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Freie Uni­versität Ber­lin - Fachbereich Physik - Insti­tut für The­or­et­ische Physik

The Clem­enti's group in the Phys­ics Depart­ment at Freie Uni­versität Ber­lin seeks a postdoc­toral researcher to work on the devel­op­ment and applic­a­tion of coarse-grain­ing meth­od­o­lo­gies to study mac­ro­molec­u­lar dynam­ics with machine learn­ing and exper­i­mental data, integ­rat­ive struc­tural bio­logy, and mem­brane pro­tein mod­el­ing. 

Our group works on the defin­i­tion and imple­ment­a­tion of strategies to study com­plex bio­phys­ical pro­cesses on long times­cales. We use data-driven meth­ods for sys­tem­atic coarse-grain­ing of mac­ro­molec­u­lar sys­tems, to bridge molecu­lar and cel­lu­lar scales. We work on a the­or­et­ical for­mu­la­tion to exploit the com­ple­ment­ary inform­a­tion that can be obtained in sim­u­la­tion and exper­i­ment, to com­bine the approx­im­ate but high-res­ol­u­tion struc­tural and dynam­ical inform­a­tion from com­pu­ta­tional mod­els with the “exact” but lower res­ol­u­tion inform­a­tion avail­able from exper­i­ments.

Research assist­ant (postdoc) (m/f/d)

Work­ing field:

  • Coup­ling of pro­ton dynam­ics with large struc­tural rearrange­ments in Phyto­chromes (WP1)

  • Struc­tural model of pro­tein M of the Dengue virus and the West Nile Virus (WP2)

The pro­ject is part of the research con­sor­tium of the CRC 1078. The can­did­ate will study global change in phytho­chromes. Using a multi-scale approach, we will com­bine this with atom­istic MD and QM/MM sim­u­la­tions, in close col­lab­or­a­tion with other pro­jects of the SFB, to under­stand the coup­ling of long-time scale con­form­a­tional changes with pro­ton­a­tion states of the chro­mo­phore bind­ing pocket. 

We will pro­ceed with the study of the dynam­ical and func­tional prop­er­ties of pro­tein M of DENV and WNV and its role in the pro­ton trans­fer activ­ity. As the atom­istic struc­ture of pro­tein M is not known for any Flavivirus, nor its oli­go­mer­iz­a­tion state in DENV and WNV, the struc­tural mod­el­ling will be the start­ing point of our pro­ject. In par­tic­u­lar, the atomic struc­ture and oli­go­mer­iz­a­tion state that will res­ult from our mod­el­ling will be the start­ing point for the study of pro­ton and cation per­meation in these viro­p­or­ins using atom­istic MD and QM/MM sim­u­la­tions.



  • Can­did­ates must have a Ph.D. in Phys­ics, Chem­istry, Applied Math­em­at­ics, or related fields.


  • Pre­vi­ous exper­i­ence with mac­ro­molec­u­lar mod­el­ing and molecu­lar dynam­ics sim­u­la­tions.
  • Excel­lent the­or­et­ical and prac­tical exper­i­ence with machine learn­ing meth­ods and the design of coarse-grain pro­tein mod­els is desir­able.
Eng­lish lan­guage flu­ent, spoken and writ­ten.

How to ap­ply:

All applic­a­tions (includ­ing a short cover let­ter out­lining your back­ground, a detailed CV includ­ing pos­sibly some ref­er­ences, and all rel­ev­ant cer­ti­fic­ates) quot­ing the ref­er­ence code should be dir­ec­ted no later than Feb­ru­ary 1st, 2021 prefer­ably elec­tron­ic­ally in one PDF-file to: Mrs. Prof. Dr. Cecilia Clem­enti: or postal to

Freie Uni­versität Ber­lin
Fachbereich Physik
Insti­tut für The­or­et­ische Physik
AG Clem­enti - The­or­et­ische und rech­nergestützte Bio­physik
Mrs. Prof. Dr. Cecilia Clem­enti
Arn­im­al­lee 14
14195 Ber­lin (Dah­lem)

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