Simplified Main Text Figure Scripts and Data for "Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light Harvesting 2 Antenna Nanoarray"
Creators: name: Varvelo, Leonel
name: Lynd, Jacob K.
name: Citty, Brian
name: Kühn, Oliver
name: Raccah, Doran I. G. B.
Publisher: name: Zenodo
Year: 2023
Subjects: Python
Open quantum systems
Photosynthetic aggregates
Matplotlib

description: (please only view version 2, version 1 is outmoded) (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.<br> - bi-exp_fit.npy is bi-exponential fit to distance from equilibrium of the monomer eigenstates, matched to T_Axis.npy.<br> - HOPS_Dynamics_Monomer is the eigenstate populations found via adHOPS at each time point of the monomer, matched to T_Axis.npy.<br> - mon_boltz_dist.npy is the Boltzmann-weighted equilibrium populations of the monomer eigenstates at 300K.<br> - mon_dist_to_eq.npy is the distance from equilibrium of the monomer eigenstates found via adHOPS, matched to T_Axis.npy.<br> - mon_equilibrium_dist.npy is the equilibrium populations of the monomer eigenstates at 300K found via adHOPS.<br> - T_Axis.npy is the time axis of the adHOPS monomer simulation.<br> - 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.<br> - HOPS_MSD.npy is the mean-squared deviation (MSD) of the 37-mer, found via adHOPS, matched to HOPS_T_Axis.npy.<br> - HOPS_Population.npy is the concentric shell populations of the 37-mer, found via adHOPS, matched to HOPS_T_Axis.npy.<br> - HOPS_T_Axis.npy is the time axis of the adHOPS simulation.<br> - Rate_MSD.npy is the MSD of the 37-mer, found via the rate model, matched to Rate_T_Axis.npy<br> - Rate_Population.npy is the concentric shell populations of the 37-mer, found via the rate model, matched to Rate_T_Axis.npy.<br> - Rate_T_Axis.npy is the time axis of the rate model dynamics.<br> - Schrodinger_MSD.npy is the MSD of the 37-mer, found via the Schrödinger equation, matched to Schrodinger_T_Axis.npy.<br> - Schrodinger_Population.npy is the concentric shell populations of the 37-mer, found via the Scrhödinger equation, matched to Schrodinger_T_Axis.npy.<br> - Schrodinger_T_Axis is the time axis of the Schrödinger equation dynamics.<br> - Simplified_Figure_2.py is the figure script that generates Figure_2.jpeg. Figure 3: The dimer rate figure from the main text.<br> - 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.<br> - 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.<br> - 65_nm_T_Axis_HOPS.npy is the time axis of the adHOPS 6.5 nm dimer simulation.<br> - 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.<br> - 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.<br> - 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.<br> - 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.<br> - R_Axis.npy is the axis of inter-ring distance (R) values.<br> - 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). <br> May your days be many and your woes few. -Jacob Lynd
description: Funding acknowledgements are listed in "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. Please do not use Version 1; it is outdated..