Related papers: Identifying interfacial molecules in nonplanar int…
Protons at the water/vapor interface are relevant for atmospheric and environmental processes, yet to characterize their surface affinity on the quantitative level is still challenging. Here we utilize phase-sensitive sum-frequency…
The quasi-neutral hybrid model with kinetic ions and fluid electrons is a promising approach for bridging the inherent multi-scale nature of many problems in space and laboratory plasmas. Here, a novel, implicit, particle-in-cell based…
We study two fundamental optimization problems: (1) scaling a symmetric positive definite matrix by a positive diagonal matrix so that the resulting matrix has row and column sums equal to 1; and (2) minimizing a quadratic function subject…
A numerical tool relying on sharp Immersed Boundary Method (IBM) is developed for the analysis of aerospace applications. The method, which is conceived for application using segregated solvers relying on implicit time discretization, uses…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Atom-probe tomography (APT) facilitates nano- and atomic-scale characterization and analysis of microstructural features. Specifically, APT is well suited to study the interfacial properties of granular or heterophase systems.…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
The insertion of solvent particles in molecular dynamics simulations of complex fluids is required in many situations involving open systems, but this challenging task has been scarcely explored in the literature. We propose a simple and…
Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified models have been proposed for different small- or…
We present a technique for analyzing the full three-dimensional density profiles of a planar crystal-fluid interface in terms of density modes. These density modes can also be related to crystallinity order parameter profiles which are used…
In this paper, we introduce the neural empirical interpolation method (NEIM), a neural network-based alternative to the discrete empirical interpolation method for reducing the time complexity of computing the nonlinear term in a reduced…
A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…
The Open Knowledgebase of Interatomic Models (OpenKIM) project is a framework intended to facilitate access to standardized implementations of interatomic models for molecular simulations along with computational protocols to evaluate them.…
The multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis is done on methane, ethylene, acetylene and benzene as selected basic hydrocarbons. This is the first report on applying the MC-QTAIM analysis on polyatomic…
Understanding the flow of deformable particles such as liquid drops, synthetic capsules and vesicles, and biological cells confined in a small channel is essential to a wide range of potential chemical and biomedical engineering…
The large quantity and high quality of modern radio and infrared line observations require efficient modeling techniques to infer physical and chemical parameters such as temperature, density, and molecular abundances. We present a computer…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…
Molecules composed of atoms exhibit properties not inherent to their constituent atoms. Similarly, meta-molecules consisting of multiple meta-atoms possess emerging features that the meta-atoms themselves do not possess. Metasurfaces…
Motivated by the study of the electrodynamics of particles, we propose in this work an arbitrary-order discrete de Rham scheme for the treatment of elliptic problems with potential and flux jumps across a fixed interface. The scheme…
Recent measurements of microsphere interactions in diverse media suggest that the standard dielectric-continuum models of solution-phase interactions are fundamentally incomplete. Experiments indicate that the interactions of charged…