Browsing by Subject "molecular dynamics"

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  • Lindblom, Otto (Helsingin yliopisto, 2020)
    Due to its exceptional thermal properties and irradiation resistance, tungsten is the material of choice for critical plasma-facing components in many leading thermonuclear fusion projects. Owing to the natural retention of hydrogen isotopes in materials such as tungsten, the safety of a fusion device depends heavily on the inventory of radioactive tritium in its plasma-facing components. The proposed methods of tritium removal typically include thermal treatment of massive metal structures for prolonged timescales. A novel way to either shorten the treatment times or lower the required temperatures is based performing the removal under an H-2 atmosphere, effectively exchanging the trapped tritium for non-radioactive protium. In this thesis, we employ molecular dynamics simulations to study the mechanism of hydrogen isotope exchange in vacancy, dislocation and grain boundary type defects in tungsten. By comparing the results to simulations of purely diffusion-based tritium removal methods, we establish that hydrogen isotope exchange indeed facilitates faster removal of tritium for all studied defect types at temperatures of 500 K and above. The fastest removal, when normalising based on the initial occupation of the defect, is shown to occur in vacancies and the slowest in grain boundaries. Through an atom level study of the mechanism, we are able to verify that tritium removal using isotope exchange depends on keeping the defect saturated with hydrogen. This study also works to show that molecular dynamics indeed is a valid tool for studying tritium removal and isotope exchange in general. Using small system sizes and spatially-parallelised simulation tools, we have managed to model isotope exchange for timescales extending from hundreds of nanoseconds up to several microseconds.
  • Zhang, Shuo; Pakarinen, Olli Heikki; Backholm, Matilda; Djurabekova, Flyura; Nordlund, Kai; Keinonen, Juhani; Wang, T.S. (2018)
    In this work, we first simulated the amorphization of crystalline quartz under 50 keV Na-23 ion irradiation with classical molecular dynamics (MD). We then used binary collision approximation algorithms to simulate the Rutherford backscattering spectrometry in channeling conditions (RBS-C) from these irradiated MD cells, and compared the RBS-C spectra with experiments. The simulated RBS-C results show an agreement with experiments in the evolution of amorphization as a function of dose, showing what appears to be (by this measure) full amorphization at about 2.2 eV.atom(-1). We also applied other analysis methods, such as angular structure factor, Wigner-Seitz, coordination analysis and topological analysis, to analyze the structural evolution of the irradiated MD cells. The results show that the atomic-level structure of the sample keeps evolving after the RBS signal has saturated, until the dose of about 5 eV.atom(-1). The continued evolution of the SiO2 structure makes the definition of what is, on the atomic level, an amorphized quartz ambiguous.
  • Byggmästar, Jesper Johan André; Nagel, Morten Jesper; Albe, Karsten; Henriksson, Krister Olof Edvin; Nordlund, Kai Henrik (2019)
    We present an analytical bond-order potential for the Fe-O system, capable of reproducing the basic properties of wustite as well as the energetics of oxygen impurities in alpha-iron. The potential predicts binding energies of various small oxygen-vacancy clusters in alpha-iron in good agreement with density functional theory results, and is therefore suitable for simulations of oxygen-based defects in iron. We apply the potential in simulations of the stability and structure of Fe/FeO interfaces and FeO precipitates in iron, and observe that the shape of FeO precipitates can change due to formation of well-defined Fe/FeO interfaces. The interface with crystalline Fe also ensures that the precipitates never become fully amorphous, no matter how small they are.
  • Allolio, Christoph; Magarkar, Aniket; Jurkiewicz, Piotr; Baxova, Katarina; Javanainen, Matti; Mason, Philip E.; Sachl, Radek; Cebecauer, Marek; Hof, Martin; Horinek, Dominik; Heinz, Veronika; Rachel, Reinhard; Ziegler, Christine M.; Schröfel, Adam; Jungwirth, Pavel (2018)
    Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.
  • 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.
