Yazar "de With, Gijsbertus" seçeneğine göre listele

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    Computing dissipative particle dynamics interactions to render molecular structure and temperature-dependent properties of simple liquids
    (Elsevier, 2022) Camoglu, Hakan; Urbic, Tomaz; de With, Gijsbertus; Kacar, Gokhan
    Simulating structural and thermodynamical properties of liquids has always been a challenge. Typical examples of liquids that demonstrate particular structure and properties are water and the low molecular weight alcohols, for which hydrogen bond interactions lead to their distinctive properties, such as cage -like structures and temperature-dependent properties. Modeling these materials at the coarse-grained level is even a bigger challenge due to the loss of atomistic-level interactions. Nevertheless, one is inter-ested in mimicking these typical properties at the coarse-grained level due to the relevance of these sys-tems in complex environments, for which fully atomistic simulations still remain a challenge. In this paper, we introduce a mesoscopic level parameterization of DPD interactions to study the particular structural and thermodynamic properties of liquid water, methanol, ethanol and 1-propanol. The conser-vative repulsive DPD interactions are explicitly computed by a bottom-up parameterization, in which experimental thermodynamics data are used. A previously developed statistical mechanics approach is used to compute the hydrogen bond strength. The transport properties, such as viscosity, and thermody-namical properties, such as isothermal compressibility, are found to agree reasonably well with experi-mental data. Moreover, the structure as characterized by the radial distribution function and angular distributions of three neighboring molecules are in line with the atomistic simulations performed in this work. Furthermore, the temperature-dependency of the repulsive DPD interactions is modeled by incor-porating the experimental isothermal compressibilities at different temperatures. The effect of the tem-perature on the hydrogen bond strengths is considered as well and the structural properties are predicted via the DPD simulations. In general, our work can be viewed as an attempt to model systems by the DPD simulations, where hydrogen bonds play a crucial role. The computed parameterization of DPD interac-tions is believed to pave the way towards extending the current applicability of DPD method to more complex systems. (c) 2022 Elsevier B.V. All rights reserved.
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    Hydrogen bonding in DPD: application to low molecular weight alcohol-water mixtures
    (Royal Soc Chemistry, 2016) Kacar, Gokhan; de With, Gijsbertus
    In this work we propose a computational approach to mimic hydrogen bonding in a widely used coarse-grained simulation method known as dissipative particle dynamics (DPD). The conventional DPD potential is modified by adding a Morse potential term to represent hydrogen bonding attraction. Morse potential parameters are calculated by a mapping of energetic and structural properties to those of atomistic scale simulations. By the addition of hydrogen bonding to DPD and with the proposed parameterization, the volumetric mixing behavior of low molecular weight alcohols and water is studied and experimentally observed negative volume excess is successfully predicted, contrary to the conventional DPD implementation. Moreover, the density-dependent DPD parameterization employed provides the asymmetrical shapes of the excess volume curves. In addition, alcohol surface enrichment at the air interface and self-assembly in the bulk is studied. The surface concentrations of alcohols at the air interface compare favorably with the experimental observations at all bulk-phase alcohol fractions and, in consonance with experiment, some clustering is observed.
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    Mesoscopic structure and swelling properties of crosslinked polyethylene glycol in water
    (Springer, 2018) Kacar, Gokhan; Albers, Peter T. M.; Esteves, A. Catarina C.; de With, Gijsbertus
    In this paper, we present our efforts in modeling and simulation of polyethylene glycol crosslinked with an isocyanate tHDI. The polymer, by its nature, is hydrophilic and has strong hydrogen bond interactions with water. The simulations are performed at coarse-grained scale by using a dissipative particle dynamics (DPD) simulation method. The effect of hydrogen bond between water and polymer beads on the structure of the crosslinked hydrophilic polymer structure is studied. The polymer is observed to phase separate with water in the absence of hydrogen bonds in DPD simulations. In the reverse case, where hydrogen bonds are explicitly included in DPD simulations, polymer mixes with water. This behavior is investigated by plotting the density profiles. Moreover, the volumetric swelling behavior in mixtures with different water contents is estimated from simulations and extrapolated by a polynomial fit to compare with experiments. It is observed that the predicted swelling ratio is in good agreement with the experimental measurements.
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    Multi-scale molecular simulations for polymer behavior and properties at different interfaces
    (Amer Chemical Soc, 2016) Kacar, Gokhan; de With, Gijsbertus
    [Abstract Not Available]
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    Parametrizing hydrogen bond interactions in dissipative particle dynamics simulations: The case of water, methanol and their binary mixtures
    (Elsevier, 2020) Kacar, Gokhan; de With, Gijsbertus
    Simulating water has always been a challenge. Due to the intrinsic hydrogen bond interactions, water exhibits structural properties, such as a tetrahedral coordination resulting in a specific Radial Distribution Function (RDF), which are not trivial to predict computationally. In this paper, we attempt to use coarse-grained Dissipative Particle Dynamics (DPD) simulations to parameterize the hydrogen bond interactions without violating the classical DPD framework. We model the hydrogen bond interactions by incorporating a Morse potential, where the parameters are computed by taking the experimental enthalpy of evaporation and hydrogen bond distances as reference. We show that with the proposed procedure the RDF, the coordination number, the isothermal compressibility, and the three-body angular distributions (to demonstrate the tetrahedral structure) of pure water are predicted in great extent compatible with the experiments. To test the applicability of the procedure to mixtures, we simulated pure methanol and methanol/water mixtures at different molar fractions. The predicted RDF profiles for methanol-methanol, methanol-water and water-water represent the characteristic experimental RDF behavior. Moreover, the calculated negative excess volumes as a function of mole fraction compare quite well with the experimentally observed excess volumes. Our findings motivate the further development and use of DPD simulations in modeling hydrogen bond interactions, which are crucial not only in water (or alcohols), but in more complex systems such as biomolecules, proteins or biopolymers. (C) 2020 Elsevier B.V. All rights reserved.