Research

Memory without a brain:

Simple organisms manage to thrive in complex environments. Having memory about the environment is key in taking informed decisions. Physarum polycephalum excels as a giant unicellular eukaryote, being even able to solve optimization problems despite the lack of a nervous system. Here, we follow experimentally the organism’s response to a nutrient source and find that memory about nutrient location is encoded in the morphology of the network-shaped organism. Our theoretical predictions in line with our observations unveil the mechanism behind memory encoding and demon- strate the P. polycephalum’s ability to read out previously stored information.

Encoding memory in tube diameter hierarchy of living flow network.
Mirna Kramar & Karen Alim,
Proc. Natl. Acad. Sci. U.S.A. 118 (10) e2007815118 (2021).
(Press English) , (Press German) .

Cost-free control of pumping efficiency:

The slime mold Physarum polycephalum can thus add another achievement to its long list of remarkable properties: it can spontaneously adjust its pumping efficiency as soon as its environmental conditions change. Thanks to the clever interaction of two superimposed pumping modes, he doesn’t even need more energy, but can still achieve a considerable increase in performance. The key physics: peristaltic contraction waves consist of a fundamental wave and an overtone at twice the frequency. Under blue light, from which the slime mold wants to escape, one of the waves shifts against the other until they have reached an optimum pumping efficiency. When the waves are in the optimum constellation, they work together to contract the tube even tighter, thereby achieving an increase in efficiency without having to put more energy into the waves themselves. In the future, the observations could be used in medical technology or in soft robotics where peristalsis is already used today.

Living system adapts harmonics of peristaltic wave for cost-efficient optimization of pumping performance.
Felix K. Bäuerle, Stefan Karpitschka & Karen Alim,
Phys. Rev. Lett. 124,098102 (2020). (PDF), (Press English) , (Press German) .

Controlling transport by vessel dilation:

The cell tissue of animals and plants is traversed by a complex vascular network, the blood vessels. The vascular network supplies cells in a tissue with nutrients. Animals can dilate individual capillaries to distribute nutrients differently in the vascular network. How do the capillaries have to be dilated to transport more nutrients to a specific area of the cell tissue? Does the change in nutrient availability for a cell strongly depend on the position of the cell in the tissue? Do vascular networks have a specific structure that allows them to precisely control nutrient supply to cells when only certain areas of cell tissue require more nutrients? Solving the supply dynamics for rat brain microvasculature, we find that the brains physical parameters are chosen as to allow for a robust increase in supply independent of the position in the network. A finding which we explain within analytical derivations.

Robust increase in supply by vessel dilation in globally coupled microvasculature.
Felix Meigel, Peter Cha, Michael P. Brenner & Karen Alim,
Phys. Rev. Lett. 123, 228103 (2019). (PDF), (Physics Synopsis) , (Physics World Research Synopsis), Press English , Press German .

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

Flows drive self-organization:

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)

Divide and conquer the fluid flow:

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)

Hijacking flows to find the shortest route through a maze:

How do apparently simple organisms coordinate sophisticated behaviors? The slime mold Physarum polycephalum solves complex problems, for example finding the shortest route between food sources, despite growing as a single cell and the lack of any neural circuitry. By carefully observing P. polycephalum’s response to a nutrient stimulus and using the data to develop a mathematical model, we identify a simple mechanism underpinning the slime mold’s behaviors: A stimulus triggers the release of a signaling molecule. The molecule is initially advected by fluid flows but also increases fluid flows, generating a feedback loop and enabling the movement of information throughout the organism’s body. This simple mechanism is sufficient to explain P. polycephalum’s emergent, complex behaviors like for example finding the shortest route through a maze.

Mechanism of signal propagation in Physarum polycephalum.
Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner ,
Proc. Natl. Acad. Sci. U.S.A.,114(20), 5236-5141 (2017). (PDF) (Press German) (Press English)

Fluid flows shaping organism morphology.
Karen Alim,
Philos. Trans. Royal Soc. B, 373, 20170112 (2018). (PDF)

Organizing flows to control behavior:

Foraging organisms such as fungi and the slime mold Physarum polycephalum grow as remarkably large networks to explore their environment and find scarce and spatially disjunct resources. The mechanisms used by these organisms to integrate disparate sources of information and regulate their growth and morphological adaptation remain unknown. We study the cytoplasmic flows within the vein networks of P. polycephalum as a mechanism to coordinate behavior and transport signals. We find that the cytoplasmic flows are driven by cross-section contractions of the veins. These contractions form a peristaltic wave. We extend the theoretical concept of peristalsis to a random network and show that transport is maximized when the network comprises a single wavelength of the peristaltic wave. Comparisons of theoretically generated contraction patterns with the patterns exhibited by individuals of P. polycephalum demonstrate that individuals maximize internal flows by adapting patterns of contraction to size, thus optimizing transport throughout an organism. This control of fluid flow may be the key to coordinating growth and behavior, including the dynamic changes in network architecture seen over time in an individual.

