Research projects (2014-15)


Germany

Supervisor: Thomas Speck - thomas.speck @ uni-mainz.de
Location: Johannes Gutenberg-Universität Mainz, Germany

Rome, Italy


Accurate and transferrable coarse-grained model for polymers solutions under external fields or confinements
Supervisors: Andrea Pelissetto & Carlo Pierleoni
- carlo.pierleoni @ roma1.infn.it
Location: Università di Roma "La Sapienza", Rome, Italy

Effective force fields for high pressure hydrogen
Supervisor: Carlo Pierleoni - carlo.pierleoni @ roma1.infn.it
Location: Università di Roma "La Sapienza", Rome, Italy

Effect of the salt on the formation of DNA gels (simulations based on the OxDNA code)
Supervisor: Francesco Sciortino - francesco.sciortino @ phys.uniroma1.it
Location: Università di Roma "La Sapienza", Rome, Italy

Partition function of dipolar hard sphere clusters
Supervisor: Francesco Sciortino - francesco.sciortino @ phys.uniroma1.it
Location: Università di Roma "La Sapienza", Rome, Italy

Liquid-Liquid transitions in water and water-like models: role of the flexibility
Supervisor: Francesco Sciortino - francesco.sciortino @ phys.uniroma1.it
Location: Università di Roma "La Sapienza", Rome, Italy

Rare events methods for the design of gas-retaining, Salvinia-like surfaces
Supervisors: A. Giacomello & C.M. Casciola - carlomassimo.casciola @ uniroma1.it
Dept. of Mechanical and Aerospace Eng., Università di Roma "La Sapienza", Rome, Italy

Turbulent multiphase flows in the two-way coupling regime
Supervisors: F. Battista, P. Gualtieri, & C.M. Casciola - carlomassimo.casciola @ uniroma1.it
Location: Dept. of Mechanical and Aerospace Eng., Università di Roma "La Sapienza", Rome, Italy  

Numerical simulations of vapor bubble collapse near solid walls
Supervisor: F. Magaletti & C.M. Casciola - carlomassimo.casciola @ uniroma1.it
Location: Dept. of Mechanical and Aerospace Eng., Università di Roma "La Sapienza", Rome, Italy

Self-assembly of hard cylinders into semi-flexible mesogenic chains: evaluation of phase diagram through Monte Carlo simulations
Supervisor: Cristiano de Michele - cristiano.demichele @ roma1.infn.it
Location: Università di Roma "La Sapienza", Rome, Italy

Investigation of antibody binding to an antigen covered surface
Supervisor: Cristiano de Michele - cristiano.demichele @ roma1.infn.it
Location: Università di Roma "La Sapienza", Rome, Italy


Lausanne, Switzerland

Non-­equilibrium molecular dynamics simulations of charge transport in a magnetic field
Supervisor: Sara Bonella - sara.bonella @ epfl.ch
Location: CECAM@EPFL, Lausanne, Switzerland       


Lyon / Grenoble / Montpellier, France


Collective motion in bacterial colonies
Supervisor: Ludovic Berthier - ludovic.berthier @ univ-montp2.fr
Location: Laboratoire Charles Coulomb, Universit ?e Montpellier 2

Modeling of turbulent flow with cavitation: application of the kinetic theory within a Lattice Boltzmann approach
Supervisors: Mikhael Gorokhovski - mikhael.gorokhovski @ ec-lyon.fr
Emmanuel Lévêque - emmanuel.leveque @ ec-lyon.fr / Loïc Méès - Loic.Mees @ ec-lyon.fr


Molecular dynamics simulations of membrane protein interaction with detergents     
Supervisor: Luca Monticelli - luca.monticelli @ ibcp.fr
Location: IBCP, CNRS, Lyon

Membrane protein insertion into membranes: comparing simulations with experiments     
Supervisor: Luca Monticelli - luca.monticelli @ ibcp.fr
Location: IBCP, CNRS, Lyon  


Molecular dynamics simulations of lipopeptides in interaction with a biomimetic membrane
Supervisor: Claire Loison - claire.loison @ univ-lyon1.fr
Location: Laboratoire Institut Lumière Matièr, UCBL

A step towards artificial photosynthesis: theoretical study of photoelectrocatalytic CO2 conversion to fuel
Advisors: Dr. Ivan Rivalta - ivan.rivalta @ ens-lyon.fr / Prof. Marco Garavelli - marco.garavelli @ ens-lyon.fr

Understanding color vision: how to tune the absorption of a chromophore?
Advisors: Marco Garavelli - marco.garavelli @ ens-lyon.fr / Ivan Rivalta - ivan.rivalta @ ens-lyon.fr

Theoretical study of the visual retinal chromophore in solvent
Advisors: Marco Garavelli - marco.garavelli @ ens-lyon.fr / Ivan Rivalta - ivan.rivalta @ ens-lyon.fr

Tracking water oxidation in natural photosynthesis

Advisors: Dr. Ivan Rivalta - ivan.rivalta @ ens-lyon.fr / Prof. Marco Garavelli - marco.garavelli @ ens-lyon.fr

