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#cell

16 posts8 participants2 posts today
Rxiv mechanobio

📰 "The role of hydrodynamics in the synchronisation of {\it Chlamydomonas} flagella"
arxiv.org/abs/2504.02680 #Physics.Bio-Ph #Mechanical #Q-Bio.Cb #Cell

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arXiv.orgThe role of hydrodynamics in the synchronisation of {\it Chlamydomonas} flagellaWhile hydrodynamic coupling has long been considered essential for synchronisation of eukaryotic flagella, recent experiments on the unicellular biflagellate model organism {\it Chlamydomonas} demonstrate that -- at the single cell level -- intracellular mechanical coupling is necessary for coordination. It is therefore unclear what role, if any, hydrodynamic forces actually play in the synchronisation of multiple flagella within individual cells, arguably the building block of large scale coordination. Here we address this question experimentally by transiently blocking hydrodynamic coupling between the two flagella of single {\it Chlamydomonas}. Our results reveal that in wild type cells intracellularly-mediated forces are necessary and sufficient for flagellar synchronisation, with hydrodynamic coupling causing minimal changes in flagellar dynamics. However, fluid-mediated ciliary coupling is responsible for the extended periods of anti-phase synchronisation observed in a mutant with weaker intracellular coupling. At the single-cell level, therefore, flagellar coordination depends on a subtle balance between intracellular and extracellular forces.
Rxiv mechanobio

📰 "Identity-Based Language Shift Modeling"
arxiv.org/abs/2504.01552 #Physics.Soc-Ph #Dynamics #Math.Na #Cs.Na #Cell

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arXiv.orgIdentity-Based Language Shift ModelingThe preservation of endangered languages is a widely discussed issue nowadays. Languages represent essential cultural heritage and can provide valuable botanical, biological, and geographical information. Therefore, it is necessary to develop efficient measures to preserve and revitalize endangered languages. However, the language shift process is complex and requires an interdisciplinary approach, including mathematical modeling techniques. This paper develops a new mathematical model that extends previous works on this topic. We introduce the factor of ethnic identity, which is a proxy for a more complex nexus of variables involved in an individual's self-identity and/or a group's identity. This proxy is socially constructed rather than solely inherited, shaped by community-determined factors, with language both indexing and creating the identity. In our model, we divide speakers into groups depending on with which language they identify themselves with. Moreover, every group includes monolinguals and bilinguals. The proposed model naturally allows us to consider cases of language coexistence and describe a broader class of linguistic situations. For example, the simulation results show that our model can result in cyclic language dynamics, drawing a parallel to cell population models. In this way, the proposed mathematical model can serve as a useful tool for developing efficient measures for language preservation and revitalization.
Rxiv mechanobio

📰 "A kinetic model of jet-corona coupling in accreting black holes"
arxiv.org/abs/2504.01062 #Physics.Plasm-Ph #Astro-Ph.He #Dynamics #Cell

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arXiv.orgA kinetic model of jet-corona coupling in accreting black holesBlack hole (BH) accretion disks are often coupled to ultramagnetized and tenuous plasma coronae close to their central BHs. The coronal magnetic field can exchange energy between the disk and the BH, power X-ray emission, and lead to jetted outflows. Up until now, the coronal physics of BH accretion has only been studied using fluid modeling. We construct the first model of a BH feeding on a zero-net-flux accretion disk corona based on kinetic plasma physics. This allows us to self-consistently capture how collisionless relativistic magnetic reconnection regulates the coronal dynamics. We present global, axisymmetric, general relativistic particle-in-cell simulation of a BH coupled, via a series of magnetic loops, to a razor-thin accretion disk. We target the jet-launching regime where the loops are much larger than the BH. We ray-trace high-energy synchrotron lightcurves and track the flow of Poynting flux through the system, including along specific field-line bundles. Reconnection on field lines coupling the BH to the disk dominates the synchrotron output, regulates the flux threading the BH, and ultimately untethers magnetic loops from the disk, ejecting them via a magnetically striped Blandford-Znajek jet. The jet is initially Poynting-dominated, but reconnection operates at all radii, depleting the Poynting power logarithmically in radius. Coronal emission and jet launch are linked through reconnection in our model. This link might explain coincident X-ray flaring and radio-jet ejections observed during hard-to-soft X-ray binary state transitions. It also suggests that striped jet launch could be heralded by a bright coronal counterpart. Our synchrotron signatures resemble variability observed from the peculiar changing-look AGN, 1ES 1927+654, and from Sagittarius A*, hinting that processes similar to our model may be at work in these contexts.
Rxiv mechanobio

📰 "Influence of erythrocyte density on aggregability as a marker of cell age: Dissociation dynamics in extensional flow"
arxiv.org/abs/2409.08877 #Physics.Bio-Ph #Mechanical #Dynamics #Cell

