Related papers: Propagation of Fluctuations in Biochemical Systems…
We explore a new framework for describing the kinetics of a heterogeneous chemical reaction where two particles of the same chemical species form a reaction product of another chemical species on the surface of a seed particle. Traditional…
We study fluctuations in diffusion-limited reaction systems driven out of their stationary state. Using a numerically exact method, we investigate fluctuation ratios in various systems which differ by their level of violation of microscopic…
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the…
Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
We study the influence of a dissipation process on diffusion dynamics triggered by fluctuations with long-range correlations. We make the assumption that the perturbation process involved is of the same kind as those recently studied…
In systems of diffusing particles, we investigate large deviations of a time-averaged measure of clustering around one particle. We focus on biased ensembles of trajectories, which realise large-deviation events. The bias acts on a single…
Propagating fronts arising from bistable reaction-diffusion equations are a purely deterministic effect. Stochastic reaction-diffusion processes also show front propagation which coincides with the deterministic effect in the limit of small…
We introduce and study a new class of fronts in finite particle number reaction-diffusion systems, corresponding to propagating up a reaction rate gradient. We show that these systems have no traditional mean-field limit, as the nature of…
We study a system of interacting particles that randomly react to form new particles. The reaction flux is the rescaled number of reactions that take place in a time interval. We prove a dynamic large-deviation principle for the reaction…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
Fluctuations in a fluid are strongly affected by the presence of a macroscopic gradient making them long-ranged and enhancing their amplitude. While small-scale fluctuations exhibit diffusive lifetimes, larger-scale fluctuations live…
Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. Here we first identify the rate constant limits under which the concentrations of a given set of species will tend to…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
We investigate a problem of the necessary and sufficient conditions for appearance of the 1/f fluctuations in the simple systems affected by the external random perturbations, i.e. the power spectral density of the flux of particles moving…