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Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
We study the flow of an electrically charged fluid through an elastic and porous medium. A three continuum model consisting of an elastic solid, a viscous fluid, and a mobile charge continuum is used. The relevant laws of physics are…
The equation governing the streaming of a quantity down its gradient superficially looks similar to the simple constant velocity advection equation. In fact, it is the same as an advection equation if there are no local extrema in the…
Cilia and flagella are hair-like appendages that protrude from the surface of a variety of eukaryotic cells and deform in a wavelike fashion to transport fluids and propel cells. Motivated by the ubiquity of non-Newtonian fluids in biology,…
A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion, which controls cellular functionality. Here, we investigated two…
Collective migration of eukaryotic cells is often guided by chemotaxis, and is critical in several biological processes, such as cancer metastasis, wound healing, and embryogenesis. Understanding collective chemotaxis has challenged…
The aim of this work is to quantify the spatio-temporal dynamics of flow-driven amoeboid locomotion in small ($\sim$100 $\mu$m) fragments of the true slime mold \phys {\it polycephalum}. In this model organism, cellular contraction drives…
Liquid-liquid phase separation is an important mechanism for compartmentalizing the cell's cytoplasm, allowing the dynamic organization of the components necessary for survival. However, it is not clear how phase separation is affected by…
Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering…
A hybrid kinetic-fluid model is used to study plasma stratification in alternating current (AC) discharges in noble gases at low plasma densities. Self-consistent coupled solutions of a nonlocal kinetic equation for electrons, a…
Flow cytometry (FC) is a single-cell profiling platform for measuring the phenotypes of individual cells from millions of cells in biological samples. FC employs high-throughput technologies and generates high-dimensional data, and hence…
We consider a Stokes flow coupled with advective-diffusive transport in an evolving domain with boundary conditions allowing for inflow and outflow. The evolution of the domain is induced by the transport process, leading to a fully coupled…
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a non-equilibrium system is crucial in elucidating the intricate…
In this work, we aimed to replicate and extend the results presented in the DiffFluid paper[1]. The DiffFluid model showed that diffusion models combined with Transformers are capable of predicting fluid dynamics. It uses a denoising…
Long, shallow microchannels embedded in thick soft materials are widely used in microfluidic devices for lab-on-a-chip applications. However, the bulging effect caused by fluid--structure interactions between the internal viscous flow and…
We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind…
Dissipative Particle Dynamics (DPD) is becoming a popular particle based method to study flow through microchannels due to the ease with which the presence of biological cells or DNA chains can be modeled. Many Lab-On-Chip (LOC) devices…
Diffusion and flow-matching have emerged as powerful methodologies for generative modeling, with remarkable success in capturing complex data distributions and enabling flexible guidance at inference time. Many downstream applications,…