Related papers: Two-scale large deviations for chemical reaction k…
We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a…
We study the large deviations of additive quantities, such as energy or current, in stochastic processes with intermittent reset. Via a mapping from a discrete-time reset process to the Poland-Scheraga model for DNA denaturation, we derive…
Sharp large deviation estimates for stochastic differential equations with small noise, based on minimizing the Freidlin-Wentzell action functional under appropriate boundary conditions, can be obtained by integrating certain matrix Riccati…
We study the spherical model of a ferromagnet in $d$-dimensional cubes $\Omega_n$ of volume $|\Omega_n|=n^d$ and investigate large deviations of the magnetization of various domains $D_k\subset \Omega_n$. We focus our attention on the…
In this article we consider an extension of the classical Curie-Weiss model in which the global and deterministic external magnetic field is replaced by local and random external fields which interact with each spin of the system. We prove…
Quantum-mechanical methods are widely used for understanding molecular interactions throughout biology, chemistry, and materials science. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple…
Drastic change in dynamics and statistics in a chemical reaction system, induced by smallness in the molecule number, is reported. Through stochastic simulations for random catalytic reaction networks, transition to a novel state is…
We consider directed polymers in random environment in the critical dimension $d = 2$, focusing on the intermediate disorder regime when the model undergoes a phase transition. We prove that, at criticality, the diffusively rescaled random…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
We give large deviation upper bounds, and discuss lower bounds, for the Gibbs-KMS state of a system of quantum spins or an interacting Fermi gas on the lattice. We cover general interactions and general observables, both in the high…
In ecological studies of pattern formation, models of the competitive-diffusion type are generally singularly perturbed, and the numerical approximation of such models is challenging. In this paper, we present finite element discretization…
We investigate Turing instability and pattern formation in two-dimensional domains for two reaction-diffusion models, obtained as diffusive limits of kinetic equations for mixtures of monatomic and polyatomic gases. The first model is of…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
A particle with internal unobserved states diffusing in a force field will generally display effective advection-diffusion. The drift velocity is proportional to the mobility averaged over the internal states, or effective mobility, while…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
We consider large deviations of empirical measures of diffusion processes. In a first part, we present conditions to obtain a large deviations principle (LDP) for a precise class of unbounded functions. This provides an analogue to the…
We establish a process level large deviation principle for systems of interacting Bessel-like diffusion processes. By establishing weak uniqueness for the limiting non-local SDE of McKean-Vlasov type, we conclude that the latter describes…