Browsing by Subject "MOLECULAR-DYNAMICS SIMULATION"

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  • 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.
  • Ambrosio, Elena; Podmore, Adrian; dos Santos, Ana L. Gomes; Magarkar, Aniket; Bunker, Alex; Caliceti, Paolo; Mastrotto, Francesca; van der Walle, Christopher F.; Salmaso, Stefano (2018)
    Peptide therapeutics have the potential to self-associate, leading to aggregation and fibrillation. Noncovalent PEGylation offers a strategy to improve their physical stability; an understanding of the behavior of the resulting polymer/ peptide complexes is, however, required. In this study, we have performed a set of experiments with additional mechanistic insight provided by in silico simulations to characterize the molecular organization of these complexes. We used palmitoylated vasoactive intestinal peptide (VIP-palm) stabilized by methoxy-poly(ethylene glycol)(skDa)-cholane (PEG-cholane) as our model system. Homogeneous supramolecular assemblies were found only when complexes of PEG-cholane/VIP-palm exceeded a molar ratio of 2:1; at and above this ratio, the simulations showed minimal exposure of VIP-palm to the solvent. Supramolecular assemblies formed, composed of, on average, 9-11 PEG-cholane/VIP-palm complexes with 2:1 stoichiometry. Our in silico results showed the structural content of the helical conformation in VIP-palm increases when it is complexed with the PEG-cholane molecule; this behavior becomes yet more pronounced when these complexes assemble into larger supramolecular assemblies. Our experimental results support this: the extent to which VIP-palm loses helical structure as a result of thermal denaturation was inversely related to the PEG-cholane:VIP-palm molar ratio. The addition of divalent buffer species and increasing the ionic strength of the solution both accelerate the formation of VIP-palm fibrils, which was partially and fully suppressed by 2 and >4 mol equivalents of PEG-cholane, respectively. We conclude that the relative freedom of the VIP-palm backbone to adopt nonhelical conformations is a key step in the aggregation pathway.
  • 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.
  • 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.
  • Kepczynski, Mariusz; Rog, Tomasz (2016)
    Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Rog. (C) 2016 Elsevier B.V. All rights reserved.
  • 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.
  • Mastrotto, Francesca; Brazzale, Chiara; Bellato, Federica; De Martin, Sara; Grange, Guillaume; Mahmoudzadeh, Mohamad; Magarkar, Aniket; Bunker, Alex; Salmaso, Stefano; Caliceti, Paolo (2020)
    The colloidal stability, in vitro toxicity, cell association, and in vivo pharmacokinetic behavior of liposomes decorated with monomethoxy-poly(ethylene glycol)-lipids (mPEG-lipids) with different chemical features were comparatively investigated. Structural differences of the mPEG-lipids used in the study included: (a) surface-anchoring moiety [1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE), cholesterol (Chol), and cholane (Chin)]; (b) mPEG molecular weight (2 kDa mPEG and 5 kDa mPEG(114)); and (c) mPEG shape (linear and branched PEG). In vitro results demonstrated that branched (mPEG(114))(2)-DSPE confers the highest stealth properties to liposomes (similar to 31-fold lower cell association than naked liposomes) with respect to all PEGylating agents tested. However, the pharmacokinetic studies showed that the use of cholesterol as anchoring group yields PEGylated liposomes with longer permeance in the circulation and higher systemic bioavailability among the tested formulations. Liposomes decorated with mPEG(114)-Chol had 3.2- and similar to 2.1-fold higher area under curve (AUC) than naked liposomes and branched (mPEG(114))(2)-DSPE-coated liposomes, respectively, which reflects the high stability of this coating agent. By comparing the PEGylating agents with same size, namely, linear 5 kDa PEG derivatives, linear mPEG(114)-DSPE yielded coated liposomes with the best in vitro stealth performance. Nevertheless, the in vivo AUC of liposomes decorated with linear mPEG(114)-DSPE was lower than that obtained with liposomes decorated with linear mPEG(114)-Chol. Computational molecular dynamics modeling provided additional insights that complement the experimental results.
  • Sahle, Christoph J.; Schroer, Martin A.; Juurinen, Iina; Niskanen, Johannes (2016)
    We present a study on the influence of the naturally occurring organic osmolytes tri-methylamine N-oxide (TMAO) and urea on the bulk structure of water using X-ray Raman scattering spectroscopy. Addition of TMAO is known to stabilize proteins in otherwise destabilizing aqueous urea solutions. The experimental X-ray Raman scattering spectra change systematically with increasing solute concentration revealing different effects on the structure of water due to the presence of the two osmolytes. Although these effects are distinct for both molecular species, they have mutually compensating influences on the spectra of the ternary water-TMAO-urea mixtures. This compensation effect seen in the spectra vanishes only at the highest studied ternary concentration of 4 M: 4 M (TMAO : urea). Our experiment shows that the hydrogen-bonding structure of water remains rather intact in the presence of the aforementioned osmolytes if both of them are present.
  • Fellman, A.; Sand, A. E.; Byggmästar, Jesper; Nordlund, Kai (2019)
    We have performed a systematic molecular dynamics investigation of the effects of overlap of collision cascades in tungsten with pre-existing vacancy-type defects. In particular, we focus on the implications for fusion neutron irradiated tungsten in relation to comparisons with damage production under ion irradiation conditions. We find that overlap of a cascade with a vacancy-type defect decreases the number of new defects with roughly the same functional dependence as previously shown for interstitial clusters. We further find that different mechanisms govern the formation of dislocation loops, resulting in different Burgers vectors, depending on the degree of overlap between the cascade and the defect. Furthermore, we show that overlapping cascades consistently decrease the size of the pre-existing defect. We also observe void-induced cascade splitting at energies far below the subcascade splitting threshold in tungsten. The impact of these mechanisms on radiation damage accumulation and dose rate effects are discussed.
  • Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S. (2016)
    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.
  • Lajunen, Tatu; Nurmi, Riikka; Wilbie, Danny; Ruoslahti, Teemu; Johansson, Niklas G.; Korhonen, Ossi; Rog, Tomasz; Bunker, Alex; Ruponen, Marika; Urtti, Arto (2018)
    Light triggered drug delivery systems offer attractive possibilities for sophisticated therapy, providing both temporal and spatial control of drug release. We have developed light triggered liposomes with clinically approved indocyanine green (ICG) as the light sensitizing compound. Amphiphilic ICG can be localized in different compartments of the liposomes, but the effect of its presence, on both triggered release and long term stability, has not been studied. In this work, we report that ICG localization has a significant effect on the properties of the liposomes. Polyethylene glycol (PEG) coating of the liposomes leads to binding and stabilization of the ICG molecules on the surface of the lipid bilayer. This formulation showed both good storage stability in buffer solution (at +4-37 degrees C) and adequate stability in serum and vitreous (at +37 degrees C). The combination of ICG within the lipid bilayer and PEG coating lead to poor stability at elevated temperatures of +22 degrees C and +37 degrees C. The mechanisms of the increased instability due to ICG insertion in the lipid bilayer was elucidated with molecular dynamics simulations. Significant PEG insertion into the bilayer was induced in the presence of ICG in the lipid bilayer. Finally, feasibility of freeze-drying as a long term storage method for the ICG liposomes was demonstrated. Overall, this is the first detailed study on the interactions of lipid bilayer, light sensitizer (ICG) and PEG coating on the liposome stability. The localization of the light triggering agent significantly alters the structure of the liposomes and it is important to consider these aspects in triggered drug delivery system design.