Project Description:

In this project, the interns will theoretically investigate the interaction of light with the Cyanine-5 (Cy5) molecule, a fluorescent dye widely used in imaging studies performed with fluorescence microscopes and will attempt to understand these processes through computer-assisted methods. Cyanine dyes are important molecules employed in many advanced technology fields such as cell imaging, sensor technologies, and optical materials. When these molecules absorb light, they can be excited to different energy levels and later return to their initial states by emitting light. During these transitions, the molecule undergoes rotational motion, which leads to changes in its physical structure.

The aim of the project is for students to learn how molecules interact with light, how these interactions can be explained through energy levels and electronic transitions and how scientists investigate these processes using computer simulations and photophysical modeling.

During the internship, students will:

• Gain fundamental knowledge about molecular interactions with light and the concept of fluorescence,
• Examine the structure and properties of the Cy5 molecule,
• Visualize the molecular structure using basic computer-based molecular modeling tools,
• Construct energy diagrams describing light absorption and emission processes,
• Solve the models developed through these diagrams using the Python programming language,
• Interpret their results and prepare a short scientific presentation or poster.

Through this project, students will become familiar with modeling and visualization methods used to understand the invisible molecular realm and will gain experience with the working approaches of biomolecular physics and computational materials science.