Related papers: Substrate geometry affects population dynamics in …
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Microcolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a…
Spiral surface growth is well understood in the limit where the step motion is controlled by the local supersaturation of adatoms near the spiral ridge. In epitaxial thin-film growth, however, spirals can form in a step-flow regime where…
We propose a biophysical model of Escherichia coli that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential…
Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…
Fluid flow has a major effect on the aggregation and fragmentation of bacterial colonies. Yet, a generic framework to understand and predict how hydrodynamics affects colony size remains elusive. This study investigates how fluid flow…
A hydrodynamic model is proposed to describe one of the most critical problems in intensive medical care units: the formation of biofilms inside central venous catheters. The incorporation of approximate solutions for the flow-limited…
Bacterial attachment to a fluid interface can lead to the formation of a film with physicochemical properties that evolve with time. We study the time evolution of interface (micro)mechanics for interfaces between oil and bacterial…
It has recently been reported that bacteria, such as E.coli and P. putida, perform distinct modes of motion when placed in porous media as compared to dilute regions or free space. This has led us to suggest an efficient strategy for active…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…
Large mm surveys of star forming regions enable the study of entire populations of planet-forming disks and reveal correlations between their observable properties. Population studies of disks have shown that the correlation between disk…
We study the growth of colonies of the yeast Pichia membranaefaciens on agarose film. The growth conditions are controlled in a setup where nutrients are supplied through an agarose film suspended over a solution of nutrients. As the…
The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal…
Predicting rapid and slower soil evolution remains a scientific challenge. This process involves poorly understood aspects of disordered granular matter and dense suspension dynamics. This study presents a novel two-dimensional experiment…
Active processes drive and guide biological dynamics across scales -- from subcellular cytoskeletal remodelling, through tissue development in embryogenesis, to population-level bacterial colonies expansion. In each of these, biological…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
Growing living cultures of Escherichia coli bacteria were investigated using real-time in situ rheology and rheo-imaging measurements. In the early stages of growth (lag phase), and when subjected to a constant stationary shear, the…
Tissue growth kinetics and interface dynamics depend on the properties of the tissue environment and cell-cell interactions. In cellular environments, substrate heterogeneity and geometry arise from a variety factors, such as the structure…
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E.…