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We describe and illustrate a simple procedure for identifying a liquid interface from atomic coordinates. In particular, a coarse grained density field is constructed, and the interface is defined as a constant density surface for this…
We propose a fourth order Navier-Stokes solver based on the immersed interface method (IIM), for flow problems with stationary and one-way coupled moving boundaries and interfaces. Our algorithm employs a Runge-Kutta-based projection method…
Fundamental properties of the multicomponent diffuse-interface model (DIM), such as the maximum entropy principle and conservation laws, are used to explore the basic interfacial dynamics and phase transitions in fluids. Flat interfaces…
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…
Simultaneously optimizing multiple, frequently conflicting, molecular properties is a key bottleneck in the development of novel therapeutics. Although a promising approach, the efficacy of multi-task learning is often compromised by…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
We propose the Compact Coupling Interface Method (CCIM), a finite difference method capable of obtaining second-order accurate approximations of not only solution values but their gradients, for elliptic complex interface problems with…
Analyzing large volumes of high-dimensional data is an issue of fundamental importance in data science, molecular simulations and beyond. Several approaches work on the assumption that the important content of a dataset belongs to a…
In this work, we investigate an original strategy in order to derive a statistical modeling of the interface in gas-liquid two-phase flows through geometrical variables. The con- tribution is two-fold. First it participates in the…
Interfacial Stokes flow can be efficiently computed using the Boundary Integral Equation method. In 3D, the fluid velocity at a target point is given by a 2D surface integral over all interfaces, thus reducing the dimension of the problem.…
This work provides the community with an easily executable open-source Python package designed to automize the evaluation of Interfacial Phonons (InterPhon). Its strategy of arbitrarily defining the interfacial region and periodicity…
We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated…
We introduce a new paradigm for immersed finite element and isogeometric methods based on interpolating function spaces from an unfitted background mesh into Lagrange finite element spaces defined on a foreground mesh that captures the…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
We develop a geometrically intrinsic formulation of the arbitrary-order Virtual Element Method (VEM) on polygonal cells for the numerical solution of elliptic surface partial differential equations (PDEs). The PDE is first written in…
The U-shape structure has shown its advantage in salient object detection for efficiently combining multi-scale features. However, most existing U-shape based methods focused on improving the bottom-up and top-down pathways while ignoring…
The local arrangement of atoms is one of the most important predictors of mechanical and functional properties of materials. However, algorithms for identifying the geometrical arrangements of atoms in complex materials systems are lacking.…
We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis…
A straightforward and computationally efficient Consecutive Cubic Spline (CCS) iterative algorithm is proposed for positioning the planar interface of the unstructured geometrical Volume-of-Fluid method in arbitrarily-shaped cells. The CCS…
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…