Related papers: The AGBNP2 Implicit Solvation Model
In this work, we introduce two novel reformulations of a recent weakly hyperbolic model for two-phase flow with surface tension. In the model, the tracking of phase boundaries is achieved by using a vector interface field, rather than a…
Turbulence constitutes an exceptionally complex and irregular flow phenomenon that manifests in liquids, gases, and plasma, making it ubiquitous in both natural processes and engineering applications. Given the relatively modest…
The Serre-Green-Naghdi (SGN) equations provide a valuable framework for modelling fully nonlinear and weakly dispersive shallow-water flows. However, their elliptic formulation can considerably increase the computational cost compared to…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…
The interaction between thin structures and incompressible Newtonian fluids is ubiquitous both in nature and in industrial applications. In this paper we present an isogeometric formulation of such problems which exploits a boundary…
Water evaporation is critically important for hydrogels in open-air applications, but theoretically modeling is difficult due to the complicated intermolecular interactions and sustained deformation. In this work, we construct a simplified…
First, two examples of 1D distributed port-Hamiltonian systems with dissipation, given in explicit (descriptor) form, are considered: the Dzekster model for the seepage of underground water and a nanorod model with non-local viscous…
We propose a generalisation of molecular density functional theory to describe inhomogeneous solvent mixture, with the objective of modelling electrolytic solutions. Two electrolytic models are presented, both within the HNC approximation.…
Symbolic Regression (SR) offers an interpretable alternative to conventional Machine-Learning (ML) approaches, which are often criticized as ``black boxes''. In contrast to standard regression models that require a prescribed functional…
A class of variational schemes for the hydrodynamic-electrodynamic model of lossless free-electron gas in a quasineutral background is developed for high-quality simulations of surface plasmon polaritons. The Lagrangian density of lossless…
In this work, third-order semi-implicit schemes on staggered meshes for the shallow water and Saint-Venant-Exner systems are presented. They are based on a third-order extension of the technique introduced in Cassulli \& Cheng [1]. The…
Changes in hydration are central to the phenomenon of biomolecular recognition, but it has been difficult to properly frame and answer questions about their precise thermodynamic role. We address this problem by introducing Grid…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
In the self-consistent continuum solvation (SCCS) approach ($\textit{J. Chem. Phys.}$ 136, 064102 (2012)), the analytical expressions of the local solute-solvent interface functions determine the interface function and dielectric function…
In this paper we combine a flexible covariant formulation of the shallow water equations with the semi-implicit numerical scheme developed over the years by Casulli and collaborators. After adopting an orthogonal, but non-orthonormal,…
A comprehensive microscopic understanding of ambient liquid water is a major challenge for $ab$ $initio$ simulations as it simultaneously requires an accurate quantum mechanical description of the underlying potential energy surface (PES)…
Coordinate-based neural networks parameterizing implicit surfaces have emerged as efficient representations of geometry. They effectively act as parametric level sets with the zero-level set defining the surface of interest. We present a…
In this paper we propose a novel and general approach to design semi-implicit methods for the simulation of fluid-structure interaction problems in a fully Eulerian framework. In order to properly present the new method, we focus on the…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…
We propose a locally adaptive non-hydrostatic model and apply it to wave propagation generated by a moving bottom. This model is based on the non-hydrostatic extension of the shallow water equations (SWE) with a quadratic pressure relation,…