2024 Lisans ve Lisansüstü Projeleri
| Department | Name and Last Name | Project Title | 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) |
| Biomedical Science and Engineering | Begüm Kübra Tokyay | CRISPR-Cas13-based miRNA biosensor for early diagnosis and monitoring of epilepsy | DxBiotech Lab (PI: Assoc. Prof. Savaş Taşoğlu) | From the first week of July to the second week of August | No | Epilepsy is a chronic neurological disease characterized by the abnormal and synchronized firing of neurons. The diagnosis of epilepsy using various techniques and patient interviews remains challenging as the disease can only be diagnosed during a seizure. The use of biomarkers for diagnostic purposes is not yet widespread and clinical studies involving epilepsy specific biomarkers only serve validation purposes. However, analysis of epilepsy related biomarkers using miRNAs is indeed feasible. The use of genetic material in epilepsy diagnosis has also drawn attention to potential correlations between genetic material and epileptogenesis, the process through which genetic influences or acquired brain injury results in structural and functional alterations in the brain. Epileptogenesis is marked by progressive pathways where acute epileptogenesis can develop within minutes or hours and can be reversible. miRNAs remain central to epigenetic mechanisms regulating epileptogenesis. Traditional methods for analyzing extracellular nucleic acids include quantitative real-time polymerase chain reaction (PCR)-based, fluorescent-based, and spectrophotometry-based approaches. In addition, these methods often require sample preparation, trained staff, consumables, and time, demonstrating the need for more innovative and less time consuming next-generation measurement systems. Biosensor systems, which are mini analyzers that combine biorecognition agents and a transducer, can address limitations of traditional techniques. Our study aims to develop a biosensor system to analyze epilepsy associated miRNAs. Micro-electrodes modified using CRISPR-associated (Cas) dCas13a proteins will be used as biorecognition agents. Using CRISPR technology, which was awarded the Nobel Prize in Chemistry in 2020, dCas13a proteins will target specific miRNAs and dCas13a-modified electrodes will bind respective miRNAs. This biosensor system based on electrochemical impedance spectroscopy will allow for label-free measurement opportunities. | |
| CHBI | 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. | |
| Chemistry | Önder Metin | Two-Dimensional Semiconductor Pnictogens: Next-Generation Photocatalysts for Solar-Driven Sustainable Organic Transformations | Nanokatalizör Laboratuvarı (Nanocatalysis Lab) | 01.07.2024-15.08.2024 | No | I am looking for students who study Chemistry or recieved B.Sc. degree in Chemistry | In this project with the acronym of 2D-PNIKtoKAT, we aim to demonstrate the unexplored potential of 2D pnictogens as a new family of photocatalysts for the realization of photocatalytic organic conversions under visible or near infrared light illumination. To achieve this goal, firstly, novel chemical synthesis protocols will be developed for the synthesis of 2D pnictogens and then their possible binary alloys. Afterwards, the synthesized 2D materials will be functionalized by covalent or non-covalent methods after the exfoliation of their layers with the help of ultrasonic waves. The activity of all 2D pnictogens to be obtained in this way as photocatalysts will first be investigated on photoredox organic transformations (C-H arylation and C-H phosphorylation) in a conventional batch reactor. Next, thin films of the 2D pnictogens, whose photocatalytic activities will be determined in the light of the results obtained from batch reactor studies, will then be prepared on suitable substrates by using van der Waals epitaxy or molecular beam epitaxy growth methods. The photocatalytic performances of the novel microfluidic photo-reactors to be designed using soft-lithography techniques on the thin films of 2D pnictogens will also be examined in photoredox organic transformations. Therefore, with this project, the photocatalytic properties of delaminated 2D pnictogens in liquid phase organic transformations will be demonstrated for the first time in both classical batch and photo-microfluid reactors with the unique design. Also, for the first time in this project, a new micro photo-flow reactor consisting of thin films of 2D pnictogens and their binary alloys will be designed for the organic transformations operating under visible region or NIR light. Next, the structures and photophysical properties of all materials synthesized in the project will be characterized by using advanced analytical techniques. Our results will provide an overview of how the chemical and physical properties of 2D pnictogens can be tuned, greatly expanding the basic knowledge of these materials, and paving the way for new applications of these materials in different fields. |
| 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. |
| Computer Science and Engineering | Emre Gursoy | Secure and Trustworthy AI | Security, Privacy and Data Engineering (SPADE) Lab | June-August | Yes | Strong background in Computer Science and Engineering, excellent programming skills in Python. Hands-on experience in machine learning and deep learning is a plus. | Artificial intelligence (AI) and machine learning (ML) are very popular nowadays, yet they are known to be susceptible to various attacks that cause the models to misbehave or leak sensitive information. In this project, students will gain hands-on experience in executing state-of-the-art security and privacy attacks on AI models. Defenses against these attacks will also be considered. |
