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Up Directory 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^ ; Dr. Miquel Huix-Rotllant (miquel.huixrotllant^

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. [1] 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),[2] molecular dynamics and ElectroStatic Potential Fitting (ESPF) quantum mechanics/molecular mechanics (QM-MM) [3] 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: [1] D. Sorigue et al., "An algal photoenzyme converts fatty acids to hydrocarbons", Science, 357, 903 (2017); [2] K. H. Marti, M. Reiher, "The Density Matrix Renormalization Group Algorithm in Quantum Chemistry", Z. Phys. Chem., 224, 583 (2010); [3] 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 ( The committee will evaluate the candidate quality thanks to a 10 minutes interview, after which a final decision will be made.

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