  • Yetukuri, Laxman; Soderlund, Sanni; Koivuniemi, Artturi; Seppanen-Laakso, Tuulikki; Niemela, Perttu S.; Hyvonen, Marja; Taskinen, Marja-Riitta; Vattulainen, Ilpo Tapio; Jauhiainen, Matti; Oresic, Matej (2010)
  • Ruskamo, Salla; Krokengen, Oda C.; Kowal, Julia; Nieminen, Tuomo; Lehtimäki, Mari; Raasakka, Arne; Dandey, Venkata P.; Vattulainen, Ilpo; Stahlberg, Henning; Kursula, Petri (2020)
    Myelin protein P2 is a peripheral membrane protein of the fatty acid?binding protein family that functions in the formation and maintenance of the peripheral nerve myelin sheath. Several P2 gene mutations cause human Charcot-Marie-Tooth neuropathy, but the mature myelin sheath assembly mechanism is unclear. Here, cryo-EM of myelin-like proteolipid multilayers revealed an ordered three-dimensional (3D) lattice of P2 molecules between stacked lipid bilayers, visualizing supramolecular assembly at the myelin major dense line. The data disclosed that a single P2 layer is inserted between two bilayers in a tight intermembrane space of ?3 nm, implying direct interactions between P2 and two membrane surfaces. X-ray diffraction from P2-stacked bicelle multilayers revealed lateral protein organization, and surface mutagenesis of P2 coupled with structure-function experiments revealed a role for both the portal region of P2 and its opposite face in membrane interactions. Atomistic molecular dynamics simulations of P2 on model membrane surfaces suggested that Arg-88 is critical for P2-membrane interactions, in addition to the helical lid domain. Negatively charged lipid headgroups stably anchored P2 on the myelin-like bilayer surface. Membrane binding may be accompanied by opening of the P2 ?-barrel structure and ligand exchange with the apposing bilayer. Our results provide an unprecedented view into an ordered, multilayered biomolecular membrane system induced by the presence of a peripheral membrane protein from human myelin. This is an important step toward deciphering the 3D assembly of a mature myelin sheath at the molecular level.
  • Seppälä, Anniina; Puhakka, Eini; Olin, Markus (2016)
    The swelling and cation exchange properties of montmorillonite are fundamental in a wide range of applications ranging from nanocomposites to catalytic cracking of hydrocarbons. The swelling results from several factors and, though widely studied, information on the effects of a single factor at a time is lacking. In this study, density functional theory (DFT) calculations were used to obtain atomic-level information on the swelling of montmorillonite. Molecular dynamics (MD) was used to investigate the swelling properties of montmorillonites with different layer charges and interlayer cationic compositions. Molecular dynamics calculations, with CLAYFF force field, consider three layer charges (-1.0, -0.66 and -0.5 e per unit cell) arising from octahedral substitutions and interlayer counterions of Na, K and Ca. The swelling curves obtained showed that smaller layer charge results in greater swelling but the type of the interlayer cation also has an effect. The DFT calculations were also seen to predict larger d values than MD. The formation of 1, 2 and 3 water molecular layers in the interlayer spaces was observed. Finally, the data from MD calculations were used to predict the self-diffusion coefficients of interlayer water and cations in different montmorillonites and in general the coefficient increased with increasing water content and with decreasing layer charge.
  • Golda-Cepa, Monika; Riedlova, Kamila; Kulig, Waldemar; Cwiklik, Lukasz; Kotarba, Andrzej (2020)
    Interactions at the solid-body fluid interfaces play a vital role in bone tissue formation at the implant surface. In this study, fully atomistic molecular dynamics (MD) simulations were performed to investigate interactions between the physiological components of body fluids (Ca2+, HPO42-, H2PO4-, Na+, Cl-, and H2O) and functionalized parylene C surface. In comparison to the native parylene C (-Cl surface groups), the introduction of -OH, -CHO, and -COOH surface groups significantly enhances the interactions between body fluid ions and the polymeric surface. The experimentally observed formation of calcium phosphate nanocrystals is discussed in terms of MD simulations of the calcium phosphate clustering. Surface functional groups promote the clustering of calcium and phosphate ions in the following order: -OH > -CHO > -Cl (parent parylene C) approximate to -COO-. This promoting role of surface functional groups is explained as stimulating the number of Ca2+ and HPO42- surface contacts as well as ion chemisorption. The molecular mechanism of calcium phosphate cluster formation at the functionalized parylene C surface is proposed.
