Browsing by Subject "MOLECULAR-DYNAMICS"

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  • Toijala, H.; Eimre, K.; Kyritsakis, A.; Zadin, Vahur; Djurabekova, F. (2019)
    In this work we combine density functional theory and quantum transport calculations to study the influence of atomic-scale defects on the work function and field emission characteristics of metal surfaces. We develop a general methodology for the calculation of the field emitted current density from nanofeatured surfaces, which is then used to study specific defects on a Cu(111) surface. Our results show that the inclusion of a defect can significantly locally enhance the field emitted current density. However, this increase is attributed solely to the decrease of the work function due to the defect, with the effective field enhancement being minute. Finally, the Fowler-Nordheim equation is found to be valid when the modified value for the work function is used, with only an approximately constant factor separating the computed currents from those predicted by the Fowler-Nordheim equation.
  • Ni, Ruiqing; Gillberg, Per-Goran; Bogdanovic, Nenad; Viitanen, Matti; Myllykangas, Liisa; Nennesmo, Inger; Langstrom, Bengt; Nordberg, Agneta (2017)
    Introduction: Amyloid imaging has been integrated into diagnostic criteria for Alzheimer's disease (AD). How amyloid tracers binding differ for different tracer structures and amyloid-beta aggregates in autosomal dominant AD (ADAD) and sporadic AD is unclear. Methods: Binding properties of different amyloid tracers were examined in brain homogenates from six ADAD with APPswe, PS1 M146V, and PS1 E Delta 9 mutations, 13 sporadic AD, and 14 control cases. Results: H-3-PIB, H-3-florbetaben, H-3-AZD2184, and BTA-1 shared a high-and a varying low-affinity binding site in the frontal cortex of sporadic AD. AZD2184 detected another binding site (affinity 33 nM) in the frontal cortex of ADAD. The H-3-AZD2184 and H-3-PIB binding were significantly higher in the striatum of ADAD compared to sporadic AD and control. Polyphenol resveratrol showed strongest inhibition on H-3-AZD84 binding followed by H-3-florbetaben and minimal on H-3-PIB. Discussion: This study implies amyloid tracers of different structures detect different sites on amyloid-beta fibrils or conformations. (C) 2016 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.
  • Holmstrom, E.; Kotakoski, J.; Lechner, L.; Kaiser, U.; Nordlund, K. (2012)
  • Malkamäki, Aapo Erkki Matias; Sharma, Vivek (2019)
    Mitochondrial cytochrome c oxidase couples the reduction of oxygen to proton pumping. Despite an overall good understanding of its molecular mechanism, the role of cardiolipin in protein function is not understood. Here, we have studied the cardiolipin-protein interactions in a dynamic context by means of atomistic molecular dynamics simulations performed on the entire structure of monomeric and dimeric forms of the enzyme. Several microseconds of simulation data reveal that the crystallographic cardiolipin molecules that glue two monomers together bind weakly in hybrid and single-component lipid bilayers and dissociate rapidly. Atomistic simulations performed in the absence of tightly bound cardiolipin molecules strongly perturb the structural integrity of subunits III and Vila, thereby highlighting an indispensable nature of lipid-protein interactions in enzyme function such as proton uptake and oxygen channeling. Our results demonstrate the strength of molecular simulations in providing direct atomic description of lipid-protein processes that are difficult to achieve experimentally.
  • Reischl, Bernhard; Rohl, Andrew L.; Kuronen, Antti; Nordlund, Kai (2017)
    Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young's moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 +/- 2, 140 +/- 4 and 108 +/- 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.
  • 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.
  • Timr, Stepan; Kadlec, Jan; Srb, Pavel; Ollila, O. H. Samuli; Jungwirth, Pavel (2018)
    The detailed functional mechanism of recoverin, which acts as a myristoyl switch at the rod outer-segment disk membrane, is elucidated by direct and replica-exchange molecular dynamics. In accord with NMR structural evidence and calcium binding assays, simulations point to the key role of enhanced calcium binding to the EF3 loop of the semiopen state of recoverin as compared to the closed state. This 2-4-order decrease in calcium dissociation constant stabilizes the semiopen state in response to the increase of cytosolic calcium concentration in the vicinity of recoverin. A second calcium ion then binds to the EF2 loop and, consequently, the structure of the protein changes from the semiopen to the open state. The latter has the myristoyl chain extruded to the cytosol, ready to act as a membrane anchor of recoverin.
