Research Project (2015-16)


Lyon / Grenoble / France

Coupling 3D organization to local biochemical state dynamics: application to chromatin folding
Supervisors: Daniel Jost and Cédric Vaillant
Laboratories: TIMC-IMAG, CNRS, Université de Grenoble Alpes and Laboratoire de Physique, CNRS, ENS Lyon

Discovery of epigenetically regulated genomic domains in lung cancer
Supervisor: Daniel Jost
Laboratories: TIMC-IMAG, Université Grenoble Alpes

Development and implementation of an efficient Bayesian inference scheme for systems biology

Supervisor;: Daniel Jost
Laboratory: TIMC-IMAG, CNRS, Université Grenoble Alpes

Dynamic response of genetic regulatory networks in fluctuating environments
Supervisor: Daniel Jost
Laboratory: TIMC-IMAG, CNRS, Université de Grenoble Alpes

Molecular dynamics simulations of lipidic membrane adhesion on a substrate

Supervisors: Claire Loison / Laurent Joly
Location: Institut Lumière Matière, Université Claude Bernard Lyon 1

Integration of NMR data into molecular dynamics for the quantitative analysis of protein/protein interactions

Supervisor: Dr. Olivier Walker
Location: Institut des Sciences Analytiques, Villeurbanne

Quantum effects on crack propagation
Supervisor David Rodney
Location: Université de Lyon 1

Rome, Italy

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

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

Rare events methods for the design of gas-retaining, Salvinia-like surfaces

Supervisors: A. Giacomello & C.M. Casciola - carlomassimo.casciola@uniroma1.it
Location: Dept of Mechanical and Aerospace Eng., Università di Roma "La Sapienza", Rome

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

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

A patchy particle model for dipolar hard-sphere gels
Supervisor F. Sciortino - f.sciortino@uniroma1.it
Location: Phys. Depp, Università di Roma "La Sapienza", Rome
We will try to develop a patchy particle model that generates a network as close as possible to the one generated by dipolar hard-spheres at low temperatures. (simulations + theory)

Phase behaviour of rods and small sticky spheres
Supervisor F. Sciortino - f.sciortino@uniroma1.it
Location: Phys. Depp, Università di Roma "La Sapienza", Rome
We will try to develop a model for describing an experimental systems studied by Erika Eiser combining DNA coated viruses and gold spheres  (mostly simulations)

Develop a model for DNA tetrahedral origami to check for liquid-liquid transition
Supervisor F. Sciortino - f.sciortino@uniroma1.it
Location: Phys. Depp, Università di Roma "La Sapienza", Rome
We will try to develop a coarse-grained for DNA origami tetrahedron explicated to undergo a liquid-liquid transition at high densities.

Salt dependence of the phase diagram of DNA trimers and tetramers
Supervisor F. Sciortino - f.sciortino@uniroma1.it
Location: Phys. Depp, Università di Roma "La Sapienza", Rome
We will investigate numerically the phase-behavior of DNA tetrahedral nanostars and the role of the ionic strength on the phase behaviour. (oxDNA code) (sim+teo)

Amsterdam, Netherlands

Protein folding dynamics investigation with multiple state transition path sampling and markov state models

Supervisor : Peter G. Bolhuis - p.g.bolhuis@uva.nl
Location: University of Amsterdam

Understanding Catalytic Water Splitting
Supervisors: Nitish Govindarajan and Evert Jan Meijer
Location: University of Amsterdam

Ab Initio Simulation of Catalysis in Solution
Supervisor: Evert Jan Meijer
Location: University of Amsterdam

Structure and Reactivity of Aqueous - Alumina Surfaces
Supervisors: Dapeng Sung and Evert Jan Meijer
Location: University of Amsterdam

Self Organization of nano-particles with mobile valence
Supervisor: Arthur Newton
Docent: Peter Bolhuis
Location: University of Amsterdam

Adsorption in nanoporous materials
Supervisor: D. Dubbeldam
Daily supervisor: Arian Torres
Location: University of Amsterdam

How do Protons Move in Water? Proton Mobility near Solid Surfaces
Supervisors evert Jan Meijer and Bernd Ensing
Location: University of Amsterdam

How do ions cross membranes?
Supervisor: P.G. Bolhuis
Location: University of Amsterdam

Investigation of the hydration properties of lactalbulmin under different type and concentration conditions
Supervisor: Phaedon Brotzakis
Docent: Peter Bolhuis
Location: University of Amsterdam

Molecular modelling of proton transfer in a binary biomimetic solution

Supervisor: Bernd Ensing and Evert Jan Meijer
Location: University of Amsterdam

Reactivity in nanoporous materials
Supervisor: Evert jan Meijer and B Ensing
Location: University of Amsterdam