Related papers: Stochastic switching between multistable oscillati…
We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at…
In E. coli, accurate cell division depends upon the oscillation of Min proteins from pole to pole. We provide a model for the polar localization of MinD based only on diffusion, a delay for nucleotide exchange, and different rates of…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
We quantify the effect of Gaussian white noise on fast--slow dynamical systems with one fast and two slow variables, which display mixed-mode oscillations owing to the presence of a folded-node singularity. The stochastic system can be…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…
Resistive switching is one of the foremost candidates for building novel types of non-volatile random access memories. Any practical implementation of such a memory cell calls for a strong miniaturization, at which point fluctuations start…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
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…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
We undertake a detailed numerical study of the twin phenomena of stochastic and vibrational resonance in a discrete model system in the presence of bichromatic input signal. A two parameter cubic map is used as the model that combines the…
Determining the middle of the bacteria cell and the proper placement of the septum is essential to the division of the bacterial cell. In E. coli, this process depends on the proteins MinC, MinD, and MinE. Here, the Lattice Boltzmann method…