had mRS assessment data at 3 months and thus were included in the analysis of the primary outcome. 76 (36%) of 211 patients in the alteplase group and 58 (29%) of 199 patients in the placebo group had achieved excellent functional outcome at 3 months (adjusted odds ratio [OR] 1.86, 95% CI 1.15-2.99, p=0.011). Symptomatic intracerebral haemorrhage was more common in the alteplase group than the placebo group (ten [5%] of 213 patients vs one [<1%] of 201 patients in the placebo group; adjusted OR 9.7, 95% CI 1.23-76.55, p=0.031). 29 (14%) of 213 patients in the alteplase group and 18 (9%) of 201 patients in the placebo group died (adjusted OR 1.55, 0.81-2.96, p=0.66). Interpretation Patients with ischaemic stroke 4.5-9 h from stroke onset or wake-up stroke with salvageable brain tissue who were treated with alteplase achieved better functional outcomes than did patients given placebo. The rate of symptomatic intracerebral haemorrhage was higher with alteplase, but this increase did not negate the overall net benefit of thrombolysis. Copyright (c) 2019 Elsevier Ltd. All rights reserved.
  • Franks, Victoria R.; Ewen, John G.; McCready, Mhairi; Thorogood, Rose (2020)
    Early independence from parents is a critical period where social information acquired vertically may become outdated, or conflict with new information. However, across natural populations, it is unclear if newly independent young persist in using information from parents, or if group-level effects of conformity override previous behaviours. Here, we test if wild juvenile hihi (Notiomystis cincta, a New Zealand passerine) retain a foraging behaviour from parents, or if they change in response to the behaviour of peers. We provided feeding stations to parents during chick-rearing to seed alternative access routes, and then tracked their offspring's behaviour. Once independent, juveniles formed mixed-treatment social groups, where they did not retain preferences from their time with parents. Instead, juvenile groups converged over time to use one access route­ per group, and juveniles that moved between groups switched to copy the locally favoured option. Juvenile hihi did not copy specific individuals, even if they were more familiar with the preceding bird. Our study shows that early social experiences with parents affect initial foraging decisions, but social environments encountered later on can update transmission of arbitrary behaviours. This suggests that conformity may be widespread in animal groups, with potential cultural, ecological and evolutionary consequences.
  • Boi, Simone; Mazzino, Andrea; Muratore-Ginanneschi, Paolo; Olivieri, Stefano (2018)
    One of the cornerstones of turbulent dispersion is the celebrated Taylor's formula. This formula expresses the rate of transport (i.e., the eddy diffusivity) of a tracer as a time integral of the fluid velocity autocorrelation function evaluated along the fluid particle trajectories. Here, we review the hypotheses which permit us to extend Taylor's formula to particles of any inertia. The hypotheses are independent of the details of the inertial particle model. We also show by explicit calculation that the hypotheses encompass cases when memory terms such as Basset's and Faxén's corrections are taken into account in the modeling of inertial particle dynamics.
  • Ahlgren, Tommy; Jalkanen, Pasi; Mizohata, Kenichiro; Tuboltsev, Vladimir; Räisänen, Jyrki; Heinola, Kalle; Tikkanen, Pertti O. (2019)
    The radiological safety of the future thermonuclear fusion devices depends critically on the total tritium inventory in the plasma-facing components. The planned method to remove tritium from the ITER reactor tungsten divertor is to perform vacuum baking. We show that tritium removal from tungsten can be enhanced by the isotope exchange mechanism by doing the baking in H-2 atmosphere. The results show that the retained deuterium from 30 keV implantation can be expected to drop almost to zero after 24h annealing at 250 degrees C in H-2 atmosphere. Annealing in vacuum requires temperatures above 400 degrees C for close to zero retention.
  • Nagarajan, Usharani; Beaune, Gregory; Lam, Andy Y. W.; Gonzalez-Rodriguez, David; Winnik, Francoise M.; Brochard-Wyart, Francoise (2021)
    While both active and granular matter have been extensively studied, here we investigate what happens when we mix the two of them, in a model system combining microparticles and cell assemblies. On a substrate covered with polystyrene or silica microparticles, we notice two regimes in the spreading of a cell aggregate: light particles are pushed by the cells and form a ring, which bonds to the substrate by adhesion forces that oppose spreading, while for heavy particles, the cell monolayer spreads above the particle bed. In both cases, cell activity is transmitted to inert beads, leading to the formation of cell-microparticle aggregates, which flicker and diffuse. We then study the formation and the spreading of hybrid aggregates of microparticles and living cells and observe phase separations and jamming transitions. Our study may have implications on processes such as cancer metastasis and development, and may guide cancer therapies based on inert particles. Interaction of active matter with geometrical and topological constraints is a topic of intense research in the recent few years due to its potential for design and control of active flow patterns. Here, the authors experimentally study the growth and expansion of cell aggregates interleaved by passive colloidal particles, showing that inert particles can reshape the collective pattern formation in cellular aggregates.
