M.S. Theses

Permanent URI for this collection

https://digitalarchive.library.bogazici.edu.tr/handle/123456789/11658

Browse

Now showing 1 - 20 of 306

A computational approach for analysis of communication in proteins
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.) Özel, Sinem.; Turgut, Pemra Doruker.
Allostery and communication in proteins are crucial for the regulation of protein functions. The binding of a ligand changes the affinity of the protein at a distal ligand binding site and leads to conformational changes which are important for its function. In other words, the functional motions of the proteins reveal the communication patterns that are inherent to native architecture. The discrete-time, discrete-state Markov process applied on the network of interacting residues determines the potential pathways of signal transduction. This novel method involves the evaluation of two basic quantities: hitting and commute times, which express the information flow between the residue pairs. Furthermore maximum likelihood communication pathways are computed based on the Markov transition probabilities. This methodology is applied to adenylate kinase, triosephosphate isomerase, PDZ signaling protein and Cdc25B. As a result, the key interactions and the communication ability of the residues in the selected networks are ascertained. It is shown that the catalytic residues are located at the minima of the mean commute time curves, which indicates their efficient signal transduction abilities. Mobile residues are found to be slow communicators and the residues in the protein core are illustrated to be efficient communicators of the network. Besides, the residues on the maximum likelihood pathways are, at large, evolutionarily conserved; this issue confirms the functional importance of the residues on the pathways. In summary, the new methodology provides insights into understanding of communication patterns in proteins.
A computational study on bacterial trigger factor and ribosome dynamics
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.) Ezeroğlu, Gökçe.; Turgut, Pemra Doruker.
Trigger factor (TF), found in bacterial cells and chloroplasts, is the first chaperone that welcomes the newly synthesized nascent polypeptide chains to acquire their native fold. In this thesis, four independent 200 ns long molecular dynamics (MD) simulations were performed in explicit solvent at different ionic strengths (29 mM, 50 mM and two simulations for 150 mM). Root mean square deviations from initial structure and residue mean square fluctuations from the average structure indicated high conformational flexibility of TF. Large oscillations in gyration radius were also observed, but a fully collapsed state reported recently was not detected. A unique coil to helix formation in the binding loop took place during 29 mM run. Principal component analysis of MD trajectories and anisotropic network modelling (ANM) calculations were carried out to reveal the collective dynamics of apo TF. Domain decompositions within TF obtained from both of these methods were consistent. In the first collective mode, there is generally an anti-correlated motion between the three major domains, namely binding (BD), core (CD) and head (HD) domains. HD motion with respect to CD is more dominant at 150 mM ionic strength, however opening/closing between BD-CD and CD-HD appear at the same time at 29 mM and 50 mM runs. All snapshots from four simulations were clustered after performing overall alignment and domain-wise alignment. Resulting clusters further elucidated the inter-domain and intra-domain conformational changes. Dynamics of TF-ribosome complex were investigated after docking centroids from major clusters of apo TF runs on to a fragment of BD that was co-crystallized with ribosome 50S subunit. ANM was applied on eight different ribosome 50S-docked TF complexes. The collective dynamics were modified upon complex formation depending on the conformation and position of TF docked on 50S. For most docked conformers, HD was larger compared to apo TF, moving again in an anti-correlated manner with respect to BD and CD. In two of the docked conformers, TF moved as a fully correlated entity on 50S. Distribution of total solvent accessiable surface values calculated for all structure was similar to the distribution of gyration radii.
A DFT study on interaction between Au, Re and Au-Re surfaces with species involved in WGS reaction
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Uzun, Ali.; Aksoylu, Ahmet Erhan.
In this study, the steps of WGS reaction was investigated through studying the adsorption/co-adsorption of its reactants, products and possible intermediate species on Au(111), Re(001) and Au-Re(001) surfaces at atomic scale via utilizing DFT modules of CASTEP. Firstly, the adsorption energies of CO, OH, CO2, H2O, HOCO molecules and H atoms on Au(111) and Re(001) surfaces, LDOS profiles of these adsorbates for their free and in adsorbed state, and the surface metal atoms on the adsorption sites of Au(111) and Re(001) surfaces for their bare and adsorbed state were analyzed. Additionally, CO-OH co-adsorption on Au(111) and Re(001) surfaces were carried out in order to analyze the reaction steps of WGS reaction on Au(111) and Re(001) surfaces. In the second part of the study, Au-Re surface alloys were generated by the addition of Au atoms on Re(001) surface as point defects. The adsorptions/co-adsorptions of CO and OH molecules on Au- Re(001) surface alloys having different Au concentration on Re(001) were carried out in order to understand the reason of high activity and selectivity of Au-Re/Ceria catalysts. The results revealed that monometallic Au and Au-Re surface alloy are active catalysts, whereas Re is not an active catalyst for WGS reaction. It was found that OH has stronger interaction with Au surface than that of CO in terms of its high binding energy, and it is inferred that the active sites on Au surface, which dominantly participate in WGS reaction steps, can be poisoned by OH molecules due to site competition. The results also showed that the binding energies of OH on Re are higher than that of OH on Au, and it is concluded that OH molecules can move from Au sites to Re sites, and the active sites on Au surface can be poisoned by OH molecules to a lesser degree. The co-adsorption of CO and OH molecules on Au(111), Re(001) and Au-Re surfaces revealed that WGS reaction takes place on Au sites of monometallic and Au-Re surface alloy, and the surface reaction between CO and OH molecules on Au is consistent with the carboxyl mechanism.
