Related papers: Coarse Grain Molecular Dynamics Simulation of Fibr…
Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. There has been longstanding scientific, engineering,…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…
The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…
Liquid crystal skyrmions are topologically protected spatially localized distortions of the director field which are fascinating from both fundamental mathematics and applied physics points of view. Skyrmions are realized in experimental…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
We present a high-fidelity three dimensional computational framework for simulating the bulk mechanical behavior of granular aggregates composed of deformable brittle grains. Departing from classical discrete element methods (DEM), our…
Computational fluid dynamics (CFD) can be used to simulate vascular haemodynamics and analyse potential treatment options. CFD has shown to be beneficial in improving patient outcomes. However, the implementation of CFD for routine clinical…
Cellular automata and other discrete dynamical systems have long been studied as models of emergent complexity. Recently, neural cellular automata have been proposed as models to investigate the emerge of a more general artificial…
Context: Complex molecules such as ethanol and dimethyl ether have been observed in a number of hot molecular cores and hot corinos. Attempts to model the molecular formation process using gas phase only models have so far been…
Under many conditions, macroscopic grains flow like a fluid; kinetic theory pred icts continuum equations of motion for this granular fluid. In order to test the theory, we perform event driven molecular simulations of a two-dimensional gas…
We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior;…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
We propose a simple model for density fluctuations of aerodynamic grains, embedded in a turbulent, gravitating gas disk. The model combines a calculation for the behavior of a group of grains encountering a single turbulent eddy, with a…
Magnetic skyrmions are magnetic quasi-particles with enhanced stability and different manipulation mechanisms using external fields and currents making them promising candidates for future applications for instance in neuromorphic…