Theoretical study of 2D-materials
Supervisors: Pascal Pochet - pascal.pochet @ cea.fr
Razvan Caracas - razvan.caracas @ ens-lyon.fr
Location: CEA Grenoble / ENS Lyon


Integration of NMR and metadynamics in the quantitative analysis of protein/ligands complexes
Supervisor: Olivier Walker - olivier.walker @ univ-lyon1.fr
Location: Institut des Sciences Analytiques, Villeurbanne

Epigenetics in 3D: The "living chromatin" model.
Application to the establishment and maintenance of dosage compensation

Supervisors: Cédric Vaillant & Daniel Jost - cedric.vaillant @ ens-lyon.fr & daniel.jost @ imag.fr
Location: Laboratoire de Physique de l'ENS Lyon & Laboratoire TIMC-IMAG, Grenoble, France


Structural regulation of the anti-cancer target HSF1
Supervisor: Martin Spichty - martin.spichty @ ens-lyon.fr
Location: Laboratoire de Biologie Moléculaire de la Cellule, ENS de Lyon, France

Dynamic response of genetic regulatory networks in fluctuating environments
Supervisor: Daniel Jost - daniel.jost @ imag.fr
Location: TIMC-­?IMAG, University of Grenoble, France

Computational modeling of replication in eukaryotes: impact of 3D chromatin organization

Supervisor:
Daniel Jost - daniel.jost @ imag.fr
Location: TIMC-­?IMAG, University of Grenoble, France

Monte-Carlo modelling of signalling pathways in living cells
Supervisors: Hugues Berry and Hedi Soula - hugues.berry @ inria.fr inria.fr / hedi.soula @ inria.fr
Location: Team Beagle, INRIA (https://team.inria.fr/beagle), Campus de la Doua, Lyon, France

Hight-troughtput single-molecule replication-pattern mapping using DNA combing image
Supervisors: Benjamin AUDIT and Stéphane ROUX - benjamin.audit @
inria.fr  ens-lyon.fr / stephane.roux @ ens-lyon.fr
Laboratoire de Physique de l'ENS de Lyon, France


Zero-point energy effect on crack propagation
Supervisor: David Rodney - david.rodney @ univ-lyon1.fr
Institut Lumière Matière, Lyon, France

From photovoltaics to photosynthesis: Novel theoretical approaches and quantum simulations

Supervisor: Xavier Blase - xavier.blase @ neel.cnrs.fr
INSTITUT NEEL Grenoble, France


Coarse-Grained Modeling of the compaction of bacterial DNA through macromolecular crowding
Supervisor: Marc Joyeux - Marc.Joyeux @ ujf-grenoble.fr
Laboratoire Interdisciplinaire de Physique, UJF Grenoble, France



Amsterdam, The Netherlands

Different types of base/pairing in DNA
Supervisors: Jocelyne Vreede - J.Vreede @ uva.nl & Célia Fonseca Guerra - c.fonsecaguerra@vu.nl


Molecular modelling of proton transfer in a binary biomimetic solution
Daily Supervisor: Wagner Brandeburgo - w.brandeburgo @ uva.nl
Supervisors: Bernd Ensing and Evert Jan Meijer - b.ensing @ uva.nl or e.j.meijer @ uva.nl

Investigation of the hydration properties of Alpha-lactalbumin under different salt type and concentration conditions
Supervisor: Phaedon Brotzakis - phaedon.brotzakis
@ gmail.com
Docent: Peter Bolhuis - p.g.bolhuis
@ uva.nl

Alpha-Synuclein aggregation using extended ensemble methods (REMD)
Supervisor: Marcin Nowosielski
- M.A.Nowosielski @ uva.nl
Docent: Peter Bolhuis
- p.g.bolhuis @ uva.nl

Zelf-organisatie van nanodeeltjes met een mobiele valentie
Supervisor: Arthur Newton
- A.C.Newton @ uva.nl
Docent: Peter Bolhuis
- p.g.bolhuis @ uva.nl

Adsorption in nanoporous materials
Supervisor: D. Dubbeldam
- d.dubbeldam @ uva.nl
Daily supervisor: Ariana Torres
- a.torresknoop @ uva.nl

Ab Initio Simulation of Catalysis in Solution

Supervisor: E.J. Meijer
- e.j.meijer @ uva.nl

Structure and Stability of Carbon Materials
Supervisor: E.J. Meijer
- e.j.meijer @ uva.nl

How do ions cross membranes?
Supervisor P.G. Bolhuis
- p.g.bolhuis @ uva.nl

Protein folding dynamics investigation with multiple state transition path sampling and markov state models
Supervisor: Peter G. Bolhuis
- p.g.bolhuis @ uva.nl

Reactivity in nanoporous materials
Supervisor: E.J. Meijer and J. Heinen
- e.j.meijer @ uva.nl

Structure and Stability of Carbon Materials
Supervisor: E.J. Meijer
- e.j.meijer @ uva.nl