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Supercomputer-Facilitated Simulation to Shed Light on Photosynthesis

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Posted August 27, 2015

Despite our substantial knowledge about the process of photosynthesis, whereby plants convert sunlight into usable form of chemical energy, scientists are still uncertain as to what happens at the exact moment when light particles hit the Light Harvesting Complex II (LHC-II) molecule, responsible for the reaction.

Basque Country scientists, in collaboration with a number of European colleagues from other universities, are running a supercomputer-facilitated simulation of the LHC-II molecule (pictured above) to figure out what happens at the moment when photons reach its surface, triggering photosynthesis. Image credit: Aegon via Wikimedia.org, CC BY-SA 3.0.

Basque Country scientists, in collaboration with a number of European colleagues from other universities, are running a supercomputer-facilitated simulation of the LHC-II molecule (pictured above) to figure out what happens at the moment when photons reach its surface, triggering photosynthesis. Image credit: Aegon via Wikimedia.org, CC BY-SA 3.0.

In order to solve this long-standing mystery, researchers at the UPV/EHU University of the Basque Country, in collaboration with scientists from several other European schools, are currently working on a large-scale simulation of said molecule that will use a number of supercomputers running specialised software.

The LHC-II molecule comprises as many as 17,000 individual atoms and thus requires the fastest computers available to simulate its internal workings. The model – said to be the largest of its kind in the field – will be developed on the German Juqueen (458,752 processing cores), the Italian Fermi (163,840 cores), the German Hydra (65,320 cores) and the Catalan MareNostrum III (48,896 cores), among others.

For the calculations themselves, the research team will employ the Octopus software package, underpinned by two theories which are the result of the reformulation of quantum mechanics and based on electronic density. With these two theories it has been possible to solve quantum mechanics problems that would otherwise be too complex even for a supercomputer.

According to Joseba Alberdi, a computer engineer at the UPV/EHU and main author on the study, the team‘s main objective was to optimize the Octopus code and achieve high performance required for obtaining the right acceleration factors in supercomputer-facilitated calculations.

Succeeding at this is a tall order, and yet, despite memory and performance problems that arose during attempts to run the software across multiple processors, the researchers have already managed to model significant parts of the target molecule.

“We have simulated systems comprising 5,759, 4,050 and 6,075 atoms; according to the data we have available, they are the biggest simulations carried out so far,” Alberdi said. In these simulations, they have been able to prove that the theory coincides with reality. “These simulations will enable us to understand, for the first time, the reactions that occur during the first femtoseconds (10–15 s) of photosynthesis“.

Perhaps just as importantly, the improvements Alberdi’s team incorporated into the Octopus package has enabled it to simulate many other systems of similar size, enabling physicists to improve their modelling endeavours. The software, licensed under the GNU General Public Licence (GPL), is free of charge and can be downloaded, used and further developed by any interested party.

Sources: study abstract, phys.org.

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