https://hdl.handle.net/2072/478914 2026-04-05T03:13:17Z 2026-04-05T03:13:17Z Qi, Kai Zhou, H.Y. Corato, Marco de Stratford, Kevin Pagonabarraga Mora, Ignacio https://hdl.handle.net/2445/228244 2026-03-19T19:52:28Z 2026-03-18T07:45:35Z

Unravel the rotational and translational behavior of a single squirmer in flexible polymer solutionsat different Reynolds numbers Qi, Kai; Zhou, H.Y.; Corato, Marco de; Stratford, Kevin; Pagonabarraga Mora, Ignacio Microorganisms such as bacteria and algae navigate complex fluids, where their dynamics are vital for medical and industrial applications. However, the influence of the Reynolds number (Re) on the transport and rotational behavior of microswimmers in viscoelastic media remains poorly understood. Here, we investigate these effects for a model squirmer in flexible polymer solutions across a range of Re using Lattice Boltzmann simulations. The interaction between swimmer activity and polymer heterogeneity strongly affects behavior, with rotational enhancement up to 1400-fold and reduced self-propulsion and diffusivity for squirmers. These effects result from hydrodynamic and mechanical interactions: polymers wrap ahead of pushers and accumulate behind pullers, enhancing rotation while hindering translation through forces and torques from direct contacts or asymmetric flows. The influence of Re and squirmer-polymer boundary conditions (no-slip vs. repulsive) is also examined. Notably, no-slip conditions intensify effects above a critical Reynolds number (). Below this value, stronger viscous drag minimizes differences. Our findings emphasize the crucial role of polymer-swimmer interactions in shaping microswimmer behavior in viscoelastic media, informing microrobotic design in complex environments.

2026-03-18T07:45:35Z Haeb, Anna-Christina Yamamoto, Hideaki Roach, Paul Merryweather, Daniel Sato, Y. Tornero, Daniel Soriano i Fradera, Jordi https://hdl.handle.net/2445/228245 2026-03-19T19:11:15Z 2026-03-18T08:32:26Z

Protocol for tailored in vitro neuronal networks on high-density microelectrode arrays with polydimethylsiloxane microstructures Haeb, Anna-Christina; Yamamoto, Hideaki; Roach, Paul; Merryweather, Daniel; Sato, Y.; Tornero, Daniel; Soriano i Fradera, Jordi Complementary metal-oxide-semiconductor (CMOS)-based high-density microelectrode arrays (HD-MEAs) enable neuronal recordings with high spatiotemporal resolution. However, integrating polydimethylsiloxane (PDMS) microstructures onto HD-MEA surfaces to control network architecture is currently challenging and platform specific. Here, we present a protocol for PDMS fabrication, HD-MEA chip preparation, PDMS-HD-MEA microstructure alignment, and cell culture, including alternatives. Our results show reproducible formation of modular networks with characteristic activity patterns across different systems. This protocol supports engineering of defined neuronal architectures while maintaining compatibility with various HD-MEA systems.

2026-03-18T08:32:26Z Mikaberidze, Guram Artime, Oriol Díaz Guilera, Albert D'Souza, Raissa M. https://hdl.handle.net/2445/228178 2026-03-18T19:49:57Z 2026-03-17T10:53:27Z

Multiscale Field Theory for Network Flows Mikaberidze, Guram; Artime, Oriol; Díaz Guilera, Albert; D'Souza, Raissa M. Network flows are pervasive, including the movement of people, transportation of goods, transmission of energy, and dissemination of information; they occur on a range of empirical interconnected systems, from designed infrastructure to naturally evolved networks. Despite the broad spectrum of applications, because of their domain-specific nature and the inherent analytic complexity, a comprehensive theory of network flows is lacking. We introduce a unifying treatment for network flows that considers the fundamental properties of packet symmetries, conservation laws, and routing strategies. For example, electrons in power grids possess interchangeability symmetry, unlike packages sent by postal mail, which are distinguishable. Likewise, packets can be conserved, such as cars in road networks, or dissipated, such as Internet packets that time out. We introduce a hierarchy of analytical field-theoretic approaches to capture the different scales of complexity required. Mean-field analysis uncovers the nature of the transition through which flow becomes unsustainable upon unchecked growth of demand. Mesoscopic field theory accurately accounts for complicated network structures, packet symmetries, and conservation laws and yet is capable of admitting closed-form solutions. Finally, the full-scale field theory allows us to study routing strategies ranging from random diffusion to shortest path. Our theoretical results indicate that flow bottlenecks tend to be near sources for interchangeable packets and near sinks for distinguishable ones, and that dissipation hinders the maximum sustainable throughput for interchangeable packets but can enhance throughput for distinguishable packets. Finally, we showcase the flexibility of our multiscale theory by applying it in two distinct domains of road networks and the C. elegans neuronal network. Our work paves the way for a more unifying and comprehensive theory of network flows.

2026-03-17T10:53:27Z Cunquero, Marina Isla-Magrane, Helena Castro-Olvera, Gustavo Soriano i Fradera, Jordi Marsal, Maria Mateos, Nicolas Zufiaurre, Maddalen Garcia-Arumi, Josep Duarri, Anna Loza-Alvarez, Pablo https://hdl.handle.net/2445/226129 2026-01-27T19:58:42Z 2026-01-26T10:23:38Z

Mapping the structure and function of whole-mount retinal organoids Cunquero, Marina; Isla-Magrane, Helena; Castro-Olvera, Gustavo; Soriano i Fradera, Jordi; Marsal, Maria; Mateos, Nicolas; Zufiaurre, Maddalen; Garcia-Arumi, Josep; Duarri, Anna; Loza-Alvarez, Pablo Cell therapy is a therapeutic avenue for retinal degenerative diseases. Photoreceptortransplantation faces challenges in obtaining high-quality and mature photoreceptors that caneffectively integrate and function, facilitating regeneration. For designing therapies we will produceretinal organoids (RO) from ihPSC. To enhance our understanding of RO maturation in a 3D anddynamic context, we aim to characterize the structure and function of retinal neurons. This will helpidentifying the optimal timing for harvesting photoreceptors for subsequent implantation. In thiswork, we focus on the characterization of RO derived from ihPSC from healthy and vision-impairedindividuals, specifically Retinitis Pigmentosa type 25. We tracked calcium activity in 3D with light-sheet fluorescence microscopy (LSFM). Thisoptical configuration allows fast tracking of dynamics (10 Z-planes at 5 Hz) occurring on a volumetricscale (600x830x100μm) with minor photo-toxic effects. For visualizing changes in the calciuminfluxes, we used viral vectors encoding for GCaMP6s. Changes in fluorescence intensity werequantified and analysed in a 3D fashion to determine the pattern and frequency of calcium waves inthe neuronal network. Subsequently to the life dynamic recordings, and to characterize thestructure of whole-mount mature ROs (up to day 250), we optimized an optical clearing method(FluoClear BABB) in combination with improved antibody permeabilization. We imaged in high-resolution the calcium activity of RO derived from healthy and vision-impaired donors and quantified differences in the functional communities of neurons by usingtransfer entropy. Using our clearing protocol, we identified the morphology and population of thethree neuron-path that provide the direct route for visual information transmission: cone and rodphotoreceptors, bipolar and ganglion cells. RO are promising in vitro models for studying retinal diseases. Our findings shed morelight on the temporal, spatial and functional organization of retinal cells within the organoid. Our LSFM can be applied to study fast events occurring in mm range samples with cellular resolution

2026-01-26T10:23:38Z