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arXiv.orgInfluence of erythrocyte density on aggregability as a marker of cell age: Dissociation dynamics in extensional flowBlood rheology and microcirculation are strongly influenced by red blood cell (RBC) aggregation. The aggregability of RBCs can vary significantly due to factors such as their mechanical and membrane surface properties, which are affected by cell aging in vivo. In this study, we investigate RBC aggregability as a function of their density, a marker of cell age and mechanical properties, by separating RBCs from healthy donors into different density fractions using Percoll density gradient centrifugation. We examine the dissociation rates of aggregates in a controlled medium supplemented with Dextran, employing an extensional flow technique based on hyperbolic microfluidic constrictions and image analysis, assisted by a convolutional neural network (CNN). In contrast to other techniques, our microfluidic experimental approach highlights the behavior of RBC aggregates in dynamic flow conditions relevant to microcirculation. Our results demonstrate that aggregate dissociation is strongly correlated with cell density and that aggregates formed from the denser fractions of RBCs are significantly more robust than those from the average cell population. This study provides insight into the effect of RBC aging in vivo on their mechanical properties and aggregability, underscoring the importance of further exploration of RBC aggregation in the context of cellular senescence and its potential implications for hemodynamics. Additionally, it suggests that this technique can complement existing methods for improved evaluation of RBC aggregability in health and disease.
Rxiv mechanobio

📰 "Active Hydrodynamic Theory of Euchromatin and Heterochromatin"
arxiv.org/abs/2503.20964 #Physics.Bio-Ph #Cond-Mat.Soft #Q-Bio.Sc #Dynamics #Cell

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arXiv.orgActive Hydrodynamic Theory of Euchromatin and HeterochromatinThe genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin and heterochromatin -- contain largely transcriptionally active and silenced genes, respectively, and exhibit distinct dynamics. In this work, we present a hydrodynamic framework that describes the large-scale behavior of euchromatin and heterochromatin, and accounts for the interplay of mechanical forces, active processes, and nuclear confinement. Our model shows contractile stresses from cross-linking proteins lead to the formation of heterochromatin droplets via mechanically driven phase separation. These droplets grow, coalesce, and in nuclear confinement, wet the boundary. Active processes, such as gene transcription in euchromatin, introduce non-equilibrium fluctuations that drive long-range, coherent motions of chromatin as well as the nucleoplasm, and thus alter the genome's spatial organization. These fluctuations also indirectly deform heterochromatin droplets, by continuously changing their shape. Taken together, our findings reveal how active forces, mechanical stresses and hydrodynamic flows contribute to the genome's organization at large scales and provide a physical framework for understanding chromatin organization and dynamics in live cells.
Rxiv mechanobio

📰 "Scalable Superconducting Nanowire Memory Array with Row-Column Addressing"
arxiv.org/abs/2503.22897 #Physics.App-Ph #Dynamics #Cell

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arXiv.orgScalable Superconducting Nanowire Memory Array with Row-Column AddressingDeveloping ultra-low-energy superconducting computing and fault-tolerant quantum computing will require scalable superconducting memory. While conventional superconducting logic-based memory cells have facilitated early demonstrations, their large footprint poses a significant barrier to scaling. Nanowire-based superconducting memory cells offer a compact alternative, but high error rates have hindered their integration into large arrays. In this work, we present a superconducting nanowire memory array designed for scalable row-column operation, achieving a functional density of 2.6$\,$Mb/cm$^{2}$. The array operates at $1.3\,$K, where we implement and characterize multi-flux quanta state storage and destructive readout. By optimizing write and read pulse sequences, we minimize bit errors while maximizing operational margins in a $4\times 4$ array. Circuit-level simulations further elucidate the memory cell's dynamics, providing insight into performance limits and stability under varying pulse amplitudes. We experimentally demonstrate stable memory operation with a minimum bit error rate of $10^{-5}$. These results suggest a promising path for scaling superconducting nanowire memories to high-density architectures, offering a foundation for energy-efficient memory in superconducting electronics.
Rxiv mechanobio

📰 "A soft particle dynamics method based on shape degrees of freedom"
arxiv.org/abs/2503.22827 #Physics.Comp-Ph #Dynamics #Cell

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arXiv.orgA soft particle dynamics method based on shape degrees of freedomIn this paper, we present a 2D numerical model developed to simulate the dynamics of soft, deformable particles. To accommodate significant particle deformations, the particle surface is represented as a narrow shell composed of mass points that interact through elasto-plastic force laws governing their linear and angular relative displacements. Particle shape changes are controlled by these interactions, in conjunction with a uniform particle core stiffness. We calibrate and verify this model by comparing the deformation of constrained beams under load with theoretical predictions. Subsequently, we explore the diametral compression of a single particle between two walls, focusing on the influence of the particle core stiffness and shell plasticity. Our findings indicate that increased core stiffness reduces particle volume change and promotes the development of faceting through flat contact areas with the walls. To further illustrate the model's capabilities, we apply it to the uniaxial compaction of a granular material composed of core-shell particles. We show that, depending on the core stiffness and shell plasticity, the compaction leads to either a significant reduction of particle volumes or an improved pore filling due to particle shape changes. At high compaction, particle shapes vary: elastic particles without core stiffness become mostly elongated, elastic particles with core stiffness form polygonal shapes, while plastic particles develop elliptical or highly irregular forms. Finally, we simulate the tensile fracture of a tissue composed of elastic or plastic cells, illustrating the model's potential applicability to soft tissues that undergo both large cell deformations and fracture.
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