Ongoing Projects

Design and Manufacturing of a High Power Optical Cavity at TARLA (120C214) (Co-Funded Brain Circulation Scheme2)

Project Period: 2021-2023

Coordinator: Baris Yildirimdemir

Mentor: Avni Aksoy

Subject and Importance: One of the complex components of a high power FEL like TARLA is the optical resonator. The optical resonator consists of two (or more) mirrors placed at the ends of the undulator and maintained in a near perfect vacuum. One mirror is preferred to have 100% reflecting while the other has a hole to transmit a small amount of light for usage. The distance between the mirrors is critical and must be constantly maintained and adjusted to ensure that successive light pulses are kept in phase with the electron pulses, while transiting through the undulator. In addition to the optical resonator, cavity length and transverse alignment must meet stringent stability requirements at all times.


TUBITAK BIDEB 2232 International Outstanding Researchers Program

Title: Structural Biology of Membrane Proteins involved in Quality Control (118C225)

Project duration: 12/2019-12/2022

Coordinator: Burak V. Kabasakal

Summary: Membrane proteins constitute an important class of proteins for medical, pharmaceutical and biotechnological reasons. They present more than 25% of the proteome of all cells. They mediate the cell’s interaction with its environment, i.e. transmission of intra- and intercellular signals, cell adhesion and transport across membranes. Membrane proteins need to be incorporated into cellular membrane, which is known as protein translocation. Protein quality control mechanisms during this process are carried out by chaperones and proteases. The aim of this project is to understand the link between membrane protein insertion, folding, and quality control. The research will be based on structural elucidation of the relevant protein components and complexes involved in this process using cryo-electron microscopy and x-ray crystallography. Sub-nanometer or atomic structures of these proteins and protein complexes will show the majority of the big picture behind this fundamental process. The structural findings will be supported by biochemical experiments, and complementary techniques such as cross-linking mass spectrometry.


HORIZON 2020 PRIMA (Partnership for Research and Innovation in the Mediterranean Area Programme)

Title: FunTomP: Functionalized Tomato Products (2032)

Project duration: 05/2021-05/2025

Project Partner: Burak V. Kabasakal

Summary: The objective of FunTomP is to reformulate traditional Mediterranean tomato products considering the current consumer trend of ‘functional foods’, using leaf proteins (by-products of sugar beet processing) by using novel and eco-friendly processing technologies that will impact the nutrients minimally. At TARLA, the extracted proteins will be purified by various chromatography methods and analyzed by reducing SDS polyacrylamide gel electrophoresis.  Purified sugar beet leaf proteins will be structurally investigated using X-ray crystallography. Based on the results of the protein characterization and proteomics studies, abundant sugar beet leaf proteins will be analyzed by a sequence-based comparison with equivalent proteins in other edible plants.



Title: Development of peptidomimetic inhibitors of HoxA9-Pbx1/3 protein-protein interaction with anticancer activity (121S519)

Proje duration: 10/2021-10/2024

Researcher: Burak V. Kabasakal

Summary: Hox and Pbx are two classes of co-operating transcription factors that play significant roles during development. Deregulations in Hox-Pbx functions lead to tumorigenesis, invasion, and resistance to cell death. Therefore, molecules that would disrupt the protein-protein interaction between Hox and Pbx would be highly valuable to decipher the roles of Hox-Pbx function in tumor development and can lead to new therapies where Hox and Pbx are deregulated. Starting from the HoxA9-Pbx1 crystal structure, we aim to develop potent, permeable, and stable peptide mimetics (peptidomimetics) of HoxA9 that would bind Pbx1 and its homolog Pbx3 (Pbx1/3) and inhibit the HoxA9-Pbx1/3 protein-protein interaction. Initially, we will develop two different biochemical assays to test the inhibitor binding to Pbx1. Then, we will determine the minimum sequence required for Pbx1 binding via a truncation study on HoxA9 peptides. Starting from the minimum sequence, we will perform a structure activity relationship (SAR) investigation in parallel to in silico studies.


Supporting Institution: International Atomic Energy Agency

Project Title: Harmonization of Radiotracer and Sealed Source Techniques for Efficient Use of Natural Resources and Environmental Monitoring

Project Duration: 2022-2025 (4 years)

Project Coordinator: Süleyman Fatih ÖZMEN

Subject and Significance: This project will support to harmonize and strengthen methodologies and strategies for the countries to explore possibilities of implementing radiotracer and sealed source methods in oil and geothermal fields, mineral processing plants, wastewater treatment ponds, cement manufacturing, chemical and petroleum industry, coastal engineering management, dam maintenance. This will also contribute to reducing carbon emissions and pollution, enhancing energy and resource efficiency, and preventing the loss of biodiversity and ecosystem services which are also in line with green economy and circular economy adopted by EU.


Producing and observing NV- Color Center in Diamond by Laser Writing Method

Project Period: 2022-2023

Coordinator: H. Gul Yaglioglu

Researchers: Eyup Duman,  H. Ozgur Cıldıroglu

Project Scholar: E. Uzay Karakaya

Subject and Importance: Quantum technologies are one of the fast developing research fields, which are the subject of many experimental and theoretical research groups. In order to realize quantum optical applications, researchers are looking for systems to be used as quantum bit (Qubit). Quantum spin systems related with the defect centers in diamonds are promising candidates. Color centers in diamonds are ideal platforms for these applications due to controllable electron spin interactions as well as ability to produce in nano spatial resolution. Among the color centers, nitrogen vacancy (NV-) color centers, which have long lived quantum states and well described optical transitions, are the most promising candidate.  In this project, R&D studies will be carried out to produce NV- centers on single crystal diamonds by using laser writing methods. Produced NV- centers will be analyzed with various experimental methods.