  • Granberg, Fredric; Byggmästar, Jesper; Nordlund, Kai (2019)
    In order to understand the effect of irradiation on the material properties, we need to look into the atomistic evolution of the system during the recoil event. The nanoscale features formed due to irradiation will ultimately affect the macroscopic properties of the material. The defect production in pristine materials have been subject to investigation previously, but as the dose increases, overlap will start to happen. This effect of cascades overlapping with pre-existing debris has only recently been touched, and mainly been investigated for interstitial-type defects. We focus on vacancy-type defect clusters in BCC Fe and start a recoil event in their near vicinity. The final defect number as well as the transformation of the defect clusters are investigated, and their behaviour is related to the distance between the defect and the cascade centre. We found that for vacancy-type defects, the suppression of defect production is not as strong as previously observed for interstitial-type defects. The cascade-induced transformation, such as change in Burgers vector or creation of dislocations, was determined for all initial defect structures.
  • 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.
  • Tossavainen, Helena; Kukkurainen, Sampo; Määttä, Juha A. E.; Kähkönen, Niklas; Pihlajamaa, Tero; Hytönen, Vesa P.; Kulomaa, Markku S.; Permi, Perttu (2014)
  • Dziubanska-Kusibab, Paulina J.; Berger, Hilmar; Battistini, Federica; Bouwman, Britta A. M.; Iftekhar, Amina; Katainen, Riku; Cajuso, Tatiana; Crosetto, Nicola; Orozco, Modesto; Aaltonen, Lauri A.; Meyer, Thomas F. (2020)
    The mucosal epithelium is a common target of damage by chronic bacterial infections and the accompanying toxins, and most cancers originate from this tissue. We investigated whether colibactin, a potent genotoxin(1) associated with certain strains of Escherichia coli(2), creates a specific DNA-damage signature in infected human colorectal cells. Notably, the genomic contexts of colibactin-induced DNA double-strand breaks were enriched for an AT-rich hexameric sequence motif, associated with distinct DNA-shape characteristics. A survey of somatic mutations at colibactin target sites of several thousand cancer genomes revealed notable enrichment of this motif in colorectal cancers. Moreover, the exact double-strand-break loci corresponded with mutational hot spots in cancer genomes, reminiscent of a trinucleotide signature previously identified in healthy colorectal epithelial cells(3). The present study provides evidence for the etiological role of colibactin in human cancer. Identification of a DNA-damage signature induced by colibactin, a toxin expressed by some strains of Escherichia coli, is enriched in human colorectal cancers.
  • 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.
  • Bhardwaj, Utkarsh; Sand, Andrea E.; Warrier, Manoj (2021)
    The morphology of defects formed in collision cascades is an essential aspect of the subsequent evolution of the microstructure. The morphological composition of a defect decides its stability, interaction, and migration properties. We compare the defect morphologies in the primary radiation damage caused by high energy collision cascades simulated using three different interatomic potentials in W. An automated method to identify morphologies of defects is used. While most defects form 1/2⟨111⟩ dislocation loops, other specific morphologies include ⟨100⟩ dislocation loops, multiple loops clustered together, rings corresponding to C15 configuration and its constituent structures, and a combination of rings and dislocations. The analysis quantifies the distribution of defects among different morphologies and the size distribution of each morphology. We show that the disagreement between predictions of the different potentials regarding defect morphology is much stronger than the differences in predicted defect numbers.
