Publications and Communications

Please also check my ResearchGate profile

Articles

Dec. 2021 Hybrid high-order methods for flow simulations in extremely large discrete fracture networks.
Preprint: HAL: hal-03480570  PDF here

Oct. 2021 Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation.
Preprint: arXiv: 2110.05427 PDF here
Published: DOI: 10.1039/D1SC05892D PDF here

Aug. 2020 A hybrid high-order method for flow simulations in discrete fracture networks,
Numerical Mathematics and Advanced Applications (ENUMATH 2019 Proceedings), Elsevier.

Preprint: HAL: hal-02315491 PDF here
Published: DOI: 10.1007/978-3-030-55874-1_51

Jan. 2019 gen.parRep: a first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems, Computer Physics Communications.
Preprint : arXiv: 1807.02431 HAL: hal-01832823  PDF here
Published : DOI: 10.1016/j.cpc.2019.01.005  PDF here

Jul. 2018 Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size, eLife Sciences.
DOI: 10.7554/elife.35560
PDF here
Response to some comments on this article:
DOI: 10.7554/eLife.45318.001
PDF here

Oct. 2017 Performance and Free Energy Estimation for Solvated Polypeptides and Proteins Using Partial Infinite Swapping.
PDF here
Supplementary Information here

Jul. 2016 A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations, J. Chem. Inf. Model.
DOI: 10.1021/acs.jcim.6b00280
PDF here
PDF correction here

Jan. 2015 Vibrational Relaxation and Energy Migration of N-methylacetamide in Water: The Role of Nonbonded Interactions, J. Phys. Chem. B
DOI: 10.1021/jp511701z
PDF here

Aug. 2014 Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules, J. Chem. Theory Comput.
DOI: 10.1021/ct500529w
PDF here

Posters (see C.V. for full list)

June 2017, Poster, CECAM workshop, Beyond Kds: New computational methods to address challenges in drug discovery, Lausanne, Switzerland.

Generalized Parallel Replica algorithm : implementation and application to chemical and biochemical systems
DOI: 10.13140/RG.2.2.34336.69129
PDF here

Oct. 2012, two Posters, Workshop. Monte Carlo Methods in the Physical and Biological Sciences, organised by Brown University, Providence, Rhode Island, U.S.A.

  1. Sampling rare events with spatial averaging: theory and applications.
    PDF here
  2. Ligand uptake in truncated hemoglobin: a Monte Carlo study.
    DOI: 10.13140/RG.2.1.2998.3600

July 2012, Poster, Energy Landscape Conference, organised by European Science Foundation, Obergurgl, Austria.

Talks / Lectures / Presentations (see C.V. for full list)

May 2018, Talk, PINT 7th workshop.

June 2016, Lecture (invited), University of Basel, “High Performance Computing” Course, Master Level.

Sept. 2013, Talk, Swiss Chemical Society Fall Meeting.

Sept. 2011, Master Thesis presentation, University of Strasbourg, France.