Browsing by Subject "Molecular dynamics"

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  • Byggmästar, Jesper; Hodille, Etienne A.; Ferro, Y.; Nordlund, Kai (2018)
    An analytical interatomic bond order potential for the Be–O system is presented. The potential is fitted and compared to a large database of bulk BeO and point defect properties obtained using density functional theory. Its main applications include simulations of plasma-surface interactions involving oxygen or oxide layers on beryllium, as well as simulations of BeO nanotubes and nanosheets. We apply the potential in a study of oxygen irradiation of Be surfaces, and observe the early stages of an oxide layer forming on the Be surface. Predicted thermal and elastic properties of BeO nanotubes and nanosheets are simulated and compared with published ab initio data.
  • Hobler, G.; Nordlund, K. (2019)
    Simulations based on the binary collision approximation (BCA) are in principle less accurate than molecular dynamics (MD) simulations. In this work, we present a comprehensive comparison between BCA and MD for Si ions impinging on a (001)-Si surface by comparing "channeling maps", i.e., projected ranges of the ions as a function of incidence direction in a representative part of the angular space. We find quantitative differences to develop as the energy decreases below similar to 100 eV, but find qualitative agreement down to similar to 10 eV. Moreover, the quality of the BCA channeling maps depends on the implementation of the BCA, which is explained in terms of double-hits and missed collisions.
  • Humisto, Anu; Jokela, Jouni; Teigen, Knut; Wahlsten, Matti; Permi, Perttu; Sivonen, Kaarina; Herfindal, Lars (2019)
    Hassallidins are cyclic glycolipopeptides produced by cyanobacteria and other prokaryotes. The hassallidin structure consists of a peptide ring of eight amino acids where a fatty acid chain, additional amino acids, and sugar moieties are attached. Hassallidins show antifungal activity against several opportunistic human pathogenic fungi, but does not harbor antibacterial effects. However, they have not been studied on mammalian cells, and the mechanism of action is unknown. We purified hassallidin D from cultured cyanobacterium Anabaena sp. UHCC 0258 and characterized its effect on mammalian and fungal cells. Ultrastructural analysis showed that hassallidin D disrupts cell membranes, causing a lytic/necrotic cell death with rapid presence of disintegrated outer membrane, accompanied by internalization of small molecules such as propidium iodide into the cells. Furthermore, artificial liposomal membrane assay showed that hassallidin D selectively targets sterol-containing membranes. Finally, in silico membrane modeling allowed us to study the interaction between hassallidin D and membranes in detail, and confirm the role of cholesterol for hassallidin-insertion into the membrane. This study demonstrates the mechanism of action of the natural compound hassallidin, and gives further insight into how bioactive lipopeptide metabolites selectively target eukaryotic cell membranes.
  • Lyashenko, A.; Safi, E.; Polvi, J.; Djurabekova, F.; Nordlund, K. (2020)
    Gaseous nitrogen is planned to be used as a seeding species to control the power flux in future fusion reactors with ITER-like divertors. Nitrogen interacts with the first wall materials, particularly with tungsten, leading to sputtering and changes of chemical composition of the material. We use the molecular dynamics methods with a recently developed WN potential to analyze the mechanisms leading to these modifications. We performed the simulations of cumulative nitrogen irradiation runs of tungsten surface. The sputtering yields obtained in our cumulative runs are in good agreement with experimental data. We observe the decrease of the tungsten sputtering yield with nitrogen accumulation and determine the reasons for the observed trend. The cluster analysis reveals the composition of the sputtered particles, suggesting the swift chemical sputtering process that occurs under the prolonged nitrogen irradiation of tungsten. We also observe and analyze the nitrogen saturation in the temperature range below the thermal stability limit. (C) 2020 Elsevier B.V. All rights reserved.
  • Haapanen, Outi; Reidelbach, Marco; Sharma, Vivek (2020)
    Respiratory complex I (NADH:quinone oxidoreductase) plays a central role in generating the proton electrochemical gradient in mitochondrial and bacterial membranes, which is needed to generate ATP. Several high-resolution structures of complex I have been determined, revealing its intricate architecture and complementing the biochemical and biophysical studies. However, the molecular mechanism of long-range coupling between ubiquinone (Q) reduction and proton pumping is not known. Computer simulations have been applied to decipher the dynamics of Q molecule in the similar to 30 angstrom long Q tunnel. In this short report, we discuss the binding and dynamics of Q at computationally predicted Q binding sites, many of which are supported by structural data on complex I. We suggest that the binding of Q at these sites is coupled to proton pumping by means of conformational rearrangements in the conserved loops of core subunits.
