Department Name and Last Name Project Title (in English) Research Center or Lab Affiliated (if applicable) Dates (Expected start and end date) Can the students participate online? Specific Requirements (if any) Project Description (in English)
Chemical and Biological Engineering Özlem Keskin Özkaya Computational drug design COSBI July 15-Aug 1, 2024 Yes Drugs perform their action by binding proteins/DNA. There finding which drug can bind to which protein is a critical step in drug design. The student will learn to use a docking tool to score molecules that can bind to a protein of interest. The student will learn how to visualize the protein structure and the drug molecule.
Computer Engineering Aykut Erdem Developing Medicine Large Language Models for KUIS AI Center 01.07.2024 – 15.08.2024 Yes A good background on deep learning This summer research project aims to pioneer the development of large language models tailored for the medical domain. Participants will engage in cutting-edge methodologies in natural language processing (NLP) and deep learning, in particular in the area of large language models.
Computer Engineering Aykut Erdem Developing Medicine Large Language Models for KUIS AI Center 01.07.2024 – 15.08.2024 Yes A good background on deep learning This summer research project aims to pioneer the development of large language models tailored for the medical domain. Participants will engage in cutting-edge methodologies in natural language processing (NLP) and deep learning, in particular in the area of large language models.
Computer Science and Engineering Öznur Özkasap Blockchain for Decentralized Healthcare Systems Distributed Systems and Reliable Networks Research Lab TBA No Preferably junior/senior students in Computer Engineering or Computer Science.
Excellent programming skills and Computer Networks background.
This project addresses usage of blockchain and key distributed system technologies in decentralized healthcare systems.The aim is to classify the existing solutions in the literature and develop a prototype decentralized healthcare system implementation using blockchain.
Mechanical Engineering Erdem Alaca MEMS Flow Sensor Mechanical Characterization Lab (MCL): July 1 – July 31 No The technology of micro- and nanoelectromechanical systems (M/NEMS) enables the creation of small force sensors that accurately measure forces in the micro-newton and sub-micro-newton ranges. Piezoresistive sensors have gained popularity due to their relative immunity to electrostatic forces, simple read-out circuitry, lower noise, ease of scaling up and integration, and potential for miniaturization. The fabricated NEMS force sensor uses piezoresistive silicon nanowires to detect multi-axis forces in the micro-newton range. Through an Arduino-based setup, we will explore the flow-sensing capabilities of these sensors, characterizing them through current-voltage measurements and analyzing their electromechanical and thermal behavior.
Mechanical Engineering B. Erdem Alaca Mechanics of Soft Matter Mechanical Characterization Lab (MCL): July 1 – July 31 No Mechanical material characterization is of paramount importance in scientific and engineering domains. While extensive research has addressed the mechanics of rigid materials, such as metals exhibiting minimal deformation under moderate loads, there is a significant research gap concerning soft materials, which undergo substantial deformation under delicate loading conditions. Precise measurement of minute loads in such materials necessitates the utilization of highly sensitive force sensors. Moreover, securing soft materials within grips poses challenges due to their delicate nature. This study proposes employing digital image correlation, a sophisticated technique for analyzing local strains from sample images coupled with sensitive force sensing, to understand the mechanics of soft materials comprehensively.
Mechanical Engineering Ismail Lazoglu Advanced Manufacturing Technology Manufacturing and Automation Research Center will be determined later No Computer Aided Design, Computer Aided Manufacturing, CNC, Machining, Additive Manufacturing
Mechanical Engineering Ismail Lazoglu Mechatronics/Robotics/Automation Manufacturing and Automation Research Center will be determined later No Mechatronics/Robotics/Automation
Mechanical Engineering Ismail Lazoglu Medical Systems/Artificial Organs/Implants Manufacturing and Automation Research Center will be determined later No Design and Development of Medical Systems/Artificial Organs/Implants
Molecular Biology and Genetics Elif Nur Firat Karalar Purification and characterization of a microtubule-associated protein linked to genetic diseases Cytoskeleton Research Laboratory 45458 No Microtubule-associated proteins bind to microtubules to assemble diverse microtubule arrays ranging from the mitotic spindle to the primary cilium. These microtubule arrays carry out vital cellular processes. Therefore, their deregulation is linked to diseases such as cancer and rare developmental disorder. In this project, the student will clone a gene that is predicted to bind to microtubules into a bacterial expression vector. Following cloning, he/she will purify the protein and characterize it using in vitro assays under supervision of a PhD student.
Molecular Biology and Genetics Halil Kavaklı Drug discovery against clock related diseases Biotechnology and Circadian Clock LAB 01.07.2024-18.082024 No The circadian rhythms are physiological, biochemical, and behavioral oscillations that cycle every 24 hours to anticipate the daily changes in the external environment. Disruption of the circadian clock in mammals results in increased susceptibility to different types of diseases such as metabolic, mood and sleep disorders and cancer. To this end, different approaches have been taken to find small molecules that have the potential to correct the disrupted circadian clock. We are currently identifying novel molecules that regulate the activities of the core clock proteins to treat cancer.
Molecular Biology and Genetics İsmail K. Sağlam Evolutionary genetics of environmental change and adaptation Biodiversity and Evolutionary Genetics Laboratory No Students will be conducting genetic research on changes that promote adaptation of organisms to environmental change
Optic MEMS Laboratory Hakan Ürey Augmented and Virtual Reality Optic MEMS Laboratory 01/07/2024-26/072024 Yes Augmented and Virtual Reality
This program provides participants with the opportunity to engage in virtual/augmented reality technology. Students are expected to apply science and technology knowledge in a real-life AR/VR project. Participants will work together on projects that simulate real-world situations and limitations. Essential project management such as development, design, implementation, teamwork, communication and presentation skills are required for program completion. Development, design, implementation, and management of a project in teams under realistic constraints and conditions.
