Welcome to...
Benjamin Bouvier's homepage


Science... but not just!


I hold a tenured senior researcher position at CNRS (French public academic research institution).


Photography has been a hobby of mine for 10+ years.


Music and other stuff... (under construction)

Science projects

I use computer simulations to study recognition processes between biomacromolecules. Please click on the thumbnails for more details on individual research projects.

Deep learning protein interfaces

Predicting structure and function from protein-protein interface shape

Oligosaccharides as protein interface mimics

Using deep learning to tap the potential for novel drugs

Ionic liquids

From green fuels to batteries and biomass extraction

Controlling membrane deformations

Facilitating the study of membrane remodeling processes

Pyoverdines as antibiotics

Fighting bacteria using their own iron acquisition machinery

Ion mobility in batteries

Exploiting the affinities of LiTFSI and silica to enhance conductivity

Multivalent antibiotics

Preventing pathogenic bacteria from recognizing their host


Cooperativity in DNA-transcription factor recognition and DNA allostery

Mechanisms of Ubiquitin Recognition

Ubiquitin: understanding the cell's postal code

DNA Recognition by the SRY Protein

Finding target DNA sequences inside a genome of several million base pairs

DNA Recognition by Anticancer Drug Daunomycin

DNA binding mechanism: one drug, several bound structures

Predicting Active Patches at Protein-Protein Interfaces

Detecting essential aminoacids using interface geometry

Slow Processes in Nucleic Acids

Essential to cell life, yet difficult to characterize...

Charge and Excitation Transfer in Biomolecules and Clusters

Collective electronic states or localized charge/excitation?


My resume

  • Education

      2000-2003: PhD thesis

      Computational chemistry, University of Paris 11. Theoretical study of charge and excitation transfer in double-stranded nucleic acids and molecular clusters.

      1998-1999: Master's degree

      Molecular physical chemistry, University of Paris 11.

      1995-1998: Chemical engineer

      École Nationale Supérieure de Chimie de Montpellier, Montpellier, France.

  • Professional experience

      2023-: Tenured research position at the Enzyme and Cell Engineering Lab (GEC), CNRS UMR 7025, Amiens (France): membrane dynamics, membrane-peptide interaction, chemobiological drug design.

      Multiscale modeling; deep learning; free energy calculations; software development.

      2014: Tenured research position at Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, CNRS UMR7378, Amiens (France): drug-pathogen recognition.

      Sugar-lectin recognition; inhibition of Gram-negative membrane transporters; development of coarse-grained models; free energy calculations; software development.

      2008: Tenured research position following postdoctoral fellowship at Institut de Biologie et Chimie des Protéines, CNRS UMR5086, Lyon (France): dynamics of protein-DNA recognition.

      Dynamics of protein-DNA and protein-protein complexes; development of generalized constraints; characterization of flexibility; free energy calculations; software development.

      2007: Postdoctoral fellowship, INRIA Sophia-Antipolis & Institut Pasteur, Paris (France): geometrical and topological methods for the study of protein flexibility and recognition.

      Modeling of protein-protein interfaces; characterization of correlated motion and conformational transitions from molecular dynamics simulations; software development.

      2004: Postdoctoral fellowship at the Max Planck Institute for Biophysical Chemistry, Göttingen (Germany): molecular dynamics study of nucleic acids at long timescales.

      Base flipping in DNA; conformational transitions of the Holliday junction; characterization of the conformational space of proteins; development of methods to study correlated motion and compute free energies; software development.

      2000: PhD thesis at Laboratoire Françis Perrin, CNRS URA2453/Commissariat à l’Énergie Atomique, Saclay (France): theoretical study of charge and excitation transfer processes in DNA strands and molecular clusters.

      Development of force fields combining classical and quantum mechanical terms; effective Hamiltonian approaches; ionized and excited states of DNA strands; energy landscape exploration methods; semi-classical molecular dynamics; software development.