| Computer Science and Engineering | Emre Gursoy | Privacy-Preserving Data Analysis | Security, Privacy and Data Engineering (SPADE) Lab | June-August | Yes | Strong background in Computer Science and Engineering, excellent math and Python programming skills. Interest in security, privacy, and theoretical research. | In this project, students will explore the applications of local differential privacy (LDP) to privacy-preserving data collection and analysis. In addition to implementing and testing existing LDP algorithms, we aim for students to develop novel LDP algorithms to improve the accuracy and speed of various data analysis tasks. |
| Computer Science and Engineering | Öznur Özkasap | Blockchain and Federated Learning Assisted Internet of Energy 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. |
In this project, the objective is to do research and develop techniques and algorithms by applying innovative distributed blockchain, smart contract and distributed system principles to key research problems and areas such as (i) Distributed energy trading and sharing, (ii) Smart microgrid energy networks, and (iii) Electric and connected vehicle management. In different simulation and deployment scenarios, the project would involve comparison of algorithms based on various performance metrics of interest. |
| Computer Science and Engineering | Öznur Özkasap | Client Selection Approaches for Federated Learning | 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 client selection in federated learning in order to enhance the communication efficiency of the system. The aim is to develop a general client selection software platform that should include different client selection strategies and various aggregation methods. |
| Electrical and Electronics Engineering | Zafer Dogan | Developing tractable deep learning models for image enhancement and restoration problems | KUIS AI Center – Machine Learning and Information Processing Group | TBA | Yes | Decent programming skill in Python, C/C++ or MATLAB A good understanding of fundamentals of machine learning and deep learning A good understanding of signal and image processing concepts |
Here we focus on image enhancement and restoration problem. Deep learning has become the method of choice for image enhancement and restoration. However, prior to the DL revolution, non-local image restoration methods, such as non-local means, and BM3D, were the dominant algorithms in the field. Here, the goal is to reconcile DL with non-local algorithms and come up with a new generation of powerful image enhancement and restoration methods. The topics include, but are not limited to: § Image/video super-resolution § Image/video denoising § Image/video inpainting § Image/video dehazing § Image/video deblurring |
| Electrical and Electronics Engineering | Zafer Dogan | Classification of EEG microstates among PNES patients before and after nonepileptic seizures using machine learning methods | KUIS AI Center | TBA | Yes | Decent programming skill in MATLAB A good understanding of signal processing Experience with the EEG signal is a plus |
The Psychogenic Nonepileptic Seizures (PNES) are attacks that may look like epileptic seizures but are not epileptic and instead are cause by psychological factors. The only reliable test to positively make the diagnosis of PNES is video electroencephalography (vEEG) monitoring, which can be very long, and time consuming. Instead, in this work, we focus on the analyzing the changes observed in EEG signal before and after the seizures among the PNES patients. In EEG, microstates emerge as distributions of activity across the scalp that persist for several tens of milliseconds before changing into a different pattern. Hence, microstate analysis will be used as a way of utilizing EEG as both temporal and spatial imaging tool. Finally, the EEG microstates of PNES patients will be classified into groups representing different time information of the seizures. |
| Electrical and Electronics Engineering | Zafer Dogan | Random feature model on reducing the attention cost in transformers | KUIS AI Lab – MLIP Group | TBA | Yes | The proposed Random Feature Attention (RFA) introduces a linear time and space attention mechanism to address the efficiency challenges associated with conventional softmax attention in transformers. By leveraging random feature methods to approximate the softmax function, RFA offers a more scalable alternative for processing long sequences. Here, our goal is to characterize the training and the generalization performance of this model under some universality constraints. | |
| International Relations | Merih Angin | IMF Decides, Machine Learns: An AI Approach to IOs | MA-CSSL | 01.07.2024 – 15.08.2024 | Yes | Students should be able to label documents in English. | This project develops a new model by utilizing a wide literature on the IMF to present a comprehensive model that takes into account all actors influencing the design of IMF programs. The following questions will be at the heart of this research: Which factors influence the terms of an IMF program (loan size, number of conditions, and granted conditionality exemptions)? And how do these factors play a role in shaping program design? In this context, the project will focus on three aspects of IMF loans: (1) the size of IMF loans; (2) the number of conditions attached to loans; and (3) the number of conditionality exemptions granted to borrowing countries during