Department of Chemical Engineering

 

CHBE 590/690 - Graduate Seminar

Spring 2017

Coordinator Assist. Prof. Dr. M. Oluş Özbek


Seminar Schedule


Topics

Speaker : Belkıs Akbulut (M.Sc.)
Instructor : Assoc. Prof. Dr. Nihan Çelebi-Ölçüm
Title : COMPUTATIONAL SCREENING OF NATURAL PROTEINS FOR MORITA-BAYLIS-HILLMAN ACTIVITY
Abstract :
The aim of this project is to computationally design new enzymes for Morita-Baylis-Hillman reaction by using naturalistic approach. In order to do that, computational screening of the natural protein database for the catalytic elements of a target reaction will be achieved. Theoretical enzymes will be used as templates and numerous CAMs will be constructed for each theozyme by using Cylview program and they all will be run by Saber program. Results obtained from Saber will be listed in Microsoft Excel and best results will be selected according to criteria such as rmsd analyzed in Pymol visualisation program to see how well they match with our theozyme. Once the pair fitting of the theozymes to proteins is achieved, these combinations will be used in molecular Dynamics simulations of 10 or 20 nanoseconds. The best candidates will be used in enzyme design.

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Speaker :Ayşe Nur Dalman (M.Sc.)
Instructor : Assist. Prof. Dr. M. Oluş Özbek
Title :COST OPTIMIZATION AND ENVIRONMENTAL PROTECTION IN THE FUEL SERVICE STATIONS
Abstract :
This study focuses on the optimization problems faced in a fuel station from a chemical engineering point of view. The chosen independent variables and the data belonging to these variables to be compiled using the existing and the real time data from an actual station. The results of the optimization process will be beneficial for the cost effective construction and running of such a station. The study is expected to be environmentally beneficial as well through the application (including improvement and development if necessary) of the methods such as the detection of losses or leaks which in the whole fuel service stations (underground storage tanks + product lines + dispensers) using real time data.

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Speaker : Beril Gülkaya (M.Sc.)
Instructor : Assoc. Prof. Dr. Nihan Çelebi-Ölçüm
Title : GENERATION AND TESTING OF QUANTUM MECHANICAL CALCULATIONS FOR ORGANOCATALYST
Abstract :
The number of reports on the use of small chiral organic molecules as catalysts and related computational efforts for understanding the origins of catalysis and selectivities keep growing. Yet, the prediction of effective catalysts is still a challenging task. The determination of effective and selective organocatalytic structures still largely relies on serendipity, and experimental trial and error.

The objective of this project is to create an organocatalyst database, involving the synthetic routes, physical properties, catalytic reactions, and commercial availabilities of small organic molecules with previously determined catalytic activity and to identify organocatalysts with the desired 3D arrangement of catalytic functional groups in this database for chosen target reaction to reduce the cost of experimental screening. This project will allow easy and cost effective determination of potential organocatalyst candidates for a selected target reaction using a new computational approach combining the quantitative power of quantum mechanical calculations with drug design tools.

Initially, an organocatalyst database as will be generated. This database will include previous studies and data collected from an extensive literature survey as well as 3D conformational library of the related structures. Theoretical active side models will be constructed using quantum mechanical calculations and catalytic group maps (CGM) will be generated. CGM will be virtually screened in the generated organocatalyst database by using the pharmacophore search algorithm and potential organocatalysts will be selected for the target reaction.

Computational determination of potential organocatalyst candidates for a selected target reaction will lead to reduction of experimental cost for industry.

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Speaker :Öykü Gizem Zaloğlu (M.Sc.)
Instructor :Assist. Prof. Levent Organ
Title :PITTING CORROSION OF AA5005 SHEETS PRODUCED BY DC CASTING AND TWIN-ROLL CAST TECHNIQUES
Abstract :
Sheets of Al alloys are widely used in industry due to their light weight and high corrosion resistance. These sheets are conventionally produced by the DC Casting technique. An alternative way of production is the so called twin-roll casting. It is known that the alloys produced by the two techniques have differences in their microstructures. Since microstructure can affect resistance of a material to corrosion, alloys produced by the two techniques are likely to differ in their resistance to corrosion. The aim of this study is to compare the pitting corrosion resistance of aluminum alloy 5005 produced by the two techniques.

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Speaker :Berat Umay Topçubaşı (Ph.D.)
Instructor : Prof. Dr. Mustafa Özilgen
Title : THERMODYNAMIC ANALYSIS OF THE WORK PERFORMANCE BY THE MYOMETRIUM IN AN IN VITRO SYSTEM WITH HORMON ACTIVATION AND INACTIVATION
Abstract :
The uterine wall muscle, myometrium, has crucial role during childbirth. Increasing work performance and efficiency of this muscle during delivery of a baby may have substantial health benefits for both baby and the mother. Thermodynamic aspects of this process with utilization of different energy sources will be researched in this study. In the present study, myometrium of the uterine wall of a group of rat will be employed in the in vitro studies by using organ bath containing Krebs’ solution at 37 0C and pH = 7.4. The organ bath will be bubbled continuously with 95 % oxygen and 5% carbon dioxide. The contraction data of the muscle will be taken from transducer on organ bath upon induction of the contractions with a hormone, with the help of the software program of bioPac Lab 3.7.7 PRO. Force versus displacement data will be recorded during contraction. Four different nutrients sucrose, glucose, lactate and pyruvate will be used as substrates of energy utilization. Thermodynamic analysis of the data obtained with these nutrients will be done to determine the magnitude of the work performance, mimicking the work done during childbirth, energy utilization, exergy destruction and entropy generation will be among the thermodynamic properties calculated with the help of MATLAB by using the force and displacement data obtained in the experiments. The metabolic pathways of the energy metabolism of the muscle cell will be slightly different with different substrates. When the sucrose is used as nutrients for energy utilization, conversion of sucrose to glucose is required for to be substrate into the glycolytic pathway. This is result in, increasing time to produce work and decreasing energy and exergy efficiency. When the glucose is used as the nutrient, simple glycolytic pathway will be obtained. When the lactate or pyruvate is used as substrate, the energy source may go directly to the mitochondria muscle work may increase drastically. Thermodynamic analysis are expected to provide meaningful outcome to be used in practice. Experiments will be repeated with rats of different age, to obtain information about the variation of the magnitude and efficiency of the muscle work performance with aging.