Related papers: Self-organization principles of intracellular patt…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Many cellular processes require a polarization axis which generally initially emerges as an inhomogeneous distribution of molecular markers in the cell. We present a simple analytical model of a general mechanism of cell polarization taking…
The bipolar organization of the microtubule-based mitotic spindle is essential for the faithful segregation of chromosomes in cell division. Despite our extensive knowledge of genes and proteins, the physical mechanism of how the ensemble…
In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial…
A collection of thin structures buckle, bend, and bump into each-other when confined. This contact can lead to the formation of patterns: hair will self-organize in curls; DNA strands will layer into cell nuclei; paper, when crumpled, will…
The interior of a living cell is an active, fluctuating, and crowded environment. Yet, it maintains a high level of coherent organization, which is readily apparent in the intracellular transport network. Membrane-bound compartments called…
The question how complex systems become more organized and efficient with time is open. Examples are, the formation of elementary particles from pure energy, the formation of atoms from particles, the formation of stars and galaxies, the…
Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using flourrescence imaging have shown that,…
We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
From tumour invasion to cell sorting and animal territoriality, many biological systems rely on nonlocal interactions that drive complex spatial organisation. Partial differential equations (PDEs) with nonlocal advection are increasingly…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
We use a combination of unsupervised clustering and sparsity-promoting inference algorithms to learn locally dominant force balances that explain macroscopic pattern formation in self-organized active particle systems. The self-organized…
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…
We motivate and analyze a simple model for the formation of banded vegetation patterns. The model incorporates a minimal number of ingredients for vegetation growth in semi-arid landscapes. It allows for comprehensive analysis and sheds new…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
Transitions from turbulence to order are studied experimentally in thin fluid layers and magnetically confined toroidal plasma. It is shown that turbulence self-organizes through the mechanism of spectral condensation. The spectral…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
Life presents fascinating examples of self-organization and emergent phenomena. In multi-cellular organisms, a multitude of cells interact to form and maintain highly complex body plans of well-defined size. In this thesis, we investigate…