program implementation. This research, creating a comprehensive and new methodology to understand IMF program design, will shed light on the processes leading to diversity in the conditions of IMF loans. At the same time, by creating an original model, this project aims to provide a significant and scalable tool for international political economy researchers and policy makers to model the program design and implementation processes with high predictive power. The project aims to make a significant contribution to the literature by creating a comprehensive machine learning (ML) model to predict the loan size, the number of IMF conditions, and the number of conditionality exemptions during program implementation. This model will complement traditional statistical models by integrating a greater number of variables and providing high prediction accuracy. The research will also create a natural language processing (NLP) tool capable of automatically and quickly analyzing the minutes of IMF Executive Board meetings, capturing alliances between representatives of different countries and the stance of the G5 with high accuracy, and recognizing the sentiments of individual Executive Board members. Another contribution of the project will be the creation of a comprehensive dataset on the various factors affecting IMF program design, covering IMF programs between 1978-2014. Examining IMF behavior while collaborating with European Union institutions, focusing on the cases of Romania and Greece, will be the fourth contribution provided by the project to illuminate existing causal mechanisms. |
| International Relations / Sociology | Ayşen Üstübici | Future aspirations and migrant use of digital space | Mirekoc | 10.07.2025-15.08.2024 | Yes | interest and prior knowledge on migration studies and / or digital ethnogrpahic methods | This proposal aims at producing a general framework for studying the processes of displacement and emplacement of recently arrived, highly skilled migrants (including but not limited to those officially categorized as refugees) to post-industrial cities where they play a key economic role. Going beyond the forced–voluntary migration binary, we will focus on professionals originating from economically and politically unstable contexts primarily from Turkey but also from Russia, Ukraine, Venezuela, Lebanon and Syria. We will seek response to following questions: How do highly skilled migrant negotiate class privileges and belonging in their first years after migrating? How they use social media to send transnational feedback to those who stay? As the final output, the research will provide a pilot study on the role of social media in representing experiences of newly arrived migrants and in shaping migration aspirations of those who stay behind. |
| Koc University Arcelik Research Center for Creative Industries | Aykut Coskun | Digital infrastructures for sustainable consumption: Redirecting, reorganizing, reducing and reimaging consumption | KUAR | TBA | No | Good Level of English, familiarity with qualitative research methods and design | Global consumption and production volumes have increased for years and are now at a non-sustainable level. This has resulted in over-exploitation of natural resources, loss of biodiversity and climate change. DISCo aims to produce knowledge on how consumption can move in a more sustainable direction by applying digital technologies. While many would agree that it is important to transition to more sustainable lifestyles to address the problems we are facing, changing current consumption patterns has proved difficult. Part of this has to do with the difficulties associated with being a sustainable consumer. Lack of information, multiple sustainability labels, and green washing create confusion among consumers. Furthermore, practices such as repairing, reusing, purchasing second hand and recycling require knowledge and can be time consuming. Digital technologies can solve many of these problems. Smartphone applications and digital platforms can assist consumers to choose sustainable products in-store, support peer-to-peer sharing networks, and facilitate the reselling of goods. Digital technologies contain thus great promise for promoting sustainable consumption. However, if this potential is to be realised, we must have a better understanding of how and with what environmental consequences these “greening” technologies become part of households’ everyday practices. What is involved in the successful introduction of these digital technologies? Do they really bring about more sustainable modes of consumption? DISCo draws on theories of practice and makes use of multiple methods to systematically investigate digital efforts reconfigure consumption in the areas of food and mobility. |
| KUYTAM | Gülsu Şimşek Franci | Statistical analysis in Archaeometry | KUYTAM | TBA | No | The student must have a profound experience about the statistical softwares like R, Matlab, Minitab, Statistica, etc. | The graduate intern will be responsible for the statistical examination of archaeometric data obtained from the analyses of tiles at Iznik Tile Kilns Excavation site with Raman and pXRF. |
| KUYTAM | Hadi Jahangiri | Investigating the Impact of Milling on the Properties of Graphene Oxide | KUYTAM | 1.07.2024 | No | Research focus on understanding how the process of milling influences the characteristics and attributes of graphene oxide. In more detail, the investigation likely involves studying the structural, chemical, and physical changes that occur in graphene oxide when subjected to milling techniques.
