Conclusions
PyFREC software provides a versatile tool for modeling excitation energy transfer in such diverse systems as light-harvesting protein complexes, fluorescents labels, and photosensitizers. The software provides alignment of molecular fragments, calculation of electronic couplings and orientation factors followed by calculations of spectral overlaps and Förster energy transfer rates. The variation method can be additionally used to analyze coupled electronic excited states. Quantum dynamics is implemented with the quantum master equation approach that provides a prediction of density matrix dynamics including populations of the electronic excited states and may be coupled to molecular vibrations. Finally, a set of additional modules provides 3D visualization, generation of audio files, PDB databank scanning, and network topology analysis functionality. Future development of PyFREC will include adding non-dipole interactions for calculations of electronic couplings in order to account for triplet excited states, since quantum dynamics of photophysical processes (fluorescence quenching, phosphorescence) proceeds with involvement of triplet states. It is also planned to implement deep learning algorithms for automation of multiple routines in PyFREC, such as recognition of molecular fragments inside proteins in PDB files, prediction of excitation energies, and electronic couplings of molecular fragments based on molecular structure (coordinates) of molecular systems that contains fragments (e.g., pigments inside a light-harvesting protein).
Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY)37 provides dynamic and supportive environment for undergraduate students and faculty involved in our research projects.1-3 The consortium promotes the development of PyFREC and helps students to gain experience in modern computational quantum chemistry.