Related papers: Relaxation to statistical equilibrium in stochasti…
We investigate a stochastic version of a simple enzymatic reaction which follows the generic Michaelis-Menten kinetics. At sufficiently high concentrations of reacting species, the molecular fluctuations can be approximated as a realization…
Biochemical reactions with oscillatory behavior play an essential role in synthetic biology at the microscopic scale. Although a robust stability theory for deterministic chemical oscillators in the macroscopic limit exists, the dynamical…
Milestoning is an accurate and efficient method for rare event kinetics calculations by constructing a continuous-time kinetic network connecting the reactant and product states. However, even with adequate sampling, its accuracy can also…
Colloids that attractively bond to only a few neighbors (e.g., patchy particles) can form equilibrium gels with distinctive dynamic properties that are stable in time. Here, we use a coarse-grained model to explore the dynamics of linked…
We study complex networks of stochastic two-state units. Our aim is to model discrete stochastic excitable dynamics with a rest and an excited state. Both states are assumed to possess different waiting time distributions. The rest state is…
When liquids are cooled sufficiently rapidly below their melting temperature, they may bypass crystalization and, instead, enter a long-lived metastable supercooled state that has long been the focus of intense research. Although they…
We investigate numerically a recent BGK-type model for a multi-component mixture of monatomic gases, undergoing a reversible bimolecular chemical reaction. The model replaces each collisional term of the Boltzmann equation with a relaxation…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
For a model long-range interacting system of classical Heisenberg spins, we study how fluctuations, such as those arising from having a finite system size or through interaction with the environment, affect the dynamical process of…
We consider the problem of parameter estimation for a stochastic McKean-Vlasov equation, and the associated system of weakly interacting particles. We study two cases: one in which we observe multiple independent trajectories of the…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high…
Recurrent neural networks with balanced excitation and inhibition exhibit irregular asynchronous dynamics, which is fundamental for cortical computations. Classical balance mechanisms require strong external inputs to sustain finite firing…
We explain the ubiquity and extremely slow evolution of non gaussian out-of-equilibrium distributions for the Hamiltonian Mean-Field model, by means of traditional kinetic theory. Deriving the Fokker-Planck equation for a test particle, one…
Reaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. In…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
We revisit here the problem of the collective non-equilibrium dynamics of a classical statistical system at a critical point and in the presence of surfaces. The effects of breaking separately space- and time-translational invariance are…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
The dynamics of randomly crosslinked liquids is addressed via a Rouse- and a Zimm-type model with crosslink statistics taken either from bond percolation or Erdoes-Renyi random graphs. While the Rouse-type model isolates the effects of the…
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…