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Tech­ni­sche Uni­ver­si­tät Dres­den - Clus­ter of Excel­lence ‘Cen­ter for Advan­cing Elec­tro­nics Dres­den’ (cfaed)

The TU Dres­den is one of ele­ven Ger­man uni­ver­si­ties that were iden­ti­fied as an “excel­lence uni­ver­sity”. TUD has about 36.500 stu­dents and almost 5319 employees, 507 pro­fes­sors among them, and, thus, is the lar­gest uni­ver­sity in Sax­ony, today.

Having been com­mit­ted to sci­en­ces and the engi­nee­ring before the reuni­fi­ca­tion of Ger­many, TU Dres­den now is a multi-disci­pline uni­ver­sity, also offe­ring huma­nities and social sci­en­ces as well as medi­cine.

Rese­arch Asso­ciate / PhD Posi­tion in Theo­re­ti­cal Bio­phy­sics

The junior research group “Bio­lo­gical Algorithms” headed by Ben­jamin Friedrich within the Cluster of Excel­lence ‘Cen­ter for Advan­cing Elec­tron­ics Dresden’ (cfaed) offers a pos­i­tion as
Research Asso­ci­ate / PhD Pos­i­tion in The­or­et­ical Bio­phys­ics (sub­ject to per­sonal qual­i­fic­a­tion employ­ees are remu­ner­ated accord­ing to salary group E 13 TV-L)

Research area: Muscle build­ing in silico: Math­em­at­ical mod­el­ing of myofib­rillo-gen­esis
cfaed Invest­ig­at­ors: PD Dr. Ben­jamin Friedrich
cfaed research path: Bio­lo­gical Sys­tems Path
Terms: The pos­i­tion will start as soon as pos­sible, entails 65% of the full­time weekly hours, and is fixed-term for 3 years. The period of employ­ment is gov­erned by the Fixed-Term Research Con-tracts Act (Wis­senschaft­szeitver­trags­ge­setz – Wis­sZeitVG). The pos­i­tion offers the chance to obtain fur­ther aca­demic qual­i­fic­a­tion (e.g. PhD).

About the “Bio­lo­gical Algorithms group”
How do struc­tures form in cells and tis­sues? The mis­sion of our “Bio­lo­gical Algorithms group” is to under­stand phys­ical prin­ciples of self-assembly and self-organ­iz­a­tion in liv­ing mat­ter. Top­ics in-clude the spon­tan­eous form­a­tion of pat­tern in the cyto­skel­eton of cells, in tis­sues, and organ-isms. In our the­or­et­ical research, we com­bine non­lin­ear dynam­ics, stat­ist­ical phys­ics, and compu-tational phys­ics to under­stand phys­ical mech­an­isms of bio­lo­gical func­tion, and its robust­ness in the pres­ence of noise and per­turb­a­tions, while closely col­lab­or­at­ing with exper­i­mental part­ners.
More inform­a­tion on cur­rent research can be found at https://cfaed.tu-dresden.de/friedrich-home. Our small group con­sists of enthu­si­astic stu­dents from dif­fer­ent coun­tries. All group meet­ings are held in Eng­lish and no know­ledge of the Ger­man lan­guage is required.

Work­ing field:

