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The actin cytoskeleton of cells is in continuous motion due to both polymerization of new filaments and their contraction by myosin II molecular motors. Through adhesion to the substrate, such intracellular flow can be converted into cell…
We develop a minimal hydrodynamic model, without an orientational order parameter, for assemblies of contractile swimmers encapsulated in a droplet of a binary-fluid emulsion. Our model uses two coupled scalar order parameters, $\phi$ and…
We investigate a two-dimensional system of active Brownian dumbbells using molecular dynamics simulations. In this model, each dumbbell is driven by an active force oriented perpendicular to the axis connecting its two constituent beads. We…
Motivation: Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information…
Shape transformations of epithelial tissues in three dimensions, which are crucial for embryonic development or in vitro organoid growth, can result from active forces generated within the cytoskeleton of the epithelial cells. How the…
Embryonic tissues deform across broad spatial and temporal scales and relax stress through active rearrangements. A quantitative link between cell-scale activity, spatial forcing, and emergent tissue-scale mechanics remains incomplete.…
There are two phases of Wnt signalling in early vertebrate embryogenesis: very early, maternal Wnt signalling promotes dorsal development, and slightly later, zygotic Wnt signalling promotes ventral and lateral mesoderm induction. However,…
In the recent years, MRI-driven turbulent transport has been found to depend in a significant way on fluid viscosity $\nu$ and resistivity $\eta$ through the magnetic Prandtl number $Pm=\nu/\eta$. In particular, the transport decreases with…
In biological systems, molecular-scale forces and motions are pivotal for enabling processes like motility, shape change, and replication. These forces and motions are organized, amplified, and transmitted across macroscopic scales by…
The Drosophila larva, a soft-body animal, can bend its body and roll efficiently to escape danger. However, contrary to common belief, this rolling motion is not driven by the imbalance of gravity and ground reaction forces. Through…
Diffusion-weighted magnetic resonance imaging (dMRI) is the only non-invasive tool for studying white matter tracts and structural connectivity of the brain. These assessments rely heavily on tractography techniques, which reconstruct…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
We analyse a generic motility model, with the motility mechanism arising by contractile stress due to the interaction of myosin and actin. A hydrodynamic active polar gel theory is used to model the cytoplasm of a cell and is combined with…
Ion channels selectively transport ions, yet the underlying mechanisms remain elusive. We propose a physical model based on the Driven Damped Harmonic Oscillator (DDHO), where self-organizing turbulent structures in the ionic flow generate…
Biological microswimmers are known to navigate upstream of an external flow (positive rheotaxis) in trajectories ranging from linear, spiral to oscillatory. Such rheotaxis stems from the interplay between the motion and complex shapes of…
Automatic analyses and comparisons of different stages of embryonic development largely depend on a highly accurate spatiotemporal alignment of the investigated data sets. In this contribution, we assess multiple approaches for automatic…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are sufficient to deform long…
We propose an agent-based model of active flexible rods. Inspired by cytoskeletal flows, we introduce activity by an internal flow that contributes to the dissipative forces. The active force between our agents is central and reciprocal,…
Active inference is a theory that underpins the way biological agent's perceive and act in the real world. At its core, active inference is based on the principle that the brain is an approximate Bayesian inference engine, building an…