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The Mechanisms of Vision Studied by Quantum Monte Carlo Calculations

Principal Investigator: Leonardo Guidoni, Computational Biophysics, Biochemistry, and Chemistry, University of L'Aquila (Italy)
HPC Platform: JUQUEEN of JSC

In the rod cells of the eyes of vertebrates, a special protein, named Rhodopsin, is responsible for the detection of the light and is directly involved in the activation of the signaling cascade that triggers the nervous pulses of the retina. The deep understanding of the early mechanisms of light vision goes beyond the scientific interest as it is also an important issue for the rationalization of many retina diseases. In Rhodopsin the light is captured by its chromophore, the Retinal Protonated Schiff Base, which, upon absorption of a photon, makes a sort of “twist” or more properly a 11-cis/trans isomerization. During this process a certain amount of energy is stored in the distorted chromophore, which subsequently relaxes triggering the protein structural changes that activate the signal cascade to vision. Even in absence of light the 11-cis to all trans isomerization can still spontaneously occur by thermal activation in the ground state, a process that is limiting visual sensitivity.

The accurate determination of the electronic properties of the Retinal and the energy profiles along different isomerization pathways is challenging the chemists and physicists due to the high degrees of correlation between the electrons of this molecule.

Massively parallel High-Performance-Computing facilities, such as provided by the Jülich Supercomputing Centre, are significantly influencing computational chemistry, since thanks to their use it is possible to tackle the description of correlated molecular systems such as the Retinal in Rhodopsin with high accuracy.

A team of researchers of the University of L’Aquila Italy led by Leonardo Guidoni, in collaboration with the research group of Sandro Sorella in Trieste was able to use Quantum Monte Carlo, which is an embarrassingly parallel technique based on random numbers, to study with unprecedented accuracy the electronic structure of Retinal models.

Geometrical relaxation of the retinal in its protein environment firstly revealed how geometrical parameters can finely tune the color of the absorbed photon. The nature of the electronic structure and the energetics along the isomerization pathways have been also studied, demonstrating how the role of electron correlation is crucial for the correct description of these biological systems.

The Mechanisms of Vision Studied by Quantum Monte Carlo CalculationsA snapshot from the random walk of the electrons (yellow and orange) during Quantum Monte Carlo calculations of the mechanisms of vision.
Copyright: Universita' degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, CBBC Group

This project was made possible through the Partnership for Advanced Computing in Europe (PRACE) using HPC system JUQUEEN of Jülich Supercomputing Centre.

Scientific Contact:
Leonardo Guidoni
Universita' degli studi dell'Aquila
Dipartimento di Scienze Fisiche e Chimiche
CBBC Group - http://bio.phys.uniroma1.it
e-mail: leonardo.guidoniv[at]univaq.it

February 2015

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