Multi-scale study of the dynamics of self-organizing molecular systems

Many research groups are studying self-assembly structures via using computational techniques to understand their behavior from a theoretical point of view. Taking different length scales into consideration becomes more important day by day. In this thesis, calculations are performed at the different length scales of meso-scale, quantum scale, and nano-scale. First of all, meso-scale calculations are performed by using the Dissipative Particle Dynamics simulation methodology to obtain the three dimensional morphologies and the corresponding equilibrium structures. These structures are obtained as a collection of beads each of which consists of several atoms. Hence, morphologies varying from spherical and cylindrical micellar to lamellar are obtained. Then, in order to understand origins of interactions between beads forming meso-scale morphologies, quantum mechanical calculations are carried out at the nanoscale by using chemical reactivities and Atoms-In-Molecules theory. The interactions that occur on the interatomic scale are found to control the meso-scale. In addition to meso-scale calculations to obtain morphology, micelles are investigated in terms of their surface-to-volume ratios to the micro-phase separation behavior. Consequently, phase change from spherical to cylindrical micellar and micellar to lamellar phase is observed in surface-to-volume versus concentration plot. Finally, molecular dynamics simulations on the atomic scale are performed to study the dynamics of self-assembled synthetic structures. A reverse mapping algorithm is developed to back fit atomistic detail to morphologies obtained from meso-scale calculations. The detailed structure is soaked into water to study the dynamics of interfacial water since the target structure is superhydrophobic

Dissipative particle dynamics simulation parameters and interactions of a hydrogel

In this work, we report a parameterization procedure to compute the parameters of a hydrogel consisting of a hydrophilic polymer and a cross-linker. The system is parameterized so that coarse-grained dissipative particle dynamics (DPD) simulations can be performed. Proper computation of the simulation parameters is crucial in order to represent the inherent chemical nature of the hydrogel and to model the correct structure. The polymer is parameterized by considering different volumes for coarse-grained beads. Moreover, the hydrogen bond interactions should be represented and properly defined in the simulations. To that purpose, we use a recently introduced parameterization procedure that incorporates the attraction as a result of the hydrogen bond interactions between relevant beads. This paper serves as an example of how the realistic simulation parameters of a hydrophilic polymer can be straightforwardly computed by leading to a proper determination of the structure and properties. The computational background, the procedures and the results of the computation are reported and discussed in this paper

Açık ocak madenciliğinde kaya kütlesi özelliklerinin patlatma performansına etkilerinin incelenmesi

This study has aimed to investigate the influences of rock mass properties on the blasting performance in open cast mines. To this end, discontinuity spacings and discontinuity orientations have been measured and full scale blasts with various designs have been observed in open cast mines of Aegean Lignite(ELI) and Bursa Lignite(BLI) Establishments belonging to Turkish Coal Enterprises (TKI). Influences of the above mentioned rock mass properties on fragmentation and blasting cost have been investigated. Fragmentation influencing the excavator productivity have been taken as a criterion in order to compare the results of blasts. Particle size distribution representing fragmentation has been determined by means of a software using image processing. 50%(K50) and 80%(K80) passing sizes and topsize values have been used in determination of blasting performance according to rock mass properties. The results show that increasing trend exists for the relationships between rock mass properties and K50, K80 and topsize values. Fragmentation parameters (K50, K80, topsize) increase as the orientation angle, which is the acute angle between the strikes of slope face and major discontinuity, increases. Additionally, these parameters increase as the discontinuity modal spacing or in-situ block size index increases. Moreover, increasing trend is observed for the relationships between rock mass properties and blasting cost, too. Blasting cost increases as the orientation angle increases. Furthermore, blasting cost increases as the discontinuity modal spacing or in-situ block size index increases.Bu çalışmada kaya kütlesi özelliklerinin açık ocak patlatma performansına etkilerinin incelenmesi amaçlamıştır. Bu doğrultuda TKİ kurumuna bağlı Ege Linyitleri ve Bursa Linyitleri İşletmeleri açık ocaklarında süreksizlikler arası uzaklıklar ve süreksizlik yönelimleri ölçülmüş ve değişik patlatma tasarımlarının uygulandığı tam ölçekli patlatma atımları izlenmiştir. Sözkonusu kaya kütlesi özelliklerinin parçalanmaya ve patlatma maliyetine etkisi incelenmiştir. Patlatma sonuçlarının karşılaştırılmasında kazıcı üretkenliliğini etkileyen parçalanma kıstas alınmıştır. Atımlardan elde edilen parçalanmayı temsil eden parça boyut dağılımı sayısal görüntü işleme sistemini kullanan bir yazılımla belirlenmiştir. Parçaların %50 (K50) ve %80'inin(K80) geçtiği elek boyut ve en büyük boyut değerleri kaya kütlesi özelliklerine göre patlatma verimliliğinin tespitinde kullanılmıştır. Sonuçlar kaya kütlesi özellikleri ile K50, K80 ve en büyük boyut değerleri arasında artan eğilim gösteren ilişkiler bulunduğunu göstermektedir. Ayna ve hakimsüreksizlik doğrultulan arasındaki açı olan yönelim açısının artmasıyla parçalanma parametreleri (K50, K80 ve en büyük boyut) artmaktadır. Ek olarak süreksizlikler arası uzaklığın veya yerinde blok boyut endeksinin artmasıyla bu parametreler artmaktadır. Ayrıca, artma eğilimli ilşkiler kaya kütlesi özellikleri ve patlatma maliyeti arasında da gözlemlenmektedir. Yönelim açısının artmasıyla patlatma maliyeti artmaktadır. Bundan başka süreksizlikler arası uzaklığın veya yerinde blok boyut endeksinin artmasıyla patlatma maliyeti artmaktadır

