PhotoCaM: Photosynthetic Antennas in a Computational Microscope

A Marie Skłodowska-Curie Actions Doctoral Network funded by the European Union

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Photosynthesis relies on harvesting the sun light and on transforming the solar energy into chemical energy to sustain almost all life on earth. An enhanced molecular-level understanding of photosynthesis and particularly of the light-harvesting process is of key significance.

In this Doctoral Network we aim at training a new generation of computational scientists which can treat complex and interdisciplinary problems such as light harvesting on a molecular level using theoretical and computational tools. The interdisciplinary nature of the problem requires a combined knowledge from biology, chemistry, physics and computer science in order to combine state-of-the-art approaches like molecular dynamics simulations, quantum chemistry, theoretical spectroscopy and machine learning into multi-scale schemes.

This joint undertaking is a unique chance in research but especially also in training young scientists in interdisciplinary teamwork, method training and high-performance computing in academic as well as non-academic settings.

The scientific approach employed in this Doctoral Network has the advantage of combining diverse aspects of computational modelling to pursue the scientific objectives of the project. While the light-harvesting complexes are large biological systems, the excited state calculations determine detailed quantum chemical knowledge. The propagation of the excitation energy and the determination of non-linear spectra are more based on the area of (bio)physics. Most of the computations are numerical expensive and together with machine learning techniques, the development, adaptation and optimization of the involved numerical codes belongs to the area of computer science.

The employed methods exert strong complementarity in a way that at the end the Doctoral Candidates will gain expertise in individual methodologies but also acquire the necessary insight into a holistic view of computational modelling, a crucial characteristic of a new generation of computational scientists in biological and biophysical applications. Molecular dynamics simulations (Projects 2, 6, 10) will give input to the quantum structure and (exciton) dynamics methodologies (Projects 1, 3, 8, 9) with the latter being necessary for the spectroscopic description of light-harvesting complexes (Projects 4, 5, 7). Despite the complementarity of the employed methodologies, the individual projects can stand also independently of each other to a large degree though they evolve their full power only in combination.

• Project 1: Exciton transfer and NPQ in diatoms: A multi-scale approach employing machine learning (Kleinekathöfer, Bremen, Germany)
• Project 2: The Configurational Space of Fucoxanthin and Chlorophyll-a/c binding proteins (FCP) in diatoms (Daskalakis, Patras, Greece)
• Project 3: Multiscale modeling of energy transport for light-harvesting and non-photochemical quenching in higher plants (Mennucci, Pisa, Italy)
• Project 4: Spectroscopic Signatures of Exciton Annihilation and Quenching (Jansen, Groningen, Netherlands)
• Project 5: Development of simulation approaches for nonlinear spectroscopy of molecular complexes (Abramavicius, Vilnius, Lithuania)
• Project 6: The configurational space of LH complexes from higher plants – sensing and response to pH changes (Liguori, Castelldefels, Spain)
• Project 7: Charge transfer states and higher excited states in light-harvesting (Renger, Linz, Austria)
• Project 8: Non-adiabatic dynamics in LH complexes with the use of Machine Learning algorithms (Elstner, Karlsruhe, Germany)
• Project 9: Environmental effects (solvent and protein chain) on high accuracy QM excited-state calculations via multiscale QM/MM on the light harvesting complex (Faccts, Cologne, Germany)
• Project 10: pKa prediction for LHC residues, in the presence of LHC-protein and LHC-carotenoid, lipid interactions (OneAngstrom, Grenoble, France)

The positions for Project 1 (Bremen), Project 2 (Patras), and Project 10 (Grenoble) are still open!

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