PhD projects, university of Basel

From October 2011 to October 2016 I was a PhD student at the University of Basel, where I used computational chemistry tools to address physical, chemical and biochemical problems.

My PhD defense was on the 22nd of September 2016 ; you can view a pdf copy of my PhD Thesis here, and my PhD defense slides here.

In the following you will find a brief description and materials for projects on which I worked  :

Spatial averaging (SA-MC) algorithm
The alanine dipeptide molecule, and the 2 dihedral angles used for building a Ramachandran plot.
Free energy surface based on ramachandran plots obtained using: [A] MD, [B] MC, [C and D] SA-MC, respectively biased and unbiased

Vibrational relaxation and energy migration in water
N-Methylacetamide molecule with atoms labeled.
Probability distribution of the postexcitation lifetime of the H-bonded water molecules on the carbonyl group of NMA. (a) 1 H-bonded molecule; (b) 2 H-bonded molecules: (blue) shorter lifetime, (red) longer lifetime, and (black) distribution of the lifetime of the remaining molecule after the first left.

Fitting Toolkit for Nonbonded Parameters

Overview of the fitting procedure when using the Fitting Wizard toolkit.

The Partial Infinite Swapping Algorithm

Molecular dynamics investigation of Human Haemoglobin Tetramer stability