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Öğe Characterizing the structure and properties of dry and wet polyethylene glycol using multi-scale simulationst(Royal Soc Chemistry, 2018) Kacar, GokhanSimulation results for polyethylene glycol by employing a multi-scale approach combining mesoscopic and atomistic scales to characterize its structural, material and thermal properties in dry and wet environments are reported. After a meso-structure is created, DPD simulations with explicit hydrogen bond attraction are run for a molecular understanding of PEG oligomers. The meso-structure is analysed by the end-to-end distance and radius of gyration values, where we notice that water has an effect that makes the chains more flexible compared to the dry material, i.e., acts as a 'plasticizer' (as observed experimentally). Moreover, the helical formation of PEG chains is monitored by mesa-scale simulations and a larger distribution of helical chain formation is found for wet PEG. Following the DPD simulations, a reverse-mapping algorithm is used to insert atomistic detail into the mesoscopic configuration in order to run atomistic molecular dynamics simulations to calculate material properties. The comparison of the elastic properties in dry and wet environments shows that PEG becomes less compressible and more elastic upon addition of water. Moreover, the estimated coefficient of thermal expansion is in good agreement with the experimental value of a lower molecular weight PEG.Öğe CMC/SWCNT biocomposites: A combined study on experiments, molecular simulations and continuum models(Elsevier, 2024) Mergen, Omer Bahadir; Gul, Ufuk; Kacar, Gokhan; Arda, Ertan; Aydogdu, MetinA comprehensive study is carried out including experimental, molecular dynamics (MD) simulations and continuum modelling of Carboxymethyl cellulose/Single walled carbon nanotube (CMC/SWCNT) biocomposites. The electrical, optical, and mechanical properties of CMC/SWCNT biocomposites were investigated in the experimental part of this work. In the result of measurements, it was determined that electrical conductivity (, d c ), absorbance level ( A ) and tensile modulus ( E ) of the composites increased significantly with the increase of SWCNT content in the CMC matrix. These physical changes in the CMC/SWCNT composites were explained by the percolation theory and the electrical and optical percolation thresholds ( R , and R op ) and the critical exponents ( fl , and fl op ) of these composites were calculated. In addition, MD simulations were performed to estimate the material properties for the polymer composite structures. The results of the tensile test experiments were found to qualitatively overlap with the experiments at low concentration range. Moreover, a homogenous distribution of SWCNTs were observed in the CMC matrix together with a strong level of interactions in between. In the continuum modelling a two parameters augmentation model is used. A coupled Mori -Tanaka -self consistent method is utilized when obtaining effective properties of composites. Experimental, MD and continuum modelling results of composites were compared and reasonable agreement was obtained between results.Öğe 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, GokhanSimulating 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.Öğe Dissipative particle dynamics parameterization and simulations to predict negative volume excess and structure of PEG and water mixtures(Elsevier Science Bv, 2017) Kacar, GokhanWe report the results of dissipative particle dynamics (DPD) parameterization and simulations of a mixture of hydrophilic polymer, PEG 400, and water which are known to exhibit negative volume excess property upon mixing. The addition of a Morse potential to the conventional DPD potential mimics the hydrogen bond attraction, where the parameterization takes the internal chemistry of the beads into account. The results indicate that the mixing of PEG and water are maintained by the influence of hydrogen bonds, and the mesoscopic structure is characterized by the trade-off of enthalpic and entropic effects. (C) 2017 Elsevier B.V. All rights reserved.Öğe Hydrogen bonding in DPD: application to low molecular weight alcohol-water mixtures(Royal Soc Chemistry, 2016) Kacar, Gokhan; de With, GijsbertusIn 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.Öğe Investigation of ibuprofen loading in PEG-PLGA-PEG micelles by coarse-grained DPD simulations(Springer Heidelberg, 2021) Yildiz, Mihriban; Kacar, GokhanInvestigation of drug encapsulation behavior is important to design efficient drug delivery materials. With this aim, we strive to perform coarse-grained simulations to study the drug encapsulation behavior of a particular micelle-forming co-polymer composed of hydrophilic PEG and hydrophobic PLGA units. The study is performed at the mesoscopic scale to overcome the time scale problem associated with the micelle formation at the atomistic scale. The structure and drug loading properties are studied at different polymer concentrations and drug loading. The resulting micellar structures that are obtained via dissipative particle dynamics simulations are observed to encapsulate the drug with high efficiency values. Moreover, the DPD simulations performed in this work reveal physical insight on the interactions and molecular structure as well as the temporal evolution of the encapsulation process. Our work can be considered as an attempt to computationally characterize the drug encapsulation behavior and structure of a prospective drug delivery system.