      2000: Military service as a corps scientist, at Institut de Recherche Criminelle de la Gendarmerie Nationale, Rosny-sous-Bois (France): development and optimization of chromatographic methods for the detection and characterization of narcotics in biological matrices.

      1999: Research internship at Laboratoire Françis Perrin, CNRS URA2453/Commissariat à l’Énergie Atomique, Saclay (France): chiral discrimination in small heteroclusters.

      1998: Engineering internship at Commissariat à l’Énergie Atomique, Saclay (France): design and synthesis of steroid hormones labeled with stable isotopes.

      1997: Internship at Institut Lavoisier, CNRS/UVSQ, Versailles (France). Synthesis and characterization of novel polyoxothiometallic compounds.

  • Research: in silico molecular modeling and simulation

      Biomolecular recognition processes

      Protein/DNA/carbohydrate/drug recognition and binding. Indirect (flexibility-related) and multivalent recognition mechanisms.

      Free energy calculations

      Binding free energies for molecular recognition. Entropic effects. Enhanced sampling molecular dynamics. Development of generalized constraints for the efficient exploration of free energy landscapes.

      Force field design

      All-atom and coarse-grained models for novel pharmaceutical compounds.

      Software development

      Scientific computing. Algorithms for the simulation and analysis of biomolecular systems.


