arXiv subjects

Jonas Ranft

Publications and source records attributed to Jonas Ranft.

11 recordsLinked to original sources

arXiv2025

Contraction waves in pulsating active liquids: From pacemaker to aster dynamics

We propose a hydrodynamic theory to examine the emergence of contraction waves in dense active liquids composed of pulsating deformable particles. Our theory couples the liquid density with a chemical phase that determines the periodic deformation of the particles. This mechanochemical coupling regulates the interplay between the flow induced by local deformation, and the resistance to pulsation stemming from steric interaction. We show that this interplay leads the emergent contraction waves to spontaneously organize into a packing of pacemakers. We reveal that the dynamics of these pacemakers is governed by a complex feedback between slow and fast topological defects that form asters in velocity flows. In fact, our defect analysis is a versatile platform for investigating the self-organization of waves in a wide range of contractile systems. Our results shed light on the key mechanisms that control the rich phenomenology of pulsating liquids, with relevance for biological systems such as tissues made of confluent pulsating cells.

cond-mat.stat-mech↗

arXiv2024

How random connectivity shapes the fluctuating dynamics of finite-size neural populations

Mesoscopic models of finite-size neuronal populations are crucial to understand the dynamics of neural networks in the brain, especially their fluctuations and response to stimuli. However, current theories to derive such models are based on homogeneous all-to-all (full) connectivity. This assumption neglects the variance in the connectivity of biologically realistic networks with connection probabilities $p<1$ (non-full connectivity). To gain insight into the different fluctuation mechanisms underlying neural variability at the population level, we derive and analyze a stochastic mean-field model for finite-size networks of Poisson neurons with random connectivity (including non-full connectivity), external noise and disordered mean inputs. We treat the quenched disorder of the connectivity by an annealed approximation enabling a doubly stochastic description of synaptic inputs for finite network size. A further reduction leads to a low-dimensional closed system of coupled Langevin equations for the mean and variance of the membrane potentials as well as a variable capturing finite-size fluctuations. Compared to microscopic simulations, the mesoscopic model describes the fluctuations and nonlinearities well and outperforms previous theories that neglected the variance in the connectivity. The joint effect of connectivity disorder and finite network size can be analytically understood by a softening of the effective nonlinearity and the multiplicative character of spiking noise. The mesoscopic theory shows that quenched disorder can stabilize the asynchronous state, and it correctly predicts large quantitative and non-trivial qualitative effects of connection probability on the variance of the population firing rate and its dependence on stimulus strength. In conclusion, our theory elucidates how disordered connectivity shapes nonlinear dynamics and fluctuations of neural populations.

q-bio.NC↗

arXiv2024

Hydrodynamics of pulsating active liquids

Inspired by dense contractile tissues, where cells are subject to periodic deformation, we formulate and study a generic hydrodynamic theory of pulsating active liquids. Combining mechanical and phenomenological arguments, we postulate that the mechanochemical feedback between the local phase, which describes how cells deform due to autonomous driving, and the local density can be described in terms of a free energy. We demonstrate that such a feedback is compatible with the coarse-graining of a broad class of microscopic models. Our hydrodynamics captures the three main states emerging in its particle-based counterparts: a globally cycling state, a homogeneous arrested state with constant phase, and a state with propagating radial waves. Remarkably, we show that the competition between these states can be rationalized intuitively in terms of an effective landscape, and argue that waves can be regarded as secondary instabilities. Linear stability analysis of the arrested and cycling states, including the role of fluctuations, leads to predictions for the phase boundaries. Overall, our results demonstrate that our minimal, yet non-trivial model provides a relevant platform to study the rich phenomenology of pulsating liquids.

cond-mat.soft↗

arXiv2024

Self-consistent autocorrelation of a disordered Kuramoto model in the asynchronous state

The Kuramoto model has provided deep insights into synchronization phenomena and remains an important paradigm to study the dynamics of coupled oscillators. Yet, despite its success, the asynchronous regime in the Kuramoto model has received limited attention. Here, we adapt and enhance the mean-field approach originally proposed by Stiller and Radons [Phys. Rev. E 58 (1998)] to study the asynchronous state in the Kuramoto model with a finite number of oscillators and with disordered connectivity. By employing an iterative stochastic mean field (IMF) approximation, the complex N-oscillator system can effectively be reduced to a one-dimensional dynamics, both for homogeneous and heterogeneous networks. This method allows us to investigate the power spectra of individual oscillators as well as of the multiplicative "network noise" in the Kuramoto model in the asynchronous regime. By taking into account the finite system size and disorder in the connectivity, our findings become relevant for the dynamics of coupled oscillators that appear in the context of biological or technical systems.

math-ph↗

arXiv2023

Non-equilibrium cluster-cluster aggregation in the presence of anchoring sites

Non-equilibrium cluster-cluster aggregation of particles diffusing in or at the cell membrane has been hypothesized to lead to domains of finite size in different biological contexts such as lipid rafts, cell adhesion complexes, or postsynaptic domains in neurons. In this scenario, the desorption of particles balances a continuous flux to the membrane, imposing a cut-off on possible aggregate sizes and giving rise to a stationary size distribution. Here, we investigate the case of non-equilibrium cluster-cluster aggregation in two dimensions where diffusing particles and/or clusters remain fixed in space at specific anchoring sites, which should be particularly relevant for synapses but may also be present in other biological or physical systems. Using an effective mean-field description of the concentration field around anchored clusters, we derive an expression for their average size as a function of parameters such as the anchoring site density. We furthermore propose and solve appropriate rate equations that allow us to predict the size distributions of both diffusing and fixed clusters. We confirm our results with particle-based simulations, and discuss potential implications for biological and physical systems.