Öğe Investigation of morphology, micelle properties, drug encapsulation and release behavior of self-assembled PEG-PLA-PEG block copolymers: A coarse-grained molecular simulations study(Elsevier, 2021) Kuru, Melike Merve; Dalgakiran, Erdal Anil; Kacar, GokhanTargeted drug delivery has become one of the key fields of personalized medicine. Developing candidate drug delivery agents requires a thorough understanding of the drug carrier materials by means of structure, drug encapsulation and release properties. To this aim, coarse-grained DPD simulations are employed to study the morphology, drug encapsulation and release of a particular amphiphilic block copolymer system. Extent of the drug encapsulation and release are observed to be mainly affected from copolymer concentration in the mixture. Mean aggregation number and average micelle volume are observed to increase as drug is encapsulated in the micelles. In addition, the shape of micelles is characterized as mainly spherical. It is observed that the drug release follows a pseudo-Fickian diffusion model and can be represented by the Korsmeyer-Peppas model. Furthermore, the diffusion rate of the drug molecules is observed to increase mainly in the release-phase. Our simulations can be viewed as a computational attempt to model the drug encapsulation and release by mimicking real experimental conditions, while yielding results on the structure and dynamics of the polymeric carrier. The results can be anticipated to find applications in understanding and controlling the parameters to design candidate drug delivery micelles at the molecular level.Öğe 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, GijsbertusIn 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.Öğe Modeling surface segregation of smart PU coatings at hydrophilic and hydrophobic interfaces via coarse-grained molecular dynamics and mesoscopic simulations(Elsevier Science Sa, 2023) Kizilkaya, Deniz; Ghermezcheshme, Hassan; Sabzevar, Sepide Eslami; Makki, Hesam; Kacar, GokhanDeveloping adaptive coatings having desired functionalities at targeted interfaces is one of the major efforts in the coatings science area. The adaptation of the surface functionality to the changing surface conditions can be maintained by introducing dangling chains with different properties to the cross-linked polymer coatings. In this work, we strive to investigate the change in interfacial morphology of PU coatings as exposed to hydrophilic (HPI) and hydrophobic (HPB) interfaces by employing molecular simulations at the coarse-grained and meso-scopic levels. The molecular structure and surface segregation dynamics are studied for PU coatings having pure HPI, mixture of HPI and HPB, and amphiphilic dangling chains. The dual-scale simulations, Dissipative Particle Dynamics (DPD) and MARTINI model, yield results about the dangling chain structures at the interface in terms of their end-to-end distances, where HPI chains adopt a more extended conformation in water in comparison to oil interfaces. The reverse is observed to be valid for the HPB chains. Regarding the dangling chain dynamics, a swift migration towards the interfaces is noticed at about 10 ns for both of the simulation methods. The struc-tures of the dangling chains and their interaction with the interfaces are also characterized by computing the radial distribution function (RDF) profiles. Preferential interactions between the HPI/water and HPB/oil are clearly noted. The switchability of the surfaces is also studied by simulating the system in cycles, such that the interface is changed from water to oil and back to water. The migration of HPI groups in the dangling chains towards water and vice versa in each cycle is clearly shown by the simulations. In all, the inherent structure and dynamics of the dangling chains is obtained at the molecular level by the dual-scale molecular simulations. Our findings reveal a significant level of understanding about interfacial morphology of thermoset coatings modified by dangling chains, where the results can be extended to find applications in guiding the experimental studies.Öğe Molecular understanding of interactions, structure, and drug encapsulation efficiency of Pluronic micelles from dissipative particle dynamics simulations(Springer, 2019) Kacar, GokhanIn this work, we employ coarse-grained dissipative particle dynamics simulations with the hydrogen bonds added explicitly to study the drug encapsulation property, structure, and interactions of Pluronic L64/ibuprofen combinations. The coarse-grained simulations reveal that the computed total drug encapsulation efficiency is around 80% and the simulations show a decrease in the micelle size upon encapsulation of the drug in line with the experimental literature. The computed radial distribution functions point out that the micelle shrinkage can be caused by an increased local packing of the hydrophobic-hydrophilic units around each other, and the absence of water molecules inside the micelles when there are drug molecules present in the system. Overall, the coarse-grained DPD simulations predict the structural and drug encapsulation properties of a polymeric system consistent with the experiments, whereby bringing new insights to its molecular understanding in terms of micelle shrinkage upon inclusion of ibuprofen.