Tutorial #1: simulate 2d spectra of light-harvesting complexes with GPU-HEOM @ nanoHub

The computation and prediction of two-dimensional (2d) echo spectra of photosynthetic complexes is a daunting task and requires enormous computational resources – if done without drastic simplifications. However, such computations are absolutely required to test and validate our understanding of energy transfer in photosyntheses. You can find some background material in the recently published lecture notes on Modelling excitonic-energy transfer in light-harvesting complexes (arxiv version) of the Latin American School of Physics Marcos Moshinsky.
The ability to compute 2d spectra of photosynthetic complexes without resorting to strong approximations is to my knowledge an exclusive privilege of the Hierarchical Equations of Motion (HEOM) method due to its superior performance on massively-parallel graphics processing units (GPUs). You can find some background material on the GPU performance in the two conference talks Christoph Kreisbeck and I presented at the GTC 2014 conference (recored talk, slides) and the first nanoHub users meeting.

GPU-HEOM 2d spectra computed at nanohub

GPU-HEOM 2d spectra computed at nanohubComputed 2d spectra for the FMO complex for 0 picosecond delay time (upper panel) and 1 ps (lower panel). The GPU-HEOM computation takes about 40 min on the nanohub.org platform and includes all six Liouville pathways and averages over 4 spatial orientations.
  1. login on nanoHub.org (it’s free!)
  2. switch to the gpuheompop tool
  3. click the Launch Tool button (java required)
  4. for this tutorial we use the example input for “FMO coherence, 1 peak spectral density“.
    You can select this preset from the Example selector.
  5. we stick with the provided Exciton System parameters and only change the temperature to 77 K to compare the results with our published data.
  6. in the Spectral Density tab, leave all parameters at the the suggested values
  7. to compute 2d spectra, switch to the Calculation mode tab
  8. for compute: choose “two-dimensional spectra“. This brings up input-masks for setting the directions of all dipole vectors, we stick with the provided values. However, we select Rotational averaging: “four shot rotational average” and activate all six Liouville pathways by setting ground st[ate] bleach reph[asing , stim[ulated] emission reph[asing], and excited st[ate] abs[orption] to yes, as well as their non-rephasing counterparts (attention! this might require to resize the input-mask by pulling at the lower right corner)
  9. That’s all! Hit the Simulate button and your job will be executed on the carter GPU cluster at Purdue university. The simulation takes about 40 minutes of GPU time, which is orders of magnitude faster than any other published method with the same accuracy. You can close and reopen your session in between.
  10. Voila: your first FMO spectra appears.
  11. Now its time to change parameters. What happens at higher temperature?
  12. If you like the results or use them in your work for comparison, we (and the folks at nanoHub who generously develop and provide the nanoHub platform and GPU computation time) appreciate a citation. To make this step easy, a DOI number and reference information is listed at the bottom of the About tab of the tool-page.

With GPU-HEOM we and now you (!) can not only calculate the 2d echo spectra of the Fenna-Matthews-Olson (FMO) complex, but also reveal the strong link between the continuum part of the vibrational spectral density and the prevalence of long-lasting electronic coherences as written in my previous posts


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