Simplified Main Text Figure Scripts and Data for "Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light Harvesting 2 Antenna Nanoarray"

(as README.txt):

Main text figure data and simplified figure generation scripts for "Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light Harvesting 2 Antenna Nanoarray" by Leonel Varvelo, Jacob K. Lynd, Brian Citty, Oliver Kuhn, and Doran I. G. B. Raccah.

Table of contents:

Figure_1: Panels (c) and (d) of the monomer figure from the main text.
- bi-exp_fit.npy is bi-exponential fit to distance from equilibrium of the monomer eigenstates, matched to T_Axis.npy.
- HOPS_Dynamics_Monomer is the eigenstate populations found via adHOPS at each time point of the monomer, matched to T_Axis.npy.
- mon_boltz_dist.npy is the Boltzmann-weighted equilibrium populations of the monomer eigenstates at 300K.
- mon_dist_to_eq.npy is the distance from equilibrium of the monomer eigenstates found via adHOPS, matched to T_Axis.npy.
- mon_equilibrium_dist.npy is the equilibrium populations of the monomer eigenstates at 300K found via adHOPS.
- T_Axis.npy is the time axis of the adHOPS monomer simulation.
- Simplified_Figure_1.py is the figure script that generates Figure_1.jpeg.

Figure 2: Panels (b), (c), (d), and (d) of the 37-mer figure from the main text.
- Haken_Strobl_Population.npy is the concentric shell populations of the 37-mer, found via the Haken-Strobl model, matched to Haken-Strobl_T_Axis.npy.
- Haken-Strobl_T_Axis is the time axis of the Haken-Strobl model dynamics, identical to Schrodinger_T_Axis.npy.
- HOPS_MSD.npy is the mean-squared deviation (MSD) of the 37-mer, found via adHOPS, matched to HOPS_T_Axis.npy.
- HOPS_Population.npy is the concentric shell populations of the 37-mer, found via adHOPS, matched to HOPS_T_Axis.npy.
- HOPS_T_Axis.npy is the time axis of the adHOPS simulation.
- Rate_MSD.npy is the MSD of the 37-mer, found via the rate model, matched to Rate_T_Axis.npy
- Rate_Population.npy is the concentric shell populations of the 37-mer, found via the rate model, matched to Rate_T_Axis.npy.
- Rate_T_Axis.npy is the time axis of the rate model dynamics.
- Schrodinger_MSD.npy is the MSD of the 37-mer, found via the Schrödinger equation, matched to Schrodinger_T_Axis.npy.
- Schrodinger_Population.npy is the concentric shell populations of the 37-mer, found via the Scrhödinger equation, matched to Schrodinger_T_Axis.npy.
- Schrodinger_T_Axis is the time axis of the Schrödinger equation dynamics.
- Simplified_Figure_2.py is the figure script that generates Figure_2.jpeg.

Figure 3: The dimer rate figure from the main text.
- 65_nm_Dynamics_HOPS.npy is the ring population dynamics of the R = 6.5 nm dimer, found via adHOPS, matched to 65_nm_T_Axis_HOPS.npy.
- 65_nm_Dynamics_Rate.npy is the ring population dynamics of the R = 6.5 nm dimer, found via the single-exponential rate fit, matched to the 65_nm_T_Axis_HOPS.npy from 600 fs onwards.
- 65_nm_T_Axis_HOPS.npy is the time axis of the adHOPS 6.5 nm dimer simulation.
- All_Couplings_Allowed_Error.npy is the error bars from the 95% confidence interval of the single-exponential rate fits  to the ring population dynamics of the 6.5, 7.5, and 8.5 nm dimers with all couplings allowed in the Hamiltonian, generated with 10,000 bootstrapped ensembles, matched to R_Axis.npy.
- All_Couplings_Allowed_Rates.npy is the single-exponential rate fits  to the ring population dynamics of the 6.5, 7.5, and 8.5 nm dimers with all couplings allowed in the Hamiltonian, matched to R_Axis.npy.
- Bright_State_Only_Error.npy is the error bars from the 95% confidence interval of the single-exponential rate fits  to the ring population dynamics of the 6.5, 7.5, and 8.5 nm dimers with only inter-ring couplings between bright states allowed in the Hamiltonian, generated with 10,000 bootstrapped ensembles, matched to R_Axis.npy.
- Bright_State_Only_Rates.npy is the single-exponential rate fits  to the ring population dynamics of the 6.5, 7.5, and 8.5 nm dimers with only inter-ring couplings between bright states allowed in the Hamiltonian, matched to R_Axis.npy.
- R_Axis.npy is the axis of inter-ring distance (R) values.
- Simplified_Figure_3.py is the figure script that generates Figure_3.jpeg.

The packaged scripts may be run with Python 3.10 and the associated versions of the os, numpy, and matplotlib packages. Please direct any questions to Jacob Lynd at jacobklynd@gmail.com (for questions about the construction of this packaged data) or Doran I. G. B. Raccah (regarding the paper at large).

May your days be many and your woes few.

-Jacob Lynd