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Exciton Dynamics Lab for Light-Harvesting Complexes (GPU-HEOM)
Non-Markovian calculation of absorption spectra, 2d echo-spectra, coherences and polulation dynamics for light-harvesting complexes.
Version 1.3 - published on 05 Jul 2017
doi:10.4231/D3RF5KH7G cite this
This tool is closed source.
For light-harvesting complexes (i.e. the Fenna-Matthews-Olson complex) or model systems with less than 8 sites, you can calculate absorption spectra, two-dimensional echo-spectra, and track the exciton populations and coherences.
This tool employs a variant of the reduced hierarchy equations of motion (HEOM) method 1 for generalized spectral densities and implemented on massively parallel graphics processing units (GPU-HEOM) 2 3.
GPU-HEOM handles non-Markovian effects and works well in the biologically relevant temperature range.
- independent phonon baths attached to each site, the same shape of the spectral density J(omega) is taken for each independent bath
- decomposition of the vibronic spectral density into a superposition of shifted Lorentzian peaks
- high-temperature approximation
- for two-dimensional spectra, the program computes up to six Feynman pathways 4, and constructs the manifolds for the two exciton states as described in 5
- convergence must be verified by increasing the hierarchy depth (be careful, this quickly exhausts the available GPU memory) and by decreasing the time-step. We recommend to start from the examples provided.
- at lower temperatures (for the FMO complex typically below 100 K), the high-temperature approximation becomes invalid
- activation of excited-state absorption mode in two-dimensional spectroscopy requires longer computation times and consumes more memory. Use this option with caution.
The examples are a good starting point for own explorations. A short tutorial will be published soon, see also quantumdynamics.wordpress.com for additional background information and tutorials.
- Y. Tanimura and R. Kubo (1989): Time Evolution of a Quantum System in Contact with a Nearly Gaussian-Markoffian Noise Bath, J. Phys. Soc. Jpn. vol. 58, p. 101
- C. Kreisbeck and T. Kramer (2012): Long-Lived Electronic Coherence in Dissipative Exciton-Dynamics of Light Harvesting Complexes, Journal of Physical Chemistry Letters, vol. 3, p. 2828
- C. Kreisbeck, T. Kramer, M. Rodríguez, B.Hein (2011): High-performance solution of hierarchical equations of motions for studying energy-transfer in light-harvesting complexes, Journal of Chemical Theory and Computation, vol. 7, p. 2166
- S. Mukamel, Principles of nonlinear optical spectroscopy
- B. Hein, C. Kreisbeck, T. Kramer, M. Rodríguez (2012): Modelling of Oscillations in Two-Dimensional Echo-Spectra of the Fenna-Matthews-Olson Complex, New Journal of Physics vol. 14, p. 023018
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