Annuaire

  https://www.sayens-materiaux-technologies.fr/modelisation-moleculaire

PHysique appliquée aux Protéines (PHaP)

Les techniques de modélisation atomistique et de simulations de dynamique moléculaire nous permettent de décrire les mécanismes d’interactions physico-chimiques de la matière à l’échelle atomique. Nous couvrons les thématiques allant des propriétés des nanomatériaux solides et de leur applications pour la détection de molécule unique à la caractérisation des molécules biologiques (protéines) et de leurs implications en tant que biomarqueurs de maladie notamment.

Membres permanents: Jeanne CHALOYARD, Patrice DELARUE, Jean-Marie HEYDEL, Fabrice NEIERS, Adrien NICOLAÏ, Catherine POTIN, Patrick SENET.

Doctorants: Andreina URQUIOLA HERNANDEZ, Nicolas PETIOT

2024:

• Single-Molecule, Sensors and Nanosystems (Paris, October 28-30th 2024): Sequencing of α-Synuclein Intrinsically Disordered Protein through single-layer MoS2 Solid-State Nanopores.

• JTMS2024 “Journées Théorie, Modélisation et Simulation 2024” (Toulouse, October 8-9th): Structural analysis of the Drosophila Melanogaster GSTome.

• ComplexBioDyn2024 (Dijon, June 9-14th 2024): MoS2 Solid-State Nanopores as Single-Biomolecule Sensors.

• Nanofluidics Conference (Lenzerheide, Jan. 21-24th 2024): Single-layer MoS2 Nanopores for Coarse-Grained Sequencing of Proteins

2023:

• Single-Molecule Sensors and nanoSystems International Conference 2023 (Barcelona, Nov. 23rd 2023): Single-layer MoS2 Nanopores for Coarse-Grained Sequencing of Proteins

• Black Forest Nanopore Meeting (Nov. 6-9th 2023): Single-layer MoS2 Nanopores for Coarse-Grained Sequencing of Proteins
• 1ère réunion de l’axe transverse “Expériences numériques, modélisations et intelligence artificielle” (Dijon, July 13th 2023): SEPIA : Nano-SEquenceur de Protéines assisté par Intelligence Artificielle
• Rencontre des Chimistes Théoriciens du Grand-Est (Reims, May 30-31st 2023): Functional modes and thermal B-factor predictions for multigenic structural analysis predicted from AlphaFold
• GGMM 2023 – Young Modellers Conference (Toulouse, May 17th 2023): Functional modes and thermal B-factor predictions for multigenic structural analysis predicted from AlphaFold
• GGMM 2023 – Young Modellers Conference (Toulouse, May 17th 2023): Identification of the Twenty Proteinogenic Amino Acids using MoS2 Solid-State Nanopores
• 1ère réunion de l’axe transverse “Matériaux innovants et Photonique pour la Santé” (Dijon, April 27th 2023): Nanodetection and neurodegenerative diseases

2022:

• 2022 MRS Fall meeting and exhibit (Boston USA, December 1st 2022): Identification of Proteinogenic Amino Acids using MoS2 Solid-State Nanopores

2021:

• Bioelectrodynamics Webinar series (December 6th 2021): Challenges in unlabelled single-biomolecule sequencing using 2-D solid–state nanopores

• NanoMedicine International Conference 2021 (Milan Italy Oct. 20-22 2021): Nanopore Sensing of Single-Biomolecule: Challenges in Protein Sequencing using Solid-State Nanopores.
• Nanopore Weekly Meeting (Webinar Sept. 13th 2021): Challenges in Protein Sequencing using 2-D MoS2 Nanopores.
• The International Society of Quantum Biology and Pharmacology (ISQBP) 2021 President’s Meeting (Online June 29th-July 1st 2021): Challenges in Protein Sequencing using 2-D MoS2 Nanopores, Answers from all-atom Molecular Dynamics.

2019:

• The SFNano C’Nano joint meeting (Dijon France, Dec. 10-12 2019): Identifying Patterns in Time Series Data: Application to Biological Peptide Translocation through single-layer MoS2 Nanopores.
• International Conference on Advanced Nanotechnology and Nanomaterials (Dubaï UAE, Nov. 20-21): Identifying Patterns in Time Series Data: Application to Biological Peptide Translocation through single-layer MoS₂ Nanopores.

2018:

• Reportage FR3 BFC: https://france3-regions.francetvinfo.fr/bourgogne-franche-comte/chercheurs-universite-bourgogne-veulent-revolutionner-dessalement-eau-mer-1449241.html
• Materials Research Society Fall Meeting (Boston USA, Nov. 25-30): Modeling the Ionic Conductivity and Biomolecule Translocation Through Solid-State MoS₂ Nanopores

2017: 

• Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments (Dijon France Sept. 3-8 2017): Computational investigation of the translocation of single polypeptide through MoS2 nanopores from ionic conductance dynamics.
• XXVIII International Materials Research Congress (Cancún México, Aug. 20-25): Biological Peptide Sequencing: Computational investigation of the performances of MoS₂ solid-state nanopores for such applications.