We are hir­ing a PhD stu­dent for a pro­ject in The­or­et­ical Bio­phys­ics, to under­stand how micro-scopic force-gen­er­at­ing units in our mus­cles self-assem­ble dur­ing devel­op­ment: Every mus­cle cell in your body con­tains highly reg­u­lar myo­fib­rils, which pro­duce act­ive mus­cle forces. Each myo­fib­ril is built by a chain of sar­come­res, com­posed of actin fil­a­ments and myo­sin molecu­lar motors, lin­ked tog­e­ther by gigan­tic titin springs. The myo­fib­rils are act­ive “bio­lo­gical crys­tals” and any alter­a­tions of their reg­u­lar archi­tec­ture are lin­ked to dis­ease sta­tes. Yet how these myo­fib­rils assem­ble dur­ing devel­op­ment is poorly under­stood in terms of phys­ical mech­an­isms.
Pre­vi­ously, we pro­posed a math­em­at­ical model of how actin and myo­sin fil­a­ments self-assem­ble into reg­u­lar sar­come­ric pat­terns by a com­bin­a­tion of act­ive forces and pass­ive cross­link­ing (Frie-drich et al. PLoS Com­pu­ta­tio­nal Bio­logy, 2012). Based on this, we want to deve­lop in this pro­ject com­puter sim­u­la­tions of a bundle of actin, myo­sin, and titin, in order to under­stand the role of act­ive ten­sion and fil­a­ment elasti­city in sar­comere self-assem­bly. You will for­mu­late altern­at­ive phys­ical mech­an­isms in terms of math­em­at­ical mod­els. You will imple­ment mech­an­isms, e.g. as agent-based sim­u­la­tions, with spe­cific inter­ac­tion rules for the dif­fer­ent fil­a­ments. You will com-pute phase dia­grams and derive test­able pre­dic­tions. In addi­tion to sim­u­la­tions, you can coarse-grain the inter­ac­tion model to devise a mean-field the­ory of sar­come­ric pat­tern form­a­tion. Final-ly, you can com­pare the­ory pre­dic­tions to quant­it­at­ive exper­i­men­tal data.
This PhD the­sis will con­sti­tute the the­ory part of a the­ory-exper­i­ment col­lab­or­a­tion with the la-bor­at­or­ies of Frank Schor­rer (IBDM, Mar­seil­les) and Oli­vier Pour­quie (HMSB, Bos­ton). You will par­ti­cip­ate in reg­u­lar inter­na­tio­nal pro­ject meet­ings. The exper­i­men­tal part­ners will pro­vide high-res­ol­u­tion time-lapse micro­scopy data of devel­op­ing myo­fib­rils, as well as molecu­lar force-sen­sor data for live force meas­ure­ments in devel­op­ing mus­cle fibers. Based on this data, we will quan­tify the gra­dual emer­gence of sar­come­ric pat­terns using con­cepts from Soft Con­den­sed Mat­ter Phys­ics (nema­tic and smec­tic order para­met­ers) to link the­ory and exper­i­ment. Full fund­ing includ­ing tra­vel funds is avail­able from the pres­ti­gi­ous Human Fron­tier Sci­ence Pro­gram.
More inform­a­tion on the pro­ject can be found here: https://cfaed.tu-dresden.de/press-releases-201/muscle-growth-in-the-computer-international-team-wants-to-unravel-the-formation-of-myofibrils

Require­ments:

We are loo­king for a theo­re­ti­cal phy­si­cist (or app­lied mathe­ma­ti­cian), who is intrigued to dis­co­ver algo­rithms of life, and meets the fol­lo­wing requi­re­ments: excel­lent uni­ver­sity degree (diploma or Mas­ter) in Bio­lo­gi­cal Phy­sics, Mathe­ma­ti­cal Bio­logy, or rela­ted field; expe­ri­ence in sta­ti­s­ti­cal phy­sics, non­linear dyna­mics, sto­cha­s­tic pro­ces­ses; expe­ri­ence in Com­pu­ta­tio­nal Phy­sics (Monte-Carlo and agent-based simu­la­ti­ons, ODEs, PDEs), and pro­gramming skills (e.g. Mat­lab, Python, C); strong inte­rest in app­ly­ing phy­sics to under­stand life, wil­ling­ness to learn some bio­logy en route; strong ana­lytic and pro­blem-sol­ving skills, crea­ti­vity; strong com­mu­nica-tion skills, espe­cially in cross-disci­pli­nary com­mu­ni­ca­tion; flu­ency in Eng­lish – oral and writ­ten.

