Research Groups

(Virtual) DPG Meeting in the Group!

And the virtual conferences aren't over yet! Next week Allyson presents How Tissue Microenvironment Impacts Pluripotent Cell Differentiation to kick off the 2021 edition of the DPG @ 9:00am CET (UTC +01:00) Monday 22 March and then Tuesday afternoon Felix has a poster on Topology Control and Pruning in Intertwined Biological Flow Networks. Check it out! 

(Virtual) APS March Meeting in the Group!

Abhijeet, Felix, Carlos, Szabolcs, and Mohammad all present short talks at this year's All-Virtual APS March Meeting next week! We gathered on Zoom as a group (pictured above) to practice and provide feedback; good luck everyone! Check out the schedule below (all times UTC -05:00) and watch them present some of their work:

Tue 16 March 4:48pm Abhijeet Krishna J11.00008 Modelling the dynamics of shape change in a patterned viscoelastic sheet

Wed 17 March 3:48pm Felix Kramer P13.00005 Topology control and pruning in intertwined biological flow networks

Thu 18 March 10:00am Carlos Duque R11.00009 Spontaneous strains in tissue mechanics: topologically driven morphogenesis

Fri 19 March 8:48am Szabolcs Horvát X16.00005 Point pattern analysis through proximity graphs

Fri 19 March 1:42pm Mohammadreza Bahadorian Y11.00010 Multi-fractal analysis of the ossification process in developing skull bone

New Publication: Connectedness Matters

Szabolcs's "Connectedness Matters" paper is now out! Read it here and learn how to effectively and efficiently sample connected networks and generate connected null models with controlled bias and no issues with unknown mixing times. We also demonstrate that commonly applied ad hoc methods to construct these null models, such as simply taking the largest connected component of an unconstrained random network sampling can lead to serious problems.

UPDATE (10 Feb): "Connectedness Matters" has been picked up by phys.org, among other science news outlets! Check it out! And h/t to Katrin Boes for writing the news article for the MPI-CBG and CSBD websites in the first place!

Rotation Student in the Lab: Welcome Iaroslav!

Iaroslav Babenko, PhD student jointly in the labs of Nils Kröger and Benjamin Friedrich, joins us for a lab rotation these next few weeks. Iaroslav will be working with Szabolcs on automated computational analysis of biosilica features during the development of diatom shells. Welcome Iaroslav!

New Preprint: Lines of Concentrated Gaussian Curvature

New preprint out! Abhijeet Krishna helps investigate the shape programming of lines of concentrated Gaussian curvature in a great collaborative project that started with Mark Warner's visit to Dresden in the summer of 2019 and grew to include the Biggins lab in the UK and the Ware lab in Texas. Have a read here.

New Preprint: Biosilica Morphology in Diatoms

New preprint out! Szabolcs Horvát in collaboration with the Schlierf and Kröger labs at the TU Dresden's BCUBE brings computational analysis to bear on the seemingly disordered biosilica patterns of the T. pseudonana diatom, finding unappreciated and unexpected features in the underlying ridge networks. Check it out here.

Home Office Time Ahead, Take 2

After enjoying a COVID-free summer and a relatively low COVID autumn, the winter wave is upon us here in Dresden. As of the close of business today, we and the rest of the CSBD are again shifting entirely to remote/home office work for the coming weeks and perhaps months. Stay healthy and safe everyone!

New Publication: Intertwined Networks

Felix's paper on topology control and pruning in intertwined and interacting spatial networks is now out! It includes identification of a new, interaction mediated nullity transition as well as a nice generalization of the classical Murray's Law scaling to cases where fluctuations or spatial interactions influence the network structure. Read it here!

Guest Lecture for the IGC Lisbon 1st Year Graduate Course

Carl gave a guest lecture via the magic of Zoom to the first year graduate students at the Instituto Gulbenkian de Ciência in Oeiras, Portugal this morning, covering "theory and modelling of morphogenesis from cells to tissues". The group was very interactive and the whole thing was quite the enjoyable time.

Welcome Alicja Szałapak!

