Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Subject: search.filters.subject.Molecular Dynamics Simulation

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  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Investigating the Behavior of D-Glucose, D-Fructose, and D-Allulose in Aqueous Media by Molecular Dynamics Simulations
    (Elsevier Sci Ltd, 2025) Bugday, Zinnur Yagmur; Bayramoglu, Beste; Oztop, Halil Mecit
    Isomeric monosaccharides may have different hydration behaviors, leading to distinct physicochemical properties in solutions. In this work, the aqueous behavior, structure, and hydration properties of D-allulose, Dglucose, and D-fructose were investigated as a function of concentration by molecular dynamics simulations. This is the first computational study investigating D-allulose compared to its two isomers. The dynamics were analyzed through self-diffusion coefficients; hydration was characterized by hydrogen bond (HB) analyses. Radial distribution functions were used to probe water structuring around sugar oxygens. Results show the hydration number and the fraction of bound water in solution were the highest for glucose, followed by fructose and allulose. The C3 epimerization of fructose into allulose highly promotes the allulose pyranoses to form intramolecular HBs, significantly limiting their water-holding capacity. This may possibly explain the favorability of furanose forms over pyranose forms in aqueous allulose solutions, opposing glucose and fructose in solution.
  • Article
    Investigation of Interactions of Acetylene Molecules With an Iron Nanowire and Its Effects on Mechanical Tensile Properties
    (Sakarya University, 2021) Aral, G.
    Understanding complex atomistic-scales interactions mechanisms of reactive acetylene (C2H2) molecules with reactive pure iron nanowires (Fe NWs) including its effects on the tensile mechanical properties of NWs is a crucial task in nanotechnology, especially having practical significance in the mechanical reliability, durability and stability. Therefore, we performed molecular dynamics (MD) simulations based on ReaxFF reactive force field interatomic potential model to investigate the interactions of C2H2 molecules with surface of cylindrical pure Fe NW and its fundamental effects on the tensile mechanical deformations properties of NWs at three different strain rates. Our results reveal that the chemical energetic reactions on the free surface of cylindrical Fe NW with C2H2 molecules in the gas phase form FexCyHz shell layer at temperature T=300 K. The presence of FexCyHz shell layer on the free surface of NW has a significant effect on the mechanical tensile deformation mechanism of the NWs. © 2021, Sakarya University. All rights reserved.