Memory without a brain:

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

Encoding memory in tube diameter hierarchy of living flow network.
Mirna Kramar and Karen Alim,
[Proc. Natl. Acad. Sci. 2021] [PDF] [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 need more energy but can still achieve a considerable increase in performance. Critical 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 it reaches an optimum pumping efficiency. When the waves are in the optimum constellation, they work together to contract the tube even tighter, increasing efficiency without putting more energy into the waves. 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, and Karen Alim,
[Phys. Rev. Lett. 2020] [PDF] [Press English]

Controlling transport by vessel dilation:

In a complex vascular network, the blood vessels traverse the cell tissue of animals and plants. The vascular network supplies cells in a tissue with nutrients. Animals can dilate individual capillaries to distribute nutrients differently in the vascular network. How must the capillaries 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 cell’s position 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 brain’s physical parameters are chosen to allow for a robust supply increase independent of the network’s position. A finding that we explain within analytical derivations.

Robust increase in supply by vessel dilation in globally coupled microvasculature.
Felix Meigel, Peter Cha, Michael P. Brenner, and Karen Alim,
[Phys. Rev. Lett. 2019] [PDF] [Physics Synopsis] [Physics World Research Synopsis] [Press English]

Flow rate of transport network controls uniform metabolite supply to tissue.
Felix J. Meigel and Karen Alim,
[Roy. Soc. Interface 2018] [PDF]

Flows drive self-organization:

Long-range fluid flows are crucial for the functioning of many organisms, as they provide force 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 is spread with the fluid flows that arise from 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 and Karen Alim,
[Proc. Natl. Acad. Sci. 2018] [PDF] [Press German] [Press English]

Divide and conquer the fluid flow:

Many materials like rocks and sediments and materials for technological applications like fuel cells contain a lot of pores. As transport through these porous materials is often driven by fluid flow, it is essential 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 defines the overall flow characteristics of a porous material. Combining experiments and computer simulation with theoretical work supports this new idea. This contrasts former models, where the pore size distribution controls the flow through a material. Our new understanding may help us better design materials, for example, fuel cells or filtration techniques.

Local pore size correlations determine flow distributions in porous media.
Karen Alim, Shima Parsa, David A. Weitz, and Michael P. Brenner,
[Phys. Rev. Lett. 2017] [PDF]

Hijacking flows to find the shortest route through a maze:

How do 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 lacking 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.

Mechanism of signal propagation in Physarum polycephalum.
Karen Alim, Natalie Andrew, Anne Pringle, and Michael P. Brenner ,
[Proc. Natl. Acad. Sci. 2017] [PDF] [Press German] [Press English]

Fluid flows shaping organism morphology.
Karen Alim,
[Philos. Trans. Royal Soc. B 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 these organisms use 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 cross-section contractions of the veins drive the cytoplasmic flows. 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 contraction patterns 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, and Michael P. Brenner ,
[Phys. Rev. Lett. 2016] [PDF]

Quickguide: Physarum.
Karen Alim, Natalie Andrew, and Anne Pringle,
[Curr. Biol. 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. 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 its function could be in the shoot apical meristem of plants. Studying a katanin mutant, we provide evidence that katanin-dependent microtubule dynamics increase 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 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. 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 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 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 2010] [arXiv 2010] [PDF]

The form of semiflexible polymer rings:

The form of semiflexible biopolymers is essential to many biological processes, 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.

Our work aims 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 nano-technological design and coarse-grained biological modeling.

Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim*, and Erwin Frey,
[Soft Matter 2010] [arXiv 2010] [PDF]

Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim, and Erwin Frey,
[Phys. Rev. E 2010] [arXiv 2010] [PDF]

Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler, and Erwin Frey,
[Nano Letters 2010] [arXiv 2010] [PDF]

Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
[Eur. Phys. J. E 2007] [arXiv 2007] [PDF]

Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
[Phys. Rev. Lett. 2007] [arXiv 2007] [PDF]