A droplet-based platform for high throughput screening of drug administered cells
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) Kasım, Müge.; Ülgen, Kutlu Ö.
Droplet-based microfluidic systems move forward since 2000s having benefits compared to the conventional methods like improved sensitivity, automated and high throughput operation. This thesis involves a combined approach of the engineering and biological principles and analyses within the droplet-based microfluidic system. The performances of di↵erent microfluidic bioreactor designs were tested, and the surfactant concentration against the toxicity to cells and the flow rates were optimized. Diploid BY4743 strain with GFP tagged Rpl5 protein and haploid EY0987 strain with Nop56 protein were treated with hydroxyurea (HU) and temsirolimus drugs to understand the functions of these proteins in ribosome biogenesis. The responses of the cells were measured based on the cell area and the amount of protein expressions. SOM analysis was performed, and several clustering approaches gather the over- and underexpressed genes together. GO analysis was applied to these clusters to understand the cumulative functions of the genes in the clusters. The experimental and computational results on the response of the cells were interpreted within the context of ribosome biogenesis. HU inhibits cell growth, decreases cell dimension and protein expression of Nop56 and Rpl5, which function in ribosome biogenesis. Temsirolimus, inhibits EY0987 yeast cell growth, decreases cell dimension and protein expression of Nop56, whereas the drug e↵ects on diploid BY4743 strain and Rpl5 protein are unclear. SOM analysis reveals that the clusters, in which NOP56, NOP58 and RPL5 are involved, are related to ribosome biogenesis, rRNA processing and nucleolus, and the genes in these clusters are suppressed after 10 to 14 minutes of rapamycin treatment. This study elucidates the role of nucleolar components, snoRNP proteins, in ribosome biogenesis and confidently lead to novel therapeutic strategies for ribosomal protein related diseases.
A finite element thermal hydraulic analysis of a plate type fuel element
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1986., 1986.) Kazan, Ş. Nejat.; Borak, Fahir.; Hortaçsu, Öner.
In this work a mathematical model and a Computer program developed to perform thermcohydraulic analysis of a plate type fueled, water cooled nuclear core is presented. A finite element numerical solution was obtained for the two dimensional heat conduction model developed. For the transient case, the finite difference method was chosen to approximate the time derivative. In the early stages of this work a lot of time and effort were necessary for the preparation and entering of the needed data for calculations. This difficulty was overcome later after using a grid generating subroutine. In the determination of coolant temperature and pressure change mass, energy and momentum balance equations were evaluated for a control volume. The computer program NEKA developed, throughout this work is used for the steady state calculations. If desired, subcooled boiling and transient calculations can also be performed using NEKA. In all cases the program may be used either interactively or using data file. Two sample reactor cores were analyzed for various operating conditions such as the steady state analysis for a given power level, transient analysis with the change of power, coolant inflmi temperature, inflowing mass flowrate as a function of time. In the lMW power generating core, the Reactor I in Çekmece Nükleer Araştırma ve Eğitim Merkezi, showed to have a maximum fuel temperature of 76.7°C under normal operatingoxditkms for 37°C coolant input temperature This temperature reached to ,66.8 °C if coolant enters at 23 °C. In the transient analysis, for a given step change 90 per cent of the total change was observed to complete within 5.2 seconds. In the case of Reactor II which produces 5MW, the maximum fuel tanperature reached to 69.2°C under normal operating conditions for 30°C coolant input temperature. If the coolant flowrate is decreased to 0.065 kg/s from 0.31 kg/s or power level is increased to 17.5 MW subcoo1ed boiling occurance was predicted. For both reactors, the operating conditions were found to be safe.
A fuzzy logic approach for regulation in flux balance analysis
(Thesis (M.S)-Bogazici University.Institute for Graduate Studies in Science and Engineering, 2006., 2006.) Tepeli, Aris.; Hortaçsu, Amable.
