Related papers: Model reduction for molecular diffusion in nanopor…
Continuum fluid dynamic models based on the Navier-Stokes equations have previously been used to simulate granular media undergoing fluid-like shearing. These models, however, typically fail to predict the flow behaviour in confined…
Geological parameterization entails the representation of a geomodel using a small set of latent variables and a mapping from these variables to grid-block properties such as porosity and permeability. Parameterization is useful for data…
We propose a general methodology for calculating the self-diffusion tensor from molecular dynamics for a liquid with a liquid-gas or liquid-solid interface. The standard method used in bulk fluids, based on computing the mean square…
Fluids confined in nanopores are ubiquitous in nature and technology. In recent years, the interest in confined fluids has grown, driven by research on unconventional hydrocarbon resources -- shale gas and shale oil, much of which are…
The problem of biological motion is a very intriguing and topical issue. Many efforts are being focused on the development of novel modeling approaches for the description of anomalous diffusion in biological systems, such as the very…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
Discontinuous transitions into absorbing states require an effective mechanism that prevents the stabilization of low density states. They can be found in different systems, such as lattice models or stochastic differential equations (e.g.…
We propose a theoretical approach for predicting thermodynamics and kinetics of guest molecules in nanoporous materials. This statistical mechanical-based method requires a minimal set of physical parameters that may originate from…
The diffusion/relaxation behavior of polarized spins of pore filling fluid, as often probed by NMR relaxometry, is widely used to extract information on the pore-geometry. Such information is further interpreted as an indicator of the key…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this…
Pore network modelling has traditionally been used to study displacement processes in idealized porous media related to geological flows, with applications ranging from groundwater hydrology to enhanced oil recovery. Very recently, pore…
Characterization of transport properties of porous media is increasingly relying on computational methods that require reconstruction of the media structure. We present a simple method of constructing the 3D surface of fibrous porous media…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
The bulk nuclear matter produced in heavy ion collisions carries a multitude of conserved quantum numbers: electric charge, baryon number, and strangeness. Therefore, the diffusion processes associated to these conserved charges cannot…
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…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
Optical micro-manipulation techniques has evolved into powerful tools to efficiently steer the motion of microscopical particles on periodic and quasi-periodic potentials, driven by the external electromagnetic field. Here, the dynamics of…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
In this article we investigate through molecular dynamics simulations the diffusion behavior of the TIP4P/2005 water when confined in pristine and deformed carbon nanotubes (armchair and zigzag). To analyze different diffusive mechanisms,…