Browsing by Subject "MOLECULAR-DYNAMICS SIMULATIONS"

Sort by: Order: Results:

Now showing items 21-25 of 25
  • Liekkinen, Juho; Enkavi, Giray; Javanainen, Matti; Olmeda, Barbara; Pérez-Gil, Jesús; Vattulainen, Ilpo (2020)
    Surfactant protein B (SP-B) is essential in transferring surface-active phospholipids from membrane-based surfactant complexes into the alveolar air-liquid interface. This allows maintaining the mechanical stability of the surfactant film under high pressure at the end of expiration; therefore, SP-B is crucial in lung function. Despite its necessity, the structure and the mechanism of lipid transfer by SP-B have remained poorly characterized. Earlier, we proposed higher-order oligomerization of SP-B into ring-like supramolecular assemblies. In the present work, we used coarse-grained molecular dynamics simulations to elucidate how the ring-like oligomeric structure of SP-B determines its membrane binding and lipid transfer. In particular, we explored how SP-B interacts with specific surfactant lipids, and how consequently SP-B reorganizes its lipid environment to modulate the pulmonary surfactant structure and function. Based on these studies, there are specific lipid-protein interactions leading to perturbation and reorganization of pulmonary surfactant layers. Especially, we found compelling evidence that anionic phospholipids and cholesterol are needed or even crucial in the membrane binding and lipid transfer function of SP-B. Also, on the basis of the simulations, larger oligomers of SP-B catalyze lipid transfer between adjacent surfactant layers. Better understanding of the molecular mechanism of SP-B will help in the design of therapeutic SP-B-based preparations and novel treatments for fatal respiratory complications, such as the acute respiratory distress syndrome. (C) 2020 The Author(s). Published by Elsevier Ltd.
  • Marian, Jaime; Becquart, Charlotte S.; Domain, Christophe; Dudarev, Sergei L.; Gilbert, Mark R.; Kurtz, Richard J.; Mason, Daniel R.; Nordlund, Kai; Sand, Andrea E.; Snead, Lance L.; Suzudo, Tomoaki; Wirth, Brian D. (2017)
    Under the anticipated operating conditions for demonstration magnetic fusion reactors beyond ITER, structural and plasma-facing materials will be exposed to unprecedented conditions of irradiation, heat flux, and temperature. While such extreme environments remain inaccessible experimentally, computational modeling and simulation can provide qualitative and quantitative insights into materials response and complement the available experimental measurements with carefully validated predictions. For plasma-facing components such as the first wall and the divertor, tungsten (W) has been selected as the leading candidate material due to its superior high-temperature and irradiation properties, as well as for its low retention of implanted tritium. In this paper we provide a review of recent efforts in computational modeling of W both as a plasma-facing material exposed to He deposition as well as a bulk material subjected to fast neutron irradiation. We use a multiscale modeling approach-commonly used as the materials modeling paradigm-to define the outline of the paper and highlight recent advances using several classes of techniques and their interconnection. We highlight several of the most salient findings obtained via computational modeling and point out a number of remaining challenges and future research directions.
  • Zadin, Vahur; Veske, Mihkel; Vigonski, Simon; Jansson, Ville; Muszynski, Johann; Parviainen, Stefan; Aabloo, Alvo; Djurabekova, Flyura (2018)
    Onset of vacuum arcing near a metal surface is often associated with nanoscale asperities, which may dynamically appear due to different processes ongoing in the surface and subsurface layers in the presence of high electric fields. Thermally activated processes, as well as plastic deformation caused by tensile stress due to an applied electric field, are usually not accessible by atomistic simulations because of the long time needed for these processes to occur. On the other hand, finite element methods, able to describe the process of plastic deformations in materials at realistic stresses, do not include surface properties. The latter are particularly important for the problems where the surface plays crucial role in the studied process, as for instance, in the case of plastic deformations at a nanovoid. In the current study by means of molecular dynamics (MD) and finite element simulations we analyse the stress distribution in single crystal copper containing a nanovoid buried deep under the surface. We have developed a methodology to incorporate the surface effects into the solid mechanics framework by utilizing elastic properties of crystals, pre-calculated using MD simulations. The method leads to computationally efficient stress calculations and can be easily implemented in commercially available finite element software, making it an attractive analysis tool.
  • Sand, A. E.; Aliaga, M. J.; Caturla, M. J.; Nordlund, K. (2016)
    We have investigated the effect of surfaces on the statistics of primary radiation damage, comparing defect production in the bcc metals iron (Fe) and tungsten (W). Through molecular dynamics simulations of collision cascades we show that vacancy as well as interstitial cluster sizes follow scaling laws in both bulk and thin foils in these materials. The slope of the vacancy cluster size distribution in Fe is clearly affected by the surface in thin foil irradiation, while in W mainly the overall frequency is affected. Furthermore, the slopes of the power law distributions in bulk Fe are markedly different from those in W. The distinct behaviour of the statistical distributions uncovers different defect production mechanisms effective in the two materials, and provides insight into the underlying reasons for the differing behaviour observed in TEM experiments of lowdose ion irradiation in these metals. Copyright (C) EPLA, 2016
  • Olzynska, Agnieszka; Kulig, Waldemar; Mikkolainen, Heikki; Czerniak, Tomasz; Jurkiewicz, Piotr; Cwiklik, Lukasz; Rog, Tomasz; Hof, Martin; Jungwirth, Pavel; Vattulainen, Ilpo (2020)
    Cholesterol renders mammalian cell membranes more compact by reducing the amount of voids in the membrane structure. Because of this, cholesterol is known to regulate the ability of cell membranes to prevent the permeation of water and water-soluble molecules through the membranes. Meanwhile, it is also known that even seemingly tiny modifications in the chemical structure of cholesterol can lead to notable changes in membrane properties. The question is, how significantly do these small changes in cholesterol structure affect the permeability barrier function of cell membranes? In this work, we applied fluorescence methods as well as atomistic molecular dynamics simulations to characterize changes in lipid membrane permeability induced by cholesterol oxidation. The studied 7 beta-hydroxycholesterol (7 beta-OH-chol) and 27-hydroxycholesterol (27-OH-chol) represent two distinct groups of oxysterols, namely, ring- and tail-oxidized cholesterols, respectively. Our previous research showed that the oxidation of the cholesterol tail has only a marginal effect on the structure of a lipid bilayer; however, oxidation was found to disturb membrane dynamics by introducing a mechanism that allows sterol molecules to move rapidly back and forth across the membranebobbing. Herein, we show that bobbing of 27-OH-chol accelerates fluorescence quenching of NBD-lipid probes in the inner leaflet of liposomes by dithionite added to the liposomal suspension. Systematic experiments using fluorescence quenching spectroscopy and microscopy led to the conclusion that the presence of 27-OH-chol increases membrane permeability to the dithionite anion. Atomistic molecular dynamics simulations demonstrated that 27-OH-chol also facilitates water transport across the membrane. The results support the view that oxysterol bobbing gives rise to successive perturbations to the hydrophobic core of the membrane, and these perturbations promote the permeation of water and small water-soluble molecules through a lipid bilayer. The observed impairment of permeability can have important consequences for eukaryotic organisms. The effects described for 27-OH-chol were not observed for 7 beta-OH-chol which represents ring-oxidized sterols.