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.