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The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
We discuss a theoretical model for bidirectional cargo transport in biological cells, which is driven by teams of molecular motors and subject to thermal fluctuations. The model describes explicitly the directed motion of the molecular…
Transport networks are crucial to the functioning of natural systems and technological infrastructures. For flow networks in many scenarios, such as rivers or blood vessels, acyclic networks (i.e., trees) are optimal structures when…
Microorganisms often encounter strong confinement and complex hydrodynamic flows while navigating their habitats. Combining finite-element methods and stochastic simulations, we study the interplay of active transport and heterogeneous…
The transport of motile entities across modulated energy landscapes plays an important role in a range of phenomena in biology, colloidal science and solid-state physics. Here, an easily implementable strategy that allows for the collective…
Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…
Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization…
In an inspiring recent study, Xu et al. [Nat. Phys. 19, 46 (2023)] observed for a living active biofilm under circular confinement two emergent dynamic modes of collective motion in the film. One corresponds to global rotational motion of…
The one-dimensional crawling movement of a cell is considered in this theoretical study. Our active gel model shows that for a cell with weakly mechanosensitive adhesion complexes, as myosin contractility increases, a cell starts to move at…
Motor-proteins are responsible for transport inside cells. Harnessing their activity is key towards developing new nano-technologies, or functional biomaterials. Cytoskeleton-like networks, recently tailored in vitro, result from the…
Flow networks are essential for both living organisms and enginneered systems. These networks often present complex dynamics controlled, at least in part, by their topology. Previous works have shown that topologically complex networks…
Neuronal function requires precise spatial organization of mitochondria to meet localized energetic demand. However, the physical constraints governing mitochondrial transport in axons remain poorly defined. Bidirectional motor-driven…
Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication.…
Most biological molecules contain acido-basic groups that modulate their structure and interactions. A consequence is that pH gradients, local heterogeneities and dynamic variations are used by cells and organisms to drive or regulate…
Transport at microscopic length scales is essential in biological systems and various technologies, including microfluidics. Recent experiments achieved self-organized transport phenomena in microtubule active matter using light to modulate…
Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the…
Acellular slime mould Physarum polycephalum is a monstrously large single cell visible by an unaided eye. It shows sophisticated behavioural traits in foraging for nutrients and developing an optimal transport network of protoplasmic tubes…
Acellular slime mould Physarum polycephalum is a popular now user-friendly living substrate for designing of future and emergent sensing and computing devices. P. polycephalum exhibits regular patterns of oscillations of its surface…
We discuss a two-dimensional model for the dynamics of axonemal deformations driven by internally generated forces of molecular motors. Our model consists of an elastic filament pair connected by active elements. We derive the dynamic…