Milling, in this context, refers to a mechanical process that involves grinding materials by ball mill to achieve a desired outcome. The primary goal of this research could be to assess the effects of milling on the size, morphology, and functional groups of graphene oxide. It may also explore how milling impacts the material’s electronic, thermal, or mechanical properties. To gain comprehensive insights, the study might employ various analytical techniques, such as microscopy, spectroscopy, and other characterization methods. The findings could provide valuable information for optimizing milling processes applied to graphene oxide and understanding its behavior under different milling conditions. Overall, the investigation aims to contribute to the knowledge of graphene oxide processing and its potential applications. |
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| KUYTAM | Hadi Jahangiri | Analyzing the Impact of Laser on the Reduction of Graphene Oxide | KUYTAM | 1.06.2024 | No | In this study, researchers likely explore the effects of laser irradiation on graphene oxide and observe how the reduction process unfolds. The use of laser-induced reduction methods in graphene oxide is of interest due to their potential in achieving precise control over the reduction process, leading to the production of graphene with tailored properties. The study may involve examining various parameters such as laser power, irradiation time, and their impact on the structural and chemical changes in graphene oxide. The goal is likely to gain insights into optimizing the reduction process for the development of graphene with specific characteristics for various applications | |
| MAVA (MEDIA AND VISUAL ARTS) | ILGIM VERYERİ ALACA | 1-CONTEMPORARY TRENDS IN ILLUSTRATION. 2-CONTEMPORARY CHILDREN’S BOOKS | ARTISTIC RESEARCH STUDIO(https://kuarc.ku.edu.tr/) & PICTUREBOOK STUDIES(https://kure.ku.edu.tr/) | JULY 2024 | Yes | DETAILED CV, TRANSCRIPT & GPA(LİSE İÇİN KARNE OLABİLİR, (OPTIONAL: PORTFOLIO), ENGLISH FLUENCY | 1-CONTEMPORARY TRENDS IN ILLUSTRATION: THE PROJECT FOCUS ON EVALUATING NEW WORK IN ILLUSTRATION STUDIES. 2-CONTEMPORARY CHILDREN’S BOOKS-EVALUATING NEW TRENDS IN CHILDREN’S BOOKS. |
| Mechanical Engineering | Erdem Alaca | MEMS Flow Sensor | Mechanical Characterization Lab (MCL): mcl.ku.edu.tr | 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): mcl.ku.edu.tr | 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 | TBA | No | Computer Aided Design, Computer Aided Manufacturing, CNC, Machining, Additive Manufacturing | |
| Mechanical Engineering | Ismail Lazoglu | Mechatronics/Robotics/Automation | Manufacturing and Automation Research Center | TBA | No | Mechatronics/Robotics/Automation | |
| Mechanical Engineering | Ismail Lazoglu | Medical Systems/Artificial Organs/Implants | Manufacturing and Automation Research Center | TBA | No | Design and Development of Medical Systems/Artificial Organs/Implants | |
| Mechanical Engineering | Ismail Lazoglu | Advanced Manufacturing Technology | Manufacturing and Automation Research Center | TBA | No | Computer Aided Design, Computer Aided Manufacturing, CNC, Machining, Additive Manufacturing | |
| Mechanical Engineering | Ismail Lazoglu | Mechatronics/Robotics/Automation | Manufacturing and Automation Research Center | TBA | No | Mechatronics/Robotics/Automation | |
| Mechanical Engineering | Ismail Lazoglu | Medical Systems/Artificial Organs/Implants | Manufacturing and Automation Research Center | TBA | No | Design and Development of Medical Systems/Artificial Organs/Implants | |
| MiReKoc | Muge Dalkiran | BROADER, SOPEMI, Research on Exploring Schengen Visa Processes and Challenges for Turkish Citizens | MiReKoc | 01.07.2024 – 15.08.2024 | Yes | BROAD-ER is a research network project aiming to enhance the scientific, technological and development-driven management capacities of Koc University (KU), Migration Research Center at Koç University (MiReKoc) in Istanbul, Turkey, by linking it with two internationally leading research institutions in the themes of migration and urban studies. It requires data collection, desk-based research and transcriptions. SOPEMI is an OECD project on data collection and research on international migration in Turkey. It requires data collection, desk-based research and transcriptions. “Research on Exploring Schengen Visa Processes and Challenges for Turkish Citizens” is a project that requires data collection, desk-based research and transcriptions. |