  • Stepien, Piotr; Augustyn, Bozena; Poojari, Chetan; Galan, Wojciech; Polit, Agnieszka; Vattulainen, Ilpo; Wisnieska-Becker, Anna; Rog, Tomasz (2020)
    Lipid nanodiscs are macromolecular assemblies, where a scaffold protein is wrapped around a nanosized disc of a lipid bilayer, thus protecting the hydrocarbon chains at the disc edges from unfavorable interactions with water. These nanostructures have numerous applications in, e.g., nanotechnology and pharmaceutics, and in investigations of membrane proteins. Here, we present results based on atomistic molecular dynamics simulations combined with electron paramagnetic spectroscopy measurements on the structure and dynamics of lipids in single-component nanodiscs. Our data highlight the existence of three distinctly different lipid fractions: central lipids residing in the center of a nanodisc, boundary lipids in direct contact with a scaffold protein, and intermediate lipids between these two regions. The central lipids are highly ordered and characterized by slow diffusion. In this part of the nanodisc, the membrane is the thickest and characterized by a gel-like or liquid-ordered phase, having features common to cholesterol-rich membranes. The boundary lipids in direct contact with the scaffold protein turned out to be less ordered and characterized by faster diffusion, and they remained in the liquid-disordered phase even at temperatures that were somewhat below the main phase transition temperature (Tm). The enthalpies associated with the central-boundary and central-intermediate transitions were similar to those observed for lipids going through the main phase transition. Overall, the study reveals lipid nanodiscs to be characterized by a complex internal structure, which is expected to influence membrane proteins placed in nanodiscs.
  • Baibuz, Ekaterina; Vigonski, Simon; Lahtinen, Jyri Kalevi; Zhao, Junlei; Jansson, Ville Bernt Christian; Zadin, Vahur; Djurabekova, Flyura Gatifovna (2018)
    Atomistic rigid lattice Kinetic Monte Carlo (KMC) is an efficient method for simulating nano-objects and surfaces at timescales much longer than those accessible by molecular dynamics. A laborious and non-trivial part of constructing any KMC 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. We have calculated three data sets of migration barriers for Cu self-diffusion with two different methods. The data sets were specifically calculated for rigid lattice KMC simulations of copper self-diffusion on arbitrarily rough surfaces, but can be used for KMC simulations of bulk diffusion as well.
  • Djurabekova, F.; Fridlund, C.; Nordlund, K. (2020)
    We present molecular dynamics simulations of atomic mixing over a Si/SiO2 heterostructure interface, induced by focused Ne+ and broad Si(+ )ion-beam irradiations, using a speed-up scheme that significantly reduces the relaxation time of the cascading recoils. To assess the qualitative reliance of the chosen method, two different potential models for Si-O, Si-Si, and O-O interactions were used: the Stillinger-Weber-like Watanabe-Samela potential and the Tersoff-like Munetoh potential. Furthermore, the molecular dynamics simulations were assessed by simulating a similar case, at a total fluence of 1 x10(15) cm(-2), with the binary collision approximation. The same general atomic density profile distributions were achieved with both models; however, the binary collision approach showed shallower penetration of Si into the SiO(2 )layer. Coordination analysis of the molecular dynamics results provides strong evidence that ion mixing at high fluences leads to coordination defects, which will affect the electronic properties of the structures unless removed with annealing.
  • Lopez-Cazalilla, A.; Djurabekova, F.; Ilinov, A.; Fridlund, C.; Nordlund, K. (2020)
    Patterns on sand generated by blowing winds are one of the most commonly seen phenomena driven by such a self-organization process, as has been observed at the nanoscale after ion irradiation. The origins of this effect have been under debate for decades. Now, a new methodology allows to simulate directly the ripple formation by high-fluence ion-irradiation. Since this approach does not pre-assume a mechanism to trigger self-organization, it can provide answers to the origin of the ripple formation mechanism. The surface atom displacement and a pile-up effect are the driving force of ripple formation, analogously to the macroscopic one. IMPACT STATEMENT The presented model allows to follow the ripple formation and propagation in different steps, at the atomic level, for the first time under low irradiation energies.
