Browsing by Subject "MD simulations"

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  • Dominguez-Gutierrez, F. J.; Byggmastar, J.; Nordlund, K.; Djurabekova, F.; von Toussaint, U. (2021)
    In this work, we study the damage in crystalline molybdenum material samples due to neutron bombardment in a primary knock-on atom (PKA) range of 0.5-10 keV at room temperature. We perform classical molecular dynamics (MD) simulations using a previously derived machine learning (ML) interatomic potential based on the Gaussian approximation potential (GAP) framework. We utilize a recently developed software workflow for fingerprinting and visualizing defects in damaged crystal structures to analyze the Mo samples with respect to the formation of point defects during and after a collision cascade. As a benchmark, we report results for the total number of Frenkel pairs (a self-interstitial atom and a single vacancy) formed and atom displacements as a function of the PKA energy. A comparison to results obtained using an embedded atom method (EAM) potential is presented to discuss the advantages and limits of the MD simulations utilizing ML-based potentials. The formation of Frenkel pairs follows a sublinear scaling law as xi ( b ) where b is a fitting parameter and xi = E (PKA)/E (0) with E (0) as a scaling factor. We found that the b = 0.54 for the GAP MD results and b = 0.667 for the EAM simulations. Although the average number of total defects is similar for both methods, the MD results show different atomic geometries for complex point defects, where the formation of crowdions by the GAP potential is closer to the DFT-based expectation. Finally, ion beam mixing results for GAP MD simulations are in a good agreement with experimental mixing efficiency data. This indicates that the modeling of atom relocation in cascades by machine learned potentials is suited to interpret the corresponding experimental findings.
  • Wilkosz, Natalia; Rissanen, Sami; Cyza, Malgorzata; Szybka, Renata; Nowakowska, Maria; Bunker, Alex; Rog, Tomasz; Kepczynski, Mariusz (2017)
    Uptake of piroxicam, a non-steroidal anti-inflammatory drug, from the intestines after oral intake is limited due to its low solubility and its wide use is associated with several side effects related to the gastrointestinal tract. In this study, all-atom molecular dynamics (MD) simulations and fluorescent spectroscopy were employed to investigate the interaction of piroxicam in neutral, zwitterionic, and cationic forms with lipid bilayers composed of phosphatidylcholine, cholesterol, and PEGylated lipids. Our study was aimed to assess the potential for encapsulation of piroxicam in liposomal carriers and to shed more light on the process of gastrointestinal tract injury by the drug. Through both the MD simulations and laser scanning confocal microscopy, we have demonstrated that all forms of piroxicam can associate with the lipid bilayers and locate close to the water-membrane interface. Conventional liposomes used in drug delivery are usually stabilized by the addition of cholesterol and have their bloodstream lifetime extended through the inclusion of PEGylated lipids in the formulation to create a protective polymer corona. For this reason, we tested the effect of these two modifications on the behavior of piroxicam in the membrane. When the bilayer was PEGylated, piroxicam localize to the PEG layer and within the lipid headgroup region. This suggests that PEGylated liposomes are capable of carrying a larger quantity of piroxicam than the conventional ones. (C) 2017 Elsevier B.V. All rights reserved.
  • Paajanen, Santeri (Helsingin yliopisto, 2022)
    NMDA receptors are ionotropic glutamate receptors (iGluRs), tetrameric proteins, mediating synaptic transmission in the brain and the whole nervous system. Together with another type of iGluRs, AMPA receptors, they are considered essential for neuronal plasticity and memory. Understanding their dynamics and different kinetics is vital for studying various neurological diseases. The relatively slow dynamics, where the time scales of related processes range up to hundreds of milliseconds, make studying them with Molecular Dynamics (MD) simulations challenging. We developed the Functional Sampling Tool (FST), a novel method for enhancing the sampling of a function of interest. Compared to existing enhanced sampling schemes it strikes a balance between generality and simplicity, minimising the need of user input, while allowing for maximal customisability. Using FST, we studied two processes of the NMDA receptor. By keeping all four ligands bound we simulated a desensitisation pathway, and by removing all four we simulated an inactivation pathway. The tool sampled both, giving a good distribution between open and closed states. The tool also allowed us to change the function in the middle of sampling. With the new function we were able to produce more data, focusing on a certain value range.
