Modeling of polystyrene under confinement: Exploring the limits of iterative boltzmann inversion

We explore the limits of a purely structure based coarse-graining technique, the iterative Boltzmann inversion (IBI), in the coarse-graining of a confined concentrated polystyrene solution. In the first place, some technical considerations and challenges encountered in the course of the optimization process are represented. The concepts of the choice of the initial potentials and the cross-dependency of the interactions as well as the order of optimization are discussed in detail. Furthermore, the transferability of a previously developed CG confined polystyrene solution model, the "parent CG confined model", to different degrees of confinement at constant concentration and temperature is examined. We investigate if a CG force field developed for a confined polymer solution by IBI is sensitive to changes in the degree of localization or arrangement of polymers near the surfaces although the concentration is kept constant. For this purpose, reference atomistic simulations on systems of different confinement levels have been performed. The differences in the structure and dynamics of the chains are addressed. Results are compared with those of an unconfined (bulk) system at the same concentration. The chain dimensions and orientations as a function of the distance from the surfaces are also reported. To the best of our knowledge, this is the first computational study that investigates the structural behavior of polymers in close proximity of the surfaces in a concentrated polymer solution rather than in a melt. Transferability of the parent CG confined model is tested by employing the parent force field in CG simulations of the reference systems. Results indicate that the degree of arrangement of monomers and solvent molecules near the surfaces is an important factor that needs to be paid attention to when considering the application of a CG force field developed by IBI to different degrees of confinement.U.S. Department of Energy, Office of Science, Basic Energy Sciences (DE-FG02-06ER46340); Scientific and Technological Research Council of Turke

Çözücüsüz mikrodalga ekstraksiyonu ve mikrodalga yardımlı hidrodistilasyon yöntemleri ile bitkilerden esansiyel yağların elde edilmesi.

The undesirable effects of conventional methods generated the need for economical and safe techniques in the extraction of essential oils. Microwave-assisted hydrodistillation (MAHD) and solvent-free microwave extraction (SFME) are recently developed techniques, which are thought to overcome this problem. Oregano (Origanum vulgare L.), laurel (Laurus nobilis L.) and rosemary (Rosmarinus officinalis L.) were chosen in this study since they have high antimicrobial and antioxidant effects and are widely grown and consumed in Turkey. The objectives of this study were to examine the applicability of SFME in the extraction of essential oils from oregano and laurel, and MAHD in the extraction of rosemary essential oil. The effects of microwave power and extraction time on the yield, composition, and other quality parameters of the extracts were also investigated. Hydrodistillation was performed as control. SFME offered significantly higher essential oil yields (0.054 mL oil/g oregano) from oregano as compared to hydrodistillation (0.048 mL oil/g oregano). Conventional process time was reduced by 80%. Main aroma compound was thymol (650-750 mg thymol/mL oil). For laurel, no significant differences were obtained in yields (about 0.022 mL oil/g laurel) obtained by SFME and hydrodistillation. Process time was reduced by 55-60%. Main aroma compound was 1,8-cineole (630-730 mg 1,8-cineole/mL oil). In the case of rosemary, no significant differences were obtained in yields (about 0.026 mL oil/g rosemary) obtained by MAHD at 622 W and hydrodistillation. The process time was reduced by about 65%. Main aroma compounds were 1,8-cineole (430-500 mg 1,8-cineole/mL oil) and camphor (150-210 mg camphor/mL oil). Keywords: Solvent-free microwave extraction (SFME), Microwave-assisted hydrodistillation (MAHD), Origanum vulgare L., Laurus nobilis L., Rosmarinus officinalis L.M.S. - Master of Scienc

Basit şekerlerin doymuş çözeltilerdeki davranışlarının moleküler dinamik (MD) simülasyon ile incelenmesi

Şekerler biyokullanılabilirliği, son ürün kalitesini ve üretim verimini etkileyen birçok yapısal özelliğe sahiptir bu sebeple değişen koşullar altındaki yapısal davranışlarının incelenmesi esastır. Bu araştırmanın amacı fruktoz ve glikoz şekerlerinin, su ile etkileşimlerini, kristalizasyon eğilimlerini, moleküller arası itme-çekme kuvvetlerini ve sulu çözeltilerdeki belirli davranışlarını Moleküler Dinamik (MD) simülasyon tekniğini kullanarak karşılaştırmak ve tekniğin gıda sistemlerine uygulanabilirliğini göstermektir. Çalışmada MD simülasyonlar GROMACS 5.1 simulasyon paketi araçları kullanılarak, şekerlerin 25 °C‘deki doyma konsantrasyonunu referans alınıp bu değerin 0,50 0,75, 1,25 ve 1,50 ile çarpılmasıyla elde edilen doymamış, aşırı doymuş sistemlerin modellenmesiyle tamamlanmıştır. Molekül yapı dosyaları Protein Veri Bankasından elde edilmiş ve CHARMM-GUI Girdi Üreticisi kullanılarak da CHARMM kuvvet alanında kullanılmak üzere topoloji dosyaları üretilmiştir. Simülasyonlar neticesindeki zaman içerisinde değişen sistem davranışları, Ortalama Karekök Sapma (RMSD), Çözgen Erişebilir Yüzey Alanı (SASA) ve eylemsizlik yarıçapı (Rg)‘ı ile izlenmiş ve sistemlerin yapısal denge özellikleri, Radyal Dağılım Fonksiyonu (RDF), Hidrojen Bağ Sayısı, RMSD, SASA, Rg ve bağlı olmayan potansiyellerin hesaplanmasıyla değerlendirilmiştir. Sonuçta kristalizasyon eğilimi beklenen sistemlerde RMSD ve SASA değerlerinin küçülerek dengeye ulaştığı, şeker molekülleri arasındaki H-bağı sayısında konsantrasyon ile artış olduğu ve kristal yapıya katılması beklenen moleküllerin arasında çekme kuvvetlerinin baskın olduğu gözlenmiştir