cond-mat.soft↗

arXiv2022

Theory of the asynchronous state of structured rotator networks and its application to recurrent networks of excitatory and inhibitory units

Recurrently coupled oscillators that are sufficiently heterogeneous and/or randomly coupled can show an asynchronous activity in which there are no significant correlations among the units of the network. The asynchronous state can nevertheless exhibit a rich temporal correlation statistics, that is generally difficult to capture theoretically. For randomly coupled rotator networks, it is possible to derive differential equations that determine the autocorrelation functions of the network noise and of the single elements in the network. So far, the theory has been restricted to statistically homogeneous networks, making it difficult to apply this framework to real-world networks, which are structured with respect to the properties of the single units and their connectivity. A particularly striking case are neural networks for which one has to distinguish between excitatory and inhibitory neurons, which drive their target neurons towards or away from firing threshold. To take into account network structures like that, here we extend the theory for rotator networks to the case of multiple populations. Specifically, we derive a system of differential equations that govern the self-consistent autocorrelation functions of the network fluctuations in the respective populations. We then apply this general theory to the special but important case of recurrent networks of excitatory and inhibitory units in the balanced case and compare our theory to numerical simulations. We inspect the effect of the network structure on the noise statistics by comparing our results to the case of an equivalent homogeneous network devoid of internal structure. Our results show that structured connectivity and heterogeneity of the oscillator type can both enhance or reduce the overall strength of the generated network noise and shape its temporal correlations.

q-bio.NC↗

arXiv2022

A model of membrane deformations driven by a surface pH gradient

Many cellular organelles are membrane-bound structures with complex membrane composition and shape. Their shapes have been observed to depend on the metabolic state of the organelle, and the mechanisms that couple biochemical pathways and membrane shape are still actively investigated. Here, we study a model coupling inhomogeneities in the lipid composition and membrane geometry via a generalized Helfrich free energy. We derive the resulting stress tensor, the Green's function for a tubular membrane and compute the phase diagram of the induced deformations. We then apply this model to study the deformation of mitochondria cristae described as membrane tubes supporting a pH gradient at its surface. This gradient in turn controls the lipid composition of the membrane via the protonation/deprotonation of cardiolipins, which are acid-based lipids known to be crucial for mitochondria shape and functioning. Our model predicts the appearance of tube deformations resembling the observed shape changes of cristea when submitted to a proton gradient.

cond-mat.soft↗

arXiv2022

A self-consistent analytical theory for rotator networks under stochastic forcing: effects of intrinsic noise and common input

Despite the incredible complexity of our brains' neural networks, theoretical descriptions of neural dynamics have led to profound insights into possible network states and dynamics. It remains challenging to develop theories that apply to spiking networks and thus allow one to characterize the dynamic properties of biologically more realistic networks. Here, we build on recent work by van Meegen & Lindner who have shown that "rotator networks," while considerably simpler than real spiking networks and therefore more amenable to mathematical analysis, still allow to capture dynamical properties of networks of spiking neurons. This framework can be easily extended to the case where individual units receive uncorrelated stochastic input which can be interpreted as intrinsic noise. However, the assumptions of the theory do not apply anymore when the input received by the single rotators is strongly correlated among units. As we show, in this case the network fluctuations become significantly non-Gaussian, which calls for a reworking of the theory. Using a cumulant expansion, we develop a self-consistent analytical theory that accounts for the observed non-Gaussian statistics. Our theory provides a starting point for further studies of more general network setups and information transmission properties of these networks.

q-bio.NC↗

arXiv2016

One-dimensional collective migration of a proliferating cell monolayer

The importance of collective cellular migration during embryogenesis and tissue repair asks for a sound understanding of underlying principles and mechanisms. Here, we address recent in vitro experiments on cell monolayers which show that the advancement of the leading edge relies on cell proliferation and protrusive activity at the tissue margin. Within a simple viscoelastic mechanical model amenable to detailed analysis, we identify a key parameter responsible for tissue expansion, and we determine the dependence of the monolayer velocity as a function of measurable rheological parameters. Our results allow us to discuss the effects of pharmacological perturbations on the observed tissue dynamics.

q-bio.QM↗

arXiv2015

Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly

Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the Enveloping Cell Layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly.

q-bio.TO↗

arXiv2014

Border forces and friction control epithelial closure dynamics

Epithelization, the process whereby an epithelium covers a cell-free surface, is not only central to wound healing but also pivotal in embryonic morphogenesis, regeneration, and cancer. In the context of wound healing, the epithelization mechanisms differ depending on the sizes and geometries of the wounds as well as on the cell type while a unified theoretical decription is still lacking. Here, we used a barrier-based protocol that allows for making large arrays of well-controlled circular model wounds within an epithelium at confluence, without injuring any cells. We propose a physical model that takes into account border forces, friction with the substrate, and tissue rheology. Despite the presence of a contractile actomyosin cable at the periphery of the wound, epithelization was mostly driven by border protrusive activity. Closure dynamics was quantified by an epithelization coefficient $D = σ_p/ξ$ defined as the ratio of the border protrusive stress $σ_p$ to the friction coefficient $ξ$ between epithelium and substrate. The same assay and model showed a high sensitivity to the RasV12 mutation on human epithelial cells, demonstrating the general applicability of the approach and its potential to quantitatively characterize metastatic transformations.

q-bio.CB↗