Technological advances in experimental observations give the ability to examinecomplex biological systems and the chance to forecast the bacterial behaviour in silico. In this thesis, the experimentally observed behavior by which bacteria are able to establish a timehierarchy of sugar utilization is examined and simulated. The optimal growth of bacteria ondefined carbon sources are now easily predicted from the solutions of constraint basedmetabolic models. However, these methods are unable to predict the sequence of carbon utilization and changes in cellular behavior of growth in mixed substrates. In this work aregulatory structure describing transcriptional regulation of catabolic genes or operonsexpressed in Fuzzy Logic Formalism is combined with dynamic Flux Balance Analysis(FBA). Since the transcription of operons is regulated by specific promoters and inducers that evolve from substrate usage, this regulatory structure is a natural part of any model of carbonsource utilization. The Fuzzy Logic Formalism is a good alternative to differential equationmodels that require kinetic parameter values and superior to Boolean Formalism whichautomatically sets regulation as "on" or "off" rules. The FBA/Fuzzy Logic combination was successfully used to simulate aerobic growth ofEscherichia coli in mixed double (glucose-lactose) or triple (glucose-lactose-galactose, glucose-sorbitol-glycerol) substrates and anaerobic growth of Lactococcus lactis in a triplesubstrate (glucose-lactose-galactose). When well-defined data are available, the computed results are in good agreement with the data. The method also allows for the prediction ofgrowth lag periods upon substrate substitution and changes in growth pattern and substrateutilization upon pulse injection of substrates in existing growth media.
A mathematical model based analysis for designing demo scale fuel processor
(Thesis (M.A.) - Bogazici University. Institute for Graduate Studies in the Social Sciences, 2017., 2017.) Demirci, Barış.; Aksoylu, Ahmet Erhan.; Bedir, Hasan.
The aim of this study is to construct a FLUENT-based mathematical model of a Demo-scale fuel processor, which will be used as the base model to obtain the optimum operating parameters of a Demo-FP that produces sufficient amount of PEM-grade H2, having CO concentration below 100 ppm, from methane in amount enough to feed a 1 kW PEMFC. In the first part, the power law type kinetic expressions obtained from kinetic studies for the FP reactions (OSR-WGS-PROX) were corrected through minimizing the difference between experimentally obtained performance test results and the results obtained from the mathematical model formed in the current study for the same reaction conditions. In the second part, the fuel processor prototype (FPP) was modeled and its performance was simulated through the use of corrected kinetic models. 16 FPP simulations of the OSR reactor were performed by using the feed composition, temperature and W/F used in the first part. First, FP reactors having ¼ inch-OD were modeled in series. Then, the same simulations were performed for 1 inch-OD of the reactors, which is the OD of the reactors has been planned to be used in Demo-FP, while the catalyst bed height of each reactor were kept fixed as in the case of ¼ inch reactors; in those simulations, the catalyst amount and the flow rate of the OSR feed was increased such as to keep W/F of the OSR reactor the same as that of the ¼ inch reactor case. Finally, the reaction conditions yielding the best performance in terms of H2 and CO level at the PROX outlet (the simulations with 400 oC OSR reactor temperature) were selected. For the selected sets, the catalyst amounts in the reactors increased while keeping the W/F fixed such as to satisfy the H2 flow of 0.00272 moles/s and CO concentration of 100 ppm. In the last part, the operation of individual OSR reactor was further simulated for granule-size technical catalyst via introducing several levels of effectiveness factor to the power-law type OSR kinetic expression. The required catalyst amounts and the pressure drop values for the particle diameters and effectiveness factors studied were calculated. The bed density change with the change in particle size was almost insignificant, and consequently almost the same bed lengths were found. On the other hand, as the particle diameter was increased, the pressure drop was reduced sharply.
A mechanistic view of cullin neddylation: allosteric conformational control of E3-ring ligases
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.) Yıldırım, Melis.; Haliloğlu, Türkan.
