Browsing by Subject "Molecular dynamics (MD)"

Sort by: Order: Results:

Now showing items 1-3 of 3
  • Postila, Pekka A.; Róg, Tomasz (2020)
    Synaptic neurotransmission is generally considered as a function of membrane-embedded receptors and ion channels in response to the neurotransmitter (NT) release and binding. This perspective aims to widen the protein-centric view by including another vital component—the synaptic membrane—in the discussion. A vast set of atomistic molecular dynamics simulations and biophysical experiments indicate that NTs are divided into membrane-binding and membrane-nonbinding categories. The binary choice takes place at the water-membrane interface and follows closely the positioning of the receptors’ binding sites in relation to the membrane. Accordingly, when a lipophilic NT is on route to a membrane-buried binding site, it adheres on the membrane and, then, travels along its plane towards the receptor. In contrast, lipophobic NTs, which are destined to bind into receptors with extracellular binding sites, prefer the water phase. This membrane-based sorting splits the neurotransmission into membrane-independent and membrane-dependent mechanisms and should make the NT binding into the receptors more efficient than random diffusion would allow. The potential implications and notable exceptions to the mechanisms are discussed here. Importantly, maintaining specific membrane lipid compositions (MLCs) at the synapses, especially regarding anionic lipids, affect the level of NT-membrane association. These effects provide a plausible link between the MLC imbalances and neurological diseases such as depression or Parkinson’s disease. Moreover, the membrane plays a vital role in other phases of the NT life cycle, including storage and release from the synaptic vesicles, transport from the synaptic cleft, as well as their synthesis and degradation.
  • Vu, T. H. Y.; Dufour, C.; Khomenkov, V.; Leino, A. A.; Djurabekova, F.; Nordlund, K.; Coulon, P. -E.; Rizza, G.; Hayoun, M. (2019)
    The elongation process under swift heavy ion irradiation (74 MeV Kr ions) of gold NPs, with a diameter in the range 10-30 nm, and embedded in a silica matrix has been investigated by combining experiment and simulation techniques: three-dimensional thermal spike (3DTS), molecular dynamics (MD) and a phenomenological simulation code specially developed for this study. 3DTS simulations evidence the formation of a track in the host matrix and the melting of the NP after the passage of the impinging ion. MD simulations demonstrate that melted NPs have enough time to expand after each ion impact. Our phenomenological simulation relies on the expansion of the melted NP, which flows in the track in silica with modified (lower) density, followed by its recrystallization upon cooling. Finally, the elongation of the spherical NP into a cylindrical one, with a length proportional to its initial size and a width close to the diameter of the track, is the result of the superposition of the independent effects of each expansion/recrystallization process occurring for each ion impact. In agreement with experiment, the simulation shows the gradual elongation of spherical NPs in the ion-beam direction until their widths saturate in the steady state and reach a value close to the track diameter. Moreover, the simulations indicate that the expansion of the gold NP is incomplete at each ion impact.
  • Granberg, F.; Wang, X.; Chen, D.; Jin, K.; Wang, Y.; Bei, H.; Weber, W. J.; Zhang, Y.; More, K. L.; Nordlund, K.; Djurabekova, F. (2021)
    Due to virtually no solubility, He atoms implanted or created inside materials tend to form bubbles, which are known to damage material properties through embrittlement. Higher He density in nano-sized bubbles was observed both experimentally and computationally in Ni(100-x)Fex-alloy samples compared to Ni. The bubbles in the Ni(100-x)Fex-alloys were observed to be faceted, whereas in elemental Ni they were more spherical. Molecular dynamics simulations showed that stacking fault structures formed around bubbles at maximum He density. Higher Fe concentrations stabilize stacking fault structures, suppress evolution of dislocation network around bubbles and suppress complete dislocation emission, leading to higher He density. (C) 2020 Acta Materialia Inc. Published by Elsevier Ltd.