2013081486 LHC-ABS - The optical absorption spectra of a real Light Harvesting Complex from first-principles: the spinach case


Status: ongoing project
Contract Number:

More than 50% of the light captured by green plants for use in photosynthesis is absorbed by the light harvesting complex (LHCII). LHCII is a trimeric protein assembly with three-fold symmetry.Each monomer unit contains, in addition to the protein, 14 chlorophyll (both type A and B) and 4 xanthophyll (lutein, neoxanthin and violoxanthin) chromophore molecules which are the key functional units of the LHC system and perform the actual light-harvesting. In all, LHCII contains approximately 16,900 atoms, 7000 of which belong to the chromophores. Although usually bound within cell membranes in vivo, LHCII is a robust structure and survives intact the processes of purification and crystallisation meaning that the crystal structure is known accurately and also that it has become possible to perform experimental studies of the isolated LHCII in a fairly routine manner.


Attempts at the theoretical/computational study of light absorption has to take in account that this is fundamentally a quantum process. The study of these complexes is usually done in a semi-empirical fashion that requires parameters to be adjusted from numerical calculations or experimental results. An ab-initio study of this system would provide more accurate results and have more predictive power to understand the electron dynamics of the system. At the moment, the only ab-initio method that can accurately treat systems containing hundreds or thousands of atoms is density functional theory (DFT), and, for the particular case of optical properties, its time-dependent extension (TDDFT). Although improvements in scientific codes and HPC infrastructures made over the last years have considerably increased the size of the systems that can be routinely be simulated using TDDFT, performing such calculations for a system as large as the full LHCII is still a significant challenge. In fact, a successful calculation of the optical absorption spectra of the full LHC

In this project we propose to study the various contributions made by each of the building
blocks of the light-harvesting antenna to its characteristic electronic structure and optical properties by performing TDDFT simulations of the optical response of the full LHCII complex and of its components. Computationally we can easily separate the protein,
chlorophyll and xanthophyll assemblies and study them in isolation and at various levels of combination whilst maintaining them at the original geometries found in the complete
complex. Thus, it will be possible to clearly separate the spectral features corresponding to the separate components and assess how the interplay between them leads to the building up of the optical response of the whole system.


Angel Rubio Secades (project leader)
Micael JT Oliveira
Fernando Nogueira
Miguel Marques
Xavier Andrade
Joseba Alberdi-Rodriguez
Joaquim Jornet-Somoza
Bruce Milne

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