Cullin-RING E3 ligases (CRLs), which constitute a superfamily of RING type E3 ligases, regulate ~20% of protein degradation by the ubiquitin-proteasome system in the cells. Cullin neddylation activates CRLs by urging a conformational transition in Cullin C-terminal domain and exposes the Rbx1 RING E3 ligase to facilitate ubiquitination. CRLs are over-activated by Cullin neddylation in myriad of human cancers; thereby the inhibition mechanism of Cullin neddylation is of significant interest for generating novel cancer therapies. To explore how the signals of Cullin neddylation are transmitted through the CRLs to control the Rbx1 conformations, we performed molecular dynamics (MD) simulations combined with Gaussian Network Model (GNM) analysis on the closed-unbound and open-bound to Nedd8 states of Cul5-Rbx1 E3 ligases. Our results display multiple Rbx1 RING domain conformations with neddylation of Cul5 where the rigid dynamics of the unbound-to-Nedd8 state CRLs is abrogated. The Rbx1 RING domain conformations of the neddylated CRLs, which are in agreement with the proposed neddylated state Rbx1 conformations for effective ubiquitin transfer, arise as a result of coupled dynamics between Nedd8 and Rbx1. A dynamic hinge plane of Cul5 hinges at R495-M496, N704-E705 and Rbx1 hinges at D51-L52, T69-V70 coordinates allosteric communication between Nedd8 and Rbx1 on the CRL structure along an H-bond between Cul5 R538, R569 and Rbx1 E67 that restricts the Rbx1 conformational space. Nedd8 predisposes Rbx1 together with Cul5 for an effective ubiquitin transfer by a plausible mechanism explaining the allosteric conformational control of Rbx1. We propose that selective interruptions in the neddylation pathway to disrupt the dynamic hinge plane coordination could shed a light on the allosteric drug design studies on Cullin neddylation inhibition.
A mechanistic view on rRNA - antibiotics binding
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Güneş, Mehmet Ünal.; Haliloğlu, Türkan.
The ribosome, which is the macromolecular machine for protein synthesis, is one of the most striking targets for the antimicrobial drugs. Antibiotics that block the protein synthesis in various ways in ribosome have different modes of action and binding sites in different microorganisms. The key interactions are mainly between ribosomal RNA (rRNA) and antibiotics. The interaction sites of these antibiotics with the rRNA, determined by biochemical, in vitro and in vivo cross-linking experiments and footprinting studies, are proved when the structures with antibiotics are discovered. We used the Gaussian Network Model (GNM) to predict antibiotic binding sites and their interactions with the ribosomal proteins. In the GNM, the structures are modeled as an elastic network, where the inter-residue interactions are harmonic. We have analyzed the vibrational modes of motion for 73 ribosome structures (64 bound, 9 unbound) from Deinococcus radiodurans, Escherichia coli, Haloarcula marismortui and Thermus thermophilus. We propose a mechanistic view for the antibiotics binding and to predict antibiotic binding sites and their interactions with the ribosomal proteins based on the dynamics of rRNA. The antibiotics binding sites are mainly located at the Peptidyl Transferase Center (PTC) and decoding center in 23S rRNA and 16S rRNA, respectively. The nucleotides showing high frequency fluctuations cluster in two regions and these two regions correspond to these two functional and known antibiotics binding sites. The nucleotides in the antibiotics binding sites and their adjacent nucleotides form a network of residues that are coupled in their high frequency fluctuations. This network may also lead to the allosteric interaction between the antibiotics binding sites and ribosomal proteins.
A microfluidic study on the regulation of ribosome biogenesis in saccharomyces cerevisiae
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2018., 2018.) Yurdakul, Ekin.; Ülgen, Kutlu Ö.; Mutlu, Şenol.
Microfluidic bioreactors are economical, efficient and usable reactors for conducting biological studies aiming to observe cells under continuous flow. In the present work, microchips from COP (cyclo olefin copolymer) material, which has high fluorescence permeability, were produced for the intended experiments. Entrance hole drilling, hot embossing and thermocompression bonding process steps and the related parameters were optimized throughout the chip production. Two simultaneous experiments, each of which is repeated eight times by means of 16 independent chambers of a single microbioreactor were conducted under steady state. The variation of cells marked with NOP56 red fluorescence during the treatment of hydroxyurea- ribonucleotidreductase inhibitor- was analyzed in the microbioreactor for 16 hours. In order to investigate the effect of various concentrations of hydroxymethylfurfural, the cell growth inhibitor on ribosome biogenesis, the same type of cells were followed in the microbioreactor using YNB medium during simultaneous experiments. The effects of metformin, the inhibitor of the rapamycin protein complex in mammals, on cell growth and ribosome biogenesis were also examined in NOP56:RFP tagged yeast cells. In these experiments, the yeast cells were periodically observed under the Nikon TI-E inverse microscope, and brightfield and fluorescence images were taken, and images taken were processed using the Fiji-ImageJ program. Based on the obtained and calculated data, the time profiles of cell area, circumference, volume and integrated fluorescence intensity were extracted and interpreted as the cells, response to the inhibitors. As a result of single cell processing of fluorescence images, hydroxymethylfurfural, hydroxyurea and metformin inhibitors suppressed the expression of NOP56 gene. In the experiments containing hydroxymethylfurfural and hydroxyurea inhibitors, it was observed that the cells recovered in 10 hours when they were fed with fresh medium.
