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Transport of colloid particles through narrow channels is ubiquitous in cell biology as well as becoming increasingly important for microfluidic applications or targeted drug delivery. Membrane channels in cells are useful models for…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has…
Collective dynamics in proliferating anisotropic particle systems arise from an interplay between growth, division, and mechanical interactions, often mediated by particle shape. In classical models of prolate, rod-like growth, flow-induced…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
With the use of the general variational principle of self-organization of systems with varying constraints, namely the principle of dynamical harmonization of systems presented in the first work of the cycle, we advance an approach to the…
Randomly moving active particles can be herded into directed motion by asymmetric geometric structures. Although such a rectification process has been extensively studied due to its fundamental, biological, and technological relevance, a…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
This paper presents a novel methodology for the direct numerical modeling and simulation of turbulent flows. The kinetic model equation is firstly extended to turbulent flow with the account of coupled evolution of kinetic, thermal, and…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
We investigate the outflux of ions through the channels in a cell membrane. The channels undergo an open/close cycle according to a periodic schedule. Our study is based both on theoretical considerations relying on homogenization theory,…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
To analyze high-dimensional systems, many fields in science and engineering rely on high-level descriptions, sometimes called "macrostates," "coarse-grainings," or "effective theories". Examples of such descriptions include the…
Driving an inertial many-body system out of equilibrium generates complex dynamics due to memory effects and the intricate relationships between the external driving force, internal forces, and transport effects. Understanding the…
Tracer diffusion in crowded environments is central to many biological and soft matter systems, but quantitative frameworks for linking tracer motion to environmental structure remain limited. Here, we study the transport of rigid tracers…
Finding optimal trajectories for multiple traffic demands in a congested network is a challenging task. Optimal transport theory is a principled approach that has been used successfully to study various transportation problems. Its usage is…
Tracking experiments in dense biological tissues reveal a diversity of sources f or local energy injection at the cell scale. The effect of cell motility has been largely studied, but much less is known abo ut the effect of the observed…