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. In the following you will find a brief description and materials for projects on which I worked or I am still working on :


Spatial averaging (SA-MC) algorithm

https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2014/jctcce.2014.10.issue-10/ct500529w/20141008/images/large/ct-2014-00529w_0006.jpeg
The alanine dipeptide molecule, and the 2 dihedral angles used for building a Ramachandran plot.

 

https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2014/jctcce.2014.10.issue-10/ct500529w/20141008/images/large/ct-2014-00529w_0007.jpeg
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

https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2015/jpcbfk.2015.119.issue-7/jp511701z/20150212/images/large/jp-2014-11701z_0002.jpeg
N-Methylacetamide molecule with atoms labeled.

 

https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2015/jpcbfk.2015.119.issue-7/jp511701z/20150212/images/large/jp-2014-11701z_0004.jpeg
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

FW-overview
Overview of the fitting procedure when using the Fitting Wizard toolkit.

The Partial Infinite Swapping Algorithm


Molecular dynamics investigation of Human Haemoglobin Tetramer stability