A parametric study of selective CO oxidation using particulate and monolithic Pt-Co-CeO2 catalysts
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Dikman, Funda.; Önsan, Zeynep İlsen.; Yıldırım, Ramazan,
The objective of this thesis was to conduct a parametric study of selective CO oxidation using particulate and monolithic Pt-Co-CeO2 catalyst supported on alumina. In this comparative study, the monolithic catalysts were prepared by applying a layer of alumina support on to the walls of a cordierite monolithic carrier by colloidal coating method, termed as wash-coating, and then impregnating active components. Colloidal alumina coated and 1.4%Pt-1.25%Co-1.25%Ce impregnated monolithic catalysts were tested for the preferential CO oxidation reaction in a micro-reactor flow system under a total flow of 100 cm3 min–1 using reaction temperatures in the 110-170°C range and typical feed compositions. The effect of calcination temperature, reaction temperature, Co content and residence time on catalyst activity and selectivity was investigated. The most suitable calcination temperature was found to be 700°C for monolithic catalysts which exhibited the highest catalytic activity towards CO oxidation approaching 100 per cent CO conversion at a temperature of 170°C in a feed containing 1.0 mol per cent CO, 1.0 mol per cent O2 and 60.0 mol per cent H2 with balance helium. The Pt and Co loadings on monolithic catalyts were determined by Inductively Coupled Plasma (ICP) analysis. In the light of ICP results indicating lower active component loadings on the cordierite structure, particulate 1.18%Pt-0.06%Co-1.25%Ce/γ-Al2O3 was prepared to match the monolithic catalyst composition and was tested for preferential CO oxidation in a microreactor flow system under a total flow of 100 cm3 min–1 using reaction temperatures in the 90-150°C range. 99.4% conversion was obtained over the particulate catalyst at 130°C in a feed containing 1.0 mol per cent CO, 1.0 mol per cent O2 and 60.0 mol per cent H2 with balance helium.
A parametric study on catalyst development for glycerol DRY reforming
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2018., 2018.) Bilgi, Selin Baç.; Avcı, Ahmet Kerim.
Glycerol reforming to hydrogen and synthesis gas has drawn much attention re cently due to increased glycerol production related with the global biodiesel demand. Among several reforming techniques, dry reforming is more promising since it involves consumption of a major greenhouse gas, CO2. Regarding the lack of information es pecially about catalysis in the literature, this study aims to develop active and stable catalysts to be used in glycerol dry reforming systems. Furthermore, eﬀects of opera tional parameters, namely reaction temperature, carbon dioxide-to-glycerol (CO2/G) molar feed ratio and residence time, on reactant conversions and production distri butions were investigated. Rh and Co based single oxide (ZrO2 and CeO2) catalysts were tested under glycerol dry reforming conditions for 72 hours to comprehend the stability of the catalysts. Catalyst characterization methods (TEM-EDX, in-situ FTIR and ex-situ Raman spectroscopic measurements) together with longevity studies sug gested that Rh and Co based single oxide catalysts were not stable due to severe coke formation and sintering. Based on the knowledge obtained from the experiments and the literature, Rh, Ni and Co based catalysts were prepared with ZrO2-TiO2 (ZT) and Al2O3-ZrO2-TiO2 (AZT). 1 wt.% Rh/AZT and Rh/ZT together with 5 wt.% Ni/AZT and Co/AZT were tested under varying temperatures between 600 and 750 ◦C, CO2/G ratios between 1 and 4 and residence time between 0.5 and 3.75 mgcat min NmL-1. At studied conditions, the highest activity was found over Rh/AZT catalyst followed by Ni/AZT, Rh/ZT and Co/AZT in decreasing order. Increasing temperature and de creasing CO2/G ratio had positive eﬀect on reactant conversion as well as desired product yields, namely H2 and CO. Stability tests and BET, TEM-EDX and in-situ FTIR spectroscopic analyses were revealed the good stability of Rh/AZT and Ni/AZT.
A preliminary work on design and development of sour water gas shift catalysts for synthetic natural gas process
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Özata, Hasretnur.; Aksoylu, Ahmet Erhan.