Öğe Multi-scale molecular simulations for polymer behavior and properties at different interfaces(Amer Chemical Soc, 2016) Kacar, Gokhan; de With, Gijsbertus[Abstract Not Available]Öğe Parametrizing hydrogen bond interactions in dissipative particle dynamics simulations: The case of water, methanol and their binary mixtures(Elsevier, 2020) Kacar, Gokhan; de With, GijsbertusSimulating 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.Öğe Properties of Pluronic F68 and F127 micelles interacting furosemide from coarse-grained molecular simulations as validated by experiments(Elsevier, 2023) Dalgakiran, Erdal Anil; Ergin, Ahmet Dogan; Kacar, GokhanUnderstanding properties of the drug delivery nanoparticles is of utmost importance to investigate the properties of the currently used systems and/or to design new drug delivery materials. Therefore, in this work we strive to study particular FDA approved drug delivery materials, namely Pluronics, to understand micellization properties and drug encapsulation behaviour at the molecular-level. Our main approach is to employ molecular simulations, which are confirmed by experiments performed within the scope of this work. To that aim, dissipative particle dynamics (DPD) simulations are employed. We quantify the encapsulation efficiency properties of Pluronics, namely F68 and F127, where furosemide as the drug. The DPD simulations predict the encapsulation efficiency of the F68 system higher than F127 system due to a shorter hydrophobic section. Moreover, the micelle properties of Pluronics are quantified by means of the number of micelles, aggregation number, surface area to volume ratio, micelle sizes; and polymer chain properties such as, chain end-to-end distance, radius of gyration prop-erties. We observe similar number of micelles for both systems and the aggregation numbers are rather higher for the F127 system. Moreover, both systems adopt alike end-to-end distance and radius-of-gyration values, and the micelle sizes agree with the experimental data in literature. Furthermore, the interactions of hydrophilic and hydrophobic groups with furosemide and water are analysed by computing the radial distribution functions.Öğe Structural and energetic properties of lecithin liposomes encapsulating coenzyme Q10 from coarse-grained simulations(Springer Int Publ Ag, 2024) Kacar, GokhanUnderstanding properties of materials at the molecular level are crucial to develop novel nano-carriers for the purpose of drug delivery. To that purpose, we perform mesoscopic simulations to study the formation mechanism and properties of lecithin liposomes encapsulating coenzyme Q10. The self-assembly process of the liposomes is monitored as well as the structural properties such as RDFs, Voronoi volumes and vesicle sizes. We found that increasing the concentration of lecithin leads to increasing vesicles size, but similar total Voronoi volumes and a decrease in the interactions between liposome and coenzyme Q10 as the number of lecithin molecules increase in solution. Moreover, steered MD simulations are performed to estimate the strength of interactions between encapsulated material and liposomes by applying a mechanical force to coenzyme Q10 beads. The computed values are observed to not to be influenced by the lecithin concentration. Finally, the computed radial density and pressure profiles indicate that the liposomal bilayer is quite homogenous in density, but exhibit interfacial pressure excess, which drives the bilayer to form spherical liposomal vesicles. The release properties of coenzyme Q10 are characterized and found that the Weibull's model is able to represent the release character as a result of the mechanical force. Our findings in this work would hopefully stimulate a better understanding of liposomal systems while introducing new computational tools to study properties of these materials.Öğe Thermodynamic stability of ibuprofen loaded poloxamer micelles(Elsevier, 2020) Kacar, GokhanThermodynamic stability of poloxamer micelles excluding and encapsulating ibuprofen drug at different concentrations is studied by means of free energies. Free energies are computed by a partitioning of the total free energy in order to consider the different parts of the co-polymers together with free co-polymer chains in solvent. Moreover, extra terms to the free energy are added to account for the drug-micelle and drug-solvent interactions. The thermodynamic stability of the system is found to be positively correlated with the drug loading for the same system. The RDFs computed between water and the drug molecules signify the decreasing neighboring between these pairs as the co-polymer and drug concentrations are increased in the mixtures as the system leans towards a higher thermodynamic stability. In this work, not only the thermodynamic stability but also its relation to the structure are discussed for a drug-laden system demonstrating the utility of the proposed procedure.
