Related papers: Lattice simulation method to model diffusion and N…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Nuclear magnetic resonance (NMR) is a powerful spectroscopic technique that is sensitive to the local atomic structure of matter. Computational predictions of NMR parameters can help to interpret experimental data and validate structural…
Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to…
Simulating reactive dissolution of solid minerals in porous media has many subsurface applications, including carbon capture and storage (CCS), geothermal systems and oil & gas recovery. As traditional direct numerical simulators are…
This paper deals with the numerical modeling of wave propagation in porous media described by Biot's theory. The viscous efforts between the fluid and the elastic skeleton are assumed to be a linear function of the relative velocity, which…
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 particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
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…
Accurate modeling of diffusive transport of nanoparticles across nanopores is a particularly challenging problem. The reason is that for such narrow pores the large surface-to-volume ratio amplifies the relevance of the nanoscopic details…
The continuous-time random walk (CTRW) model is useful for alleviating the computational burden of simulating diffusion in actual media. In principle, isotropic CTRW only requires knowledge of the step-size, $P_l$, and waiting-time, $P_t$,…
We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
A non-equilibrium thermodynamics model able to analyze the combined effect of diffusion and adsorption in porous materials is proposed. The model considers the coupled dynamics of the diffusive phase, described by a diffusion type equation,…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
In this paper, we propose a computational framework,which is based on a domain decomposition technique, to employ both finite element method (which is a popular continuum modeling approach) and lattice Boltzmann method (which is a popular…
Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of one-dimensional models of single ion transport. Ions move through pores of length $L$, under the action of a…
Nuclear magnetic resonance is widely used as a probe of pore geometry and fluid composition in well logging. One of the critical assumptions often made is that the diffusion of fluid molecules is sufficiently fast to warrant the condition…
The process of liquid silicon infiltration is investigated for channels with radii from $0.25$ to $0.75$ [mm] drilled in compact carbon preforms. The advantage of this setup is that the study of the phenomenon results to be simplified. For…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
The relaxation of polarized spins in a porous medium has been utilized as a probe of its structure. We note that the governing diffusion problem has a close parallel to that of a particle in a box, an elementary Quantum mechanics toy model.…