  • Granberg, F.; Byggmästar, J.; Nordlund, K. (2020)
    The understanding of materials' behaviour during continuous irradiation is of great interest for utilizing materials in environments where harsh radiation is present, like nuclear power plants. Most power plants, both current and future ones, are based, at least partially, on Fe or FeCr alloys. In this study, we investigate the response of BCC Fe and several FeCr alloys to massively overlapping cascades. The effect of the added chromium on the defect accumulation and defect evolution was studied. Both a bulk setup, for observing the evolution deep inside the material far from grain boundaries and surfaces, and a setup with a nearby open surface, to investigate the effect of a permanent defect sink, were studied. We found that the primary defect production is similar in all materials, and also the build-up before serious overlap is comparable. When cascade overlap starts, we found that different sized clusters are formed in the different materials, depending on the setup. The defect cluster evolution was followed and could be related to the dislocation reactions in the materials. We found that the irradiation mixing was specific to the different chromium concentrations, the low chromium-containing alloy showed ordering, whereas the highest chromium-containing sample showed segregation. (C) 2019 The Authors. Published by Elsevier B.V.
  • Kadribasic, Fedja; Mirabolfathi, Nader; Nordlund, Kai; Holmström, Eero; Djurabekova, Flyura (2018)
    A large body of astrophysical observations indicate that around 85% of the matter in the universe is not made of recognized standard model particles. Understanding the nature of this so-called dark matter is of fundamental importance to cosmology, astrophysics, and high-energy particle physics. We examine the response of commonly used semiconductor materials to low-mass WIMP interactions using numerical simulations based on classical interatomic potentials in these materials. These simulations, backed up by more precise density functional theory simulations and experiments, predict a nonlinear energy loss that never produces phonons due to the nonzero energy required to form crystallographic defects. We argue that such nonlinear effects related to defect formation in electron-volt-scale resolution semiconductor detectors allows for very effective directional sensitivity and possible statistical nuclear recoil discrimination to dark matter signals for masses below 1 GeV/c(2).
  • Sand, A.E.; Byggmästar, J.; Zitting, A.; Nordlund, K. (2018)
    Most experimental work on radiation damage is performed to fairly high doses, where cascade overlap effects come into play, yet atomistic simulations of the primary radiation damage have mainly been performed in initially perfect lattice. Here, we investigate the primary damage produced by energetic ion or neutron impacts in bcc Fe and W. We model irradiation effects at high fluence through atomistic simulations of cascades in pre-damaged systems. The effects of overlap provide new insights into the processes governing the formation under irradiation of extended defects. We find that cascade overlap leads to an increase in the numbers of large clusters in Fe, while in W such an effect is not seen. A significant shift in the morphology of the primary damage is also observed, including the formation of complex defect structures that have not been previously reported in the literature. These defects are highly self-immobilized, shifting the damage away from the predominance of mobile 1/2〈111〉 loops towards more immobile initial configurations. In Fe, where cascade collapse is extremely rare in molecular dynamics simulations of individual cascades, we observe the formation of vacancy-type dislocation loops from cascade collapse as a result of cascade overlap.
  • Xydou, A.; Parviainen, S.; Djurabekova, F. (2020)
    Diffusion bonding of copper disks is an important step during the assembly of accelerating structures -the main components of power radio-frequency linear accelerators-. During the diffusion bonding copper disks are subjected to pressure at high temperatures. Finding the optimal combination of pressure and temperature will enable an accurate design of manufacturing workflow and machining tolerances. However, required optimization is not possible without good understanding of physical processes developed in copper under pressure and high temperature. In this work, the combined effect of temperature and pressure on closing time of inter-granular voids is examined by means of molecular dynamics simulations. In particular, a nano-void of 3.5–5.5 nm in diameter representing a peak and a valley of surface roughness facing each other was inserted between identical copper grains. The simulations performed at T = 1250 K, the temperature used in experimental condition, and the 300–800 MPa pressure range indicated the dislocation-mediated enhancement of atomic diffusion leading to full void closure.
  • Granberg, F.; Byggmästar, J. (2021)
    Ion sputtering of surfaces is a widely used technique, for instance utilized to modify surfaces or surface features. Another commonly used technique is the utilization of sputtering to coat another material, where sputtering targets are used to release atoms in order to redeposit them. In self-ion molecular dynamics sputtering simulations, the interatomic potential between the ion and the matrix material is usually the same as for the matrix material. However, for sputtering by ions of different type, the choice is not as self-evident. For most elements, a well-fitted many-body interatomic potential is not available in the literature, and simple pair potentials are used. Quite commonly, the potential between the ion and the matrix is used with no further validation. In this article, we investigate the effect of choice of interatomic potential on the sputtering yield of the sample material palladium by argon ions. We utilize three commonly used pair potential forms, as well as modify these to obtain in total 11 different interatomic potentials for the Ar-Pd interaction. We found that the choice of interatomic potential can drastically affect the low energy sputtering of the surfaces. Additionally, four different surface orientations were simulated to see possible differences. To investigate continuous irradiation, in order to obtain the evolution of surface during prolonged irradiation, cumulative sputtering simulations were carried out.
  • Byggmästar, J.; Granberg, F.; Nordlund, K. (2018)
    Recent work has shown that the repulsive part of the interatomic potential at intermediate atomic separations strongly affects the extent and morphology of the damage produced by collision cascades in molecular dynamics simulations. Here, we modify an existing embedded atom method interatomic potential for iron to more accurately reproduce the threshold displacement energy surface as well as the many-body repulsion at intermediate and short interatomic distances. Using the modified potential, we explore the effects of an improved repulsive potential on the primary damage production and the cumulative damage accumulation in iron. We find that the extent of the damage produced by single cascades, in terms of surviving Frenkel pairs, directly correlates with the change in threshold displacement energies. On the other hand, the damage evolution at higher doses is more dependent on the formation and stability of different defect clusters, defined by the near-equilibrium part of the interatomic potential.
  • Leino, Aleksi A.; Samolyuk, German; Sachan, Ritesh; Granberg, Fredric; Weber, William J.; Bei, Hongbin; Lie, Jie; Zhai, Pengfei; Zhang, Yanwen (2018)
    Concentrated solid solution alloys have attracted rapidly increasing attention due to their potential for designing materials with high tolerance to radiation damage. To tackle the effects of chemical complexity in defect dynamics and radiation response, we present a computational study on swift heavy ion induced effects in Ni and equiatomic Ni -based alloys (Ni50Fe50, Ni50Co50) using two-temperature molecular dynamics simulations (2T-MD). The electronic heat conductivity in the two-temperature equations is parameterized from the results of first principles electronic structure calculations. A bismuth ion (1.542 GeV) is selected and single impact simulations performed in each target. We study the heat flow in the electronic subsystem and show that alloying Ni with Co or Fe reduces the heat dissipation from the impact by the electronic subsystem. Simulation results suggest no melting or residual damage in pure Ni while a cylindrical region melts along the ion propagation path in the alloys. In Ni50Co50 the damage consists of a dislocation loop structure (d = 2 nm) and isolated point defects, while in Ni50Fe50, a defect cluster (d = 4 nm) along the ion path is, in addition, formed. The simulation results are supported by atomic-level structural and defect characterizations in bismuth-irradiated Ni and Ni50Fe50. The significance of the 2T-MD model is demonstrated by comparing the results to those obtained with an instantaneous energy deposition model without consideration of e-ph interactions in pure Ni and by showing that it leads to a different qualitative behavior.