Alicja joins us to complete the spontaneous strain and topology mediated morphogenesis team. She will be looking at the comparative efficiency of different routes to the same shape outcomes as well as implications for engineering and device design as part of the EU FET-OPEN PRIME project. She arrived in Dresden today, but due to quarantine requirements she will need to wait until early October to join us in person at the CSBD. Welcome Alicja!

New Preprint: Connectivity Matters!

New preprint out! Szabolcs Horvát shows an efficient new method to randomly sample connected realizations of a network degree sequence. Read it here and see how to improve your network null models and be more confident that observed phenomena arise from specific proposed properties and not simply from the general constraints.

Welcome Carlos Duque!

Carlos joins us to work on a range of exciting projects connected to spontaneous strain and topology mediated morphogenesis, including the SPlaT-DM project in collaboration with the Sbalzarini and Jülicher groups on building a comprehensive simulation platform for topology driven morphogenesis. Due to COVID travel restrictions and quarantine requirements he is only able to join remotely for the time being, but we're looking forward to his arrival in the CSBD. Welcome Carlos!

Lab Outing: Photo Scavenger Hunt / Schnitzeljagd

Group activity this afternoon, an outdoor photo-scavenger hunt across Dresden on a beautiful, warm and sunny day! We started over a delicious Chinese lunch at Mandarin in Altstadt, where Carl distributed the first clue, and proceeded to hop across the city solving clues and taking pictures. The final clue (whose solution is being attempted in the pic in front of Schloss Albrechtsberg above, bottom right) led to a nearby beer garden for a relaxing evening to cap off the day.

Volkswagen Foundation Grant in the Lab!

The Modes Lab in collaboration with the labs of Alf Honigmann and André Nadler has been awarded a grant under the Volkswagen Foundation's 2020 version of the initiative "Life? – A fresh scientific approach to the basic principles of life". The joint project, "Cellular Reconstitution of Complex 3D Tissue Shapes”, seeks to tackle the mechanisms of how complex shapes emerge in multicellular life and ultimately open a new research field of complex tissue reconstitution. Read the institute's news article on the grant here and keep an eye out for hiring calls on the project from us and from the Honigmann and Nadler labs!

Remembering Suzanne Eaton

Today marks one year since we tragically lost our dear colleague, collaborator, and friend Suzanne Eaton. We and all the MPI-CBG remember her with deep admiration and respect, and we gather today to comfort one another, pay tribute to her memory, and inaugurate the site of a new contemplative garden at the institute that will bear her name. Read more here

New Publication: The Gift of Gab, Communication and Estimation

Mohammad's paper (in a fun collaboration between us and the Zechner Lab!) on dynamical communication or Poissonian and super Poissonian estimators over complex networks is out! Read it at Physical Review Research here  

Home Office Time Ahead

As of the close of business today, we and the rest of the CSBD are shifting entirely to remote/home office work for the coming weeks and perhaps months. We've been very fortunate not to have any COVID cases in the lab, or at the institute more broadly, but given the world numbers and the trends in Germany we don't want to press our luck any further. Stay healthy and safe everyone!

Lab Dinner and Exit Game!

 

Pizza and puzzles! We escaped being stranded on a desert island and will return to the CSBD and CBG tomorrow no worse for wear...

2020 DIPP Outstanding Mentor Award

Carl Modes has been awarded the Dresden International PhD Program Outstanding Mentor Award for 2020! He is very thankful and appreciative of his students for nominating him and hopes to continue being worthy of the honor in the future as well.

Joining the MPI-PKS Biophysics Retreat

This week we trek to snowy (or, rather, not-forecasted-to-be-so-snowy) Oberwiesenthal in the Erzgebirge mountains on retreat with Frank Jülicher, the rest of the the MPI-PKS Biophysics Department, and guests. Looking forward to a fun- and physics-packed time!