  • Lassmann-Klee, Paul Guenther; Lehtimäki, Lauri; Lindholm, Tuula; Malmberg, L. Pekka; Sovijärvi, Anssi; Piirilä, Päivi (2018)
    Fractional exhaled nitric oxide (F-ENO) is used to assess eosinophilic inflammation of the airways. F-ENO values are influenced by the expiratory flow rate and orally produced NO. We measured F-ENO at four different expiratory flow levels after two different mouthwashes: tap water and carbonated water. Further, we compared the alveolar NO concentration (C-ANO), maximum airway NO flux (J(awNO)) and airway NO diffusion (D-awNO) after these two mouthwashes. F-ENO was measured in 30 volunteers (healthy or asthmatic) with a chemiluminescence NO-analyser at flow rates of 30, 50, 100 and 300mL/s. A mouthwash was performed before the measurement at every flow rate. The carbonated water mouthwash significantly reduced F-ENO compared to the tap water mouthwash at all expiratory flows: 50mL/s (p
  • Rieppo, Lassi; Kokkonen, Harri T.; Kulmala, Katariina A. M.; Kovanen, Vuokko; Lammi, Mikko J.; Töyräs, Juha; Saarakkala, Simo (2017)
    Collagen forms an organized network in articular cartilage to give tensile stiffness to the tissue. Due to its long half-life, collagen is susceptible to cross-links caused by advanced glycation end-products. The current standard method for determination of cross-link concentrations in tissues is the destructive high-performance liquid chromatography (HPLC). The aim of this study was to analyze the cross-link concentrations nondestructively from standard unstained histological articular cartilage sections by using Fourier transform infrared (FTIR) microspectroscopy. Half of the bovine articular cartilage samples (n = 27) were treated with threose to increase the collagen cross-linking while the other half (n = 27) served as a control group. Partial least squares (PLS) regression with variable selection algorithms was used to predict the cross-link concentrations from the measured average FTIR spectra of the samples, and HPLC was used as the reference method for cross-link concentrations. The correlation coefficients between the PLS regression models and the biochemical reference values were r = 0.84 (p <0.001), r = 0.87 (p <0.001) and r = 0.92 (p <0.001) for hydroxylysyl pyridinoline (HP), lysyl pyridinoline (LP), and pentosidine (Pent) cross-links, respectively. The study demonstrated that FTIR microspectroscopy is a feasible method for investigating cross-link concentrations in articular cartilage. (C) The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.
  • Karjalainen, A.; Weiser, P. M.; Makkonen, I.; Reinertsen, V. M.; Vines, L.; Tuomisto, F. (2021)
    Positron annihilation spectroscopy, Fourier transform-infrared absorption spectroscopy, and secondary ion mass spectrometry have been used to study the behavior of gallium vacancy-related defects and hydrogen in deuterium (D) implanted and subsequently annealed beta-Ga2O3 single crystals. The data suggest the implantation generates a plethora of V-Ga-related species, including V-Ga1- and V-Ga2-type defects. The latter's contribution to the positron signal was enhanced after an anneal at 300 degrees C, which is driven by the passivation of Vib Ga by hydrogen as seen from infrared measurements. Subsequent annealing near 600 degrees C returns the positron signal to levels similar to those in the as-received samples, which suggests that split V-Ga-like defects are still present in the sample. The almost complete removal of the V(Ga)(ib-)2D vibrational line, the appearance of new weak O-D lines in the same spectral region, and the lack of D outdiffusion from the samples suggest that the 600 degrees C anneal promotes the formation of either D-containing, IR-inactive complexes or defect complexes between V-Ga(ib)-2D and other implantation-induced defects. The degree of electrical compensation is found to be governed by the interactions between the Ga vacancies and hydrogen.Published under an exclusive license by AIP Publishing.
  • Jansson, V.; Baibuz, E.; Djurabekova, F. (2016)
    Sharp nanoscale tips on the metal surfaces of electrodes enhance locally applied electric fields. Strongly enhanced electric fields trigger electron field emission and atom evaporation from the apexes of nanotips. Together, these processes may explain electric discharges in the form of small local arcs observed near metal surfaces in the presence of electric fields, even in ultra-high vacuum conditions. In the present work, we investigate the stability of nanoscale tips by means of computer simulations of surface diffusion processes on copper, the main material used in high-voltage electronics. We study the stability and lifetime of thin copper (Cu) surface nanotips at different temperatures in terms of diffusion processes. For this purpose we have developed a surface kinetic Monte Carlo (KMC) model where the jump processes are described by tabulated precalculated energy barriers. We show that tall surface features with high aspect ratios can be fairly stable at room temperature. However, the stability was found to depend strongly on the temperature: 13 nm nanotips with the major axes in the <110 > crystallographic directions were found to flatten down to half of the original height in less than 100 ns at temperatures close to the melting point, whereas no significant change in the height of these nanotips was observed after 10 mu s at room temperature. Moreover, the nanotips built up along the <110 > crystallographic directions were found to be significantly more stable than those oriented in the <100 > or <111 > crystallographic directions. The proposed KMC model has been found to be well-suited for simulating atomic surface processes and was validated against molecular dynamics simulation results via the comparison of the flattening times obtained by both methods. We also note that the KMC simulations were two orders of magnitude computationally faster than the corresponding molecular dynamics calculations.
