Related papers: Gated reactions in discrete time and space
We consider the dynamics of diffusing particles in one space dimension with annihilation on collision and nucleation (creation of particles) with constant probability per unit time and length. The cases of nucleation of single particles and…
Reactions are an important tool to study nuclear structure and for extracting reactions relevant for astrophysics. In this paper we focus on deuteron induced reactions which can provide information on neutron shell evolution as well as…
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…
In a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
We analyse the problem of meeting times for interdependent stochastic agents: random walkers whose behaviour is stochastic but controlled by their selections from some set of allowed actions, and the inference problem of when these agents…
The control of chemical reactions is a recurring theme in physics and chemistry. Traditionally, chemical reactions have been investigated by tuning thermodynamic parameters, such as temperature or pressure. More recently, physical methods…
There are a wide range of first passage time (FPT) problems in the physical and life sciences that can be modelled in terms of a Brownian particle binding to a reactive surface (absorption). However, prior to absorption, the particle may…
We investigate how confinement may drastically change both the probability density of the first-encounter time and the related survival probability in the case of two diffusing particles. To obtain analytical insights into this problem, we…
New theorems for the moments of the first passage time of one dimensional nonlinear stochastic processes with an entrance boundary are formulated. This important class of one dimensional stochastic processes results among others from…
Calculating how long a coupled multi-species reactive-diffusive transport process in a heterogeneous medium takes to effectively reach steady state is important in many applications. In this paper, we show how the time required for such…
An autocatalytic reacting system with particles interacting at a finite distance is studied. We investigate the effects of the discrete-particle character of the model on properties like reaction rate, quenching phenomenon and front…
We investigate transport properties of molecular junctions under two types of bias--a short time pulse or an AC bias--by combining a solution for the Green functions in the time domain with electronic structure information coming from ab…
Stochastic reaction networks, which are usually modeled as continuous-time Markov chains on $\mathbb Z^d_{\ge 0}$, and simulated via a version of the "Gillespie algorithm," have proven to be a useful tool for the understanding of processes,…
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…
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…
Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the…
Motivated by the diffusion-reaction kinetics on interstellar dust grains, we study a first-passage problem of mortal random walkers in a confined two-dimensional geometry. We provide an exact expression for the encounter probability of two…
Whereas collisions between atoms and molecules are largely understood, collisions between two molecules have proven much harder to study. In both experiment and theory, our ability to determine quantum state-resolved bimolecular cross…