IMPRS First Year Pre-Doc Course begins

The 2019 first year PhD student course began today with a completely new format as teams of four students will work together on month-long projects guided by two or three different labs at the institute. This year, the Modes and Tang Labs will run a project on diffusive signalling in complex spaces viewed through the lens of bottom-up synthetic biology. The R2-D2s team of Chi Fung Chow (Toth-Petroczy Lab), Marina Cuenca (Tomancak Lab), Anna Gonchorova (Jug/Honigmann Labs), and Abhinav Singh (Sbalzarini Lab) is ready and rarin' to go, let's have a fun month!

Welcome Allyson Ryan!

Allyson joins us as well as the Tabler and Jug labs as a new ELBE Postdoctoral Fellow to work on an exciting collaborative project centered around the early growth of the skull plate. Welcome Allyson!

New Preprint: Communication and Estimation

Another new preprint is out now with Mohammad's paper on Poissonian and super Poissonian estimators communicating across a network of cells, a fun collaboration with the Zechner Lab. Have a look here.

We are hiring!

We have two open positions for postdoctoral researchers. The first position is related to theoretical and computational modelling of morphogenesis integrating experimental data. The second position is for designing active components in next-generation microfluidic circuits. Apply soon! Deadline : 6th October!

New Preprint: Intertwined Networks

Our new preprint is online, coming from the very first pre-doc of the lab : Felix! Check it out here. We model two intertwined and interacting 3D flow network systems and find interesting new topological phase transitions in the reticulation of the networks.

Lab Retreat

It’s retreat time! Like our last publication, this retreat was a fruitful collaboration with the Norden lab. The idea was for a theoretical and experimental lab to go on a retreat in order to understand the ideology and methodology of the “other side”. We spent three wonderful days in the Czech Republic in the village of Oparno. We would collectively recommend trying to give a presentation among the sounds of goats bleating.

New Publication: Nuclear Pushing in PSE

A schematic of the novel pushing mechanism for the nucleus proposed in the paper

Our new publication in collaboration with the Norden lab at MPI-CBG is out. The paper studies the migration of nuclei in the optic cup. The work was supported by a theoretical proof of principle model for a novel pushing mechanism for nuclear migration. We hope for many more collaborations with the amazing Norden lab in the future.

Visitor in lab : Prof. Mark Warner

CSBD is fortunate to host Prof. Mark Warner this summer. Mark is a Professor of Theoretical Physics at the Cavendish Laboratory at the Cambridge University. During his time here, he will collaborate closely with Carl to establish connections between his work on shape programmable materials and Developmental Biology.

Visitor in lab : Fionnuala Curran

As part of the IMPRS Student Research Internship, Fionnuala Curran has joined the Modes lab for the summer of 2019. She is an incoming fourth year undergraduate of theoretical physics in University College Dublin. For the next three months, she has joined forces with Szabolcs to study triangle constraints in stochastic block model graphs. In her free time, she is also working on her foosball skills.

Long Night of Science Dresden

The Modes lab participated in the Dresden Science Night. We demonstrated the Chain Fountain experiment. It was great fun demonstrating this phenomenon in the exciting environment. We thank the organisers for this event which attracted around 900 visitors!

Fun with Minimal Surfaces

Minimal surfaces : helicoid (left), catenoid (top-right).

On a sunny afternoon, our theoretical lab was literally converted into a “wet” lab. We decided to have some fun with soap films on wireframes. For a given boundary condition (the wire frame), the soap solution forms a film which has the minimum surface area possible. Hence, these surfaces are called minimal surfaces. Interestingly, the mean curvature at each point of such a surface is zero.
Having failed at making stable films two days back, we learnt that mixing soap, water and glycerol in the correct proportion was the key to success. We were able to generate some interesting films including a catenoid and a helicoid. Later during the week, Carl used this setup as props for a talk.

Imaging multiple samples using SPIM

We are very happy to announce our new publication in Development led by Stephan Daetwyler (lab alumni). This work was in collaboration with Ulrik Günther (Sbalzarini lab), Kyle Harrington (University of Idaho and former CSBD visiting faculty) and Jan Huisken (UoW Madison and former CSBD group leader). We present a new workflow for imaging multiple samples for several days using SPIM. The workflow is quite comprehensive starting from sample preparation and includes 3D segmentation, data processing, visualisation and analysis of vasculature growth.