Related papers: Numerical Methods for a Poisson-Nernst-Planck-Ferm…
Ion transport, the movement of ions across a cellular membrane, plays a crucial role in a wide variety of biological processes and can be described by the Poisson-Nernst-Planck equations with steric effects (PNP-steric equations). In this…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
The transport and distribution of charged particles are crucial in the study of many physical and biological problems. In this paper, we employ an Energy Variational Approach to derive the coupled Poisson-Nernst-Planck-Navier-Stokes system.…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
Mean-field molecular dynamics based on path integrals is used to approximate canonical quantum observables for particle systems consisting of nuclei and electrons. A computational bottleneck is the sampling from the Gibbs density of the…
The normalization constraint on probability density poses a significant challenge for solving the Fokker-Planck equation. Normalizing Flow, an invertible generative model leverages the change of variables formula to ensure probability…
We develop a fully continuous model for colloidal suspensions with hydrodynamic interactions. The Navier Stokes Phase Field Crystal (NS-PFC) model combines ideas of dynamic density functional theory with particulate flow approaches and is…
We develop a fast and scalable numerical approach to solve Wasserstein gradient flows (WGFs), particularly suitable for high-dimensional cases. Our approach is to use general reduced-order models, like deep neural networks, to parameterize…
Aging and stability of gaseous ionization detectors are intricately related to charging up, accumulation of space charge and formation of discharges. All these phenomena, in their turn, depend on the dynamics of charged particles within the…
We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum effects (NQE). The inclusion of CF…
The steady, asymmetric and two-dimensional flow of viscous, incompressible, and Newtonian fluid through a rectangular channel with splitter plate parallel to walls is investigated numerically. In the past, the position of the splitter plate…
Nonlinear non-Gaussian state-space models are ubiquitous in statistics, econometrics, information engineering and signal processing. Particle methods, also known as Sequential Monte Carlo (SMC) methods, provide reliable numerical…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
A numerical method based upon the immersed boundary technique for the fluid-solid coupling and on a soft-sphere approach for solid-solid contact is used to perform direct numerical simulation of the flow-induced motion of a thick bed of…
In this paper, we develop a novel numerical framework, namely the stochastic interacting particle-field method with particle-in-cell acceleration (SIPF-PIC), for the efficient simulation of the three-dimensional (3D) parabolic-parabolic…
We present a new parallel spectral element solver, FNPF-SEM, for simulating linear and fully nonlinear potential flow-based water waves and their interaction with offshore structures. The tool is designed as a general-purpose wave model for…
We theoretically study the electrokinetic transport properties of nano-fluidic devices under the influence of a pressure, voltage or salinity gradient. On a microscopic level the behaviour of the device is quantified by the Onsager matrix…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
Antiferroelectric liquid crystals can be considered as a promising alternative to nematic mixtures in the area of microdisplays. Switching behaviour of the molecules has been modelled as two adjacent smectic layers. However, some studies…