Related papers: Adaptation and Optimal Chemotactic Strategy for E.…
Motivated by the problem of estimating the bacterial growth rates for genome assemblies from shotgun metagenomic data, we consider the permuted monotone matrix model $Y=\Theta\Pi+Z$, where $Y\in \mathbb{R}^{n\times p}$ is observed,…
We consider an initial-boundary value problem describing the formation of colony patterns of bacteria Escherichia coli. This model consists of reaction-diffusion equations coupled with the Keller-Segel system from the chemotaxis theory in a…
Eukaryotic cells perform chemotaxis by determining the direction of chemical gradients based on stochastic sensing of concentrations at the cell surface. To examine the efficiency of this process, previous studies have investigated the…
Chemotaxis can be defined as an innate behavioural response by an organism to a directional stimulus, in which bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their…
We have investigated the growth of Escherichia coli E.coli, a mesophilic bacterium, as a function of pressure $P$ and temperature $T$. E.coli can grow and divide in a wide range of pressure (1-400atm) and temperature ($23-40^{\circ}$C). For…
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but…
Robust radiative transfer techniques are requisite for efficiently extracting the physical and chemical information from molecular rotational lines.We study several hypotheses that enable robust estimations of the column densities and…
We review recent work on the statistical mechanics of Von Neumann's growth model and discuss its application to cellular metabolic networks. In this context, we present a detailed analysis of the physiological scenario underlying optimality…
The effects of internal adaptation dynamics on the self-organized aggregation of chemotactic bacteria are investigated by Monte Carlo (MC) simulations based on a two-stream kinetic transport equation coupled with a reaction-diffusion…
In proliferating cell populations, adaptive changes to biochemical reactions can change a cell's division time, which in turn can change the population size. However, biochemical reactions are subject to noise, and therefore the conditions…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
Electroporation (EP), the temporary or permanent permeabilization of the cell membrane induced by an electric field, is the basis of various applications in medicine and food processing. In EP-based protocol optimization in terms of pulse…
Many studies have shown that Physarum polycephalum slime mold is able to find the shortest path in a maze. In this paper we study this behavior in a network, using a hyperbolic model of chemotaxis. Suitable transmission and boundary…
Collective cell migration in response to a chemical cue occurs in many biological processes such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems are capable of responding to gradients of less than 1%…
Experimentalists have observed phenotypic variability in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log growth rate, potentially…
We have developed and implemented a numerical evolution scheme for a class of stochastic problems in which the temporal evolution occurs on widely-separated time scales, and for which the slow evolution can be described in terms of a small…
The E. coli chemosensory lattice, consisting of receptors, kinases, and adaptor proteins, is an important test case for biochemical signal processing. Kinase output is characterized by precise adaptation to a wide range of background ligand…
Adaptive measurements were recently shown to significantly improve the performance of quantum state tomography. Utilizing information about the system for the on-line choice of optimal measurements allows to reach the ultimate bounds of…
Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without…
E.coli serves as prototype for the study of peritrichous enteric bacteria that perform runs and tumbles alternately. Bacteria run forward as a result of the counterclockwise (CCW) rotation of their flagella bundle and perform tumbles when…