Related papers: Dynamic compartmentalization of bacteria: accurate…
To explore the coupling between a growing population of microorganisms such as E. coli and a nonuniform nutrient distribution, we formulate a minimalistic model. It consists of active Brownian particles that divide and grow at a…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in…
{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
We study the random walk of a particle in a compartmentalized environment, as realized in biological samples or solid state compounds. Each compartment is characterized by its length $L$ and the boundaries transmittance $T$. We identify two…
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and artificial environments. Here, we experimentally investigate sedimentation of passive particles in water containing various…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, in response to a diffusing spatial…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection…
Motile eukaryotic cells display distinct modes of migration that often occur within the same cell type. It remains unclear, however, whether transitions between the migratory modes require changes in external conditions, or whether the…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Diffusion in an evolving environment is studied by continuos-time Monte Carlo simulations. Diffusion is modelled by continuos-time random walkers on a lattice, in a dynamic environment provided by bubbles between two one-dimensional…
Microorganisms are ubiquitous in nature and technology. They inhabit diverse environments ranging from small river tributaries and lakes to oceans, as well as wastewater treatment plants and food manufacturing. In many of these…
The swimming properties of an E. coli-type model bacterium are investigated by mesoscale hy- drodynamic simulations, combining molecular dynamics simulations of the bacterium with the multiparticle particle collision dynamics method for the…
Under special conditions bacteria excrete an attractant and aggregate. The high density regions initially collapse into cylindrical structures, which subsequently destabilize and break up into spherical aggregates. This paper presents a…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…