2024:

• Journal of Physical Chemistry: Molecular Dynamics of Peptide Sequencing through MoS2 Solid-State Nanopores for Binary Encoding Applications
• Biomolecules: Structural Analysis of the Drosophila melanogaster
• Biomolecules: Structural and Thermodynamic Insights into Dimerization Interfaces of Drosophila Glutathione Transferases
• Carbon: Molecular Dynamics Simulations of 2D-layered Graphene Sheets with Tandem Repeat Proteins

2023 :

• Frontiers in Nanotechnology: Single-layer MoS2 Solid-State Nanopores for Coarse-Grained Sequencing of Proteins
• FEBS Letters: Structure–activity analysis suggests an olfactory function for the unique antennal delta glutathione transferase of Apis mellifera
• Molecules: Einstein Model of a Graph to Characterize Protein Folded/Unfolded States
• Biomolecules: Role of Insect and Mammal Glutathione Transferases in Chemoperception

2022 :

• Applied Science: Free-Energy Landscape Analysis of Protein-Ligand Binding: The Case of Human Glutathione Transferase A1
• Frontiers in Molecular Biosciences: Wild-Type α-Synuclein and Variants Occur in Different Disordered Dimers and Pre-Fibrillar Conformations in Early Stage of Aggregation.
• Single Molecule Sensing Beyond Fluorescence (Springer): Challenges in Protein Sequencing Using 2-D MoS2 Nanopores

2021:

• Frontiers in Molecular Biosciences: Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic

2020:

• Nanoscale: Nanopore Sensing of Single-Biomolecule: A New Procedure to Identify Protein Sequence Motifs from Molecular Dynamics.
• The Journal of Physical Chemistry B: Curvature and torsion of protein main chain as local order parameters of protein unfolding

2019:

• The Journal of Physical Chemistry B: Molecular Dynamics Investigation of Polylysine Peptide Translocation through MoS₂ Nanopores.
• Applied Physics Letter: Improved model of ionic transport in 2-D MoS₂ membranes with sub-5 nm pores.
• Chemistry–A European Journal: On‐Surface Synthesis and Characterization of Acene‐Based Nanoribbons Incorporating Four‐Membered Rings.
• Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes (Springer): Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis.

2018:

• Insect Biochemistry and Molecular Biology: Characterization of a Drosophila glutathione transferase involved in isothiocyanate detoxification.
• Nano Letters: Angstrom-Size Defect Creation and Ionic Transport through Pores in Single-Layer MoS₂.

2017:

• WSEAS Trans. Circuits Syst: Computational investigation of the ionic conductance through molybdenum disulfide (MoS2) nanopores.
• Journal of the American Chemical Society: On-Surface Cyclization of ortho-Dihalotetracenes to Four- and Six-Membered Rings.
• Journal of Materials Chemistry C: Charge transport in highly ordered organic nanofibrils: lessons from modelling.
• Chemical Science: Photochromic Torsional Switch (PTS): a light-driven actuator for the dynamic tuning of π-conjugation extension.

2016:

• Journal of Physical Chemistry Letters: Theoretical Insights into Sub-Terahertz Acoustic Vibrations of Proteins Measured in Single-Molecule Experiments.
• Journal of Computational Chemistry: Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry.
• Carbon: Structural, energetic, and electronic properties of gyroidal graphene nanostructures.
• ACS Omega: Fingerprints of conformational states of human Hsp70 at sub-THz frequencies.

2015:

• Journal of Physical Chemistry Letters: Exploiting dispersion-driven aggregators as a route to new one-dimensional organic nanowires.
• ACS Nano: On-surface synthesis of BN-substituted heteroaromatic networks.
• ACS Applied Materials & Interfaces: Temperature-dependent and bistable current–voltage measurements in zinc porphyrin molecular junctions.
• The Journal of Physical Chemistry C: Electrolyte Diffusion in Gyroidal Nanoporous Carbon.
• Scientific Reports: Intrinsic localized modes in proteins.
• ACS Nano: DNA translocation in nanometer thick silicon nanopores.

2014:

• Accounts of Chemical Research: Interfacial properties and design of functional energy materials.
• Physical Chemistry Chemical Physics: Tunable water desalination across graphene oxide framework membranes.

2013:

• PLOS Computational Biology: Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.
• Journal of Chemical Theory and Computation: Molecular dynamics simulations of graphene oxide frameworks.
• Journal of Biomolecular Structure and Dynamics: Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent.
• Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes (Springer): Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis.

2010:

• Journal of Chemical Theory and Computation: Human inducible Hsp70: structures, dynamics, and interdomain communication from all-atom molecular dynamics simulations.

Licence Sciences et Techniques :

• L1: Physique Générale
• L2: Outils Informatiques pour la Physique et la Chimie
• L3: Physique de la Matière Condensée et Introduction à la Physique Statistique

Master Physics Photonics Nanotechnology :

• M1: Soft Matter (Practical)
• M2: Nanobiomodelling (Practical)

Master Santé :

• M1: Bioinformatique au service de la décarbonation