MOLECULAR MODELLING AND SIMULATION: FROM SOFT CONDENSED MATTER TO BIOLOGICAL SYSTEMS

Here I briefly introduce the body of my memoire. I had been a PhD student for about three years and about nine years for the post-doc. Then I spent about two years as a temporary principal investigator before being hired as CR1 researcher at CNRS and join the Laboratoire de Biochimie Th\'eorique at IBPC. During this long period I have had opportunities to challenge myself in different fields of research and to acquire deep expertise in computer simulations as well as to be exposed to various scientific environments. During my PhD work in the field of soft condensed matter simulation, I had been trained in simulation of coarse-grained liquid crystalline systems using classical Monte Carlo technique. This required intensive coding of the simulation programs and analytical derivations related to the liquid state density functional theory. I started to learn biomolecules, specifically protein and RNA during my postdoc. During this time, I had been trained in equilibrium and nonequilibrium molecular dynamics simulations of atomistic protein models. The experience in both coarse-grained and atomistic simulations was the key for acquiring expertise in my current research activity which focuses on the development and application of computational methods for studying the equilibrium and nonequilibrium structure, dynamics, thermodynamics of single proteins and amyloids at all-atom and coarse-grained levels. Personally, my idea in the development is that the developed methods should be as simple as possible, yet efficient. Also, I am more interested in principals governing the system rather than going into details. During my PhD and postdoc I had been involved in supervising master and PhD students. I had also been regularly involved in teaching activity. In particular, I was in charge of the tutoring associated to the Mathematics course for undergraduate students for eight years of my postdoc. Since this year, I have been involved in giving some lectures on advanced topics of computer simulations such as simulated tempering, metadynamics as well as weighted histogram analysis method and disconnectivity graph