  • Willmann, Knut; Vent-Schmidt, Thomas; Rasanen, Markku; Riedel, Sebastian; Khriachtchev, Leonid (2015)
    The HKrCCH center dot center dot center dot HCCH complex is identified in a Kr matrix with the H-Kr stretching bands at 1316.5 and 1305 cm(-1). The monomer-to-complex shift of the H-Kr stretching mode is about +60 cm(-1), which is significantly larger than that reported previously for the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix (about +25 cm(-1)). The HKrCCH center dot center dot center dot HCCH complex in a Kr matrix is formed at similar to 40 K via the attachment of mobile acetylene molecules to the HKrCCH monomers formed at somewhat lower annealing temperatures upon thermally-induced mobility of H atoms (similar to 30 K). The same mechanism was previously proposed for the formation of the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix. The assignment of the HKrCCH center dot center dot center dot HCCH complex is fully supported by the quantum chemical calculations. The experimental shift of the H-Kr stretching mode is comparable with the computational predictions (+46.6, +66.0, and +83.2 cm(-1) at the B3LYP, MP2, and CCSD(T) levels of theory, respectively), which are also bigger that the calculated shift in the HXeCCH center dot center dot center dot HCCH complex. These results confirm that the complexation effect is bigger for less stable noble-gas hydrides.
  • Snellman, J. E.; Rheinhardt, M.; Käpylä, P. J.; Mantere, M. J.; Brandenburg, A. (2012)
  • Kuva, J.; Voutilainen, M.; Mattila, K. (2019)
    The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous matrix. Simulations with several flow rates, diffusion coefficients, and matrix porosities indicate good agreement between the numerical approximations and analytical solutions.
  • Wijsen, N.; Aran, A.; Pomoell, J.; Poedts, S. (2019)
    Aims. We introduce a new solar energetic particle (SEP) transport code that aims at studying the effects of different background solar wind configurations on SEP events. In this work, we focus on the influence of varying solar wind velocities on the adiabatic energy changes of SEPs and study how a non-Parker background solar wind can trap particles temporarily at small heliocentric radial distances (less than or similar to 1.5AU) thereby influencing the cross-field diffusion of SEPs in the interplanetary space. Methods. Our particle transport code computes particle distributions in the heliosphere by solving the focused transport equation (FTE) in a stochastic manner. Particles are propagated in a solar wind generated by the newly developed data-driven heliospheric model, EUHFORIA. In this work, we solve the FTE, including all solar wind effects, cross-field diffusion, and magnetic-field gradient and curvature drifts. As initial conditions, we assume a delta injection of 4 MeV protons, spread uniformly over a selected region at the inner boundary of the model. To verify the model, we first propagate particles in nominal undisturbed fast and slow solar winds. Thereafter, we simulate and analyse the propagation of particles in a solar wind containing a corotating interaction region (CIR). We study the particle intensities and anisotropies measured by a fleet of virtual observers located at different positions in the heliosphere, as well as the global distribution of particles in interplanetary space. Results. The differential intensity-time profiles obtained in the simulations using the nominal Parker solar wind solutions illustrate the considerable adiabatic deceleration undergone by SEPs, especially when propagating in a fast solar wind. In the case of the solar wind containing a CIR, we observe that particles adiabatically accelerate when propagating in the compression waves bounding the CIR at small radial distances. In addition, for r greater than or similar to 1.5AU, there are particles accelerated by the reverse shock as indicated by, for example, the anisotropies and pitch-angle distributions of the particles. Moreover, a decrease in high-energy particles at the stream interface (SI) inside the CIR is observed. The compression /shock waves and the magnetic configuration near the SI may also act as a magnetic mirror, producing long-lasting high intensities at small radial distances. We also illustrate how the efficiency of the cross-field diffusion in spreading particles in the heliosphere is enhanced due to compressed magnetic fields. Finally, the inclusion of cross-field diffusion enables some particles to cross both the forward compression wave at small radial distances and the forward shock at larger radial distances. This results in the formation of an accelerated particle population centred on the forward shock, despite the lack of magnetic connection between the particle injection region and this shock wave. Particles injected in the fast solar wind stream cannot reach the forward shock since the SI acts as a diffusion barrier.