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Karen Alim

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Published work

9 published item(s)

preprint2026arXiv

Coexistence of trapped and flow-transported nuclei enables fast pigeon post communication across multinucleated cell

Multi-nucleated cells exist in all domains of life, ranging from animals, plants and fungi to single-celled organisms such as the slime mold Physarum polycephalum. The large cell size, in the case of Physarum reaching centimeters and more, challenges the coordination of nuclei activity as signals need to cross large distances. In search for a mechanism for fast long-ranged communication among nuclei, we quantify nuclei dynamics and cytoplasmic flows in Physarum's tubular network. We observe nuclei in two interchangeable, dynamic states: mobile, flowing within the cytoplasmic shuttle flow, or trapped in the tube's porous cell cortex. As we find nuclei to accumulate at the tube's inner fluid-porous interface we theoretically explore and confirm, with physiological parameters, that slowing down of mobile nuclei during flow is sufficient for diffusible signal exchange between mobile and trapped nuclei. We analytically derive that communication akin to pigeon-post with mobile nuclei serving as pigeons shuttling between trapped nuclei acting as waypoints, gives rise to signaling velocities that account for the rapid intracellular reorganization observed in Physarum. Since signal transfer by flow-transported nuclei outcompetes the mere diffusion of signals encoded in cytosolic proteins, pigeon-post communication surpasses alternative signaling mechanisms, even diffusive relay signaling up to twenty-fold in velocity. The key ingredients of pigeon-post communication, namely alternating flows and waypoints, exist in other multi-nucleated cells and may also be generalized beyond intracellular signaling.

preprint2020arXiv

Feedback from tissue mechanics self-organizes efficient outgrowth of plant organ

Plant organ outgrowth superficially appears like the continuous mechanical deformation of a sheet of cells. Yet, how precisely cells as individual mechanical entities can act to morph a tissue reliably and efficiently into three dimensions during outgrowth is still puzzling especially when cells are tightly connected as in plant tissue. In plants, the mechanics of cells within a tissue is particularly well defined as individual cell growth is essentially the mechanical yielding of cell-wall in response to internal turgor pressure. Cell wall stiffness is controlled by biological signalling and, hence, cell growth is observed to respond to mechanical stresses building up within a tissue. What is the role of the mechanical feedback during morphing of tissue in three dimensions? Here, we develop a three dimensional vertex model to investigate tissue mechanics at the onset of organ outgrowth at the tip of a plant shoot. We find that organ height is primarily governed by the ratio of growth rates of faster growing cells initiating the organ to slower growing cells surrounding them. Remarkably, the outgrowth rate is higher when cells growth responds to the tissue-wide mechanical stresses. Our quantitative analysis of simulation data shows that tissue mechanical feedback on cell growth can act via twofold mechanism. First, the feedback guides patterns of cellular growth. Second, the feedback modifies the stress patterns on the cells, consequently amplifying and propagating growth anisotropies. This mechanism may allow plants to grow organs efficiently out of the meristem by reorganizing the cellular growth rather than inflating growth rates.

preprint2019arXiv

Controlling effective dispersion within a channel with flow and active walls

Channels are fundamental building blocks from biophysics to soft robotics, often used to transport or separate solutes. As solute particles inevitably transverse between streamlines along the channel by molecular diffusion, the effective diffusion of the solute along the channel is enhanced - an effect known as Taylor dispersion. Here, we investigate how the Taylor dispersion effect can be suppressed or enhanced in different settings. Specifically, we study the impact of flow profile and active or pulsating channel walls on Taylor dispersion. We derive closed analytic expressions for the effective dispersion equation in all considered scenarios providing hands-on effective dispersion parameters for a multitude of applications. In particular, we find that active channel walls may lead to three regimes of dispersion: either dispersion decrease by entropic slow down at small Peclet number, or dispersion increase at large Peclet number dominated either by shuttle dispersion or by Taylor dispersion. This improves our understanding of solute transport e.g. in biological active systems such as blood flow and opens a number of possibilities to control solute transport in artificial systems such as soft robotics.

preprint2016arXiv

Leaf growth is conformal

Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

preprint2016arXiv

Pruning to Increase Taylor Dispersion in Physarum polycephalum Networks

How do the topology and geometry of a tubular network affect the spread of particles within fluid flows? We investigate patterns of effective dispersion in the hierarchical, biological transport network formed by Physarum polycephalum. We demonstrate that a change in topology - pruning in the foraging state - causes a large increase in effective dispersion throughout the network. By comparison, changes in the hierarchy of tube radii result in smaller and more localized differences. Pruned networks capitalize on Taylor dispersion to increase the dispersion capability.

preprint2010arXiv

Buckling of stiff polymer rings in weak spherical confinement

Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak spherical confinement imposed by an impenetrable shell. We develop an analytic argument for the dominating polymer trajectory depending on polymer flexibility considering elastic and entropic contributions. Monte Carlo simulations are performed to assess polymer ring conformations in probability densities and by the shape measures asphericity and nature of asphericity. Comparison of the analytic argument with the mean asphericity and the mean nature of asphericity confirm our reasoning to explain polymer ring conformations in the stiff regime, where elastic response prevails.

preprint2010arXiv

Excluded volume effects on semiflexible ring polymers

Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of the different models over the full range of flexibilities shows that excluded volume caused by finite thickness induces an anisotropic increase of the main axes of the conformations, a change of shape, accomplished by an enhanced correlation along the contour.

preprint2010arXiv

Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves

The dynamic patterning of the plant hormone auxin and its efflux facilitator the PIN protein are the key regulator for the spatial and temporal organization of plant development. In particular auxin induces the polar localization of its own efflux facilitator. Due to this positive feedback auxin flow is directed and patterns of auxin and PIN arise. During the earliest stage of vein initiation in leaves auxin accumulates in a single cell in a rim of epidermal cells from which it flows into the ground meristem tissue of the leaf blade. There the localized auxin supply yields the successive polarization of PIN distribution along a strand of cells. We model the auxin and PIN dynamics within cells with a minimal canalization model. Solving the model analytically we uncover an excitable polarization front that triggers a polar distribution of PIN proteins in cells. As polarization fronts may extend to opposing directions from their initiation site we suggest a possible resolution to the puzzling occurrence of bipolar cells, such we offer an explanation for the development of closed, looped veins. Employing non-linear analysis we identify the role of the contributing microscopic processes during polarization. Furthermore, we deduce quantitative predictions on polarization fronts establishing a route to determine the up to now largely unknown kinetic rates of auxin and PIN dynamics.