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 :
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.
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.
(Ala10): extended starting structure (blue), and folded structure (red) obtained after 100 ns of MD with GENBORN implicit solvent. In cyan and orange, the carbonyl carbon atoms define the end-to-end distance ξ in Å, used for following compactification and building ∆F surfaces. The extended structure has ξ = 31.04 Å, and the α-helical structure is characterised by a ξ = 14.13 Å.Free Energy as a function of ξ for Ala10 in explicit TIP3P water from 4 μs MD simulation. The red vertical line marks the point where ∆F = 0 kcal/mol for ξ = 22.75 Å, i.e. the most sampled extended (non-helical) state. The 4 displayed configurations are examples of structures for which ∆F ≤ 1 kcal/mol.
![Free energy surface based on ramachandran plots obtained using: [A] MD, [B] MC, [C and D] SA-MC, respectively biased and unbiased.](https://fhedin.com/wp-content/uploads/2019/06/samc-fe.jpg)