The main goal of this study is to design and develop a model sour water gas shift catalyst showing high performance in terms of activity, stability & selectivity and conducting performance screening by mimicking the syngas composition of the potential coal gasifier under ideal, sulfur-free conditions. According to the literature, dry powder entrained-bed type gasifier seems potential gasifier for the Synthetic Natural Gas (SNG) production processes, and it contains low steam/CO ratio, below 0.8. On the other hand, classical sour water gas shift (SWGS) catalysts work under high steam/CO ratio, specifically, above 2 or 3. In this context, from literature, one of the potential SWGS catalysts which is suitable for dry-powder syngas composition was chosen as a reference. Activated carbon supported KCoRe as the model SWGS catalysts were developed and these catalysts were tested under ideal, sulfur-free syngas composition. The effect of reaction conditions (i.e., reaction temperature and steam to carbon monoxide ratio) and catalyst preparation & support pre treatment methods (i.e., impregnation method, air & nitric acid pre-treatment on the Activated Carbon support) were investigated on the prepared catalyst. Activity and selectivity were determined in terms of conversions of CO and H₂, respectively. Experimental results showed that reaction conditions are very important parameters on the performance of the catalysts. At low steam/CO ratios, it is necessary to increase the temperature in order to get high activity. The effect of the impregnation method may vary from support to support since impregnation depends on the surface chemistry of the support material. Co-impregnation method may not be suitable for air oxidized AC supported catalysts. Both air and nitric acid treatments are helpful to increase the performance of the catalysts by increasing the oxygen bearing surface groups on the AC support.
A process variable study of apple pectin extraction
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1985., 1985.) Dereboylu, E. Ayça.; Hortaçsu, Öner.; Arıcan, Haluk.
Dried Amasya apple pomace was used for extraction of apple pectin in this process variable study. Process variables of the extraction process were chosen as extraction temperature, duration of the extraction and acidity of the extraction medium. The effect of these variables on the yield and quality of pectin obtained were studied. To determine the quality of pectins their equivalent weights and methylester contents were measured. by titrating 0.5 per cent water solutions of pectins obtained with dilute alkali. Using the titration results total anhydrouronic acid contents of pectins were calculated. Absolute viscosities of one per cent water solutions of pectins obtained were measured. The results showed that pectin yield increased with time and temperature. It was seen that yield increase was directly related to the extraction time and the temperature effect was similar in all levels studied. The anhydrouronic acid content·of pectins increased with temperature. The methylester content of pectins- showed similar behaviour. as anhydrouronic acid content. The constant temperature lines crossed each other near 750 °C - 45 min point. At lower temperatures pectins with higher degree of esterification were obtained. The results showed also that pectin yield increased with increasing acidity. Anhydrouronic acid content was highest acidity and pectin with lower methylester content was obtained. Degree of esterification of pectins extracted increased with decreasing acidity of extraction medium. Experimehtal runs showed deviations from the literature as a result of the clqrification problem.
A QM study on determination of vibrational frequencies of the surface coordinated species involved in CDRM
(Thesis (M.A.) - Bogazici University. Institute for Graduate Studies in the Social Sciences, 2013., 2014.) Karagöz, Burcu.; Aksoylu, Ahmet Erhan.
The determination of the sites participating the reaction mechanism is of crucial importance in catalysis. Ni- and Co- based catalysts have been studied by our group for their activity in Catalytic Dry Reforming of Methane (CDRM). Although in-situ FTIRDRIFT tests have been conducted on those catalysts under adsorption and reaction conditions, and the vibrational spectra were obtained, the available information in the literature is not detailed and surface specific enough to allow the determination of the active sites on the catalyst. The aim of this study is to obtain a vibrational frequency database for the species involved in CDRM reaction mechanism occurs on the possible active faces of the Co- and Ni- based catalysts. In the formation of the database, quantum mechanical simulations utilizing Density Functional Theory (DFT) calculations are used. In the simulations, the metallic faces whose presences have been confirmed for our CDRM catalysts by XRD were considered. Vibrational frequencies of CHx(x=0-4), CO2, CO, O and H on Co(111) flat surface, Ni(220) and NiPt(220) terraced surfaces were calculated for each possible sites via DMol3 tool of Accelrys Materials Studio. Calculated vibrational frequencies of CO2, CO, CH3, and CH2 on Co(111) are in good agreement with the literature. Adsorption energies of CO2, CO, O, CH4, CH3, and CH2 on Co(111) are inversely related with their stretching frequencies whereas there is a linear relationship for adsorbed CH, C, and H on Co(111). Furthermore, calculated vibrational frequencies of CO2, CO and CH2 on Ni(220) are consistent with the literature, while stretching frequency of CH3 is far different from experimental findings, due to possible alloy formation, and geometry and/or support effect. Comparative analysis of the results obtained for Ni(220) and NiPt(220) revealed that for NiPt(220) surface, Pt existence affect the vibrational frequencies of all species. Moreover, CO2 and CO vibrational frequencies on NiPt(220) are considerably close to experimental findings. Vibrational frequency of CH4 is inconsistent with the literature for all surfaces, most probably because the weak CH4 adsorption on these surfaces may not be precisely calculated by DFT.