  • Kauppala, Juuso (Helsingin yliopisto, 2021)
    The rapidly increasing global energy demand has led to the necessity of finding sustainable alternatives for energy production. Fusion power is seen as a promising candidate for efficient and environmentally friendly energy production. One of the main challenges in the development of fusion power plants is finding suitable materials for the plasma-facing components in the fusion reactor. The plasma-facing components must endure extreme environments with high heat fluxes and exposure to highly energetic ions and neutral particles. So far the most promising materials for the plasma-facing components are tungsten (W) and tungsten-based alloys. A promising class of materials for the plasma-facing components is high-entropy alloys. Many high-entropy alloys have been shown to exhibit high resistance to radiation and other wanted properties for many industrial and high-energy applications. In materials research, both experimental and computational methods can be used to study the materials’ properties and characteristics. Computational methods can be either quantum mechanical calculations, that produce accurate results while being computationally extremely heavy, or more efficient atomistic simulations such as classical molecular dynamics simulations. In molecular dynamics simulations, interatomic potentials are used to describe the interactions between particles and are often analytical functions that can be fitted to the properties of the material. Instead of fixed functional forms, interatomic potentials based on machine learning methods have also been developed. One such framework is the Gaussian approximation potential, which uses Gaussian process regression to estimate the energies of the simulation system. In this thesis, the current state of fusion reactor development and the research of high-entropy alloys is presented and an overview of the interatomic potentials is given. Gaussian approximation potentials for WMoTa concentrated alloys are developed using different number of sparse training points. A detailed description of the training database is given and the potentials are validated. The developed potentials are shown to give physically reasonable results in terms of certain bulk and surface properties and could be used in atomistic simulations.
  • Herbig, Charlotte; Åhlgren, E. Harriet; Jolie, Wouter; Busse, Carsten; Kotakoski, Jani; Krasheninnikov, Arkady V.; Michely, Thomas (2014)
  • Manna, Moutusi; Javanainen, Matti; Monne, Hector Martinez-Seara; Gabius, Hans-Joachim; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Extracellular and cytosolic leaflets in cellular membranes are distinctly different in lipid composition, yet they contribute together to signaling across the membranes. Here we consider a mechanism based on long-chain gangliosides for coupling the extracellular and cytosolic membrane leaflets together. Based on atomistic molecular dynamics simulations, we find that long-chain GM1 in the extracellular leaflet exhibits a strong tendency to protrude into the opposing bilayer leaflet. This interdigitation modulates the order in the cytosolic monolayer and thereby strengthens the interaction and coupling across a membrane. Coarse-grained simulations probing longer time scales in large membrane systems indicate that GM1 in the extracellular leaflet modulates the phase behavior in the cytosolic monolayer. While short-chain GM1 maintains phase-symmetric bilayers with a strong membrane registration effect, the situation is altered with long-chain GM1. Here, the significant interdigitation induced by long-chain GM1 modulates the behavior in the cytosolic GM1-free leaflet, weakening and slowing down the membrane registration process. The observed physical interaction mechanism provides a possible means to mediate or foster transmembrane communication associated with signal transduction. (C) 2017 Elsevier B.V. All rights reserved.
