Related papers: Computing Biomolecular System Steady-states
On the basis of the transfer matrix technique an analytical method to investigate the stationary states, for an electron in one-dimensional periodic structures in an external electrical field, displaying the symmetry of the problem is…
Understanding which system structure can sustain stable dynamics is a fundamental step in the design and analysis of large scale dynamical systems. Towards this goal, we investigate here the structural stability of systems with a random…
We consider a generational and continuous-time two-phase model of the cell cycle. The first model is given by a stochastic operator, and the second by a piecewise deterministic Markov process. In the second case we also introduce a…
Mathematical models for physiological processes aid qualitative understanding of the impact of various parameters on the underlying process. We analyse two such models for human physiological processes: the Mackey-Glass and the Lasota…
We introduce structured random matrix ensembles, constructed to model many-body quantum systems with local interactions. These ensembles are employed to study equilibration of isolated many-body quantum systems, showing that rather complex…
A basic model of a dynamical distribution network is considered, modeled as a directed graph with storage variables corresponding to every vertex and flow inputs corresponding to every edge, subject to unknown but constant inflows and…
We have developed a steady state theory of complex transport networks used to model the flow of commodity, information, viruses, opinions, or traffic. Our approach is based on the use of the Markov chains defined on the graph…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
In this article, we consider a dynamic model of a three-phase power system including nonlinear generator dynamics, transmission line dynamics, and static nonlinear loads. We define a synchronous steady-state behavior which corresponds to…
A stochastic model for a continuous photon counting and heterodyne measurement of a coherent source is proposed. A nonlinear filtering equation for the posterior state of a single-mode field in a cavity is derived by using the methods of…
A recently introduced particle-based model for fluid flow, called Stochastic Rotation Dynamics, can be made Galilean invariant by introducing a random shift of the computational grid before collisions. In this paper, it is shown how the…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
We present an ongoing development of an existing code for calculating ground-state, steady-state, and transient properties of many-particle systems. The development involves the addition of the full four-index two electron integrals, which…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
The steady states of an isotone electric system are described by an isotone function with respect to the componentwise order. When there are steady states, we highlight a dominant steady state and we study its domain of attraction for the…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
This article reviews the mechanical bidomain model, a mathematical description how the extracellular matrix and intracellular cytoskeleton are coupled by integrin proteins. The fundamental hypothesis is that differences between…
This paper presents a novel approach to the description and understanding of two-dimensional binary cellular automata with the Moore neighborhood that preserve the number of active cells. Such dynamical systems are known to successfully…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…