- statut_ub:
- batiment:
- equipe_1:
- OCS
- fonction_equipe_1:
- Agent(e) de service
- mots_cles:
- adresse:
- onglets:
- {tab=Carrière} # {tab=Projets} # {tab=Publications} # {tab=Communications} # {tab=Enseignements} # {tab=Administration} # {/tabs}
- telephone:
- 03-80-39-60-93
- e-mail:
- adrien.nicolai@u-bourgogne.fr
- site_web:
- departement:
- a:1:{i:0;s:12:"Nanosciences";}
- fonction:
Maître de conférences / Assistant professor
- localisation:
- Bâtiment MIRANDE - Aile D bureau 316
- texte_onglets:
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- kc_raw_content:
- carriere:
CV:
I studied Physics at Université de Bourgogne (uB), where I got a master degree in Nanotechnology and Nanobiosciences in 2009. I earned a PhD from uB in 2012 under the supervision of Professor Patrick Senet. I was postdoctoral research associate at Renselaer Poytechnic Institute (NY, USA) in 2013-2014, joining the group of Professor Vincent Meunier and at Ecole Polytechnique Federale de Lausanne (Switzerland) in the group of Professor Clémence Corminboeuf (LCMD) until 2015 when I joined uB as an associate professor.Research interests:
My domains of expertise are condensed matter physics, physics and chemistry of nanomaterials and biophysics. My research uses computation and numerical simulations to examine and describe mechanisms of interactions between Nanomaterials and biomolecules (proteins) at the atomic level. I am particularly interested in the characterization and detection of single biomolecules using devices based on Nanomaterials (spectroscopic and sequencing techniques). [video width="700" height="500" mp4="https://icb.u-bourgogne.fr/wp-content/uploads/2018/08/animation.mp4" loop="true" autoplay="true"][/video]- projets:
-
Deciphering the free-energy landscape of GST enzymes induced by ligand binding. M1 internship of Nicolas Petiot (2022).
- Nano-SEquenceur de Protéines assisté par Intelligence Artificielle (SEPIA). PhD thesis of Andreina Urquiola Hernandez (started Oct. 1st, 2021).
- Nanopore Sensing of Single Biomolecule Assisted by Machine Learning. M2 internship of Andreina Urquiola Hernandez (2021).
- Design and computer simulations of 2D MeX2 (Me = transition metal) nanopores for DNA and protein detection and analysis. PhD thesis of Maria Daniela Barrios Pérez (defended Jan. 7th, 2020).
https://www.theses.fr/2020UBFCK003
- Identifying patterns in Time series Data from Nanopore sensing of single-biomolecules experiments. M1 internship of Aniket Rath (2019).
- Simulation des spectres infrarouge basses fréquences (<300 GHz) à haute résolution de la conalbumine. Rôle de l’anharmonicité et comparaison avec les données expérimentales. M1+M2 internships of Mohamed Ahmed Khaireh (2017-2018).
- Translocation of biomolecules through solid-state nanopores. M2 internship of Daniela Barrios Pérez (2016).
-
- communications:
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.
- publications:
2023:
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.
- enseignements:
Licence Sciences et Techniques:
- L1: Physique Générale
- L2: Outils Informatiques pour la Physique et la Chimie
- L3: Physique de la Matière Condensée
Master Physics Photonics Nanotechnology:
- M1: Soft Matter (Practical)
- M2: Nanobiomodelling (Practical)
- administration:
- switch:
- 0