Related papers: Model reduction for molecular diffusion in nanopor…
Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static…
Pore-scale modeling and simulation of reactive flow in porous media has a range of diverse applications, and poses a number of research challenges. It is known that the morphology of a porous medium has significant influence on the local…
We consider in this paper a solvable model for the motion of molecular motors. Based on the averaging principle, we reduce the problem to a diffusion process on a graph. We then calculate the effective speed of transportation of these…
The diffusion of atoms and radicals on interstellar dust grains is a fundamental ingredient for predicting accurate molecular abundances in astronomical environments. Quantitative values of diffusivity and diffusion barriers usually rely…
Probabilistic denoising diffusion models (DDMs) have set a new standard for 2D image generation. Extending DDMs for 3D content creation is an active field of research. Here, we propose TetraDiffusion, a diffusion model that operates on a…
Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…
We propose a stochastic model for intracellular transport processes associated with the activity of molecular motors. This out-of-equilibrium model, based on a generalized Langevin equation, considers a particle immersed in a viscoelastic…
A practical correction formula relating the self-diffusion coefficient of dense liquids from molecular dynamics simulations with periodic boundary conditions to the self-diffusion coefficient in the thermodynamic limit is discussed. This…
This article presents a numerical simulation of solvent diffusion in transition metal dichalcogenide based nanomaterials during solvothermal reaction, leading to layer exfoliation and, consequently, a reduction in the average nanoparticle…
The description of the dynamics of a complex, high-dimensional system in terms of a low-dimensional set of collective variables Y can be fruitful if the low dimensional representation satisfies a Langevin equation with drift and diffusion…
This work presents a data-driven framework for multi-scale parametrization of velocity-dependent dispersive transport in porous media. Pore-scale flow and transport simulations are conducted on periodic pore geometries, and volume-averaging…
We use Langevin dynamics simulations to study the mass diffusion problem across two adjacent porous layers of different transport property. At the interface between the layers, we impose the Kedem-Katchalsky (KK) interfacial boundary…
Particle diffusion in rotating drums is studied via computer simulations using a full 3-D model which does not involve any arbitrary input parameters. The diffusion coefficient for single-component systems agree qualitatively with previous…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
An overview is presented of the various phases predicted to occur when gases are absorbed within a bundle of carbon nanotubes. The behavior may be characterized by an effective dimensionality, which depends on the species and the…
Diffusion in an evolving environment is studied by continuos-time Monte Carlo simulations. Diffusion is modelled by continuos-time random walkers on a lattice, in a dynamic environment provided by bubbles between two one-dimensional…
We introduce the concept of Randomly Modulated Gaussian Processes as a unifying framework for modeling, analyzing and classifying anomalous diffusion models in heterogeneous media. This formulation incorporates correlations in the…
The motion of molecules on solid surfaces is of interest for technological applications such as catalysis and lubrication, but it is also a theoretical challenge at a more fundamental level. The concept of activation barriers is very…
We present a numerical and partially analytical study of classical particles obeying a Langevin equation that describes diffusion on a surface modeled by a two dimensional potential. The potential may be either periodic or random. Depending…