  • Granberg, F.; Litnovsky, A.; Nordlund, K. (2020)
    Surfaces of materials subject to irradiation will be affected by sputtering, which can be a beneficial effect, like in the coating industry where a material is sputtered and redeposited on to another material to coat it. However, in most cases sputtering is an unwanted side-effect, for instance in nuclear fusion reactors, where the wall material will be degraded. This effect needs to be understood in order to be able to predict its consequences. To understand the sputtering, on an atomistic level, we have thoroughly investigated molybdenum surface sputtering by computational means. Molybdenum was chosen as detailed experimental studies have been carried out on it and it is one candidate material for the diagnostic mirrors in ITER, facing the plasma. In this study, we thoroughly investigate the molybdenum samples of different surface orientations, and their response to low energy argon plasma irradiation, by molecular dynamics simulations. We find both a surface orientation and ion energy specific sputtering yield of the samples, and a very good agreement with the experiments available in the literature. A few different setups were investigated to observe differences as well as to understand the key features affecting the sputtering events. The different simulation setups revealed the optimal one to represent the experimental conditions as well as the mechanisms behind the observed discrepancies between different modelling setups. (C) 2020 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (
  • Liu, Jian; Muinos, Henrique Vazquez; Nordlund, Kai; Djurabekova, Flyura (2020)
    As a promising material used in accelerators and in space in the future, it is important to study the property and structural changes of graphene and diamond-like carbon on the surface as a protective layer before and after swift heavy ion irradiation, although this layer could have a loose structure due to the intrinsic sp(2) surrounding environment of graphene during its deposition period. In this study, by utilizing inelastic thermal spike model and molecular dynamics, we simulated swift heavy ion irradiation and examined the track radius in the vertical direction, as well as temperature, density, and sp(3) fraction distribution along the radius from the irradiation center at different time after irradiation. The temperature in the irradiation center can reach over 11000 K at the beginning of irradiation while there would be a low density and sp(3) fraction area left in the central region after 100 ps. Ring analysis also demonstrated a more chaotic cylindrical region in the center after irradiation. After comprehensive consideration, diamond-like carbon deposited by 70 eV carbon bombardment provided the best protection.
  • Granberg, F.; Byggmastar, J.; Nordlund, K. (2021)
    Tungsten has been chosen as the plasma-facing wall material in fusion reactors, due to its high density and melting point. The wall material will not only be sputtered at the surface, but also damaged deep inside the material by energetic particles. We investigate the high-dose damage production and accumulation by computational means using molecular dynamics. We observe that the choice of interatomic potential drastically affects the evolution. The structure and stability of the obtained defect configurations are validated using a quantum-accurate Gaussian approximation potential. (c) 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license ( )
  • Oeemig, Jesper S.; Ollila, O.H. Samuli; Iwaï, Hideo (2018)
    The TonB protein plays an essential role in the energy transduction system to drive active transport across the outer membrane (OM) using the proton-motive force of the cytoplasmic membrane of Gram-negative bacteria. The C-terminal domain (CTD) of TonB protein is known to interact with the conserved TonB box motif of TonB-dependent OM transporters, which likely induces structural changes in the OM transporters. Several distinct conformations of differently dissected CTDs of Escherichia coli TonB have been previously reported. Here we determined the solution NMR structure of a 96-residue fragment of Pseudomonas aeruginosa TonB (PaTonB-96). The structure shows a monomeric structure with the flexible C-terminal region (residues 338-342), different from the NMR structure of E. coli TonB (EcTonB-137). The extended and flexible C-terminal residues are confirmed by N-15 relaxation analysis and molecular dynamics simulation. We created models for the PaTonB-96/TonB box interaction and propose that the internal fluctuations of PaTonB-96 makes it more accessible for the interactions with the TonB box and possibly plays a role in disrupting the plug domain of the TonB-dependent OM transporters.
