@article{KramerRodriguezZelinskyi2017, author = {Kramer, Tobias and Rodriguez, Mirta and Zelinskyi, Yaroslav}, title = {Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems}, volume = {121}, journal = {Journal of Physical Chemistry B}, arxiv = {http://arxiv.org/abs/1811.10683}, doi = {10.1021/acs.jpcb.6b09858}, pages = {463 -- 470}, year = {2017}, abstract = {Time-resolved spectroscopy provides the main tool for analyzing the dynamics of excitonic energy transfer in light-harvesting complexes. To infer time-scales and effective coupling parameters from experimental data requires to develop numerical exact theoretical models. The finite duration of the laser-molecule interactions and the reorganization process during the exciton migration affect the location and strength of spectroscopic signals. We show that the non-perturbative hierarchical equations of motion (HEOM) method captures these processes in a model exciton system, including the charge transfer state.}, language = {en} } @article{ReimersBiczyskoBruceetal.2016, author = {Reimers, Jeffrey R. and Biczysko, Malgorzata and Bruce, Douglas and Coker, David F. and Frankcombe, Terry J. and Hashimoto, Hideki and Hauer, J{\"u}rgen and Jankowiak, Ryszard and Kramer, Tobias and Linnanto, Juha and Mamedov, Fikret and M{\"u}h, Frank and R{\"a}tsep, Margus and Renger, Thomas and Styring, Stenbj{\"o}rn and Wan, Jian and Wang, Zhuan and Wang-Otomo, Zheng-Yu and Weng, Yu-Xiang and Yang, Chunhong and Zhang, Jian-Ping and Freiberg, Arvi and Krausz, Elmars}, title = {Challenges facing an understanding of the nature of low-energy excited states in photosynthesis}, volume = {1857}, journal = {BBA Bioenergetics}, number = {9}, doi = {10.1016/j.bbabio.2016.06.010}, pages = {1627 -- 1640}, year = {2016}, abstract = {While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.}, language = {en} } @inproceedings{NoackReinefeldKrameretal.2018, author = {Noack, Matthias and Reinefeld, Alexander and Kramer, Tobias and Steinke, Thomas}, title = {DM-HEOM: A Portable and Scalable Solver-Framework for the Hierarchical Equations of Motion}, booktitle = {2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018)}, isbn = {978-1-5386-5555-9}, doi = {10.1109/IPDPSW.2018.00149}, pages = {947 -- 956}, year = {2018}, abstract = {Computing the Hierarchical Equations of Motion (HEOM) is by itself a challenging problem, and so is writing portable production code that runs efficiently on a variety of architectures while scaling from PCs to supercomputers. We combined both challenges to push the boundaries of simulating quantum systems, and to evaluate and improve methodologies for scientific software engineering. Our contributions are threefold: We present the first distributed memory implementation of the HEOM method (DM-HEOM), we describe an interdisciplinary development workflow, and we provide guidelines and experiences for designing distributed, performance-portable HPC applications with MPI-3, OpenCL and other state-of-the-art programming models. We evaluated the resulting code on multi- and many-core CPUs as well as GPUs, and demonstrate scalability on a Cray XC40 supercomputer for the PS I molecular light harvesting complex.}, language = {en} } @article{KramerNoackReinefeldetal.2018, author = {Kramer, Tobias and Noack, Matthias and Reinefeld, Alexander and Rodr{\´i}guez, Mirta and Zelinskyi, Yaroslav}, title = {Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM)}, volume = {39}, journal = {Journal of Computational Chemistry}, number = {22}, publisher = {Wiley Periodicals, Inc.}, arxiv = {http://arxiv.org/abs/arXiv:1803.03498}, doi = {doi:10.1002/jcc.25354}, pages = {1779 -- 1794}, year = {2018}, abstract = {Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes.}, language = {en} } @article{KramerNoackReimersetal.2018, author = {Kramer, Tobias and Noack, Matthias and Reimers, Jeffrey R. and Reinefeld, Alexander and Rodr{\´i}guez, Mirta and Yin, Shiwei}, title = {Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM}, volume = {515}, journal = {Chemical Physics}, publisher = {Elsevier B.V.}, arxiv = {http://arxiv.org/abs/arXiv:1805.10484}, doi = {10.1016/j.chemphys.2018.05.028}, pages = {262 -- 271}, year = {2018}, abstract = {We analyze the exciton dynamics in PhotosystemI from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Foerster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results.}, language = {en} } @article{KramerRodriguez2020, author = {Kramer, Tobias and Rodr{\´i}guez, Mirta}, title = {Effect of disorder and polarization sequences on two-dimensional spectra of light harvesting complexes}, volume = {144}, journal = {Photosynthesis Research}, arxiv = {http://arxiv.org/abs/1912.03003}, doi = {10.1007/s11120-019-00699-6}, pages = {147 -- 154}, year = {2020}, abstract = {Two-dimensional electronic spectra (2DES) provide unique ways to track the energy transfer dynamics in light-harvesting complexes. The interpretation of the peaks and structures found in experimentally recorded 2DES is often not straightforward, since several processes are imaged simultaneously. The choice of specific pulse polarization sequences helps to disentangle the sometimes convoluted spectra, but brings along other disturbances. We show by detailed theoretical calculations how 2DES of the Fenna-Matthews-Olson complex are affected by rotational and conformational disorder of the chromophores.}, language = {en} } @article{KramerRodriguez2017, author = {Kramer, Tobias and Rodriguez, Mirta}, title = {Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria}, volume = {7}, journal = {Scientific Reports}, doi = {10.1038/srep45245}, pages = {45245}, year = {2017}, abstract = {Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. From our calculation one can infer the coupling of the antenna chlorosome with the environment and the coupling between the chlorosome and the Fenna-Matthews-Olson complex. We show that environment assisted transport between the subunits is the required mechanism to reproduce the experimental two-dimensional electronic spectra.}, language = {en} } @inproceedings{Noack2017, author = {Noack, Matthias}, title = {OpenCL in Scientific High Performance Computing: The Good, the Bad, and the Ugly}, booktitle = {Proceedings of the 5th International Workshop on OpenCL}, doi = {10.1145/3078155.3078170}, pages = {12:1 -- 12:3}, year = {2017}, abstract = {For writing a new scientific application, portability across existing and future hardware should be the major design goal, as there is a multitude of different compute devices, and programme codes typically outlive systems by far. Unlike other programming models that address parallelism or heterogeneity, OpenCL does provide practical portability across a wide range of HPC-relevant architectures. Other than that, it has a range of further advantages like being a library-only implementation, and using runtime kernel-compilation. We present experiences with utilising OpenCL alongside C++, MPI, and CMake in two real-world scientific codes. Our targets are a Cray XC40 supercomputer with multi- and many-core (Xeon Phi) CPUs, as well as multiple smaller systems with Nvidia and AMD GPUs. We shed light on practical issues arising in such a scenario, like the interaction between OpenCL and MPI, discuss solutions, and point out current limitations of OpenCL in the domain of scientific HPC from an application developer's and user's point of view.}, language = {en} }