As a scientist I want to calculate MCFRET rates so I can understand weakly coupled systems better.

[marickmanrho]

Problem description

MCFRET is a an acronym for Multi Chromophoric Förster Resonant Energy Transfer. Its classical use case is found in donor-acceptor systems, but other applications are also possible. It is a method of computing the energy transfer between two groups of chromophores. In calculating MCFRET it is assumed that the coupling between the groups can be treated perturbatively.

For details on the MCFRET method we refer to the following references:

1. J. Chem. Phys. 142, 094108 (2015); https://doi-org.proxy-ub.rug.nl/10.1063/1.4908601

Problem solution

(written by @GHlacour ) We want to use NISE to compute the time evolution of the system. Then we fit the excitation population transfer to an exponential and extract rates. This is not the same as MCFRET but gives approximately the same answer when the coupling between the subsystems is indeed perturbatively small.

For the MCFRET project we need a number of functionalities as discussed at our previous meeting. Below are the ideas for each of these functionalities with the idea that each will be separated in a different function and a proposed keyword for running the code part separately. The main keyword MCFRET should result in all relevant subroutines being called in the correct order.

• A management/main routine that direct NISE to the desired subroutines.
• Autodetect coherently connected parts (segments) MCFRET-autodetect. This code should also be called if the user does not provide segments via input.
• Calculate the Absorption Matrices for the defined segments MCFRET-Absorption.
• Calculate the Emission Metrics for the defined segments MCFRET-Emission. Note this can be done with the same code as for the Absorption Matrices if a flag for including the thermal equilibrium density matrix is used. For the high-temperature approximation the Absorption matrices should be used if they were already calculated.
• Determine the (average) couplings between segments. MCFRET-Coupling.
• Determine the rate matrix between all segments. MCFRET-rate.
• Analyse the validity of the outcome. Make various checks as if the transfer is actually incoherent and if the amount of averaging is reasonable. Give the user warnings if the coherence time is too short or there are other reasons that the results may be inaccurate.
• Analyse the determined rate-matrix by diagonalization and providing the eigenvalues and eigen vectors MCFRET-analyse.

Alternatives

The alternative is to not implement specific MCFRET code into NISE and leave it to the end-user to develop this. However, the usage of MCFRET methods is sufficiently large that it would be a waste of time for every user to develop their own code. Furthermore, this code may become a benchmark for MCFRET studies.

[GHlacour]

This is essentially done. Paper in progress.