A study of penetration of oil into sorbents
(Thesis (M.S.)- Bogazici University. Institute for Graduate Studies in Science and Engineering, 1982., 1982.) Orhan, Metin.; Dinçer, Salih.; Tekeli, Sahim.
This study was initiated to absorb petroleum spills in sea waters. For this purpose, polyurethane and polypropylene were used as sorbents, and SAE 20W-20 motor oil and SAE 90W gear oil were used as oils. To observe the penetration of oils into sorbents, four groups of experiments were carried out the horizontal penetration of oils into dry polyurethanes, the horizontal displacement of water from polyurethanes (pre-wetted with water) by oil, the vertical penetration of oils into drypolypropylenes, and the vertical retention of oils by polyurethanes (pre-wetted with oil). Sorbents are characterized by their porosities, thicknesses, and fiber diameters. Such properties of .the sorbents used were obtained from the literature. The important properties of an oil are the density, the viscosity and the surface tension coefficient. The values for the density and the viscosity of oils used were supplied by Mobil Oil Company in Istanbul. The surface tension coefficients of these oilS also were measured in Bogaziçi University Labs. The sorbent/oil contact angle, which is another important parameter, was taken as zero by assuming that the sorbents were completely wetted with oil. A linear model, developed in literature for the horizontal penetration of oils into sorbents, was used in this study, and the experimental results obtained in this study did not agree with this model. Here, the distance penetrated by oil into sorbents was observed to be directly proportional to the square root of time. In addition, the horizontal displacement of water from sorbents by oil was also studied here. The polyurethane samples (pre-wetted with water) did not absorb oil, that is, water prevented the penetration of oil into Sorbent. Therefore, the displacement of water from sorbents by oil could not be achieved. This indicates that the sorbents can absorb oil from the surface of sea waters, if they are prevented from being wetted. The verticalpenetratjon rate model, taken from the literature, is nonlinear. The vertical retention model, which was·developed in this study, is also nonlinear. The experimental and the theoretical results showed that both the vertical penetration rate and the vertical retention were nonlinear. In the vertical penetration rate experiments, the rate at which oil climbed up the soroont was measured. In the vertical retention experiments, the rate at which oil drained from the sorbent was measured. The evalua.tions were based on these measurements.
A study of polymer-metal-protein complexes and effects of irradiation
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1995., 1995.) Taşdelen, Dinçer Betül.; Borak, Fahir.
In the present work, complex formation of some water soluble polymers (polyacrylic acid, polyacrylamide containing amino acid end group, and polyacrylamide containing no end group) with Bovine Serum Albumin (as a model protein) in the presence of divalent copper ions (Cu2+) was investigated using High Performance Liquid Chromatography (HPLC) before evaluating their possible usage as a radioprotector. For this purpose, polyacrylamide with and without functional end groups were synthesized. The molecular weight (MW) distributions of the polymers synthesized at different reaction conditions were analyzed by High Performance Liquid Chromatography (HPLC). In order to facilitiate an understanding of the complex formation mechanism of the triple complexes, the HPLC analysis of polymer-metal and polymer-protein complexes were also performed. Finally, aqueous solutions of polyacrylic acid (PAA), BSA, PAA-Cu2+, PAA-Cu2+- BSA, and PAA-BSA were irradiated using a Co-60 gamma source for a total dose of 1.2 kGy and ultimately, HPLC and spectrophotometric methods were employed to these samples in order to investigate the effect of irradiation on them.
A study on biometallic water gas shift catalysts to be used ın fuel processing
(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Güven, Sabriye.; Aksoylu, Ahmet Erhan.
The aim of this study is to design and develop a Au-based, bimetallic WGS catalyst which has suitable activity and selectivity characteristics to be used in a fuel processor. The catalyst composition, preparation method, calcination temperature, reduction temperature and reduction mixture composition, and feed composition were the parameters used in the catalyst design and testing studies. Nine different catalyst samples were prepared, tested and they are characterized by SEM. The optimum catalyst composition for WGS reaction was found to be 1% Re-2% Au/ZrO2, prepared by impregnation of Re on ZrO2 followed by deposition precipitation of Au (Re+Au). Addition of Re in this sequence was observed to improve the catalytic activity significantly, suggesting that rhenium is a good promoter for bimetallic gold based WGS catalysts. Together with five other different realistic feed compositions, a reaction mixture of 6% CO, 36% H2O, 39% H2, 10% CO2, 9% He was used for most of the reaction tests performed. The WGS activities of the samples were determined for 250-350 ˚C range. Effect of W/F ratio (0.02, 0.03, 0.06) and H2O/CO ratio (5, 6 and 7) on the WGS performance of Re-Au bimetallic catalysts were also investigated, and as expected, the general trend observed was that the catalytic activity increases with increasing W/F and H2O/CO ratios, with the exception that the catalytic activity was found to be very close for all W/F ratios at 350 ˚C. For optimum catalyst composition and reaction conditions, the catalytic activity was observed to reach as high as 55% CO conversion at 350 ˚C. Trace amounts of methane formation was observed only for the samples prepared by Au+Re sequence at 350 ˚C. No methane activity was observed for the rest of the samples. The results of the current study indicate that the bimetallic Re-Au catalyst supported on zirconia has a real potential to be used in the WGS unit of a real fuel processor.
