Related papers: Derivation of the bacterial run-and-tumble kinetic…
This paper presents a novel methodology for the direct numerical modeling and simulation of turbulent flows. The kinetic model equation is firstly extended to turbulent flow with the account of coupled evolution of kinetic, thermal, and…
In the present work we simulate the basic two-dimensional dynamics of swarming E. coli bacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with…
A phenomenological model for the dissipation of scalar fluctuations due to the straining by the fluid motion is proposed in this letter. An explicit equation is obtained for the time evolution of the probability distribution function of a…
Bacterial cells navigate around their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories.…
The large-scale collective behavior of biological systems can be characterized by macroscopic transport, which arises from the non-equilibrium microscopic interactions among individual constituents. A prominent example is the formation of…
Transport through molecular devices with strong coupling to a single vibrational mode is considered in the case where the vibration is damped by coupling to the environment. We focus on the weak tunneling limit, for which a rate equation…
We numerically study the dynamics of run-and-tumble particles confined in two chambers connected by thin channels. Two dominant dynamical behaviors emerge: (i) an oscillatory pumping state, in which particles periodically fill the two…
We study a system of two coupled nonlinear parabolic equations. It constitutes a variant of the Keller-Segel model for chemotaxis, i.e. it models the behaviour of a population of bacteria that interact by means of a signalling substance. We…
In the classical transport theory, the coefficients such as the diffusion, thermal conductivity and viscosity of fluid are usually expressed in a form proportional to the mean free path of molecules. We point out that this may cause a great…
We recently found that marine bacteria Vibrio alginolyticus execute a cyclic 3-step (run- reverse-flick) motility pattern that is distinctively different from the 2-step (run-tumble) pattern of Escherichia coli. How this novel swimming…
The chemotaxis pathway in the bacterium Escherichia coli allows cells to detect changes in external ligand concentration (e.g. nutrients). The pathway regulates the flagellated rotary motors and hence the cells' swimming behaviour, steering…
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
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…
Chemotaxis is a directed cell movement in response to external chemical stimuli. In this paper, we propose a simple model for the origin of chemotaxis - namely how a directed movement in response to an external chemical signal may occur…
Collective motion is a phenomenon observed across length scales in nature, from bacterial swarming and tissue migration to the flocking of animals. The mechanisms underlying this behavior vary significantly depending on the biological…
In molecular dynamics, transport coefficients measure the sensitivity of the invariant probability measure of the stochastic dynamics at hand with respect to some perturbation. They are typically computed using either the linear response of…
In this paper we present a hydrodynamic approach to describe the motion of migrating bacteria as a special class of self-propelled systems. Analytical and numerical calculations has been performed to study the behavior of our model in the…
Run-and-tumble is a basic model of persistent motion and a motility strategy widespread in micro-organisms and individual cells. In many natural settings, movement occurs in the presence of confinement. While accumulation at the surface has…
Bacterial chemotactic sensing converts noisy chemical signals into running and tumbling. We analyze the static sensing limits of mixed Tar/Tsr chemoreceptor clusters in individual Escherichia coli cells using a heterogeneous…