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Tech­ni­sche Uni­ver­si­tät Dres­den - Clus­ter of Excel­lence ‘Cen­ter for Advan­cing Elec­tro­nics Dres­den’ (cfaed), junior rese­arch group “Bio­lo­gi­cal Algo­rithms”

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 or Post­doc 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: PhD: 65% of the full­time weekly hours, fixed-term until 06/2021. Pro­lon­ga­tion pos­si­ble depen­ding on the likely no-cost exten­sion of the HFSP grant bey­ond the sche­du­led ter­mi­na­tion date. Post­docs: 100%, fixed-term for about 2 years. The posi­tion starts as soon as pos­si­ble. The period of employ­ment is gover­ned by the Fixed-Term Rese­arch Con­tracts Act (Wis­sen­schafts­zeit­ver­trags­ge­setz – Wiss­ZeitVG). The posi­tion offers the chance to obtain fur­ther aca­de­mic qua­li­fi­ca­tion (e.g. PhD or habi­li­ta­tion the­sis).

Work­ing field:

About the “Bio­lo­gi­cal Algo­rithms group”
The mis­sion of our “Bio­lo­gi­cal Algo­rithms group” is to under­stand phy­si­cal prin­ci­ples of self-assem­bly and self-orga­niza­t­ion in bio­lo­gi­cal cells and tis­sues, and their robust­ness to noise and per­tur­ba­ti­ons. Topics include cel­lu­lar moti­lity con­trol and pat­tern for­ma­tion of the cytos­ke­le­ton. We pur­sue a Quan­ti­ta­tive Bio­lo­gi­cal Phy­sics approach that com­bi­nes non­linear dyna­mics, sta­ti­s­ti­cal phy­sics, com­pu­ta­tio­nal phy­sics and state-of-the-art image/data ana­ly­sis. More infor­ma­tion on cur­rent rese­arch can be found at https://cfaed.tu-dresden.de/friedrich-home.

About the pro­ject
https://cfaed.tu-dresden.de/press-releases-201/muscle-growth-in-the-computer-international-team-wants-to-unravel-the-formation-of-myofibrils
We are hiring a rese­arch asso­ciate for a pro­ject on mathe­ma­ti­cal mode­ling of myo­fi­bril­lo­ge­ne­sis, to under­stand how micro­sco­pic force-gene­ra­ting units in our mus­cles self-assem­ble during de-velop­ment.
Human mus­cle fibers are cen­ti­me­ter-long cells, packed with long linear myo­fi­brils that span throughout the fiber. Every myo­fi­bril is built by a chain of sar­co­me­res, which pro­duce active mus­cle forces. Each sar­co­mere is com­po­sed of actin fil­aments and myo­sin mole­cu­lar motors, lin­ked toge­ther by gigan­tic titin springs. The sar­co­me­res are strikingly regu­lar, con­sti­tu­ting an example of a dyna­mic bio­lo­gi­cal crys­tal. How the myo­fi­brils assem­ble during deve­lop­ment is poorly unders­tood. Pre­viously, we sug­gested a mathe­ma­ti­cal model of how actin and myo­sin fil­aments self-assem­ble into regu­lar sar­co­me­ric pat­terns by a com­bi­na­tion of active forces and pas­sive cross­lin­king (Fried­rich et al. PLoS Com­pu­ta­tio­nal Bio­logy, 2012). Based on this, we pro­pose agent-based simu­la­ti­ons of a bundle of actin, myo­sin, and titin, in order to under­stand the role of active ten­sion in sar­co­mere self-assem­bly. You will for­mu­late and imple­ment alter­na­tive phy­si­cal mecha­nisms and com­pare pre­dic­tions to quan­ti­ta­tive expe­ri­men­tal data.
This posi­tion will con­sti­tute the theory part of a theory-expe­ri­ment col­la­bo­ra­tion with the labo­ra­to­ries of Frank Schor­rer (IBDM, Mar­seil­les) and Oli­vier Pour­quie (HMSB, Bos­ton). The expe­ri­men­tal part­ners will pro­vide high-reso­lu­tion time-lapse fluo­re­scence micro­scopy data from the fruit fly and stem-cell deri­ved human mus­cle cells with GFP-tag­ged sar­co­me­ric pro­te­ins, as well as mole­cu­lar force-sen­sor data for live force mea­su­re­ments in deve­lo­ping mus­cle fibers. You will deve­lop auto­ma­ted image ana­ly­sis pipe­lines, and the­r­eby quan­tify the gra­dual emer­gence of sar­co­me­ric pat­terns using con­cepts from Soft Con­den­sed Mat­ter Phy­sics. Full fun­ding is avail­able from the pres­ti­gious Human Fron­tier Sci­ence Pro­gram.
Loo­king bey­ond this spe­ci­fic bio­lo­gi­cal model sys­tem, our group will explore also pos­si­ble app­li­ca­ti­ons of bio­lo­gi­cal self-orga­niza­t­ion and bot­tom-up self-assem­bly of bio­mole­cu­lar cir­cuits, e.g. motor-fil­ament arrays for bio­mole­cu­lar com­pu­ting, in tight col­la­bo­ra­tion with the engi­nee­ring paths of the cfaed. Dres­den unites excel­lence in infor­ma­tion and life sci­en­ces. 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, which allows fruit­ful inter­ac­tions with the strong Bio­lo­gi­cal Phy­sics rese­arch in Dres­den.

