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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 Posi­tion in Theo­re­ti­cal Bio­lo­gi­cal Phy­sics

(sub­ject to per­so­nal qua­li­fi­ca­tion employees are remu­n­e­ra­ted accord­ing to salary group E 13 TV-L)
Rese­arch area: Mus­cle buil­ding in silico: Mathe­ma­ti­cal mode­ling of myo­fi­bril­lo­ge­ne­sis
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 until June 30, 2021 with the pos­si­bi­lity of exten­sion. 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).

Work­ing field:

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.

About the pro­ject
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.
In this pro­ject, phy­si­cal mecha­nisms of myo­fi­bril self-assem­bly shall be inves­ti­ga­ted, with a focus the role of active ten­sion and fil­ament elas­ti­city for sar­co­mere self-assem­bly. We will for­mu­late alter­na­tive phy­si­cal mecha­nisms in terms of mathe­ma­ti­cal models, study these nume­ri­cally and ana­lyti­cally, and test these by com­pa­ri­son to expe­ri­men­tal data. Spe­ci­fi­cally, we plan agent-based simu­la­ti­ons of initi­ally unor­de­red acto-myo­sin bund­les, with spe­ci­fic inter­ac­tion rules for the dif-ferent fil­aments. In addi­tion to com­pu­ter simu­la­ti­ons, we will deve­lop a mean-field theory of sar-come­ric pat­tern for­ma­tion that coarse-grains the inter­ac­tion model. We will com­pute phase-dia­gram of liquid crys­tal order in nas­cent myo­fi­brils. We will derive tes­ta­ble pre­dic­tions that will be com­pa­red to quan­ti­ta­tive expe­ri­men­tal data (time-lapse fluo­re­scence micro­scopy, elec­tron micro­scopy, mole­cu­lar force sen­sor data).
Pre­viously, our group pro­po­sed a first mecha­nism 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), which will pro­vide a star­ting point for the pro­ject.
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 fund-ing 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 com­mu­ni­ca­tion 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 (500000 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 pro-ces­sing 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/

Addi­tio­nally, our rese­arch group is part of the new Clus­ter of Excel­lence “Phy­sics of Life” and affi­liat-ed with the “Cen­ter for Sys­tems Bio­logy Dres­den”.

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-Bio-w517 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 07.01.2019 (stam­ped arri­val date of the uni­ver­sity cen­tral mail ser­vice app­lies). Please sub­mit copies only, as your ap-pli­ca­tion will not be retur­ned to you.

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