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| MiReKoç | Muge Dalkiran | (Revised form) Comparative Study of Post-industrial Transition of Istanbul Golden Horn and Bilbao; BROADER; SOPEMI; Research on Schengen Visa Processes for Turkish Citizens | MiReKoç | 01.07.2024 – 15.08.2024 | Yes | The projects will require desk-based research, transcription, and support to data collection. | Comparative Study of Post-industrial Transition of Istanbul Golden Horn and Bilbao is a comparative analysis between Istanbul and Bilbao in terms of late capitalism and post-industrial development. It aims to identify common challenges and opportunities in post-industrial transitions, and to enable UNIC cities to formulate better informed strategies. BROADER aims to build a Research Excellence Network which will foster interdisciplinary research and training at the nexus of migration and urban studies. SOPEMI is an OECD project to support data collection on migration processes in Turkey. Research on Schengen Visa Processes for Turkish citizens is an ongoing research that explores the Schengen visa processes and the challenges that Turkish citizens face. |
| Molecular Biology and Genetics | İsmail K. Sağlam | Evolutionary genetics of environmental change and adaptation | Biodiversity and Evolutionary Genetics Laboratory | 01.07.2024 – 01.08.2024 | 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. |
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| Psychology | Aysecan Boduroglu | Visual Perceptual Representation: Ensemble and Serial Dependency Effects | CABLAB (Cognitive and Behavior Lab) | July-August | No | This project is a multi experiment project in which we investigate limitations and biases in visual representations. We are specifically interested in the impact of time on visual reprsesentations. We address this question by focusing on 1) how the brain extracts summary information across time and 2) how item representations are biased towards this summary and the preceeding items. | |
| Psychology | Aysecan Boduroglu | Visual Reasoning | Cognition and Behavior Lab instagram: cblab.ku | July-August | Yes | This is a broad project in which we investigate how format (table vs. graph) and structure of data patterns ( linear, exponential, with outliers etc.) impact processing and subsequent reasoning and decision processing. A subset of experiments we plan to carry out is linked to the cognitive basis of financial literacy and cognition based interventions to improve it. | |
| 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, Graduate School of Health Sciences | Irem Durmaz Sahin | Investigation of drug-resistance mechanisms in ovarian cancer and the role of miRNAs on drug-resistance; and characterization of novel anti-cancer agents in ovarian cancer | KUTTAM | 1.06.2024 | No | Investigation of drug-resistance mechanisms in ovarian cancer and the role of miRNAs on drug-resistance; and characterization of novel anti-cancer agents in ovarian cancer | |
| School of Medicine | Tamer Onder | Reprogramming, Stem cells, epigenetics | KUTTAM | 1.07.2024 | No | The Stem Cell Laboratory at KUTTAM (https://scl.ku.edu.tr/) 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. | |
| ELEC – Electrical and Electronics Engineering | Murat Kuscu | Adaptive molecular communication systems | Nano/Bio/Physical Information and Communications Laboratory (CALICO Lab) | June 15 – August 15 | Yes | Strong background in probability/random processes is required. | “Molecular Communications (MC) underpins signaling in biological systems, enabling information transfer through biochemical molecules. The prospect of engineering this natural communication mechanism has inspired the emerging Internet of Bio-Nano Things (IoBNT) framework, which relies on heterogeneous collaborative networks of bio-nano things, such as engineered or artificial biological cells (biotic), as well as artificial micro/nanomachines (abiotic), to enable paradigm-shifting applications, particularly in the healthcare domain, such as intrabody continuous health monitoring.
