Related papers: Stochastic Control Analysis for Biochemical Reacti…
Model Predictive Control is an extremely effective control method for systems with input and state constraints. Model Predictive Control performance heavily depends on the accuracy of the open-loop prediction. For systems with uncertainty…
The recently established connection between stochastic thermodynamics and fluctuating hydrodynamics is applied to a study of efficiencies in the coupled transport of heat and matter on a small scale. A stochastic model for a mesoscopic cell…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
The study of density-dependent stochastic population processes is important from a historical perspective as well as from the perspective of a number of existing and emerging applications today. In more recent applications of these…
We generalize and extend the recently proposed method to account for contributions of system size (or volume/participant) fluctuations to the experimentally measured moments of particle multiplicity distributions. We find that in the…
Text-book concepts of diffusion- versus kinetic-control are well-defined for reaction-kinetics involving macroscopic concentrations of diffusive reactants that are adequately described by rate-constants -- the inverse of the…
The rates of activated processes, such as escape from a metastable state and nucleation, are exponentially sensitive to an externally applied field. We describe how this applies to modulation by high-frequency fields and illustrate it with…
The currently existing theory of fluorescence correlation spectroscopy(FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in…
Many biological activities are induced by cellular chemical reactions of diffusing reactants. The dynamics of such systems can be captured by stochastic reaction networks. A recent numerical study has shown that diffusion can significantly…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X. Assuming the distribution of reacting particles in the system volume to be uniform, we introduced the notion of the point model of reaction…
We investigate the effect of noisy feed rates on the behavior of a cubic autocatalytic chemical reaction model. By combining the renormalization group and stoichiometric network analysis, we demonstrate how externally adjustable random…
Reaction-diffusion systems, which consist of the reacting particles subject to diffusion process, constitute one of the common examples of non-linear statistical systems. In low space dimensions $d \leq 2$ the usual description by means of…
Stochastic reaction-diffusion models can be analytically studied on complex networks using the linear noise approximation. This is illustrated through the use of a specific stochastic model, which displays traveling waves in its…
We study the impact of stochastic perturbations to deterministic dynamical systems using the formalism of the Ruelle response theory and explore how stochastic noise can be used to explore the properties of the underlying deterministic…
In a previous work, we presented a model that integrates cancer cell differentiation and immunotherapy, analysing a particular therapy against cancer stem cells by cytotoxic cell vaccines. As every biological system is exposed to random…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
Time delay in general leads to instability in some systems, while a specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a non-stationary stochastic…