  • Owen, Michael C.; Kulig, Waldemar; Poojari, Chetan; Rog, Tomasz; Strodel, Birgit (2018)
    To resolve the contribution of ceramide-containing lipids to the aggregation of the amyloid-β protein into β-sheet rich toxic oligomers, we employed molecular dynamics simulations to study the effect of cholesterol-containing bilayers comprised of POPC (70% POPC, and 30% cholesterol) and physiologically relevant concentrations of sphingomyelin (SM) (30% SM, 40% POPC, and 30% cholesterol), and the GM1 ganglioside (5% GM1, 70% POPC, and 25% cholesterol). The increased bilayer rigidity provided by SM (and to a lesser degree, GM1) reduced the interactions between the SM-enriched bilayer and the N-terminus of Aβ42 (and also residues Ser26, Asn27, and Lys28), which facilitated the formation of a β-sheet in the normally disordered N-terminal region. Aβ42 remained anchored to the SM-enriched bilayer through hydrogen bonds with the side chain of Arg5. With β-sheets in the at the N and C termini, the structure of Aβ42 in the sphingomyelin-enriched bilayer most resembles β-sheet-rich structures found in higher-ordered Aβ fibrils. Conversely, when bound to a bilayer comprised of 5% GM1, the conformation remained similar to that observed in the absence of GM1, with Aβ42 only making contact with one or two GM1 molecules. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
  • Nordlund, Kai (2018)
    Using energy degrading foils to slow down antiprotons is of interest for producing antihydrogen atoms. I consider here the slowing down of 100 keV antiprotons, that will be produced in the ELENA storage ring under construction at CERN, to energies below 10 keV. At these low energies, they are suitable for efficient antihydrogen production. I simulate the antihydrogen motion and slowing down in Al foils using a recently developed molecular dynamics approach. The results show that the optimal Al foil thickness for slowing down the antiprotons to below 5 keV is 910 nm, and to below 10 keV is 840 nm. Also the lateral spreading of the transmitted antiprotons is reported and the uncertainties discussed. (C) 2018 The Author. Published by Elsevier B.V.
  • Fellman, Aslak (Helsingin yliopisto, 2021)
    The plasma-facing materials of future fusion reactors are exposed to high doses of radiation. The characterization of the radiation damage is an essential part in the study of fusion relevant materi- als. Electron microscopy is one of the most important tools used for characterization of radiation damage, as it provides direct observations of the microstructure of materials. However, the char- acterization of defects from electron microscope images remains difficult. Simulated images can be used to bridge the gap between experimental results and models. In this thesis, scanning transmission electron microscope (STEM) images of radiation damage were simulated. Molecular dynamics simulations were employed in order to create defects in tungsten. STEM images were simulated based on the created systems using the multislice method. A data- base of images of h001i dislocation loops and defects produced from collision cascade simulations was generated. The simulated images provide insight into the observed contrast of the defect structures. Differences in the image contrast between vacancy and interstitial h001i dislocation loops were reported. In addition to this, the results were compared against experimental images and used in identification of a dislocation loop. The simulated images demonstrate that it is feasible to simulate STEM images of radiation damage produced from collision cascade simulations.
  • Laulumaa, Saara; Nieminen, Tuomo; Raasakka, Arne; Krokengen, Oda C.; Safaryan, Anushik; Hallin, Erik I.; Brysbaert, Guillaume; Lensink, Marc F.; Ruskamo, Salla; Vattulainen, Ilpo; Kursula, Petri (2018)
    Background: Myelin is a multilayered proteolipid sheath wrapped around selected axons in the nervous system. Its constituent proteins play major roles in forming of the highly regular membrane structure. P2 is a myelin-specific protein of the fatty acid binding protein (FABP) superfamily, which is able to stack lipid bilayers together, and it is a target for mutations in the human inherited neuropathy Charcot-Marie-Tooth disease. A conserved residue that has been proposed to participate in membrane and fatty acid binding and conformational changes in FABPs is Phe57. This residue is thought to be a gatekeeper for the opening of the portal region upon ligand entry and egress. Results: We performed a structural characterization of the F57A mutant of human P2. The mutant protein was crystallized in three crystal forms, all of which showed changes in the portal region and helix a2. In addition, the behaviour of the mutant protein upon lipid bilayer binding suggested more unfolding than previously observed for wild-type P2. On the other hand, membrane binding rendered F57A heat-stable, similarly to wild-type P2. Atomistic molecular dynamics simulations showed opening of the side of the discontinuous beta barrel, giving important indications on the mechanism of portal region opening and ligand entry into FABPs. The results suggest a central role for Phe57 in regulating the opening of the portal region in human P2 and other FABPs, and the F57A mutation disturbs dynamic cross-correlation networks in the portal region of P2. Conclusions: Overall, the F57A variant presents similar properties to the P2 patient mutations recently linked to Charcot-Marie-Tooth disease. Our results identify Phe57 as a residue regulating conformational changes that may accompany membrane surface binding and ligand exchange in P2 and other FABPs.