Realistic Simulations of Photoactive Systems on HPC Clusters with Many-Core Processors
Photosynthesis fuels life on Earth by converting incoming solar radiation into chemical energy.
Different strategies emerged during the evolution of natural photosynthesis to collect light in antenna systems and to guide it into the reaction center.
Recent pulsed-laser experiments on parts of photosynthetic complexes reveal a time-resolved picture of the energy transport.
The presence of coherent osciullations in the dynamics of the energy transfer suggests that classical transport models need to be revised to take quantum mechanical effects into account, which do assist the transport.
The better understanding of quantum effects on the transfer through molecular networks at ambient room temperature will help to optimize light emitting OLEDs and organic photovoltaics.
The physical simulation of energy pathways requires to design new scalable algorithms for current and future many-core supercomputers.
The combined expertise of computer scientists and physicists at ZIB allows us to remove obstacles for efficient computations during the development of new tools and to explore and develop novel parallelization schemes across future processor architectures.
The resulting techniques will be integrated into the publicly available exciton dynamics simulation toolbox available at nanoHUB.
Publikationen
2020 |
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Tobias Kramer, Mirta Rodríguez | Effect of disorder and polarization sequences on two-dimensional spectra of light harvesting complexes | Photosynthesis Research, Vol.144, pp. 147-154, 2020 |
BibTeX
arXiv DOI |
2018 |
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Matthias Noack, Alexander Reinefeld, Tobias Kramer, Thomas Steinke | DM-HEOM: A Portable and Scalable Solver-Framework for the Hierarchical Equations of Motion | 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018), pp. 947-956, 2018, ISBN: 978-1-5386-5555-9 |
BibTeX
DOI |
Tobias Kramer, Matthias Noack, Alexander Reinefeld, Mirta Rodríguez, Yaroslav Zelinskyi | Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM) | Journal of Computational Chemistry, 39(22), pp. 1779-1794, 2018 |
BibTeX
arXiv DOI |
Tobias Kramer, Matthias Noack, Jeffrey R. Reimers, Alexander Reinefeld, Mirta Rodríguez, Shiwei Yin | Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM | Chemical Physics, Vol.515, pp. 262-271, 2018 |
BibTeX
arXiv DOI |
2017 |
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Tobias Kramer, Mirta Rodriguez, Yaroslav Zelinskyi | Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems | Journal of Physical Chemistry B, Vol.121, pp. 463-470, 2017 |
BibTeX
DOI arXiv |
Matthias Noack | OpenCL in Scientific High Performance Computing: The Good, the Bad, and the Ugly | Proceedings of the 5th International Workshop on OpenCL, pp. 12:1-12:3, IWOCL 2017, 2017 |
BibTeX
DOI |
Tobias Kramer, Mirta Rodriguez | Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria | Scientific Reports, Vol.7, p. 45245, 2017 |
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2016 |
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Jeffrey R. Reimers, Malgorzata Biczysko, Douglas Bruce, David F. Coker, Terry J. Frankcombe, Hideki Hashimoto, Jürgen Hauer, Ryszard Jankowiak, Tobias Kramer, Juha Linnanto, Fikret Mamedov, Frank Müh, Margus Rätsep, Thomas Renger, Stenbjörn Styring, Jian Wan, Zhuan Wang, Zheng-Yu Wang-Otomo, Yu-Xiang Weng, Chunhong Yang, Jian-Ping Zhang, Arvi Freiberg, Elmars Krausz | Challenges facing an understanding of the nature of low-energy excited states in photosynthesis | BBA Bioenergetics, 1857(9), pp. 1627-1640, 2016 |
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