相关论文: A Unified Approach to Gated Reactions on Networks

How much time does it take two molecules to react? If a reaction occurs upon contact, the answer to this question boils down to the classic first-passage time problem: find the time it takes the two molecules to meet. However, this is not…

First-passage times provide invaluable insight into fundamental properties of stochastic processes. Yet, various forms of gating mask first-passage times and differentiate them from actual detection times. For instance, imperfect conditions…

Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…

In this paper we study the kinetics of diffusion-limited, pseudo-first-order A + B -> B reactions in situations in which the particles' intrinsic reactivities vary randomly in time. That is, we suppose that the particles are bearing "gates"…

Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…

The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…

The work is presented, leading to the universal contact molecular mechanism of phase transitions and other reactions in solid state. The two components of the mechanism - nucleation and interface propagation - are investigated in detail and…

We consider stochastic models of chemical reaction networks with time dependent input rates and several types of molecules. We prove that, in despite of strong time dependence of input rates, there is a kind of homeostasis phenomenon: far…

Gated first-passage processes, where completion depends on both hitting a target and satisfying additional constraints, are prevalent across various fields. Despite their significance, analytical solutions to basic problems remain unknown,…

The standard analysis of reaction networks based on deterministic rate equations fails in confined geometries, commonly encountered in fields such as astrochemistry, thin film growth and cell biology. In these systems the small reactant…

We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…

Gated networks are networks that contain gating connections, in which the outputs of at least two neurons are multiplied. Initially, gated networks were used to learn relationships between two input sources, such as pixels from two images.…

We study the efficiency of a two-channel reaction between two walkers on a finite one-dimensional periodic lattice. The walkers perform a combination of synchronous and asynchronous jumps on the lattice and react instantaneously when they…

`Gating' is a widely observed phenomenon in biochemistry that describes the transition between the activated (or open) and deactivated (or closed) states of an ion-channel, which makes transport through that channel highly selective. In…

A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…

Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…

We present a stochastic lattice theory describing the kinetic behavior of trapping reactions $A + B \to B$, in which both the $A$ and $B$ particles perform an independent stochastic motion on a regular hypercubic lattice. Upon an encounter…

Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…

Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 years various criteria have been developed that can answer this…

In biochemical reaction networks, the first passage time (FPT) of a reaction quantifies the time it takes for the reaction to first occur, from the initial state. While the mean FPT historically served as a summary metric, a far more…