Patients' perceptions and preferences of oral and maxillofacial surgeons in a university dental hospital

Purpose: There is a lack of information regarding the dental patient's point of view of oral and maxillofacial surgeons (OMFSs). The aim of this study was to evaluate the perceptions and preferences of a group of university dental hospital patients for OMFSs.Materials and methods: This study was based on patients' self-assessment using a questionnaire. A total of 530 patients were enrolled for the study. The patients' preferences regarding the surgeons' age, gender, religion, race and experience were determined and compared statistically.Results: A total of 506 questionnaires were considered as complete and used in the analysis. Female patients preferred female practitioner more than male patients did (p=0.002), but no significant difference was found between male and female patients regarding preference for the age (p=0.464), ethnicity (p=0.926) and religion (p=0.261) of the OMFS. The educational status of the patients did not have an effect on the gender preference for the OMFS (p=0.114); however, educational status significantly affected the preferences for the ethnicity and religion of the practitioners (p=0.001).Conclusion: Today patient expectations and perceptions take place in post graduate education programs. In this study we determined a wide range of different factors for choosing an OMFS. The diversity of these factors may affect the quality of the health service and thus must be considered in determining the content of oral and maxillofacial curriculum

İnvestigation of the drug encapsulatıon efficiency of block copolymers contaınıng peg-pia via molekular Simülations

