Related papers: On Boolean gates in fungal colony
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
Identifying dynamically influential nodes in biological networks is a central problem in systems biology, particularly for prioritizing intervention targets in gene regulatory networks. In this paper, we propose a Shapley-value-based…
The soft character of organic materials leads to strong coupling between molecular nuclear and electronic dynamics. This coupling opens the way to control charge transport in organic electronic devices by inducing molecular vibrational…
We propose a road-map to experimental implementation of cytoskeleton-based computing devices. An overall concept is described in the following. Collision-based cytoskeleton computers implement logical gates via interactions between…
Biocomputing systems based on engineered bacteria can lead to novel tools for environmental monitoring and detection of metabolic diseases. In this paper, we propose a Bacterial Molecular Computing on a Chip (BMCoC) using microfluidic and…
Electrochemical gradient of protons, or proton motive force (PMF), is at the basis of bacterial energetics. It powers vital cellular processes and defines the physiological state of the cell. Here we use an electric circuit analogy of an…
We apply the framework of optimal nonlinear control to steer the dynamics of a whole-brain network of FitzHugh-Nagumo oscillators. Its nodes correspond to the cortical areas of an atlas-based segmentation of the human cerebral cortex, and…
We show that the flagellar beat of bull spermatozoa and Chlamydomonas Reinhardtii can be modelled by a minimal, geometrically nonlinear reaction-diffusion system. Model solutions are spatio-temporally animated patterns describing flagellar…
In this paper, experimental data is presented and a simple model is developed for the time evolution of a F-amp \textit{E. Coli} culture population. In general, the bacteria life cycle as revealed by monitoring a culture's population…
The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial…
The stochastic FitzHugh-Nagumo (FHN) model is a two-dimensional nonlinear stochastic differential equation with additive degenerate noise, whose first component, the only one observed, describes the membrane voltage evolution of a single…
We study a cellular automaton (CA) model of information dynamics on a single hypha of a fungal mycelium. Such a filament is divided in compartments (here also called cells) by septa. These septa are invaginations of the cell wall and their…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The effect of molecular vibrations on electronic transport is investigated with the smallest fullerene C20 bridge, utilizing the Keldysh nonequilibrium Green's function techniques combined with the tight-binding molecular-dynamics method.…
Signal propagation over long distances is a ubiquitous feature of multicellular communities. In biofilms of the bacterium Bacillus subtilis, we recently discovered that some, but not all, cells participate in the propagation of an…
The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is…
A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on…
Neurons are the central biological objects in understanding how the brain works. The famous Hodgkin-Huxley model, which describes how action potentials of a neuron are initiated and propagated, consists of four coupled nonlinear…
Because the attractors of biological networks reflect stable behaviors (e.g., cell phenotypes), identifying control interventions that can drive a system towards its attractors (attractor control) is of particular relevance when controlling…
The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a…