  • Kaptan, Shreyas; Vattulainen, Ilpo (2022)
    Machine learning has rapidly become a key method for the analysis and organization of large-scale data in all scientific disciplines. In life sciences, the use of machine learning techniques is a particularly appealing idea since the enormous capacity of computational infrastructures generates terabytes of data through millisecond simulations of atomistic and molecular-scale biomolecular systems. Due to this explosion of data, the automation, reproducibility, and objectivity provided by machine learning methods are highly desirable features in the analysis of complex systems. In this review, we focus on the use of machine learning in biomolecular simulations. We discuss the main categories of machine learning tasks, such as dimensionality reduction, clustering, regression, and classification used in the analysis of simulation data. We then introduce the most popular classes of techniques involved in these tasks for the purpose of enhanced sampling, coordinate discovery, and structure prediction. Whenever possible, we explain the scope and limitations of machine learning approaches, and we discuss examples of applications of these techniques.
  • Kuppart, Kristian; Vigonski, Simon; Aabloo, Alvo; Wang, Ye; Djurabekova, Flyura; Kyritsakis, Andreas; Zadin, Veronika (2021)
    We present a credible mechanism of spontaneous field emitter formation in high electric field applications, such as Compact Linear Collider in CERN (The European Organization for Nuclear Research). Discovery of such phenomena opens new pathway to tame the highly destructive and performance limiting vacuum breakdown phenomena. Vacuum breakdowns in particle accelerators and other devices operating at high electric fields is a common problem in the operation of these devices. It has been proposed that the onset of vacuum breakdowns is associated with appearance of surface protrusions while the device is in operation under high electric field. Moreover, the breakdown tolerance of an electrode material was correlated with the type of lattice structure of the material. Although biased diffusion under field has been shown to cause growth of significantly field-enhancing tips starting from initial nm-size protrusions, the mechanisms and the dynamics of the growth of the latter have not been studied yet. In the current paper we conduct molecular dynamics simulations of nanocrystalline copper surfaces and show the possibility of protrusion growth under the stress exerted on the surface by an applied electrostatic field. We show the importance of grain boundaries on the protrusion formation and establish a linear relationship between the necessary electrostatic stress for protrusion formation and the temperature of the system. Finally, we show that the time for protrusion formation decreases with the applied electrostatic stress, we give the Arrhenius extrapolation to the case of lower fields, and we present a general discussion of the protrusion formation mechanisms in the case of polycrystalline copper surfaces.
  • Hooda, Sonu; Avchachov, Konstantin; Khan, S. A.; Djurabekova, Flyura; Satpati, B.; Nordlund, Kai; Bernstorff, Sigrid; Ahlawat, Sarita; Kanjilal, D.; Kabiraj, D. (2017)
    The formation of nanoscale voids in amorphous-germanium (a-Ge), and their size and shape evolution under ultra-fast thermal spikes within an ion track of swift heavy ion, is meticulously expatiated using experimental and theoretical approaches. Two step energetic ion irradiation processes were used to fabricate novel and distinct embedded nanovoids within bulk Ge. The 'bow-tie' shape of voids formed in a single ion track tends to attain a spherical shape as the ion tracks overlap at a fluence of about 1 x 10(12) ions cm(-2). The void assumes a prolate spheroid shape with major axis along the ion trajectory at sufficiently high ion fluences. Small angle x-ray scattering can provide complementary information about the primary stage of void formation hence this technique is applied for monitoring simultaneously their formation and growth dynamics. The results are supported by the investigation of cross-sectional transmission and scanning electron micrographs. The multi-time-scale theoretical approach corroborates the experimental findings and relates the bow-tie shape void formation to density variations as a result of melting and resolidification of Ge within the region of thermal spike generated along an ion track, plus non-isotropic stresses generated towards the end of the thermal spike.
