Rational Design of Photoactivated BiologicalMaterials

This thesis presents the design of new sensing systems that can be used in the future generation of bio-imaging optical techniques to enhance understanding of complex biological
environments. In the last two decades, the development of multi-scale methods opened the possibility of studying optical processes involving several thousands of atoms. Since the light-triggered process occurs in a localized volume, the total system can be split into different layers that will be treated with different models depending on the required accuracy. Therefore, it is possible to use quantum mechanics methods to describe the
light interacting molecule while all the surrounding environment, acting as a contour, can be described with a still atomistic but less accurate method. In this thesis, we have used polarizable embedding methods to introduce the environment’s effect in calculating spectroscopic properties central in optical techniques for bio-imaging. In these models, every atom in the environment is represented by a set of parameters, and they can mutually polarize each other and the quantum region. As a result, the environmental effect is directly included in the calculation of the molecular properties of the fluorophore. Therefore, the one- and two-photon properties calculated in this thesis closely resemble
the experimental values and can be used to get insight into the light-initiated processes here analyzed.