Related papers: Analytical methods for cytoplasmic streaming in el…
We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case…
These lectures start with the mean field theory for a symmetric binary fluid mixture, addressing interfacial tension, the stress tensor, and the equations of motion (Model H). We then consider the phase separation kinetics of such a…
Many biological systems evolve through continuous local dynamics while switching between latent regimes defined by learning, stimulus context, internal state, or developmental stage. These processes are often observed only as unpaired…
Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer…
The leading-order far-field scattered flow produced by a particle in a parallel-wall channel under creeping flow conditions has a form of the parabolic velocity field driven by a 2D dipolar pressure distribution. We show that in a system of…
Two fundamental problems in unsupervised learning are efficient inference for latent-variable models and robust density estimation based on large amounts of unlabeled data. Algorithms for the two tasks, such as normalizing flows and…
The ocean is filled with microscopic microalgae called phytoplankton, which together are responsible for as much photosynthesis as all plants on land combined. Our ability to predict their response to the warming ocean relies on…
Animal morphogenesis often involves significant shape changes of epithelial tissue sheets. Great progress has been made in understanding the underlying cellular driving forces and their coordination through biomechanical feedback loops.…
Many fundamental biological processes are dependent on cellular migration. Although the mechanical mechanisms of single-cell migration are relatively well understood, those underlying migration of multiple cells adhered to each other in a…
The seemingly simple process of inhalation relies on a complex interplay between muscular contraction in the thorax, elasto-capillary interactions in individual lung branches, propagation of air between different connected branches, and…
We propose a one-way coupled model that tracks individual primary particles in a conceptually simple cellular flow setup to predict flocculation in turbulence. This computationally efficient model accounts for Stokes drag, lubrication,…
Obtaining sparse, interpretable representations of observable data is crucial in many machine learning and signal processing tasks. For data representing flows along the edges of a graph, an intuitively interpretable way to obtain such…
Flowing blood displays a phenomenon called margination, in which leukocytes and platelets are preferentially found near blood vessel walls, while erythrocytes are depleted from these regions. Here margination is investigated using direct…
Flow cytometry mainly used for detecting the characteristics of a number of biochemical substances based on the expression of specific markers in cells. It is particularly useful for detecting membrane surface receptors, antigens, ions, or…
The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations challenging, especially when capillary effects are essential for the dynamics of the flow.…
Modeling dynamical systems and unraveling their underlying causal relationships is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and…
Classical thermodynamics and statistical mechanics describe systems in which nothing interacts with nothing. Even the highly refined theory of simple fluids does not deal very well with electrical interactions, boundary conditions, or…
In many applications, the two-dimensional trajectories of fluid particles are available, but little is known about the underlying flow. Oceanic floats are a clear example. To extract quantitative information from such data, one can measure…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…