Related papers: Reaction-diffusion kinetics on lattice at the micr…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
In this work, we establish a direct connection between generative diffusion models (DMs) and stochastic quantization (SQ). The DM is realized by approximating the reversal of a stochastic process dictated by the Langevin equation,…
The birth of the lattice Boltzmann method (LBM) fulfils a dream that simple arithmetic calculations can simulate complex fluid flows without solving complicated partial differential flow equations. Its power and potential of resolving more…
Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are…
Ab initio quantum Monte Carlo (QMC) is a stochastic approach for solving the many-body Schr\"odinger equation without resorting to one-body approximations. QMC algorithms are readily parallelizable via ensembles of $N_w$ walkers, making…
The lattice Boltzmann method (LBM) is a popular numerical framework to investigate single and multiphase flow though porous media. For estimation of absolute permeability based on micro-tomographic images of the porous medium, the…
Particle-based stochastic reaction-diffusion (PBSRD) models are a popular approach for capturing stochasticity in reaction and transport processes across biological systems. In some contexts, the overdamped approximation inherent in such…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
A general and local reactive boundary condition (RBC) for studying first-order equilibrium reactions using the lattice Boltzmann method (LBM) is presented. Its main characteristics are accurate reproduction of wall diffusion, invariance to…
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…
Reaction-diffusion PDEs and particle-based stochastic reaction-diffusion (PBSRD) models are commonly-used approaches for modeling the spatial dynamics of chemical and biological systems. Standard reaction-diffusion PDE models ignore the…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
In this work, we aimed to replicate and extend the results presented in the DiffFluid paper[1]. The DiffFluid model showed that diffusion models combined with Transformers are capable of predicting fluid dynamics. It uses a denoising…
The role of dimensionality (Euclidean versus fractal), spatial extent, boundary effects and system topology on the efficiency of diffusion-reaction processes involving two simultaneously-diffusing reactants is analyzed. We present…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Theory of diffusion-mediated reactions is already established for the target problem in the dilute limit, where the immobile target is surrounded by many quenchers. For lattice random walks in the crowded situation, each quencher is…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
Lattice Boltzmann models provide better understanding with mesoscopic eyesight on multi-component diffusion than macroscopic models. Based on the kinetic theory and starting from the He-Luo model, the state-of-the-art multi-component…