{"id":63,"date":"2017-02-08T13:08:26","date_gmt":"2017-02-08T12:08:26","guid":{"rendered":"https:\/\/fhedin.com\/?page_id=63"},"modified":"2019-06-24T15:19:50","modified_gmt":"2019-06-24T13:19:50","slug":"phd-projects-unibas","status":"publish","type":"page","link":"https:\/\/fhedin.com\/?page_id=63","title":{"rendered":"PhD projects, university of Basel"},"content":{"rendered":"

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

My PhD defense was on the 22nd of September 2016 ; you can view a pdf copy of my PhD Thesis here<\/a><\/strong>, and my PhD defense slides here<\/strong><\/a>.<\/p>\n

In the following you will find a brief description and materials for projects on which I worked\u00a0 :<\/p>\n

\n

Spatial averaging (SA-MC) algorithm<\/a><\/p>\n

\"The<\/a>
The alanine dipeptide molecule, and the 2 dihedral angles used for building a Ramachandran plot.<\/figcaption><\/figure>\n
\"Free<\/a>
Free energy surface based on ramachandran plots obtained using: [A] MD, [B] MC, [C and D] SA-MC, respectively biased and unbiased.<\/figcaption><\/figure>\n
\n

Vibrational relaxation and energy migration in water<\/a><\/p>\n

\"N-Methylacetamide<\/a>
N-Methylacetamide molecule with atoms labeled.<\/figcaption><\/figure>\n
\"Probability<\/a>
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.<\/figcaption><\/figure>\n
\n

Fitting Toolkit for Nonbonded Parameters<\/a><\/p>\n

\"Overview<\/a>
Overview of the fitting procedure when using the Fitting Wizard toolkit.<\/figcaption><\/figure>\n
\n

The Partial Infinite Swapping Algorithm<\/a><\/p>\n

\"\"<\/a>
(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 \u03be in \u00c5, used for following compactification and building \u2206F surfaces. The extended structure has \u03be = 31.04 \u00c5, and the \u03b1-helical structure is characterised by a \u03be = 14.13 \u00c5.<\/figcaption><\/figure>\n
\"\"<\/a>
Free Energy as a function of \u03be for Ala10 in explicit TIP3P water from 4 \u03bcs MD simulation. The red vertical line marks the point where \u2206F = 0 kcal\/mol for \u03be = 22.75 \u00c5, i.e. the most sampled extended (non-helical) state. The 4 displayed configurations are examples of structures for which \u2206F \u2264 1 kcal\/mol.<\/figcaption><\/figure>\n

\"\"<\/a><\/p>\n

\n

Molecular dynamics investigation of Human Haemoglobin Tetramer stability<\/a><\/p>\n

\"\"<\/a><\/p>\n

\n","protected":false},"excerpt":{"rendered":"

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 …<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":6,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-63","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/pages\/63","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/fhedin.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=63"}],"version-history":[{"count":18,"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/pages\/63\/revisions"}],"predecessor-version":[{"id":366,"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/pages\/63\/revisions\/366"}],"up":[{"embeddable":true,"href":"https:\/\/fhedin.com\/index.php?rest_route=\/wp\/v2\/pages\/6"}],"wp:attachment":[{"href":"https:\/\/fhedin.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=63"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}