junipertcy/network_light-harvesting

My network research in theoretical light-harvesting

network_light-harvesting

My network research in theoretical light-harvesting The duration of this study spanned from Feb 2013 to Jul 2013, by Tzu-Chi Yen, under the supervision of Professor Yuan-Chung Cheng.

The package component

• [code-network] code for calculating the quantum yield and excitation lifetime of random networks

[code-network]

• MAIN:

  • box_properness.m (draw the pairwose distribution function for different geometry)
  • DipoleCoupling.m
  • FRate.m
  • rateM.m
  • whatsDE_rand.m

• CONFIGURATION GENERATION:

  • realn_box_p2.m
  • realn_box_p6.m
  • realn_sphere.m

• QY CALAULATION:

  • rate_box.m
  • rate_ps_1.m
  • rate_ps_1_rand.m (ploting with randomized energy configuration for PSI)
  • rate_box_rand.m (ploting with randomized energy for 5 highest/lowest QY configuration for random network with box geometry)

• MINOR CODES:

  • drawbox_ps1.tcl (code to draw the box of figure-1 in VMD)
  • rate_ps1_p6_pert (code to randomly shuffle dipole orientation in PSI stucture, except the central 6 chromophores remain fixed)
  • plot_fig_2b_ps1.m (for plotting figure-2b)
  • plot_fig_2b.m (for plotting figure-2b)