    B. Bouvier, ‘Substituted oligosaccharides as protein mimics: deep learning free energy landscapes’, Journal of Chemical Information and Modeling, doi:10.1021/acs.jcim.3c00179, 2023. [pdf]
    C. Ferreira Funes, B. Bouvier, C. Cézard, C. Fuentealba, A. Jamali, M. Courty, C. Hadad, A. Nguyen Van Nhien, ‘Theoretical and experimental studies of chitin nanocrystals treated with ionic liquid or deep eutectic solvent to afford nanochitosan sheets’, Journal of Molecular Liquids 375, 121350, 2023. [pdf]
    J. Bidal, C. Cézard, B. Bouvier, C. Hadad, A. Nguyen Van Nhien, M. Becuwe, ‘Fundamental insight into the interaction between a lithium salt and an inorganic filler for ion mobility using a synergic theoretical-experimental approach’, Journal of Colloid and Interface Science 625, 734, 2022. [pdf]
    B. Bouvier, ‘Protein-protein interface topology as a predictor of secondary structure and molecular function using convolutional deep learning’, Journal of Chemical Information and Modeling 61, 3292, 2021. [pdf]
    G. Huet, M. Araya-Farias, R. Alayoubi, S. Laclef, B. Bouvier, I. Gosselin, C. Cézard, R. Roulard, M. Courty, C. Hadad, E. Husson, C. Sarazin, A. Nguyen Van Nhien, ‘New biobased-zwitterionic ionic liquids: efficiency and biocompatibility for the development of sustainable biorefinery processes’, Green Chemistry 22, 2935, 2020. [pdf]
    B. Bouvier, ‘Curvature as a collective coordinate in enhanced sampling membrane simulations’, Journal of Chemical Theory and Computation 15, 6551, 2019. [pdf]
    C. Cézard, P. Sonnet, B. Bouvier, ‘Ironing out pyoverdine’s chromophore structure: serendipity or design?’, Journal of Biological Inorganic Chemistry 24, 659, 2019. [pdf]
    B. Bouvier, C. Cézard, ‘Impact of iron coordination isomerism on pyoverdine recognition by the FpvA membrane transporter of Pseudomonas aeruginosa’, Physical Chemistry Chemical Physics 19, 29498, 2017. [pdf]
    B. Bouvier, ‘Optimizing the multivalent binding of bacterial lectin LecA by glycopeptide dendrimers for therapeutic purposes’, Journal of Chemical Information and Modeling 56, 1193, 2016. [pdf]
    C. Cézard, B. Bouvier, A. Dassonville-Klimpt, P. Sonnet , ‘The origin of the stereoselective alkylation of 3-substituted-2-oxopiperazines: A computational investigation’, Computational and Theoretical Chemistry 1078, 1, 2016. [pdf]
    B. Bouvier, C. Cézard, P. Sonnet , ‘Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations’, Physical Chemistry Chemical Physics 17, 18022, 2015. [pdf]
    F. Merino, B. Bouvier, V. Cojocaru , ‘Cooperative DNA recognition modulated by an interplay between protein-protein interactions and DNA-mediated allostery’, PLoS Computational Biology, e1004287, 2015. [pdf]
    B. Bouvier, ‘Decoding the patterns of uniquitin recognition by ubiquitin-associated domains from free energy simulations’, Physical Chemistry Chemical Physics 16, 48, 2014. [pdf]
    M. Wilhelm, A. Mukherjee, B. Bouvier , K. Zakrzewska, J. T. Hynes, R. Lavery, ‘Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA’, Journal of the American Chemical Society 134, 8588, 2012. [pdf]
    B. Bouvier, K. Zakrzewska, R. Lavery, ‘Protein-DNA recognition triggered by a DNA conformational switch’, Angewandte Chemie 50, 6516, 2011. [pdf]
    K. Zakrzewska, B. Bouvier, A. Michon, C. Blanchet, R. Lavery, ‘Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies’, Physical Chemistry Chemical Physics 11, 10712, 2009. [pdf]
    B. Bouvier, R. Lavery, ‘A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations’, Journal of the American Chemical Society 131, 9864, 2009. [pdf]
    B. Bouvier, R. Grünberg, M. Nilges, F. Cazals, ‘Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition’, Proteins: Structure, Function and Bioinformatics 76, 677, 2009. [pdf]
    B. Bouvier, H. Grubmüller, ‘A molecular dynamics study of slow base flipping in DNA using conformational flooding’, Biophysical Journal 93, 770, 2007. [pdf]
    B. Bouvier, H. Grubmüller, ‘Molecular dynamics study of slow base flipping in DNA using conformational flooding’, Abstracts of Papers of the American Chemical Society 229, 775, 2005.
    B. Bouvier, P. Millié, M. Mons, ‘Investigation of the photoionization mechanism of small aromatic homoclusters’, Journal of Physical Chemistry A 108, 4254, 2004. [pdf]
    C. Cézard, B. Bouvier, V. Brenner, M. Defranceschi, P. Millié, J.-M. Soudan, J.-P. Dognon, ‘Theoretical investigation of small alkali cation-molecule clusters : a model potential approach’, Journal of Physical Chemistry B 108, 1497, 2004. [pdf]
    B. Bouvier, ‘Theoretical study of charge and excitation transfer in molecular assemblies: applications to van der Waals clusters and double-stranded oligonucleotides’, PhD thesis, University of Paris XI – Orsay, 2003. [pdf]
    B. Bouvier, J.-P. Dognon, R. Lavery, D. Markovitsi, P. Millié, D. Onidas, K. Zakrzewska, ‘Influence of conformational dynamics on the exciton states of DNA oligomers’, Journal of Physical Chemistry B 107, 13512, 2003. [pdf]
    B. Bouvier, V. Brenner, P. Millié, J.-M. Soudan, ‘A model potential approach to charge transfer phenomena in aromatic cluster ions’, Journal of Physical Chemistry A 106, 10326, 2002. [pdf]
    B. Bouvier, T. Gustavsson, D. Markovitsi, P. Millié, ‘Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices’, Chemical Physics 275, 75, 2002. [pdf]
    C. Crépin, P. de Pujo, B. Bouvier, V. Brenner, P. Millié, ‘A simulation of naphthalene matrix isolation: comparison with experiments’, Chemical Physics 272, 243, 2001. [pdf]


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Benjamin Bouvier

Enzyme and Cell Engineering Lab (GEC)
UMR7025 CNRS - Université de Picardie Jules Verne
10, rue Baudelocque
F-80039 Amiens Cedex, France