Related papers: Ribosome flow model with different site sizes
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
Inertial particles are often observed to be trapped, temporarily or permanently, by recirculation cells which are ubiquitous in natural or industrial flows. In the limit of small particle inertia, determining the conditions of trapping is a…
We present a model of traffic flow, with rules that describe the behaviour of automated vehicles in an open system. We show first of all that the fundamental diagram of this system collapses to a point, where states of free and jammed…
Macroscopic traffic flow is stochastic, but the physics-informed deep learning methods currently used in transportation literature embed deterministic PDEs and produce point-valued outputs; the stochasticity of the governing dynamics plays…
We consider an inhomogeneous symmetric simple exclusion process on a one-dimensional lattice with open boundary conditions. The time scale is continuous. Particles of different types arrive to the utmost left and the utmost right site. If a…
We examine a biomolecular machine involving a driven, observable process coupled to a hidden process in a kinetically cooperative manner. A stochastic thermodynamics framework is employed to analyze a fluctuation theorem for the…
Starting with a many-atom master equation of a kinetic, restricted solid-on-solid (KRSOS) model with external material deposition, we investigate nonlinear aspects of the passage to a mesoscale description for a crystal surface in 1+1…
Suspensions of finite-size solid particles in a turbulent pipe flow are found in many industrial and technical flows. Due to the ample parameter space consisting of particle size, concentration, density and Reynolds number, a complete…
Fundamental to many transportation network studies, traffic flow models can be used to describe traffic dynamics determined by drivers' car-following, lane-changing, merging, and diverging behaviors. In this study, we develop a…
One great challenge of modeling granular systems lies in capturing the rheologic dependencies on scale. For example, there are marked differences between quasi-static, intermediate, and rapid flow regimes. In this study, we demonstrate that…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
The cohesive collective motion (flocking, swarming) of autonomous agents is ubiquitously observed and exploited in both natural and man-made settings, thus, minimal models for its description are essential. In a model with continuous space…
Lattice-based random walk models are widely used to study populations of migrating cells with motility bias and proliferation. Crowding is typically represented by volume exclusion, where each lattice site can be occupied by at most one…
We study several one dimensional step flow models. Numerical simulations show that the slope of the profile exhibits scaling in all cases. We apply a scaling ansatz to the various step flow models and investigate their long time evolution.…
Using a non-perturbative classical approach, we study the dynamics of a mobile particle interacting with an infinite one-dimensional (1D) chain of harmonic oscillators. This minimal system is an effective model for many 1D transport…
In order to develop a toy model for car's traffic in cities, in this paper we analyze, by means of numerical simulations, the transition among fluid regimes and a congested jammed phase of the flow of "kinetically constrained" hard spheres…
This work proposes a method for the two-dimensional simulation of Brownian particles in a fluid with restrictions. The method is based on simple numerical rules between two matrices. One of the matrix represent the identification of all…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
We consider transport networks with nodes scattered at random in a large domain. At certain local rates, the nodes generate traffic flowing according to some navigation scheme in a given direction. In the thermodynamic limit of a growing…
Granular materials are inherently out-of-equilibrium systems due to energy dissipation through inelastic collisions and friction. When driven by mechanical agitation such as vibration, they exhibit rich collective behaviors including…