Pruning to increase Taylor dispersion in Physarum polycephalum networks.
Sophie Marbach, Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner ,
Phys. Rev. Lett., 117, 178103 (2016). (PDF)

Quickguide: Physarum.
Karen Alim, Natalie Andrew and Anne Pringle,
Curr. Biol., 23(24), R1082-R1083 (2013). (PDF) .

Random network peristalsis in Physarum polycephalums organizes fluid flows across an individual.
Karen Alim*, Gabriel Amselem*, François Peaudecerf, Michael P. Brenner and Anne Pringle,
Proc. Natl. Acad. Sci. U.S.A., 110(33), 13306-13311 (2013). (PDF) .

Growth control in plant tissue:

A central question in biology is how cells within a tissue coordinate their growth. We investigated how growth heterogeneity is controlled and what could be its function in the shoot apical meristem of plants. Studying a katanin mutant we provide evidence that katanin-dependent microtubule dynamics increases cell competence to respond to mechanical stress, allowing cells to adapt their growth parameters to that of their neighbors. While this mechanism could mediate growth homeostasis, we surprisingly found that it enhances growth heterogeneity. We generated a model of cell tissue growth exploring the strength of the cell response to mechanical stress. The model shows that mechanical forces may decrease growth variability, even providing a theoretical optimum of homogeneity. However, the model also shows that the existence of large stress feedback, and most clearly for low fluctuations in growth, can on the contrary increase growth variability. Validation of the latter by our growth measurements suggests that, despite the existence of a theoretical optimum where growth is homogeneous, growth in plants is suboptimal to maintain an ability to generate and amplify differential growth during organogenesis.

Regulatory role of cell division rules on tissue growth heterogeneity.
Karen Alim, Olivier Hamant and Arezki Boudaoud,
Front. Plant Sci. 3, 00174 (2012). (PDF) .
Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.
Magalie Uyttewaal*, Agata Burian*, Karen Alim*, Benoît Landrein, Dorota Borowska-Wykręt, Annick Dedieu, Alexis Peaucelle, Michał Ludynia, Jan Traas, Arezki Boudaoud**, Dorota Kwiatkowska** and Olivier Hamant**,
Cell 149, 439-451 (2012). (PDF) .

Leaf vein initiation during plant development:

Plant cells grow, divide, and differentiate in response to the concentration of the hormone auxin. This hormone has the property that it induces the polar distribution of its own efflux facilitator, PIN, in a cell’s membrane. By this mechanism dynamic patterns of auxin and PIN arise on a multicellular level. This is in many parts of plants the first step to development and growth, such as in the formation of veins in the evolving leaf. During vein initiation auxin flows very localized from outer cell layers into the ground meristem. There it induces the polarization of PIN distribution along a strand of cells. Our work identifies the role of the kinetic processes in auxin and PIN dynamics during this polarization. We deduce quantitative predictions based on rigorous mathematical results that enable the determination of the kinetic parameters in future experiments. Furthermore, our analysis suggests the occurrence of bipolar cells. As bipolar cells lie at the origin of the yet puzzling formation of closed, looped veins, we provide a further understanding of vein formation.

Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 33, 165 (2010). arXiv:1005.3768. (PDF) .

The form of semiflexible polymer rings:

The form of semiflexible biopolymers is essential to many biological processes, as for example for the protein target search along a DNA. Also considering biopolymers like actin, microtubules and poly- nucleotides as nano-sized building blocks their conformations are of eminent concern. We study how the shape of semiflexible polymer rings is governed by inherent factors such as flexibility and filament diameter and external constraints like confinement. Especially the topological constraint of a ring, ubiquitously occurring in biological systems, results in astonishingly rich polymer configurations. It is the aim of our work to give an intuitive understanding of polymer shapes by rationalizing conformations observed within Monte Carlo Simulations with straightforward analytic arguments. Thereby we provide tools to estimate the shape of semiflexible polymer rings for the design of nano-technological design and coarse-grained biological modelling.

Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim* and Erwin Frey,
Soft Matter 6, 3467-3471 (2010). arXiv:1004.4574. (PDF) .

Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim and Erwin Frey,
Phys. Rev. E 81, 061802 (2010). arXiv:1003.4267. (PDF) .

Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler and Erwin Frey,
Nano Letters 10, 1445-1449 (2010). arXiv:0906.3991. (PDF) .

Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 24, 185-191 (2007). arXiv:0708.0111. (PDF) .

Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
Phys. Rev. Lett. 99, 198102 (2007). arXiv:q-bio/0703049. (PDF) .