Related papers: Explicit formulas for reaction probability in reac…
Motivated by a problem in heterogeneous catalysis, we study a model for irreversible first-order reactions in which gas transport occurs only by diffusion, and reaction occurs only at a small number of well-localized sites. The main problem…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
A general framework for the simulation of reaction-diffusion systems with probabilistic cellular automata is presented. The basic reaction probabilities of the chemical model translate directly into the transition rules of the automaton,…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
To capture the dynamic behaviors of reaction-subdiffusion in flow fields, in the present paper we analyze a simple monomolecular conversion A $\rightarrow$ B. We derive the corresponding master equations for the distribution of A and B…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for…
Patterns in reaction-diffusion systems near primary bifurcations can be studied locally and classified by means of amplitude equations. This is not possible for excitable reaction-diffusion systems. In this Letter we propose a global…
We provide a computational method for quickly determining the correct distribution of optically active nanoparticles for a desired response. This is achieved by simulating the optical response of single nanoparticles and performing a…
The reaction of volatile matter plays an important role in the process of bringing matter from the surface of the planet to the atmosphere. Therefore, by simulating the mixing and chemical reaction process of volatile matter in the…
The primary goal of this paper is to characterize solutions to coupled reaction-diffusion systems. Indeed, we use operators theory to show that under suitable assumptions, then the solutions to the reaction-diffusion equations exist. As…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
In this article, we study the large-population limit of interacting particle systems posed on weighted random graphs. In that aim, we introduce a general framework for the construction of weighted random graphs, generalizing the concept of…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Hydrocarbon pyrolysis is a complex chemical reaction system at extreme temperature and pressure conditions involving large numbers of chemical reactions and chemical species. Only two kinds of atoms are involved: carbons and hydrogens. Its…
We develop an efficient method to calculate probabilities of large deviations from the typical behavior (rare events) in reaction--diffusion systems. The method is based on a semiclassical treatment of underlying "quantum" Hamiltonian,…
Quantum chemical studies of reactivity involve calculations on a large number of molecular structures and comparison of their energies. Already the set-up of these calculations limits the scope of the results that one will obtain, because…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…