Upon completion of the program, attending participants will be able to:
● Follow a process and solve a real-life engineering problem.
● Design a system or algorithm to meet defined functional requirements.
● Practice group dynamics and team building.
● Follow a project plan for completing and managing a project.
● Test and troubleshooting of a system, script, and algorithm.
● Demonstrate the functionality and operation of their project for a general audience.
Robotics and Mechatronics Laboratory, College of Engineering Cagatay Basdogan Haptic Vest for Indoor Navigation of Blind People Robotics and Mechatronics Laboratory, College of Engineering June 25-July 25 No Good programming skills A haptic vest designed for indoor navigation of blind people would utilize tactile feedback to guide users through environments without the need for sight. This technology would convert spatial information into touch-based signals that the wearer can understand, enabling them to navigate around obstacles, through doorways, and towards destinations within buildings.
School of Medicine Tamer Onder Reprogramming, Stem cells, epigenetics KUTTAM June-July No The Stem Cell Laboratory at KUTTAM ( studies the molecular mechanisms of cellular reprogramming. Reprogramming of differentiated cells, such as skin cells, to induced pluripotent stem cells (iPSCs) has revolutionized the field of stem cell biology and greatly increased the opportunities for disease modeling and cell-based regenerative therapies. While iPSCs offer tremendous potential, a number of technical challenges remain in the generation of iPSCs that hamper their use in clinical settings. A comprehensive understanding of the molecular mechanisms of cellular reprogramming is essential for devising methods to overcome these challenges. Our research is aimed at understanding the molecular mechanisms of reprogramming and identifying genes that are important for iPSC generation. Specifically, we utilize forward genetics tools such as CRISPR-Cas9 technology and chemical screens using small molecule inhibitors to identify the role chromatin modifying enzymes play during reprogramming.
School of Medicine Fulya Dal Yöntem Development of an inhibitor targetting Drp1-MiD49/51 interaction at mitochondrial fission machinery Koc University Translational Medicine Research Center (KUTTAM) 01.07.2024-01.08.2024 No “Aim of this project is to develop a novel and specific inhibitor targeting mitochondrial fission machinery which plays role in development and progression of cancer, diabetes and neurodegenerative diseases. Mitochondria is considered as an organelle responsible for energy production through oxidative phosphorylation in cell. Today besides its energy production mitochondria also participates in many different physiological processes such as programmed cell death, mitophagy, redox signalization and calcium homeostasis. Mitochondria is a highly dynamic organelle responding to cellular stress conditions through mitochondrial mass alterations, fusion and fission and location changes in cell. Mitochondrial fusion can be explained by mitochondria’s forming an elongated mitochondrial network and vice versa small fragmented mitochondria’s are formed by mitochondrial fission. Mitochondrial functions and mitochondrial dynamics (fission and fusion) has an important role in understanding the biological processes like apoptosis and aging and molecular mechanisms of many diseases such as obesity, diabetes, complex diseases like Parkinson’s and Alzheimer’s and cancer. Recent studies revealed that cancer cells alter mitochondrial dynamics (increase mitochondrial fission protein, Drp1) to gain resistance against apoptosis and regulate bioenergetics and biosynthetic requirements to support proliferation, migration and therapeutic resistance acting on tumor origination and transformation characteristics. It has been reported that at type 1 diabetes and neurodegenerative diseases Drp1 expression was increased. Therefore, development of new inhibitors targeting mitochondrial fission become important for improving treatment of diseases which mitochondrial dynamic alteration processes act and for studying biology of mitochondrial dynamics.
This project mainly comprises of two parts. In first part mitochondrial fission inhibitor design will be performed by computational methods. Target inhibitor molecule will inhibit the interaction between Drp1 and mitochondrial outer membrane proteins, which carry and localize Drp1 to mitochondria outer membrane, MiD49/51. MiD49 and MiD51 cytosolic regions and MiD49/Drp1 complex structures have been revealed by experiments. Therefore, structure-based drug design approaches will be used in this project to design inhibitor molecules. Candidate molecules for bioactivity tests will be determined by virtual screens of 3.6 million molecules with docking calculations. At second part effects of synthesized inhibitor molecules on Drp1-MiD49/51 protein interactions and mitochondrial fission will be studied. In this context effect of the inhibitors will be studied by using confocal and real time fluorescent microscopes. Effects of new Drp1-MiD49/51 inhibitors on mitochondrial functions will be tested by mitochondrial membrane potential, oxygen consumption rate, mitochondrial complex activities, cellular reactive oxygen species, cell viability and apoptosis studies. Lastly effect of developed inhibitors on receptor-ligand kinetics of Drp1-MiD49/51 will be studied. Developing a new inhibitor for MiD49/51 and Drp1 interaction has a great importance of being novel and specific and also has a drug potential. Accomplishing the aims of this project will also help our country to take part in this field in international arena.”
Economics Seda Ertaç Improving Non-Cognitive Skills and Achievement Outcomes in Education: An Experimental Study TBD None


Aşkın Kocabaş


Physics of Living Things

Between 15 June-15 August (specific weeks to be determined)

Physical Only

This research project is designed to educate students on the fundamental physical principles involved in controlling robotic systems within complex environments. Participants will design and build various robots that navigate through challenging settings, especially viscous media. The principles learned here are also applicable in biomedical contexts, helping to elucidate the motility of cancer cells and bacterial movement. This project will equip students with crucial knowledge on the universal principles of locomotion that apply to both robotic systems and small biological organisms