Probing molecular environments through fluorescence-based photophysics: transient-state dynamics, spectroscopy and predictive modeling
Abstract
Photoinduced transitions to long-lived, non-emissive electronic states play a fundamental role in determining the photophysical behavior of fluorescent molecules. Although these transient states often limit fluorescence brightness and photostability, their population kinetics are highly sensitive to local physicochemical conditions, offering additional observables for molecular characterization and optical sensing. This seminar addresses how such dynamics can be quantitatively investigated and exploited by combining experimental fluorescence spectroscopy, analytical theory and computational modeling methods.
Time-resolved fluorescence correlation spectroscopy (FCS) and transient state (TRAST) spectroscopy techniques provide complementary approaches for resolving singlet-triplet transitions, photoinduced trans-cis isomerization and radical-state dynamics in organic fluorophores. Applications to brominated-fluoresceins reveal the influence of internal and external heavy-atom effects on intersystem crossing and triplet-state relaxation, while the environmental sensitivity of fluorescence blinking enables characterization of membrane microenvironments, RNA G-quadruplex folding and fluorescence-based chromophore multiplexing. Extending these principles from wide-field illumination scheme to microfluidic systems, flow-controlled fluorescence microscopy provides a useful framework for investigating the interplay between molecular transport, optical excitation and transient-state populations of fluorophores. Experimentally informed numerical simulations further predict distinct photoisomerization responses of free and vesicle-bound cyanine dyes under varying flow and excitation conditions. Complementary analytical solutions based on eigenmode decomposition establish explicit relationships between photophysical transition rates, excitation parameters and time-dependent fluorescence responses.
Beyond synthetic fluorophores, conventional UV-visible absorption and steady-state fluorescence spectroscopy measurements are employed to investigate the molecular interactions and quenching behavior of intrinsically fluorescent tyrosine amino acid in the presence of ionic quenchers and sodium ascorbate. Molecular dynamics simulations provide complementary insight into the intermolecular interactions and solvation structures underlying these spectroscopic responses. In parallel, machine learning approaches applied to carbon nanotube-based polymer nanocomposites demonstrate the importance of physically interpretable and rigorously validated predictive models for identifying electrical conductivity regimes. Altogether, the investigations that will be presented in this seminar highlight the integration of optical spectroscopy, kinetic theory and computational methods as a versatile strategy for understanding molecular dynamics and developing quantitative approaches to molecular sensing in life-sciences and materials characterization.
Short Bio: Dr. Barış Demirbay received his B.Sc. degree in Physics Engineering from Istanbul Technical University in 2015, ranking third among the graduates of his department. He earned his M.Sc. degree from the same department in 2017. He subsequently joined the Department of Materials Science and Nanoengineering at Sabancı University as a research assistant and doctoral student. In early 2018, he moved to KTH Royal Institute of Technology in Stockholm, Sweden, where he pursued his doctoral research in the Department of Applied Physics and received his Ph.D. in Experimental Biomolecular Physics in June 2023.
Following his doctoral studies, he served as a research engineer in the Department of Applied Physics at KTH, where he also provided training in fluorescence-based spectroscopic techniques employed during his doctoral research. In October 2023, he joined the Department of Natural and Mathematical Sciences at Özyeğin University as a part-time lecturer, teaching undergraduate physics courses in the Faculty of Engineering. Since September 2024, he has been serving as a full-time lecturer and academic researcher at Özyeğin University, where he teaches undergraduate physics courses and conducts independent scientific research projects. His research interests are mainly focused on experimental and theoretical biomolecular physics, molecular photophysics, the development of time-resolved fluorescence spectroscopy and imaging techniques, microfluidic detection systems, mathematical and computational modeling, polymer physics and applications of machine learning methods in materials science.