  • Mason, D. R.; Sand, A. E.; Yi, X.; Dudarev, S. L. (2018)
    Recently we have presented direct experimental evidence for large defect clusters being formed in primary damage cascades in self-ion irradiated tungsten [Yi et al., EPL 110:36001 (2015)]. This large size is significant, as it implies that strong elastic interaction between the defects will affect their subsequent evolution, especially if defects are formed close together. Here we present a direct experimental observation of the separation between visible defects in self-ion irradiated tungsten, in the form of a 2d pairwise radial distribution function extracted from transmission electron micrographs (TEM). We also present a detailed analysis of the observed radial distribution function, and infer the probable size and shape of individual cascades. We propose and validate a simple exponential form for the spatial distribution of defects within a single cascade. The cascade statistics necessary have been acquired by developing an automated procedure for analysing black-dot damage in TEM micrographs. We confirm that the same model also produces a high-quality fit to the separation between larger defects observed in MD simulations. For the first time we present experimental evidence for the sub-nanometre-scale spatial distribution of defect clusters within individual cascades. (C) 2017 EURATOM. Published by Elsevier Ltd on behalf of Acta Materialia Inc. All rights reserved.
  • Kaurola, Petri; Sharma, Vivek; Vonk, Amanda; Vattulainen, Ilpo; Rog, Tomasz (2016)
    Quinone and its analogues (Q) constitute an important class of compounds that perform key electron transfer reactions in oxidative- and photo-phosphorylation. In the inner membrane of mitochondria, ubiquinone molecules undergo continuous redox transitions enabling electron transfer between the respiratory complexes. In such a dynamic system undergoing continuous turnover for ATP synthesis, an uninterrupted supply of substrate molecules is absolutely necessary. In the current work, we have performed atomistic molecular dynamics simulations and free energy calculations to assess the structure, dynamics, and localization of quinone and its analogues in a lipid bilayer, whose composition mimics the one in the inner mitochondrial membrane. The results show that there is a strong tendency of both quinone and quinol molecules to localize in the vicinity of the lipids' acyl groups, right under the lipid head group region. Additionally, we observe a second location in the middle of the bilayer where quinone molecules tend to stabilize. Translocation of quinone through a lipid bilayer is very fast and occurs in 10-100 ns time scale, whereas the translocation of quinol is at least an order of magnitude slower. We suggest that this has important mechanistic implications given that the localization of Q ensures maximal occupancy of the Q-binding sites or Q-entry points in electron transport chain complexes, thereby maintaining an optimal turnover rate for ATP synthesis. (C) 2016 Elsevier B.V. All rights reserved.
  • Uno, Shinpei; Masuya, Takahiro; Zdorevskyi, Oleksii; Ikunishi, Ryo; Shinzawa-Itoh, Kyoko; Lasham, Jonathan; Sharma, Vivek; Murai, Masatoshi; Miyoshi, Hideto (2022)
    The ubiquinone (UQ) reduction step catalyzed by NADH-UQ oxidoreductase (mitochondrial respiratory complex I) is key to triggering proton translocation across the inner mitochondrial membrane. Structural studies have identified a long, narrow, UQ-accessing tunnel within the enzyme. We previously demonstrated that synthetic oversized UQs, which are unlikely to transit this narrow tunnel, are catalytically reduced by native complex I embedded in submitochondrial particles but not by the isolated enzyme. To explain this contradiction, we hypothesized that access of oversized UQs to the reaction site is obstructed in the isolated enzyme because their access route is altered following detergent solubilization from the inner mitochondrial membrane. In the present study, we investigated this using two pairs of photoreactive UQs (pUQ(m-1)/pUQ(p-1) and pUQ(m-2)/pUQ(p-2)), with each pair having the same chemical properties except for a similar to 1.0 angstrom difference in side-chain widths. Despite this subtle difference, reduction of the wider pUQs by the isolated complex was significantly slower than of the narrower pUQs, but both were similarly reduced by the native enzyme. In addition, photoaffinity-labeling experiments using the four [I-125]pUQs demonstrated that their side chains predominantly label the ND1 subunit with both enzymes but at different regions around the tunnel. Finally, we show that the suppressive effects of different types of inhibitors on the labeling significantly changed depending on [I-125]pUQs used, indicating that [I-125]pUQs and these inhibitors do not necessarily share a common binding cavity. Altogether, we conclude that the reaction behaviors of pUQs cannot be simply explained by the canonical UQ tunnel model.