Researcher profile

Karen Alim

Karen Alim contributes to research discovery and scholarly infrastructure.

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Published work

3 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.