  • Bunker, Alex; Rog, Tomasz (2020)
    In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
  • Lolicato, Fabio; Juhola, Hanna; Zak, Agata; Postila, Pekka A.; Saukko, Annina; Rissanen, Sami; Enkavi, Giray; Vattulainen, Ilpo; Kepczynski, Mariusz; Rog, Tomasz (2020)
    Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitters first partition to the lipid headgroup region and then diffuse along the membrane plane to their membrane-buried receptors. However, to date, this mechanism has not been demonstrated for any neurotransmitter-receptor complex. Here, we combined isothermal calorimetry measurements with a diverse set of molecular dynamics simulation methods to investigate the partitioning of an amphipathic neurotransmitter (dopamine) and the mechanism of its entry into the ligand-binding site. Our results show that the binding of dopamine to its receptor is consistent with the membrane-dependent binding and entry mechanism. Both experimental and simulation results showed that dopamine favors binding to lipid membranes especially in the headgroup region. Moreover, our simulations revealed a ligand-entry pathway from the membrane to the binding site. This pathway passes through a lateral gate between transmembrane alpha-helices 5 and 6 on the membrane-facing side of the protein. All in all, our results demonstrate that dopamine binds to its receptor by a membrane-dependent mechanism, and this is complemented by the more traditional binding mechanism directly through the aqueous phase. The results suggest that the membrane-dependent mechanism is common in other synaptic receptors, too.
  • Hodille, E. A.; Byggmästar, J.; Safi, E.; Nordlund, K. (2019)
    The sputtering and reflection properties of wurtzite beryllium oxide (BeO) subjected to deuterium (D) ions bombardment at 300 K with ion energy between 10 eV and 200 eV is studied by classical molecular dynamics. Cumulative irradiations of wurtzite BeO show a D concentration threshold above which an 'unphysical dramatic' sputtering is observed. From the cumulative irradiations, simulation cells with different D concentrations are used to run non-cumulative irradiations at different concentrations. Using a D concentration close to the experimentally determined saturation concentration (0.12 atomic fraction), the simulations are able to reproduce accurately the experimental sputtering yield of BeO materials. The processes driving the sputtering of beryllium (Be) and oxygen (O) atoms as molecules are subsequently determined. At low irradiation energy, between 10 eV and 80 eV, swift chemical sputtering (SCS) is dominant and produces mostly ODz molecules. At high energy, the sputtered molecules are mostly BexOy molecules (mainly BeO dimer). Four different processes are associated to the formation of such molecules: the physical sputtering of BeO dimer, the delayed SCS not involving D ions and the detachment-induced sputtering. The physical sputtering of BeO dimer can be delayed if the sputtering event implies two interactions with the incoming ion (first interaction in its way in the material, the other in its way out if it is backscattered). The detachment-induced sputtering is a characteristic feature of the 'dramatic' sputtering and is mainly observed when the concentration of D is close to the threshold leading to this sputtering regime.
  • Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M. (2016)
    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called 'fuzz' structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers than He diffusion through fuzz nanorods. Instead of trying to grow a fuzz layer starting from a flat piece of bulk W, a new approach of creating a fully formed fuzz structure 0.43 mu m thick out of ellipsoidal pieces of W is employed. Lack of detailed experimental knowledge of the 3D structure of fuzz is dealt with by simulating He bombardment on five different structures of 15 vol% W and determining the variation in He penetration for each case. The results show that by far the most important factor determining He penetration is the amount of open channels through which He ions can travel unimpeded. For a more or less even W density distribution He penetration into fuzz falls off exponentially with distance and can thus be described by a 'half depth'. In a 15 vol% fuzz structure, the half depth can reach 0.18 mu m. In the far sparser fuzz structures that were recently reported, the half depth might be 1 mu m or more. This means that ballistic He penetration offers a more likely scenario than He diffusion through nanorods for how He moves through fuzz and may provide an adequate explanation for how He penetrates through the thickest fuzz layers reported so far. Furthermore, the exponential decrease in penetration with depth would follow a logarithmic dependence on fluence which is compatible with experiments. A comparison of these results and molecular dynamics calculations carried out in the recoil interaction approximation shows that results for W fuzz are qualitatively very different from conventional stopping power calculations on W with a similarly low but homogeneous density distribution.