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Type: Text × Subject: molecular dynamics simulations ×

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Now showing 1 - 4 of 4
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    Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7 + O3 Complex in Solution
    (Weinheim : Wiley-VCH Verl., 2021) Kozari, Eve; Sigalov, Mark; Pines, Dina; Fingerhut, Benjamin P.; Pines, Ehud
    Infrared (IR) absorption in the 1000-3700 cm-1 range and 1 H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7 + O3, in acetonitrile. The core H7 + O3 motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H7 + O3 structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H7 + O3 in the OH stretch region, which reaffirms the assignment of the H7 + O3 spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H7 + O3 structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H7 + O3 structures may support proton transport within larger water solvates.
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    Gold-Induced Fibril Growth: The Mechanism of Surface-Facilitated Amyloid Aggregation
    (Weinheim : Wiley-VCH, 2016) Gladytz, Anika; Abel, Bernd; Risselada, Herre Jelger
    The question of how amyloid fibril formation is influenced by surfaces is crucial for a detailed understanding of the process in vivo. We applied a combination of kinetic experiments and molecular dynamics simulations to elucidate how (model) surfaces influence fibril formation of the amyloid-forming sequences of prion protein SUP35 and human islet amyloid polypeptide. The kinetic data suggest that structural reorganization of the initial peptide corona around colloidal gold nanoparticles is the rate-limiting step. The molecular dynamics simulations reveal that partial physisorption to the surface results in the formation of aligned monolayers, which stimulate the formation of parallel, critical oligomers. The general mechanism implies that the competition between the underlying peptide–peptide and peptide–surface interactions must strike a balance to accelerate fibril formation.
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    Ultrathin 2D Titanium Carbide MXene (Ti3C2Tx) Nanoflakes Activate WNT/HIF-1α-Mediated Metabolism Reprogramming for Periodontal Regeneration
    (Weinheim : Wiley-VCH, 2021) Cui, Di; Kong, Na; Ding, Liang; Guo, Yachong; Yang, Wenrong; Yan, Fuhua
    Periodontal defect regeneration in severe periodontitis relies on the differentiation and proliferation of periodontal ligament cells (PDLCs). Recently, an emerging 2D nanomaterial, MXene (Ti3C2Tx), has gained more and more attention due to the extensive antibacterial and anticancer activity, while its potential biomedical application on tissue regeneration remains unclear. Through a combination of experimental and multiscale simulation schemes, Ti3C2Tx has exhibited satisfactory biocompatibility and induced distinguish osteogenic differentiation of human PDLCs (hPDLCs), with upregulated osteogenesis-related genes. Ti3C2Tx manages to activate the Wnt/β-catenin signaling pathway by enhancing the Wnt-Frizzled complex binding, thus stabilizing HIF-1α and altering metabolic reprogramming into glycolysis. In vivo, hPDLCs pretreated by Ti3C2Tx display excellent performance in new bone formation and osteoclast inhibition with enhanced RUNX2, HIF-1α, and β-catenin in an experimental rat model of periodontal fenestration defects, indicating that this material has high efficiency of periodontal regeneration promotion. It is demonstrated in this work that Ti3C2Tx has highly efficient therapeutic effects in osteogenic differentiation and periodontal defect repairment. © 2021 The Authors. Advanced Healthcare Materials published by Wiley-VCH GmbH
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    Molecular structure of bottlebrush polymers in melts
    (Washington, DC [u.a.] : Assoc., 2016) Paturej, Jarosław; Sheiko, Sergei S.; Panyukov, Sergey; Rubinstein, Michael
    Bottlebrushes are fascinating macromolecules that display an intriguing combination of molecular and particulate features having vital implications in both living and synthetic systems, such as cartilage and ultrasoft elastomers. However, the progress in practical applications is impeded by the lack of knowledge about the hierarchic organization of both individual bottlebrushes and their assemblies. We delineate fundamental correlations between molecular architecture, mesoscopic conformation, and macroscopic properties of polymer melts. Numerical simulations corroborate theoretical predictions for the effect of grafting density and side-chain length on the dimensions and rigidity of bottlebrushes, which effectively behave as a melt of flexible filaments. These findings provide quantitative guidelines for the design of novel materials that allow architectural tuning of their properties in a broad range without changing chemical composition.