Related papers: Solv-eze: Automated Placement of Explicit Water Mo…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…
Engineering simulations are usually based on complex, grid-based, or mesh-free methods for solving partial differential equations. The results of these methods cover large fields of physical quantities at very many discrete spatial…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
We introduce a simple and efficient algorithm for diffusion in smoothed particle hydrodynamics (SPH) simulations and apply it to the problem of chemical mixing. Based on the concept of turbulent diffusion, we link the diffusivity of a…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
In this paper we present a novel algorithm for simulating geometrical flows, and in particular the Willmore flow, with conservation of volume and area. The idea is to adapt the class of diffusion-redistanciation algorithms to the Willmore…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
In this work we study and contrast implicit solvation models against explicit atomistic, quantum mechanical models in the description of the band alignment of semiconductors in aqueous environment, using simulations based on density…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
Localized representation of the Kohn-Sham subspace plays an important role in quantum chemistry and materials science. The recently developed selected columns of the density matrix (SCDM) method [J. Chem. Theory Comput. 11, 1463, 2015] is a…
Solute transport in fluid-particle systems is a fundamental process in numerous scientific and engineering disciplines. The simulation of it necessitates the consideration of solid particles with intricate shapes and sizes. To address this…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct…
This paper presents an efficient solution to 3D-LiDAR-based Monte Carlo localization (MCL). MCL robustly works if particles are exactly sampled around the ground truth. An inertial navigation system (INS) can be used for accurate sampling,…