Bilgisayar simülasyonları, farklı zaman ve uzunluk ölçeklerinde moleküllerin termodinamik ve fiziksel özelliklerinden yola çıkarak moleküler sistemlerin davranışlarını ve yapılarını incelemede kullanılmaktadır. Bu tezdeki simülasyon çalışmasında kaba tanecikli bir simülasyon tekniği olan Dağılıcı Parçacık Dinamiği (DPD) yöntemi ile polietilen glikol-polilaktik asit-polietilen glikol (PEG-PLA-PEG) sisteminin moleküler seviyede simülasyonları gerçekleştirilmiştir. Bu tezin amacı incelenen polimerik ilaç taşıyıcı sistemin moleküler seviyedeki etkileşimlerinin, moleküler yapısının ve ilaç hapsetme verimliliğinin moleküler simülasyonlarla belirlenmesidir. Triblok kopolimer yapısındaki hidrofilik ve hidrofobik grupları içeren, PEG-PLA-PEG polimerik zincirinde hidrofilik grupları polietilen glikol, hidrofobik grupları ise polilaktik asit oluşturmaktadır. Öncelikle, uygun ilaç taşıyıcı sistem konsantrasyonunun tespiti için polimerik zincirin ilaç bulunmayan ortamda sadece su ile etkileşimi sonucu faz diyagramı oluşturulmuş, ardından bu faz diyagramından yola çıkılarak belirlenen küresel misel yapılara ibuprofen ve aspirin ilaçları yüklenmiştir. İbuprofen ve aspirin ilaçlarının seçilmesindeki sebep bu ilaçların görece basit bir kimyasal yapıya sahipolması ve hidrofobik yapıda olmasıdır. İbuprofen ve aspirinin PEG-PLA-PEG sistemi içindeki ilaç yükleme verimi yazılan bir bilgisayar kodu ile hesaplanmış ve hidrofilik ve hidrofobik grupların ilaç ile etkileşimleri Radyal Dağılım Fonksiyonu (RDF) hesaplanarak belirlenmiştir. İlaç yükleme verimliliğinin ibuprofen için aspirine göre yaklaşık üç kat daha yüksek bir değerde olduğu hesaplanmıştır. Bunun yanında, hidrofobik ilaçların polimerin hidrofobik kısımlarıyla daha baskın bir etkileşime girdiği gözlenmiştir. Tez kapsamında gerçekleştirilen moleküler simülasyonlar sonucu PEG-PLA-PEG sisteminin ilaç hapsetme verimliliği en fazla %56 olarak hesaplanmış ve ibuprofen ilacı için geliştirilmeye aday bir ilaç taşıyıcı sistem olarak kullanabileceği değerlendirilmiştir.Computer simulations are being used to investigate the behavior and structures of molecules at different time and length scales by considering their thermodynamic and physical properties. In this thesis, the simulation study of coarse-grained Dissipative Particle Dynamics (DPD) methods employed to study the drug encapsulation property of a polyethylene glycol-polylactic acid-polyethylene glycol (PEG-PLA-PEG) system. The aim of the simulation study in this thesis that is performed as an alternative to the experimental studies is to compute the molecular-level interactions, molecular structure and drug encapsulation efficiency of the system of interest. The PEG-PLA-PEG triblock copolymer structure contains hydrophilic and hydrophobic groups, and hydrophilic and hydrophobic groups are composed of polyethylene glycol polylactic acid, respectively. Initially, the concentration of the drug encapsulating system is obtained by running simulations to construct the phase diagram in order to decide the concentrations of the spherical micelles without drug but water present in the simulation environment. The spherical micelles are later used to encapsulate the ibuprofen and aspirin. The motivation to select such drugs in this thesis is that both structures have relatively simple chemical structures and both are hydrophobic. The drug encapsulation efficiencies are computed by a computer code written in-house and the interactions of the hydrophilic and hydrophobic groups with the drug are characterized by computing Radial Distribution Functions (RDF). The drug encapsulation efficiency of ibuprofen is observed to be higher with a times 3 difference compared to aspirin. In addition, hydrophobic drug is having a stronger interaction with the hydrophobic groups of the block copolymer. The results of the molecular simulations performed in this thesisshow that the PEG-PLA-PEG system encapsulates the ibuprofen drug at a maximum value of %56 meaning that this system can be considered as a candidate drug delivery systemfor ibuprofen

Surfactant formation efficiency of fluorocarbon-hydrocarbon oligomers in supercritical CO2

We use dissipative particle dynamics simulations to explore the phase behavior and solution properties of ABCBA type model surfactants in near-supercritical CO2 environment. We present design guidelines for functional surfactants with tunable properties. The block co-oligomers used in this study are made up of a CO2-phobic block having ethyl propionate and nine different types of ethylene monomers, flanked on either side by eight repeat units of fluorinated CO2-philic blocks. The most promising design block co-oligomer in the series is that with the longest CO2-phobic group in the ethylene monomers. For this particular oligomer, we systematically analyze the effect of concentration on the self-assembly behavior. Spherical micelles form in the 5%–65% volume fraction range for this oligomer, with the highest number of spherical micelles occurring at 45% surfactant in CO2. When the volume fraction of the surfactant is increased from 70% to 85%, cylindrical micelles occur. We further investigate the effect of the length of the solvophilic fluorinated segments on self-assembly and find that stable micelles occur in a window of 8–14 repeat units. We find that the most critical contribution to stability is due to the mixing free energy between the chain tails residing in the outer layers and the interpenetrating molecules

Skeletal changes following surgically assisted rapid maxillary expansion (SARME)

Purpose Surgically assisted rapid maxillary expansion (SARME) is a common treatment technique in the correction of maxillary transverse deficiency. The purpose of this study was to evaluate nasal and palatal skeletal changes following SARME using Cone Beam Computed Tomography (CBCT) and posterior anterior (PA) cephalograms. Materials and Methods In this retrospective study, the radiographic images obtained from 14 patients with transverse maxillary deficiency before treatment and 6 months after SARME operations were evaluated. The changes in nasal bone width and palatal bone width were measured on CBCT. The changes in basal maxillary width, nasal cavity width and angular measurements were evaluated on PA cephalograms. Results Nasal floor width was measured at the levels of upper first premolar teeth and molar teeth which significantly increased following SARME (p=0.005 and 0.017 respectively). Palatal bone width between first premolar teeth and molar teeth also significantly increased (p=0.003 and 0.002 respectively). Basal maxillary width (p=0.026), nasal cavity width (p=0.024) and other angular measurements also significantly increased (p<0.05). Conclusion Nasal and palatal skeletal transverse dimensions increased following SARME. Due to the enlargement of the nasal floor and nasal cavity, it is likely to improve air pass through the nose