Require­ments:

We are loo­king for a theo­re­ti­cal phy­si­cist or app­lied mathe­ma­ti­cian, who is intrigued to dis­co­ver algo­rithms of life, and meets the fol­lo­wing requi­re­ments: For PhD stu­dents: excel­lent uni­ver­sity degree (Mas­ter) in Bio­lo­gi­cal Phy­sics, Mathe­ma­ti­cal Bio­logy, or rela­ted field; for Post­docs: an out­stan­ding uni­ver­sity degree and doc­to­ral degree in Bio­lo­gi­cal Phy­sics, Mathe­ma­ti­cal Bio­logy, or rela­ted field; strong ana­lytic skills, crea­ti­vity, effi­ci­ent pro­blem sol­ving skills; an apti­tude for data-dri­ven sci­ence and nume­ric com­pu­ting (e.g. Mat­lab, python, C); high moti­va­tion to work on ins­pi­ring rese­arch pro­blems at the inter­face of phy­sics, bio­logy and com­pu­ter sci­ence; excel­lent com-muni­ca­tion skills, espe­cially in cross-disci­pli­nary com­mu­ni­ca­tion; an inde­pen­dent, result-dri­ven work atti­tude; flu­ency in Eng­lish – oral and writ­ten.

What we of­fer:

You will join a team of enthu­si­a­s­tic sci­en­tists who pur­sue crea­tively their indi­vi­dual rese­arch agenda inspi­red by the clus­ter’s inno­va­tive approach and sup­port. Your rese­arch will be fos­te­red by the cfaed phi­lo­so­phy to pro­mote young rese­ar­chers which inclu­des: access to state of the art rese­arch of lea­ding aca­de­mic insti­tu­tes, indi­vi­dual super­vi­sion by a The­sis Advi­sory Com­mit­tee, pos­si­bi­lity to earn (seed) grants of up to € 10.000, pro­mo­tion of gen­der equa­lity and family-fri­endly work envi­ron­ment.
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.

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:

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-Bio1807 in the sub­ject hea­der to recruiting.cfaed@tu-dresden.de or alter­na­tively by post to: TU Dres­den, cfaed, Frau Dr. P. Grün­berg, Helm­holtz­str. 10, 01069 Dres­den, Ger­many. The clo­sing date for app­li­ca­ti­ons is 24.07.2018 (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.