|CCL 19.02.18 PhD POSITION - Multiscale modeling of a photoenzyme - AIX-MARSEILLE UNIVERSITY, FRANCE.|
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Date: Mon Feb 18 12:44:44 2019
Subject: 19.02.18 PhD POSITION - Multiscale modeling of a photoenzyme - AIX-MARSEILLE UNIVERSITY, FRANCE.
The theoretical chemistry group at the Institut of Radical Chemistry in Aix-Marseille University (France) is proposing a 3-year PhD grant:
Salary: ~1400 EUR/MONTH
Starting date: September/October 2019
Contact: Dr. Anouk Siri (anouk.siri^univ-amu.fr) ; Dr. Miquel Huix-Rotllant (miquel.huixrotllant^univ-amu.fr)
Topic:Photoinduced decarboxylation of fatty acids in hydrocarbons: a multiscale theoretical study of a flavin photoenzyme
Photoenzymes are class of of biocatalysts whose activity is driven by sunlight. They are involved in important biological functions such as photosynthesis, vision, vitamin D synthesis, DNA repair, plant development control, etc. Recently, a novel photoenzyme has been discovered in microalga Chlorella variabilis which converts fatty acids into hydrocarbons.  This reaction can potentially be used to generate biofuel, especially suitable for aviation. The photodecarboxylase enzyme contains a flavin adenine dinucleotide (FAD) cofactor in its active center. After blue light absorption, FAD undergoes a photoinduced electron transfer that generates a carboxylate radical that reacts leading to CO2 and a hydrocarbon.
In this PhD project, we will study the mechanism of photodecarboxylase enzyme by implementing a multi-scale simulation protocol, combining state-of-the-art methods like density-matrix renormalization group complete active space self-consistent field (DMRG-CASSCF), molecular dynamics and ElectroStatic Potential Fitting (ESPF) quantum mechanics/molecular mechanics (QM-MM)  to account for the effect of the protein in the chromophore and radicals chemistry. The main objectives are: (i) to establish a multi-scale protocol able to describe accurately radicals in proteins; (ii) to determine the reaction mechanism as well as the main spectroscopic properties (absorption, emission, magnetic properties, etc.) and the reaction kinetics; (iii) to improve enzyme efficiency by simulating the effect of mutations on the protein structure.
References:  D. Sorigue et al., "An algal photoenzyme converts fatty acids to hydrocarbons", Science, 357, 903 (2017);  K. H. Marti, M. Reiher, "The Density Matrix Renormalization Group Algorithm in Quantum Chemistry", Z. Phys. Chem., 224, 583 (2010);  F. Melaccio et al., "Unique QM/MM potential energy surface exploration using microiterations", Int. J. Quantum Chem., 111, 3339 (2011);
Profile of the candidate: Candidates should be in the last year of a master program or have a master's degree in chemistry or physics with a solid background in quantum chemistry or biophysics. It is desirable a prior knowledge of quantum chemistry codes (Gaussian, Orca, OpenMolcas, GAMESS-US, CHARMM, AMBER, etc.), Linux computer skills and programming (Fortran, Python, scripting).
Interested candidates should send their candidature to one of the PhD directors containing: (1) a letter of motivation, (2) the master thesis (if available) and (3) a detailed CV (basic information, publications, marks of all masters courses). Recommendation letters might be asked if the candidate is short listed.
PhD grant information: The PhD grant is offered by the French Ministry of Higher Education, Research and Innovation, and it is bound to the decision of a scientific committee organized by the Doctoral College of Chemical Sciences (https://ecole-doctorale-250.univ-amu.fr). The committee will evaluate the candidate quality thanks to a 10 minutes interview, after which a final decision will be made.NOTE THAT E-MAIL ADDRESSES HAVE BEEN MODIFIED!!!
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