3/10/18 PNAS on flows driving scaling published!

Flows drive self-organization:

long-range flows in Physarum

Long-range fluid flows are crucial for the functioning of many organisms, as they provide forcing for migration and development and spread resources and signals. How flows can span vastly different scales is unclear. Here, we develop a minimal, two-component model, coupling the mechanics of a cell’s cortex to a contraction-triggering chemical. The chemical itself is spread with the fluid flows that arise due to the cortex contractions. Through theoretical and numerical analysis, we find that the oscillatory component of the flows can give rise to robust scaling of contraction waves with system size—much beyond predicted length scales. This mechanism is likely to work in a broad class of systems.

Oscillatory fluid flow drives scaling of contraction wave with system size.
Jean-Daniel Julien & Karen Alim,
Proc. Natl. Acad. Sci. U.S.A., 115, 10612–10617 (2018). (PDF) (Press German) (Press English)

27/9/18. Our new lab is finished!

We are so happy about our new lab! Now both microscopes, cell culture and leisurely office space are in one big spacious room. We are truly enjoying the new atmosphere and will even do better science. Find us in 1.32 now.

03/05/18 Felix’s paper on supply in vascular networks is out

Life and functioning of higher organisms depends on the continuous supply of metabolites to tissues and organs. What are the requirements on the transport network pervading a tissue to provide a uniform supply of nutrients, minerals or hormones? To theoretically answer this question, we present an analytical scaling argument and numerical simulations on how flow dynamics and network architecture control active spread and uniform supply of metabolites by studying the example of xylem vessels in plants. We identify the fluid inflow rate as the key factor for uniform supply. While at low inflow rates metabolites are already exhausted close to flow inlets, too high inflow flushes metabolites through the network and deprives tissue close to inlets of supply. In between these two regimes, there exists an optimal inflow rate that yields a uniform supply of metabolites. We determine this optimal inflow analytically in quantitative agreement with numerical results. Optimizing network architecture by reducing the supply variance over all network tubes, we identify patterns of tube dilation or contraction that compensate sub-optimal supply for the case of too low or too high inflow rate.

Flow rate of transport network controls uniform metabolite supply to tissue.
Felix J. Meigel & Karen Alim,
Roy. Soc. Interface, 15, 20180075 (2018). (PDF)

10/4/18 Franz’s paper on nuclei ordering in fruit fly embryo is out

In the early fruit fly embryo before cellularisation, the organism is challenged to ensure that its up to 6000 cortical nuclei exhibit the order necessary for robust development. Nuclei order has to be maintained despite repeating rounds of nuclei division disrupting nuclei order. We investigated how mechanical forces between nuclei control nuclei order during these crucial early stages of a budding life. We devised a continuum mechanical model of nuclei interactions by combining passive elastic interactions mediated by the shared cytoplasm with stochastic forces arising between nuclei due to motor protein activity to understand how stochastic forces are tamed. Comparing model simulations with experimental recordings of nuclei dynamics we find excellent agreement if motor protein activity is diluted upon successive rounds of nuclei divisions. A finding that we substantiate with independent experimental measurements of motor cluster lifetimes. We thereby uncover a simple mechanism to control stochasticity during development namely downregulating stochastic versus mechanical forces by diluting the molecules driving stochasticity.


Mechanical model of nuclei ordering in Drosophila embryos reveals dilution of stochastic forces.

Franz Kaiser, Zhiyi Lv, Daniel Marques Rodrigues, Jan Rosenbaum, Timo Aspelmeier, Jörg Großhans, Karen Alim,
Biophys. J., 114(7), 1730-1740 (2018). (PDF)

5/10/17 Congrats to Felix and Mirna on their first Physarum paper!

Wounding is a severe impairment of function, especially for an exposed organism like the network-forming true slime mould Physarum polycephalum. The tubular network making up the organism’s body plan is entirely interconnected and shares a common cytoplasm. Oscillatory contractions of the enclosing tube walls drive the shuttle streaming of the cytoplasm. Cytoplasmic flows underlie the reorganization of the network for example by movement toward attractive stimuli or away from repellants. Here, we follow the reorganization of P. polycephalum networks after severe wounding. Spatial mapping of the contraction changes in response to wounding reveal a multi-step pattern. Phases of increased activity alternate with cessation of contractions and stalling of flows, giving rise to coordinated transport and growth at the severing site. Overall, severing surprisingly acts like an attractive stimulus enabling healing of severed tubes. The reproducible cessation of contractions arising during this wound-healing response may open up new venues to investigate the biochemical wiring underlying P. polycephalum‘s complex behaviours.

Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum.
Felix Bäuerle, Mirna Kramar & Karen Alim,
J. Phys. D: Appl. Phys., 50, 434005 (2017). (PDF)

3/10/17 PRL on flow in porous media published

flow pattern in a porous medium

Many materials like rocks and sediments but also materials for technological application like fuel cells contain a lot of pores. As transport through these porous materials is often driven by fluid flow it is important to understand how material architecture determines the landscape of flow velocities within such a medium. We find that local partitioning of fluid flow between adjacent pores define the overall flow characteristics of a porous material. Combining experiments and computer simulation with theoretical work supports this new idea. This is in contrast to former models where the flow through a material is controlled by the pore size distribution. Our new understanding may help us in better design of materials for example for fuel cells or filtration techniques.

Local pore size correlations determine flow distributions in porous media.
Karen Alim, Shima Parsa, David A. Weitz, & Michael P. Brenner,
Phys. Rev. Lett, 119, 144501 (2017). (PDF)

19/9/17 João Ramos joins us for his PhD. Welcome!

fbaeuerle João Ramos obtained his Bachelor and Master in Physics from the University of Coimbra (Portugal) in 2014 and 2016, respectively. For his Master, he specialized in Computational Modelling and Simulation. During his time at Coimbra, he worked with Dr. Rui Travasso and Dr. João Carvalho from the Soft and Biological Matter group at the Center for Physics of the University of Coimbra (CFisUC). This included developing a cellular automata model for tumor induced angiogenesis during his Bachelor and, for his Master thesis, simulating mechanically-driven pattern formation in cell cultures using a cellular Potts model coupled with a finite element method as well as employing image analysis techniques for characterising the morphology of emerging patterns. In 2017, he joined Biological Physics and Morphogenesis group led by Dr. Karen Alim at the Max Planck Institute for Dynamics and Self-Organisation as a PhD student working on auxin transport during plant development.

16/5/17 PNAS + PNAS cover on slime mold behavior published

We have discovered the mechanism underlying the slime mold’s (Physarum polycephalum) complex behavior, work just published in the recent issue of Proceedings of the National Academy of Science (PNAS). Our finding: Despite lacking a nervous system, a simple feedback allows the network-forming slime mold to find the shortest path through a maze. The slime mold sends information in the form of signaling molecules throughout its network of veins. Signaling molecules are transported by flowing fluids and cause fluid flow to increase. This positive feedback loop, on the one hand, speeds up information transfer, but at the same time fosters the growth of veins, precisely those that are tracing the shortest path between stimuli. With their project the scientists illuminate the mystery behind the ‘intelligent’ slime mold. We hope that the feedback mechanism found in nature may in future help develop artificial systems permitting self-organizing adaptation.