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Many parts of biological organisms are comprised of deformable porous media. The biological media is both pliable enough to deform in response to an outside force and can deform by itself using the work of an embedded muscle. For example,…

We present a model for unicellular algal growth as motivated by several experiments implicating the importance of calcium ions and ``loosening'' enzymes in morphogenesis. A growing cell at rest in a diffusive calcium solution is viewed as…

The microalga Chlamydomonas Reinhardtii (CR) is used here as a model system to study the effect of complex environments on the swimming of micro-organisms. Its motion can be modelled by a run and tumble mechanism so that it describes a…

From the Golgi apparatus to endosomes, organelles in the endomembrane system exhibit complex and varied morphologies that are often related to their function. Such membrane-bound organelles operate far from equilibrium due to directed…

Biofilms are bacterial aggregates that grow on moist surfaces. Thin homogeneous biofilms naturally formed on the walls of conducts may serve as biosensors, providing information on the status of microsystems (MEMS) without disrupting them.…

Flagella and cilia are cellular appendages that inherit essential functions of microbial life including sensing and navigating the environment. In order to propel a swimming microorganism they displace the surrounding fluid by means of…

Motility is a fundamental survival strategy of bacteria to navigate porous environments. Swimming cells thrive in quiescent wetlands and sediments at the bottom of the marine water column, where they mediate many essential biogeochemical…

Confined granular fluids, placed in a shallow box that is vibrated vertically, can achieve homogeneous stationary states thanks to energy injection mechanisms that take place throughout the system. These states can be stable even at high…

Organisms are composed of multiple chemical elements such as carbon, nitrogen, and phosphorus. The scarcity of any of these elements can severely restrict organismal and population growth. However, many trophic interaction models only…

Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way…

Biological functionality of cellular aggregates is largely influenced by the activity and displacements of individual constituent cells. From a theoretical perspective this activity can be characterized by hydrodynamic transport…

A promising approach to transport cargo at the microscale lies within the use of self-propelled microorganisms, whose motion entrains that of passive particles. However, most applications remain limited to just a few passive particles of…

Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better…

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…

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…

Several recent experiments investigate the orientational and transport behavior of self-driven bacteria and colloidal particles in nematic liquid crystals. Correspondingly, we study theoretically the dynamics of a minimal model microswimmer…

In tissues as diverse as amphibian skin and the human airway, the cilia that propel fluid are grouped in sparsely distributed multiciliated cells (MCCs). We investigate fluid transport in this "mosaic" architecture, with emphasis on the…

Environmental science almost invariably proposes problems of extreme complexity, typically characterized by strongly nonlinear evolution dynamics. The systems under investigation have many degrees of freedom - which makes them complicated -…

Continuum models of active nematic gels have proved successful to describe a number of biological systems consisting of a population of rodlike motile subunits in a fluid environment. However, in order to get a thorough understanding of the…

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule…