Related papers: Computing Biomolecular System Steady-states
We search for steady states in a class of fluctuating and driven physical systems that exhibit sustained currents. We find that the physical concept of a steady state, well known for systems at equilibrium, must be generalised to describe…
In this article we describe the incoherent and coherent spin and charge dynamics of a single electron quantum dot. We use a stochastic master equation to model the state of the system, as inferred by an observer with access to only the…
We describe the notion of stability of coherent systems as a framework to deal with redundancy. We define stable coherent systems and show how this notion can help the design of reliable systems. We demonstrate that the reliability of…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The kinetic energy distribution function satisfying the Boltzmann equation is studied analytically and numerically for a system of inelastic hard spheres in the case of binary collisions. Analytically, this function is shown to have a…
Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at…
The equations governing the conditions of mechanical equilibrium in fluid membranes subject to bending are revisited thanks to the principle of virtual work. The note proposes systematic tools to obtain the shape equation and the line…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Considering increasing distributed energy resources and responsive loads in smart grid, this paper proposes a stochastic simulation approach for stability analysis of a power system having stochastic loads. The proposed approach solves a…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
We propose an analytic approach for the steady-state dynamics of Markov processes on locally tree-like graphs. It is based on time-translation invariant probability distributions for edge trajectories, which we encode in terms of infinite…
We propose a simple model for a binary decision making process on a graph, motivated by modeling social decision making with cooperative individuals. The model is similar to a random field Ising model or fiber bundle model, but with key…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics,…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
We present a new solution for fundamental problems in nonlinear dynamical systems: finding, verifying, and stabilizing cycles. The solution we propose consists of a new control method based on mixing previous states of the system (or the…
Biochemical mechanisms with mass action kinetics are often modeled by systems of polynomial differential equations (DE). Determining directly if the DE system has multiple equilibria (multistationarity) is difficult for realistic systems,…
This paper is concerned with the existence and stability of phase transition steady states to a quasi-linear hyperbolic-parabolic system of chemotactic aggregation, which was proposed in \cite{ambrosi2005review, gamba2003percolation} to…