BME MS Thesis Defense - Eren Ergene

Title: "Bulk-effect-free Binding Kinetics Measurements and Quantitative Refractive Index Detection By Multicolor Imaging"

Advisory Committee: Irving J. Bigio, PhD – BU BME (Chair) M. Selim Unlu, PhD - BU ECE, MSC, BME (Advisor) Diane Joseph-McCarthy, PhD - BU BME

Abstract: The development of label-free optical biosensors is motivated by the need for highly accurate and sensitive measurement of biomolecular interactions. The Interferometric Reflectance Imaging Sensor (IRIS) delivers precise and multiplexed detection of these interactions. A major challenge in label-free sensing is the bulk effect, which is the presence of unwanted signals caused by variations in refractive index that can obscure true binding interactions and lead to inaccurate measurements. This thesis presents multiple advancements to IRIS technology focusing on the quantitative detection and elimination of the bulk effect using the principles of light reflection in different colors. A novel bulk-effect-free signal calculation method is introduced, significantly reducing sensitivity to refractive index variations. Additionally, a methodology for real-time refractive index detection is developed. Both systems are theoretically validated through MATLAB simulations. Experiments were conducted to demonstrate the effectiveness of the bulk-effect-free signal measurement and the refractive index detection system. Two main types of experiments were performed: with solutions of varying refractive indices without actual binding to detect refractive index changes, and binding experiments to test the new systems' effectiveness in detecting true biomolecular interactions. Novel experimental procedures with the combination of these methods were introduced to completely eliminate the bulk effect. This thesis establishes the foundation for the next-generation multicolor IRIS system, enhancing its potential for accurate detection of biomolecular interactions by eliminating the bulk effect and incorporating refractive index detection.