  • Domínguez-Gutiérrez, F.J.; Byggmästar, J.; Nordlund, K.; Djurabekova, F.; von Toussaint, U. (2020)
    The analysis of the damage on plasma facing materials (PFM), due to their direct interaction with the plasma environment, is needed to build the next generation of nuclear fusion reactors. After systematic analyses of numerous materials over the last decades, tungsten has become the most promising candidate for a nuclear fusion reactor. In this work, we perform molecular dynamics (MD) simulations using a machine learned interatomic potential, based on the Gaussian Approximation Potential framework, to model better neutron bombardment mechanisms in pristine W lattices. The MD potential is trained to reproduce realistic short-range dynamics, the liquid phase, and the material recrystallization, which are important for collision cascades. The formation of point defects is quantified and classified by a descriptor vector (DV) based method, which is independent of the sample temperature and its constituents, requiring only modest computational resources. The locations of vacancies are calculated by the k-d-tree algorithm. The analysis of the damage in the W samples is compared to results obtained by Finnis–Sinclair and Tersoff–Ziegler–Biersack–Littmark potentials, at a sample temperature of 300 K and a primary knock-on atom (PKA) energy range of 0.5–10 keV, where a good agreement with the reported number of Frenkel pair is observed. Our results provide information about the advantages and limits of the machine learned MD simulations with respect to the standard ones. The formation of dumbbell and crowdion defects as a function of PKA energy were identified and distinguished by our DV method.
  • Karaseov, P. A.; Karabeshkin, K. V.; Titov, A. I.; Ullah, Mohammad W.; Kuronen, A.; Djurabekova, F.; Nordlund, K.; Ermolaeva, G. M.; Shilov, V. B. (2017)
    An investigation of mechanisms of enhancement of irradiation-induced damage formation in GaN under molecular in comparison to monatomic ion bombardment is presented. Ion-implantation-induced effects in wurtzite GaN bombarded with 0.6 keV amu(-1) F, P, PF2, PF4, and Ag ions at room temperature are studied experimentally and by cumulative MD simulation in the correct irradiation conditions. In the low dose regime, damage formation is correlated with a reduction in photoluminescence decay time, whereas in the high dose regime, it is associated with the thickness of the amorphous/disordered layer formed at the sample surface. In all the cases studied, a shift to molecular ion irradiation from bombardment by its monatomic constituents enhances the damage accumulation rate. Implantation of a heavy Ag ion, having approximately the same mass as the PF4 molecule, is less effective in surface damage formation, but leads to noticeably higher damage accumulation in the bulk. The cumulative MD simulations do not reveal any significant difference in the total amount of both point defects and small defect clusters produced by light monatomic and molecular ions. On the other hand, increased production of large defect clusters by molecular PF4 ions is clearly seen in the vicinity of the surface. Ag ions produce almost the same number of small, but more large defect clusters compared to the others. These findings show that the higher probability of formation of large defect clusters is important mechanism of the enhancement of stable damage formation in GaN under molecular, as well as under heavy monatomic ion irradiation.
  • Malkamäki, Aapo; Meunier, Brigitte; Reidelbach, Marco; Rich, Peter R.; Sharma, Vivek (2019)
    Cytochrome c oxidases (CcOs) in the respiratory chains of mitochondria and bacteria are primary consumers of molecular oxygen, converting it to water with the concomitant pumping of protons across the membrane to establish a proton electrochemical gradient. Despite a relatively well understood proton pumping mechanism of bacterial CcOs, the role of the H channel in mitochondrial forms of CcO remains debated. Here, we used site-directed mutagenesis to modify a central residue of the lower span of the H channel, Q413, in the genetically tractable yeast Saccharomyces cerevisiae. Exchange of Q413 to several different amino acids showed no effect on rates and efficiencies of respiratory cell growth, and redox potential measurements indicated minimal electrostatic interaction between the 413 locus and the nearest redox active component heme a. These findings clearly exclude a primary role of this section of the H channel in proton pumping in yeast CcO. In agreement with the experimental data, atomistic molecular dynamics simulations and continuum electrostatic calculations on wildtype and mutant yeast CcOs highlight potential bottlenecks in proton transfer through this route. Our data highlight the preference for neutral residues in the 413 locus, precluding sufficient hydration for formation of a proton conducting wire.