SANA BOUGUEROUA

Expertise : Application of Graph theory for post-processing MD simulations

I. From a 3D structure to a topological 2D-MolGraph: a molecular system is defined as a mixed-coloured graph (2D-MolGraph) such that vertices represent atoms and edges represent the bonds formed between them. The exploration of different conformations along a MD trajectory can be seen as an exploration of different graph topologies using isomorphism.

II. From 2D-MolGraphs to a coarse-grained polygraph: a molecular system is defined as a colored graph (Polygraph) such that vertices represent polycycles (Hbonded rings/cycles) and edges represent interactions between the polycycles present in the conformers. The difficulty remains in finding a clustering that minimizes polymorphic cycles.

III. From 2D-MolGraphs to Motifs: recognizing, characterizing, and comparing motifs (sub-graphs) in amorphous silica interfaces using a brute force algorithm, and creating a database of these motifs.

IV. Graph-theoretic-based method for the vibrational mode's assignment: recognizing, characterizing, and comparing vibrational modes using indirect weighted colored graphs that represent the spectral data. Proof of principle has been done for the IR spectroscopy of gas-phase molecules.

Internal scientific collaboration

• Development of tools  based on graph theory for the analysis and characterization of MD trajectories of 'simple' gas phase molecules to much more complex heterogeneous aqueous interfaces in the condensed phase and catalysis for the members of the Theory and Modeling Team of LAMBE.

1. High-Throughput Reactivity Exploration for Extended Databases of Transition Metal Catalysts. A. Hashemi, S. Bougueroua M.-P. Gaigeot, and E. Pidko. Journal of Chemical Information and Modeling, 2023.
   DOI: 10.1021/acs.jcim.3c00660
2. Algorithmic graph theory, reinforcement learning and game theory in MD simulations: from 3D-structures to topological 2D-MolGraphs and backwards.  S. Bougueroua, M. Bricage, Y. Aboulfath, D. Barth, M.-P. Gaigeot. Molecules, 2023
   DOI: 10.3390/molecules28072892
3. Algorithmic graph theory for post-processing molecular dynamics trajectories. Bougueroua, Sana and Aboulfath, Ylène and Barth, Dominique and Gaigeot, Marie-Pierre. Molecular Physics, 2023.
   DOI: 10.1080/00268976.2022.2162456
4. ReNeGate: A Reaction Network Graph-Theoretical Tool for Automated Mechanistic Studies in Computational Homogeneous Catalysis. A. Hashemi, S. Bougueroua, M.-P. Gaigeot, E. Pidko. J. Chem. Theo. Comput. , 2022
   DOI: 10.1021/acs.jctc.2c00404
5. Direct Dynamics for Vibrational Spectroscopy: From Large Molecules in the Gas Phase to the Condensed Phase. Bougueroua, S.; Chantitch, V.; Chen, W.; Pezzotti, S.; Gaigeot, M.-P. Vibrational Dynamics Of Molecules, 2022
   DOI:10.1142/9789811237911_0011
6. Enhanced conductivity of water at the electrified air–water interface: a DFT-MD characterization. F. Creazzo, S. Pezzotti, S. Bougueroua, A. Serva, J. Sponer, F. Saija, G. Cassone, M-P. Gaigeot. Physical Chemistry Chemical Physics 2020.
   DOI: 10.1039/C9CP06970D
7. Conformational assignment of gas phase peptides and their H-Bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and Graph Theory for modes assignment. D. Ruth Galimberti, S. Bougueroua, J. Mahé, M. Tommasini, A. M. Rijs, and M.-P. Gaigeot. Faraday Discussions 'Advances in Ion Spectroscopy' 2019.
   DOI:10.1039/C8FD00211H
8. Combining ab-initio and classical molecular dynamics simulations to unravel the structure of the 2D-HB-network at the air-water interface. Serva A, Pezzotti S, Bougueroua S, Galimberti DR, Gaigeot M-P. Journal of Molecular Structure 2018.
   DOI: 10.1016/201803074
9. Graph theory for automatic structural recognition in molecular dynamics simulations. Bougueroua, S.; Barth, D.; Quessette, F.; Spezia, R.; Vial, S.; and Gaigeot, M.-P. J. Chem. Phys. 2018.
   DOI: 10.1063/1.5045818
10. A new graph algorithm for the analysis of conformational dynamics of molecules. Barth, D.; Bougueroua, S.; Gaigeot, M.-P.; Quessette, F.; Spezia, R.; and Vial, S. In Information Sciences and Systems 2015, pages 319–326. Springer 2016.
    DOI:10.1007/978-3-319-22635429