What we of­fer:

Dres­den is a European hub for Bio­lo­gical Phys­ics that unites excel­lence in inform­a­tion and life sci­ences. You will be embed­ded in the Clus­ter of Excel­lence cfaed, where we con­trib­ute bio-inspi­red algo­rithms of molecu­lar self-assem­bly and self-organ­iz­a­tion. Addi­tion­ally, we enjoy the close prox­im­ity of col­lab­or­a­tion part­ners at the Max-Planck Insti­tute of Molecu­lar Cell Bio­logy and Genet­ics, the Bio­tech­no­logy Centre, and the new Cen­ter for Sys­tems Bio­logy Dres­den.
For infor­mal enquir­ies, please con­tact Dr. Ben­jamin Fried­rich at benjamin.m.friedrich@tu-dresden.de.
App­lic­a­tions from women are par­tic­u­larly wel­come. The same app­lies to people with dis­ab­il­it­ies.
Dres­den is a medium-sized city (5˖105 inhab­it­ants) with a rich cul­tural life, baro­que archi­tec­ture, and afford­able rents. Ber­lin and Pra­gue are only a hop away (2h by train).

About cfaed
cfaed is a clus­ter of excel­lence wit­hin the Ger­man Excel­lence Ini­ti­at­ive. As a cent­ral sci­ent­i­fic unit of TU Dres­den, it brings tog­e­ther 300 rese­arch­ers from the uni­ver­sity and 10 other rese­arch insti­tutes in the areas of Elec­tri­cal and Com­puter Engin­eer­ing, Com­puter Sci­ence, Mater­i­als Sci­ence, Phys­ics, Che­mis-try, Bio­logy, and Math­em­at­ics. cfaed add­res­ses the advance­ment of elec­tro­nic inform­a­tion pro­ces­sing sys­tems through explor­ing new tech­no­lo­gies which over­come the lim­its of today’s pre­dom­in­ant CMOS tech­no­logy. For more inform­a­tion please see https://cfaed.tu-dresden.de/

About TU Dres­den
The TU Dres­den is among the top uni­ver­sit­ies in Ger­many and Europe and one of the ele­ven Ger­man uni­ver­sit­ies that were iden­ti­fied as an ‘elite uni­ver­sity’ in June 2012. As a mod­ern full-sta­tus uni­ver­sity with 14 depart­ments it offers a wide aca­demic range mak­ing it one of a very few in Ger­many.

How to ap­ply:

Applic­a­tion Pro­ced­ure
Your applic­a­tion (in Eng­lish only) should include: a motiv­a­tion let­ter, your CV with pub­lic­a­tion list, the names and con­tact details of two ref­er­ences, copy of degree cer­ti­fic­ate, and tran­script of grades (i.e. the offi­cial list of course­work includ­ing your grades). Please include also a link to your Mas­ter’s or PhD thesis. Com­plete applic­a­tions should be sub­mit­ted prefer­ably via the TU Dresden Secure­Mail Portal https://securemail.tu-dresden.de by send­ing it as a single pdf doc­u­ment quot­ing the ref­er­ence num­ber PhD-Bio0519 in the sub­ject header to recruiting.cfaed@tu-dresden.de or altern­at­ively by post to:

TU Dresden
cfaed
Herrn Dr. Ben­jamin Friedrich
Helm­holtz­str. 10
01069 Dresden
Ger­many.

The clos­ing date for applic­a­tions is 11.06.2019 (stamped arrival date of the uni­versity cent­ral mail ser­vice applies). Please sub­mit cop­ies only, as your applic­a­tion will not be returned to you. Expenses incurred in attend­ing inter­views can­not be reim-bursed.

Ref­er­ence to data pro­tec­tion: Your data pro­tec­tion rights, the pur­pose for which your data will be pro-cessed, as well as fur­ther inform­a­tion about data pro­tec­tion is avail­able to you on the web­site:
https://tu-dresden.de/karriere/datenschutzhinweis