A study on catalytic dimethyl ether production from synthesis gas with CO2
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.) Altınsoy, Necdet Semih.; Avcı, Ahmet Kerim.; Önsan, Zeynep İlsen.
Increasing concerns on the emissions of hazardous species have boosted efforts towards development of cleaner alternatives of the conventional, crude-oils based fuels. In this respect, dimethyl ether (DME) is envisioned as a promising replacement of the present fuels due its numerous benefits such as non-toxicity, SO2 and soot free combustion and compatibility with the existing fuel distribution and processing infrastructures. DME synthesis involves conversion of synthesis gas (H2+CO+CO2) on methanol synthesis and dehydration catalysts. If catalysts are present in the same reactor, used method is called direct DME synthesis, otherwise is called indirect DME synthesis. The present study involves the direct route, i.e. the physical mixture of Cu-ZnO/-Al2O3 and -Al2O3, catalysts for methanol synthesis and dehydration, respectively. Synthesis gas (syngas) is formulated either as CO+H2 or CO2+H2, with the latter being much less studied and technically more dicult. Catalyst configuration, GHSV and pressure tests were conducted when the carbon source in syngas was CO. Replacement of CO with CO2 necessitated a more active dehydration catalyst, which was obtained by impregnating PTA on -Al2O3. Relative amounts of the catalysts and molar inlet H2/CO2 ratio were also studied as additional parameters. Moreover, sorption assisted CO2-to-DME conversion was also investigated. For the mixed configuration of catalysts and sorbent (Zeolite 3A), 30 wt.% PTA impregnation on -Al2O3 and 3 g sorbent addition were found as the optimum case at 225 0C, 30 bar, H2/CO2 = 3, dehydration to synthesis catalysts ratio = 2, GHSV = ⇠ 1750 h-1. Sorbent addition led to a notable increase in CO2 conversion and DME yield without sacrificing from the exit DME molar flow rate. Sorption capacity recovery of the sorbent upon regeneration was also investigated.
A study on enhancing thermal stability of alumina
(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2021., 2021.) Çelebi, Gülten.; Aksoylu, Ahmet Erhan.
The use of temperature resistant support is a prerequisite for successful catalysts prepared to be used in reactions which need high temperature, like Dry and Mixed Reforming of Methane, catalytic oxidation, and combustion reactions. Alumina is a common and cheap catalyst support for achieving high metal dispersion, e.g., γ-Al2O3 has a surface area of 220 m2/g. However, as high temperature leads to phase change from high- to low-SA alumina phases, i.e. γδθα, preventing surface area loss requires to shift the phase change temperatures up to higher levels. In the current study, the thermal stability of commercial γ-Al2O3 samples was enhanced via doping with stabilizers La, Ba and Pt through application of various preparation and pre-treatment parameters such as; pre-doping temperature, vacuum pressure, drying temperature, pH of the precursor solution, and heat treatment applied upon doping. Total of 142 samples were prepared in 19 sets of samples, and all samples were characterized by their surface area, pore volume and pore size distribution. Selected samples chosen to represent each set were furtherly tested by XRD and Raman spectroscopy. Reference γ-Al2O3 calcined at the highest temperature applied, 1150 oC, for 2 hours had BET surface area of 8.81 m2/g. Under the same conditions, thermally resistant 1%La/Al2O3 and 1%Ba/Al2O3 samples prepared by incipient-to-wetness impregnation have BET surface areas of 61.74 m2/g and 38.26 m2/g, respectively. Results indicated that the effect of vacuum pressure and drying temperature applied during preparation were ambiguous. Changing only the pH of impregnation solution from pH1(acidic) to pH2(basic) led to decreased surface area values. While combination of pH regulation and post heat treatment significantly have a stabilizing effect leading 68.27 m2/g surface area for 1%La/Al2O3 upon calcination at 1150 °C for 2 hours, further elaboration of pre-doping temperature applied led to the highest BET surface area of 70 m2/g. XRD analysis confirmed the effect of pre-doping temperature on shifting the phase transfer temperature of alumina.

Browse

Browsing M.S. Theses by Title

Results Per Page

Sort Options