Related papers: Identifying interfacial molecules in nonplanar int…
The diffuse-interface model (DIM) is a tool for studying interfacial dynamics. In particular, it is used for modeling contact lines, i.e., curves where a liquid, gas, and solid are in simultaneous contact. As well as all other models of…
A very simple and efficient local variational iteration method for solving problems of nonlinear science is proposed in this paper. The analytical iteration formula of this method is derived first using a general form of first order…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Using Molecular Dynamics (MD) and Monte Carlo (MC) simulations interfacial properties of crystal-fluid interfaces are investigated for the hard sphere system and the one-component metallic system Ni (the latter modeled by a potential of the…
Shape optimization methods have been proven useful for identifying interfaces in models governed by partial differential equations. Here we consider a class of shape optimization problems constrained by nonlocal equations which involve…
Understanding the interactions of a solute with its environment is of fundamental importance in chemistry and biology. In this work, we propose a deep neural network architecture for atom type embeddings in its molecular context and…
One of the molecular properties most intuitive to the human perception is the geometrical shape. However, when exploring a large chemical space the determination of shape needs to be automated. We present a fast and simple approach to…
We develop a new interior-point method (IPM) for symmetric-cone optimization, a common generalization of linear, second-order-cone, and semidefinite programming. In contrast to classical IPMs, we update iterates with a geodesic of the cone…
Fluid-particle systems are very common in many natural processes and engineering applications. However, accurately and efficiently modelling fluid-particle systems with complex particle shapes is still a challenging task. Here, we present a…
Relevant to broad applied fields and natural processes, interfacial ionic hydrates has been widely studied by ultrahigh-resolution atomic force microscopy (AFM). However, the complex relationship between AFM signal and the investigated…
This article introduces a new fast direct solver for linear systems arising out of wide range of applications, integral equations, multivariate statistics, radial basis interpolation, etc., to name a few. \emph{The highlight of this new…
Biomolecular condensates organize biochemical processes by spatially concentrating molecules while allowing for dynamic exchange with their surroundings. However, transport across their interface can be strongly attenuated, leading to…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
The aim of this paper is to analyze from a mathematical perspective some existing schemes to partition a molecular density into several atomic contributions, with a specific focus on Iterative Stockholder Atom (ISA) methods. We provide a…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
Since shape optimization methods have been proven useful for identifying interfaces in models governed by partial differential equations, we show how shape optimization techniques can also be applied to an interface identification problem…
The Intrinsic Surface Finite Element Method (ISFEM) was recently proposed to solve Partial Differential Equations (PDEs) on surfaces. ISFEM proceeds by writing the PDE with respect to a local coordinate system anchored to the surface and…
When modeling scientific and industrial problems, geometries are typically modeled by explicit boundary representations obtained from computer-aided design software. Unfitted (also known as embedded or immersed) finite element methods offer…