Related papers: Reconstructing the kinetic chemotaxis kernel using…
One of simplest examples of navigation found in nature is run-and-tumble chemotaxis. Tumbles reorient cells randomly, and cells can drift toward attractants or away from repellents by biasing the frequency of these events. The post-tumble…
Chemotaxis refers to the directed movement of cells in response to a chemical signal called chemoattractant. A crucial point in the mathematical modeling of chemotactic processes is the correct description of the chemotactic sensitivity and…
Models for chemotaxis are based on gradient sensing of individual organisms. The key contribution of Keller and Segel is showing that erratic movements of individuals may result in an accurate chemotaxis phenomenon as a group. In this paper…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates…
Cells encounter a diverse array of physical and chemical signals as they navigate their natural surroundings. However, their response to the simultaneous presence of multiple cues remains elusive. Particularly, the impact of topography…
Organisms must acquire and use environmental information to guide their behaviors. However, it is unclear whether and how information quantitatively limits behavioral performance. Here, we relate information to behavioral performance in…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Bacterial motility, and in particular repulsion or attraction towards specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory…
Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
Kernel-based multivariate statistical process control (K-MSPC) extends classical monitoring to nonlinear industrial processes. Its performance depends critically on kernel parameters such as lengthscales and variance terms. In current…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Three-dimensional cultures of cells are gaining popularity as an in vitro improvement over 2D Petri dishes. In many such experiments, cells have been found to organize in aggregates. We present new results of three-dimensional in vitro…
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system.…
Mechanical stresses stemming from environmental factors are a key determinant of cellular behavior and physiology. Yet, the role of self-induced biomechanical stresses in growing bacterial colonies has remained largely unexplored. Here, we…
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model…
Low-level database operators often admit multiple physical implementations ("kernels") that are semantically equivalent but have vastly different performance characteristics depending on the input data distribution. Existing database…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions. One example is the immune system signalling, where infected tissues release chemokines…