IoBNT applications, functioning in dynamic biochemical environments with time-varying complexity, such as human body, require adaptability of MC systems akin to biological systems to ensure reliability. However, current research on adaptivity in engineered MC systems is limited to algorithmic or ‘software’ solutions (modulation and detection techniques) and does not extend to the opportunities offered by the flexible and dynamic nature of the physical architectures or ‘hardware’ of the potential MC transceivers. Natural cells implement various adaptation strategies to optimize information transfer from their environments for maintaining homeostasis in fluctuating conditions. Many such strategies involve the modulation of signal transduction through dynamic regulation of cell-surface receptors, i.e., ligand receptors, optimizing their sensitivity, dynamic range, and selectivity for time-varying statistics of the environment. The strategies range from regulating receptor cooperativity and allostery to the expression of new receptor types on the cell surface. This flexibility of cell sensory systems has inspired the development of dynamic bio-interfaces, functionalized with biomolecules whose reaction kinetics can be dynamically tuned via external stimuli, such as thermal, and electrical. These interfaces enable various functionalities including on-demand cell adhesion, drug delivery systems, and bioanalysis/bioseparation systems. The objective of this project is to harness these opportunities by developing adaptive and dynamically reconfigurable biosynthetic receiver architectures that leverage the tunability of ligand-receptor interactions to maintain high detection performance under time-varying MC scenarios. The project involves the design, modeling and simulation of intracellular stochastic chemical reaction networks that can enable adaptive tuning of ligand-receptor interactions in biosynthetic receivers to optimize MC performance under time-varying environments. Simulations will be carried out in open-source, particle-based, spatial stochastic simulators such as Smoldyn.” |
| ELEC – Electrical and Electronics Engineering | Murat Kuscu | Microfluidic molecular communication systems | Nano/Bio/Physical Information and Communications Laboratory | June 15 – August 15 | No | The project involves the design, implementation and experimental characterization of PDMS-based microfluidic chips for modulating the transmission and propagation of messages encoded in the concentration of various biochemicals, as well as optimizing and controlling the reception of these messages by lateral flow sensors, i.e., DNA, pH, ions sensors fabricated in our laboratory. The microfluidic chips will be fabricated by graduate students in our group. The summer research intern will be expected to perform the validation experiments using microfluidic flow control equipment available in our lab and analyze the experimental results using image/video processing tools, for example, in MATLAB or Python. | |
| College of Science th Sciences | Barış Yağcı | Fundamentals of The Scanning Electron Microscopy | KUYTAM | 01.7.2024-15.08.2024 | No | Chemistry, Chemical Engineering, or Materials Engineering students will be preferred | Within the scope of this project, the researcher will gain fundamental knowledge about SEM and its usage methods while performing hands-on characterizations of various samples received from Koç University and other service takers. |
| College of Science | Barış Yağcı | Fundamentals of X-Ray Photoelectron Spectroscopy | KUYTAM | 01.7.2024-15.8.2024 | No | Chemistry, Chemical Engineering, or Materials Engineering students will be preferred | Within the scope of this project, the researcher will gain fundamental knowledge about XPS and its usage methods while performing hands-on characterizations of various samples received from Koç University and other service takers. |
| Computer Engineering | Fatma Guney | Understanding Intermediate Representations in Self-Driving | KUIA AI and Autonomous Vision Group (AVG) | As long as possible, at least 2 months | Yes | Computer Scienece/engineering, 3rd year students – Good grades from Programming (Python/C++) and Math courses (Probability, Linear Algebra, Calculus) | We will focus on learning object-centric representations for self-driving starting with slot attention from videos (SAVi). We will extend SAVi to a commonly used representation in self-driving called Bird’s Eye View (BEV) representation. We will identify and sovle the challenges of learning object-centric representations in BEV. |
| 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.” |
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| School of Medicine | All Faculty Affiliated with the Center | KUISCID’s all project | Center for Infectious Diseases (KUISCID) | TBD | No | Research Areas – KUISCID | |
| School of Medicine | Tuğba Bağcı Önder | Epigenetics and cancer therapies | Koc University Translational Medicine Research Center (KUTTAM) | TBD | Yes | The student will gain theoretical knowledge on fundamentals of cancer biology, and familiarize with molecular techniques examining the epigenetic mechanisms in cancer cell lines. | |
| Economics | Seda Ertaç | Improving Non-Cognitive Skills and Achievement Outcomes in Education: An Experimental Study | TBD | Yes | https://sedaertac.com/field-experiments | ||
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Physics |
Aşkın Kocabaş |
Robo-Physics |
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 |