Related papers: Identifying interfacial molecules in nonplanar int…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
Interferometric Particle Imaging (IPI) is a powerful technique to characterize aerosol particles, which so far has been applied only to particles larger than about 100 wavelengths. We extend its applicability to smaller ice crystals,…
Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex…
A new diffuse interface model for a two-phase flow of two incompressible fluids with different densities is introduced using methods from rational continuum mechanics. The model fulfills local and global dissipation inequalities and is also…
For cellular functions like division and polarization, protein pattern formation driven by NTPase cycles is a central spatial control strategy. Operating far from equilibrium, no general theory links microscopic reaction networks and…
This study presents an advanced sharp-interface immersed boundary method (IBM) integrated with the blastFOAM library on the OpenFOAM platform for high-speed compressible flow simulations. The developed solver extends the existing IBM…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
The determination of depth profiles across interfaces is of primary importance in many scientific and technological areas. Photoemission spectroscopy is in principle well suited for this purpose, yet a quantitative implementation for…
Recently, the theory of diffusion maps was extended to a large class of local kernels with exponential decay which were shown to represent various Riemannian geometries on a data set sampled from a manifold embedded in Euclidean space.…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
We devise a numerical method for passive advection of a surface, such as the interface between two incompressible fluids, across a computational mesh. The method is called isoAdvector, and is developed for general meshes consisting of…
In this work we present and study an iterative algorithm used to asymptotically solve nonlinear differential equations. This algorithm (Iterative First Order HAM or IFOHAM) is based on the first order equation of the Homotopy Analysis…
The Immersed Interface Method is employed to solve the time-varying electric field equations around a three-dimensional vesicle. To achieve second-order accuracy the implicit jump conditions for the electric potential, up to the second…
We study an elliptic interface problem with discontinuous diffusion coefficients on unfitted meshes using the CutFEM method. Our main contribution is the reconstruction of conservative fluxes from the CutFEM solution and their use in a…
The orientational correlation scheme introduced earlier for tetrahedral molecules is extended for being able to classify orientational correlations between pairs of high symmetry molecules. While in the original algorithm a given…
In this paper, we combine discrete empirical interpolation techniques, global mode decomposition methods, and local multiscale methods, such as the Generalized Multiscale Finite Element Method (GMsFEM), to reduce the computational…
Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…
In network analysis, the core structure of modeling interest is usually hidden in a larger network in which most structures are not informative. The noise and bias introduced by the non-informative component in networks can obscure the…
In the present paper, a fluid-particle coupling method is directly derived from the Navier-Stokes equations (NSE) by applying the concept of volume-filtering, yielding a physically consistent methodology to incorporate solid wall boundary…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…